Final Program and Abstracts

Sponsored by the SIAM Activity Group on the Life Sciences The SIAM Activity Group on the Life Sciences was established to foster the application of mathematics to the life sciences and research in mathematics that leads to new methods and techniques useful in the life sciences.

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Society for Industrial and Applied Mathematics 3600 Market Street, 6th Floor Philadelphia, PA 19104-2688 USA Telephone: +1-215-382-9800 Fax: +1-215-386-7999 Conference E-mail: [email protected] Conference Web: www.siam.org/meetings/ Membership and Customer Service: (800) 447-7426 (US & Canada) or +1-215-382-9800 (worldwide) www.siam.org/meetings/ls14 2 2014 SIAM Conference on the Life Sciences

Table of Contents SIAM Registration Desk Child Care The SIAM registration desk is located For local child care information, please Program-at-a-Glance.... Separate handout in the Symphony Preconvene. It is open contact the concierge at the Sheraton General Information...... 2 during the following hours: Charlotte, at +1-704-372-4100. Get-togethers...... 4 Sunday, August 3 Minitutorial...... 7 4:00 PM – 8:00 PM Corporate Members Invited Plenary Presentations...... 8 and Affiliates Program Schedule...... 11 Monday, August 4 SIAM corporate members provide Poster Session...... 34 7:00 AM – 5:00 PM their employees with knowledge about, Abstracts...... 57 access to, and contacts in the applied Speaker and Organizer Index...... 134 mathematics and computational sciences Conference Budget.... Inside Back Cover Tuesday, August 5 community through their membership Hotel Meeting Room Map…Back Cover 7:30 AM – 5:00 PM benefits. Corporate membership is more than just a bundle of tangible products and services; it is an expression of Organizing Committee Co-Chairs Wednesday, August 6 support for SIAM and its programs. Robert Guy 7:30 AM – 5:00 PM SIAM is pleased to acknowledge its University of California, Davis, USA corporate members and sponsors. In recognition of their support, non- Thursday, August 7 Mette Sofie Olufsen member attendees who are employed by North Carolina State University, USA 7:30 AM – 3:00 PM the following organizations are entitled to the SIAM member registration rate. Organizing Committee Dean Bottino Hotel Address Takeda Pharmaceuticals, USA Corporate Institutional Sheraton Charlotte Members Paul C. Bressloff 555 South McDowell Street University of Utah, USA The Aerospace Corporation Charlotte, North Carolina, 28204 Air Force Office of Scientific Research Robert Stephen Cantrell Phone Number: +1-704-372-4100 University of Miami, USA AT&T Laboratories - Research Toll Free Reservations (USA and Bechtel Marine Propulsion Laboratory Gerardo Chowell-Puente Canada): +1-800-325-3535 The Boeing Company Arizona State University, USA Fax: +1-704-348-4646 CEA/DAM Hotel web address: Leah Edelstein-Keshet Department of National Defence University of British Columbia, Canada http://www.sheratoncharlottehotel.com/ (DND/CSEC) Nicholas A. Hill DSTO- Defence Science and University of Glasgow, Scotland Hotel Telephone Number Technology Organisation To reach an attendee or leave a message, Hewlett-Packard Anita Layton call +1-704-372-4100. If the attendee IBM Corporation Duke University, USA is a hotel guest, the hotel operator can connect you with the attendee’s room. IDA Center for Communications Simon A. Levin Research, La Jolla Princeton University, USA IDA Center for Communications Hotel Check-in Research, Princeton Eduardo D. Sontag and Check-out Times Institute for Computational and Rutgers University, USA Check-in time is 3:00 PM and check-out Experimental Research in time is 12:00 PM. Mathematics (ICERM) Institute for Defense Analyses, Center for Computing Sciences Lawrence Berkeley National Laboratory 2014 SIAM Conference on the Life Sciences 3

Lockheed Martin Leading the applied Join onsite at the registration desk, go to Los Alamos National Laboratory mathematics community . . . www.siam.org/joinsiam to join online or download an application form, or contact Mathematical Sciences Research Join SIAM and save! SIAM Customer Service: Institute SIAM members save up to $130 on Telephone: +1-215-382-9800 Max-Planck-Institute for Dynamics of full registration for the 2014 SIAM (worldwide); or 800-447-7426 (U.S. and Complex Technical Systems Conference on the Life Sciences! Join Canada only) Mentor Graphics your peers in supporting the premier Fax: +1-215-386-7999 professional society for applied National Institute of Standards and E-mail: [email protected] Technology (NIST) mathematicians and computational scientists. SIAM members receive Postal mail: Society for Industrial and National Security Agency (DIRNSA) subscriptions to SIAM Review, SIAM Applied Mathematics, 3600 Market Oak Ridge National Laboratory, News and Unwrapped, and enjoy Street, 6th floor, Philadelphia, PA 19104- managed by UT-Battelle for the substantial discounts on SIAM books, 2688 USA Department of Energy journal subscriptions, and conference Sandia National Laboratories registrations. Schlumberger-Doll Research Standard Audio/Visual Tech X Corporation If you are not a SIAM member and paid Set-Up in Meeting Rooms U.S. Army Corps of Engineers, Engineer the Non-Member or Non-Member Mini SIAM does not provide computers for Research and Development Center Speaker/Organizer rate to attend the any speaker. When giving an electronic conference, you can apply the difference presentation, speakers must provide their United States Department of Energy between what you paid and what a own computers. SIAM is not responsible member would have paid ($130 for a for the safety and security of speakers’ Non-Member and $65 for a Non-Member computers. List current June 2014 Mini Speaker/Organizer) towards a SIAM membership. Contact SIAM Customer Service for details or join at The Plenary Session Room will have Funding Agency the conference registration desk. two (2) screens, one (1) data projector and one (1) overhead projector. Cables SIAM and the conference organizing or adaptors for Apple computers are not committee wish to extend their thanks If you are a SIAM member, it only costs supplied, as they vary for each model. and appreciation to the U.S. National $10 to join the SIAM Activity Group Please bring your own cable/adaptor if Science Foundation for its support of this on the Life Sciences (SIAG/LS). As using an Apple computer. conference. a SIAG/LS member, you are eligible All other concurrent/breakout rooms for an additional $10 discount on this will have one (1) screen and one (1) data conference, so if you paid the SIAM projector. Cables or adaptors for Apple member rate to attend the conference, computers are not supplied, as they vary you might be eligible for a free for each model. Please bring your own SIAG/LS membership. Check at the cable/adaptor if using an Apple computer. registration desk. Overhead projectors will be provided only if requested. Free Student Memberships are available to students who attend an institution that Funding Panel If you have questions regarding is an Academic Member of SIAM, are Funding Agency Panel availability of equipment in the meeting members of Student Chapters of SIAM, Monday, August 4 room of your presentation, or to request or are nominated by a Regular Member 8:45 PM - 9:30 PM an overhead projector for your session, of SIAM. Symphony II please see a SIAM staff member at the registration desk. 4 2014 SIAM Conference on the Life Sciences

Internet Access SIAM Books and Journals Get-togethers The Sheraton Charlotte offers wireless Display copies of books and • Welcome Reception Internet access to hotel guests in the complimentary copies of journals Sunday, August 3 sleeping rooms at no additional charge. are available on site. SIAM books 6:00 PM – 8:00 PM Complimentary wireless Internet access are available at a discounted price in the meeting space is also available to during the conference. If a SIAM SIAM attendees. books representative is not available, • Poster Session completed order forms and payment In addition, a limited number of (credit cards are preferred) may be taken Tuesday, August 5 computers with Internet access will be to the SIAM registration desk. The 8:00 PM – 10:00 PM available during registration hours. books table will close at 9:30 AM on Thursday, August 7. • Business Meeting Registration Fee Includes (open to SIAG/LS members) • Admission to all technical sessions Wednesday, August 6 Table Top Displays • Business Meeting (open to 8:00 PM – 8:45 PM Princeton University Press SIAG/LS members) Complimentary beer and wine will SIAM • Coffee breaks daily be served. Springer • Poster Session • Room set-ups and audio/visual Please Note equipment Name Badges SIAM is not responsible for the safety • Welcome Reception A space for emergency contact and security of attendees’ computers. information is provided on the back of Do not leave your laptop computers your name badge. Help us help you in unattended. Please remember to turn Job Postings the event of an emergency! off your cell phones, pagers, etc. during sessions. Please check with the SIAM registration desk regarding the availability of job postings or visit http://jobs.siam.org. Comments? Recording of Presentations Comments about SIAM meetings are Audio and video recording of encouraged! Please send to: presentations at SIAM meetings is Important Notice to Poster Cynthia Phillips, SIAM Vice President prohibited without the written Presenters for Programs ([email protected]). permission of the presenter and SIAM. The poster session is scheduled for Tuesday, August 5 at 8:00 PM. Poster Social Media presenters may set up their poster SIAM is promoting the use of social material on the provided poster boards media, such as Facebook and Twitter, in the Symphony IV Room beginning in order to enhance scientific discussion Monday, August 4 at 2:00 PM. All at its meetings and enable attendees materials must be posted by 8:00 PM to connect with each other prior to, on Tuesday, August 5, the official start during and after conferences. If you time of the session. Posters will remain are tweeting about a conference, please on display through Thursday, August use the designated hashtag to enable 7 and must be removed by 11:30 AM. other attendees to keep up with the Posters remaining after this time will be Twitter conversation and to allow better discarded. SIAM is not responsible for archiving of our conference discussions. discarded posters. The hashtag for this meeting is #SIAMLS14. 2014 SIAM Conference on the Life Sciences 5

SIAM Activity Group on Life Sciences (SIAG/LS) www.siam.org/activity/life-sciences A GREAT WAY TO GET INVOLVED! Collaborate and interact with mathematicians and applied scientists whose work involves the application of mathematics to the life sciences and research that leads to new methods and techniques useful in the life sciences.

ACTIVITIES INCLUDE: • Special sessions at SIAM Annual Meetings • Biennial conference • Talks about topics in the life sciences available online via “SIAM Presents” • Website

BENEFITS OF SIAG/LS membership: • Free electronic subscription to SIAM Journal on Applied Dynamical Systems • Listing in the SIAG’s online membership directory • Additional $10 discount on registration at the SIAM Conference on Life Sciences (excludes student) • Electronic communications about recent developments in your specialty • Eligibility for candidacy for SIAG/LS office • Participation in the selection of SIAG/LS officers

ELIGIBILITY: • Be a current SIAM member.

COST: • $10 per year • Student members can join two activity groups for free!

2013-14 SIAG/LS OFFICERS • Chair: Gregory Forest, University of North Carolina at Chapel Hill • Vice Chair: Maia Martcheva-Drashanska, University of Flordia • Program Director: Robert Guy, University of California at Davis • Secretary: Janet Best, Ohio State University TJOIN TO JOIN: SIAG/LS: my.siam.org/forms/join_siag.htm SIAM: www.siam.org/joinsiam 6 2014 SIAM Conference on the Life Sciences

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Minitutorials

Monday, August 4 9:30 AM – 11:30 AM Mecklenburg II

MT1: Algebra in Life Sciences Algebra, in particular algebraic geometry, is playing an increasingly important role in many areas of biology, such as phylogenetics and biochemical reaction networks. Here, the modeling equations often form a polynomial or rational system of equations and might thus be studied using techniques from algebra and algebraic geometry. Recent years have seen much progress towards an algebraic understanding of reaction networks. In this tutorial it will be demonstrated how such techniques can be applied in concrete examples of reaction networks, backed by theoretical results.

Organizers and Speakers: Elisenda Feliu, University of Copenhagen, Denmark Nicolette Meshkat, North Carolina State University, USA Carsten Wiuf, University of Copenhagen, Denmark

Wednesday, August 6 9:30 AM – 11:30 AM Symphony VI

MT2: Modelling Arterial Wall Mechanics and Adaption using Structurally Based Constitutive Laws This minitutorial will introduce the four different aspects of modelling in arterial wall mechanics.

Organizers and Speakers: Yibin Fu, Keele University, United Kingdom Nicholas A. Hill, University of Glasgow, Scotland, UK Xiaoyu Luo, University of Glasgow, Scotland, United Kingdom Leif Hellevik, Norwegian University of Science and Technology, Norway 8 2014 SIAM Conference on the Life Sciences

Invited Plenary Speakers ** All Invited Plenary Presentations will take place in Symphony I, II & III**

Monday, August 4 8:15 AM – 9:00 AM IP1 Perceptual Dynamics in an Ambiguous World John Rinzel, New York University, USA

1:00 PM – 1:45 PM IP2 Patient-specific Mathematical Neuro-Oncology: Every Patient Deserves Their Own Equation Kristin Rae Swanson, Northwestern University, USA

Tuesday, August 5 8:15 AM – 9:00 AM IP3 Modelling Plant Cell and Tissue Growth Oliver E. Jensen, University of Manchester, United Kingdom

1:00 PM – 1:45 PM IP4 Robustness, Control and the Organization of Cell Lineages Arthur Lander, University of California, Irvine, USA

Wednesday, August 6 8:15 AM – 9:00 AM IP5 Deterministic and Stochastic Thresholds for Disease Extinction in Infectious Disease Models Linda J. Allen, Texas Tech University, USA

1:00 PM – 1:45 PM IP6 Is “Good Cholesterol” Always “Good”? New Insights about HDL from an In-Silico Model of Lipoprotein Metabolism and Kinetics Norman Mazer, F. Hoffmann-La Roche Ltd., Switzerland 2014 SIAM Conference on the Life Sciences 9

Invited Plenary Speakers ** All Invited Plenary Presentations will take place in Symphony I, II & III**

Thursday, August 7 8:15 AM – 9:00 AM IP7 Early Warning Signs and Critical Transitions in Ecology: Corals, Theory, Pitfalls, and Advances Alan M. Hastings, University of California, Davis, USA

1:00 PM – 1:45 PM IP8 Synthetic Biology and Biocomputation: Life Redesigned James J. Collins, Boston University, USA 10 2014 SIAM Conference on the Life Sciences

Notes 2014 SIAM Conference on the Life Sciences 11

LS14 Program 12 2014 SIAM Conference on the Life Sciences

Sunday, August 3 Monday, August 4 Monday, August 4 MT1 Registration Registration Algebra in Life Sciences 4:00 PM-8:00 PM 7:00 AM-5:00 PM 9:30 AM-11:30 AM Room:Mecklenburg II Room:Symphony Preconvene Area Room:Symphony Preconvene Area Chair: Carsten Wiuf, University of Copenhagen, Denmark Welcome Reception Welcoming Remarks Algebra, in particular algebraic geometry, is playing an increasingly important 6:00 PM-8:00 PM 8:00 AM-8:15 AM role in many areas of biology, such as Room:Mecklenburg I, II & III Room:Symphony I, II & III phylogenetics and biochemical reaction networks. Here, the modeling equations often form a polynomial or rational system of equations and might thus be IP1 studied using techniques from algebra Perceptual Dynamics in an and algebraic geometry. Recent years have seen much progress towards an Ambiguous World algebraic understanding of reaction 8:15 AM-9:00 AM networks. In this tutorial it will be demonstrated how such techniques can Room:Symphony I, II & III be applied in concrete examples of Chair: Mette Olufsen, North Carolina reaction networks, backed by theoretical State University, USA results. When experiencing an ambiguous Algebra in Reaction Network Theory sensory stimulus (e.g., the vase-faces Carsten Wiuf and Elisenda Feliu, University image), subjects may report haphazard of Copenhagen, Denmark; Nicolette alternations (time scale, seconds) Meshkat, North Carolina State University, between the possible interpretations. USA I will describe dynamical models for Determining the Steady States of neuronal populations that compete Biochemical Reaction Networks through mutual inhibition for dominance Elisenda Feliu, University of Copenhagen, - showing alternations, behaving as noisy Denmark oscillators or as multistable systems Structural Identifiability of Reaction subject to noise-driven switching. In Networks using Differential Algebra highly idealized formulations networks Nicolette Meshkat, North Carolina State are percept specific without direct University, USA representation of stimulus features. Our recent work involves perception of ambiguous auditory stimuli (e.g., http://auditoryneuroscience.com/ topics/streaming-galloping-rhythm- paradigm ); the models incorporate feature specificity, tonotopy, so that perceptual selectivity is emergent rather than built-in. John Rinzel New York University, USA

Coffee Break 9:00 AM-9:30 AM Room:Symphony Preconvene Area 2014 SIAM Conference on the Life Sciences 13

Monday, August 4 Monday, August 4 Monday, August 4 MS1 MS2 MS3 Recent Advances in Applications of Dynamical Physiological Modeling of Mathematical Epidemiology Systems to Biology and Soft Tissues via Approach of of Infectious Diseases - Part Medicine - Part I of II Bio-mechanics I of II 9:30 AM-11:30 AM 9:30 AM-11:30 AM 9:30 AM-11:30 AM Room:Symphony II Room:Symphony III Room:Symphony I For Part 2 see MS10 Mechanical forces are significant For Part 2 see MS9 Over the last decades mathematical factors for genesis of some diseases This minisymposium will bring models have been used to identify and physiological processes occurring researchers who are actively involved in important features of immune responses in soft tissues. Several tubular organs development of mathematical approaches during disease. In this minisymposium are studied to demonstrate the power of in mathematical biology. The purpose of we bring together experts in modeling bio-mechanical modeling for analyzing the minisymposium is to address recent immune responses and infectious these alterations. Tracheal angioedema advances of mathematical methods disease dynamics. Our sessions will is modeled to see how swelling may used to study dynamics of infectious focus on challenges and new directions hurt the tissue by forming stress diseases and discuss a wide range of in the study of viral kinetic dynamics, concentration. Two another models topics: computational, mathematical immune responses, drug and vaccine show respectively the function of the and statistical techniques to study the efficacy, and the best strategies to use stress of arterial wall in mediating infectious diseases. the available biological data to identify arterial growth, and how the arterial parameters and propose new designs for residual stress is estimated via inverse Organizer: Necibe Tuncer experiments. spectral techniques. One last example University of Tulsa, USA Organizer: Stanca Ciupe is about the mechanical forces driving Organizer: Maia Martcheva Virginia Tech, USA the embryonic tubular brain to twist and University of Florida, USA bend for brain morphogenesis. 9:30-9:55 Modeling Avian Influenza Organizer: Matthias Chung Virginia Tech, USA Organizer: Kun Gou and Implications for Control Michigan State University, USA Maia Martcheva, University of Florida, 9:30-9:55 Parameter Identifiability in USA Virus Infection Models Organizer: Zi Chen Washington University, USA 10:00-10:25 Mathematics of Anti-Hpv Matthias Chung and Stanca Ciupe, Virginia Vaccines Tech, USA 9:30-9:55 Bio-Mechanical Modeling Abba Gumel, University of Manitoba, 10:00-10:25 Coping with Model of Tracheal Angioedema by Canada Uncertainty in the Analysis of Acute Nonlinear Finite Elasticity Hiv Infection Datasets Kun Gou and Thomas Pence, Michigan 10:30-10:55 Transient Periodic State University, USA Oscillations and the Dynamics of CTL Sivan Leviyang, Georgetown University, Response to Viral Infections USA 10:00-10:25 A Continuum Mechanics Michael Li, University of Alberta, Canada 10:30-10:55 Early {HIV} Infection Model of Stress Mediated Arterial Predictions: Role of Viral Replication Growth During Hypertension Using An 11:00-11:25 A Structured Model Errors Eulerian Frame. for the Transmission Dynamics of Jessica M. Conway and Alan S. Perelson, Maya E. Johnson and Jay R. Walton, Texas Mycobacterium Marinum Between A&M University, USA Aquatic Animals Los Alamos National Laboratory, USA Azmy S. Ackleh, University of Louisiana, 11:00-11:25 Multi-Scale Modeling 10:30-10:55 Estimating Residual Lafayette, USA of Immune Response to Influenza Stresses in Soft Tissues by An Inverse Infection Spectral Technique Hulin Wu, University of Rochester, USA Sunnie Joshi, Temple University, USA; Jay R. Walton, Texas A&M University, USA 11:00-11:25 Mechanical Forces Drive Morphogenesis: How the Embryonic Brain Twists Zi Chen, Washington University, USA; Qiaohang Guo, Fuzhou University, China; Eric Dai and Larry Taber, Washington University, USA 14 2014 SIAM Conference on the Life Sciences

Monday, August 4 Monday, August 4 Monday, August 4 MS4 MS5 MS6 Dynamics of Melanopsin Biofluids: Biological and Dynamics and Connectivity and Collective Physical Complexity in of Complex Networks in the Cell Migration: Two Fluid Structure Interaction Brain - Part I of II Collaborative Studies Problems - Part I of II 9:30 AM-11:30 AM 9:30 AM-11:30 AM 9:30 AM-11:30 AM Room:Symphony VII Room:Symphony V Room:Symphony VI For Part 2 see MS14 Two pairs of mathematics and biology For Part 2 see MS13 The dynamics of model neuronal faculty members present results Fluids are the natural environment networks have helped to explain from undergraduate teams formed of virtually every organism and fluid many aspects of cognitive function. in response to an NSF UBM grant structure interaction problems are As more realism is incorporated into awarded at UMBC. One team focuses ubiquitous in biology. While Newtonian these models, novel dynamical features on the dynamics of melanopsin, a light fluids and linearly elastic structures are often arise which further enrich our sensitive protein. They have modeled found in nature, many important fluids understanding of the brain. This the activation and inactivation of the and materials exhibit nonlinearities minisymposium explores this theme by phototransduction cascade using both or other complex properties. The aim discussing recent work in the modeling deterministic and stochastic models. of this minisymposium is to present of both individual neuron dynamics A second team studies the acquisition examples of such behavior in biological and network topology, focusing upon and persistence of cell motility. systems and the techniques used to implications on network behavior They have modeled the intracellular address these problems. The first half and information coding. The speakers signaling that triggers motility and, focuses on complex fluids and other will draw particular attention to new through force balance dynamics, the environmental considerations while the mathematical approaches in explaining migration of cell clusters. Here they second half focuses on properties of the sensory processing and information describe the extracellular signal that immersed structures. The systems vary propagation. initiates the intracellular signaling across multiple scales and present a Organizer: Victor Barranca cascade and newly discovered activation range of biofluids problems. New York University, USA asymmetries. Organizer: Christina Hamlet Organizer: Douglas Zhou Organizer: Bradford E. Peercy Tulane University, USA Shanghai Jiao Tong University, China University of Maryland, Baltimore Organizer: Jacek K. Wrobel 9:30-9:55 Improved Estimation of County, USA Tulane University, USA Neural Correlations Suggests Detailed Interactions in Visual Cortex 9:30-9:55 Phototransduction in 9:30-9:55 Sperm Altruism and Motility Kresimir Josic, University of Houston, Melanopsin Expressing Retinal Near Surfaces Ganglion Cells USA; Yu Hu, University of Washington, Julie Simons, Lisa J. Fauci, and Ricardo USA; James Trousdale, University Phyllis R. Robinson, University of Cortez, Tulane University, USA Maryland, Baltimore County, USA of Houston, USA; Eric Shea-Brown, 10:00-10:25 Modeling Tumor and University of Washington, USA 10:00-10:25 Modeling the Melanopsin Microenvironment Interactions under 10:00-10:25 Sparsity and Compressed Phototransduction Cascade Treatment: the Role of the Interstitial Coding in Sensory Systems Kathleen A. Hoffman, University of Fluid Gregor Kovacic, Rensselaer Polytechnic Maryland, Baltimore County, USA Katarzyna A. Rejniak, H. Lee Moffitt Institute, USA; Victor Barranca, New York Cancer Center & Research Institute, USA 10:30-10:55 Genetic Regulation of University, USA; Douglas Zhou, Shanghai Cell Motility 10:30-10:55 Swimming Through Highly Jiao Tong University, China; David Cai, Michelle Starz-Gaiano and Lathiena Heterogeneous, Viscoelastic Media Shanghai Jiao Tong University, China Manning, University of Maryland, Jacek K. Wrobel, Ricardo Cortez, and Lisa and Courant Institute of Mathematical Baltimore County, USA J. Fauci, Tulane University, USA Sciences, New York University, USA 11:00-11:25 Collective Cell 11:00-11:25 Marine Invertebrate Migration: Modeling from Initiation to Sperm Chemotaxis: Search Destination Trajectories David Stonko, Bradford E. Peercy, and Sarah D. Olson, Worcester Polytechnic continued on next page Michelle Starz-Gaiano, University of Institute, USA Maryland, Baltimore County, USA 2014 SIAM Conference on the Life Sciences 15

10:30-10:55 Spatiotemporal Dynamics Monday, August 4 Monday, August 4 of Neuronal Population Response in the Primary Visual Cortex MS7 MS8 Douglas Zhou, Shanghai Jiao Tong University, China; Aaditya Rangan, David Convergence of Appled Structured Population McLaughlin, and David Cai, Courant Mathematics and Oncology Dynamics: Modeling, Institute of Mathematical Sciences, New 9:30 AM-11:30 AM Estimation, and Validation - York University, USA Part I of II 11:00-11:25 Novel Characterization Room:Mecklenburg I of Brain Networks Through Low-Rank Cancer research has become increasingly 9:30 AM-11:30 AM Network Decomposition quantitative in scope and content; Room:Mecklenburg III Victor Barranca, New York University, however, a variety of challenges remain For Part 2 see MS16 USA; Douglas Zhou, Shanghai Jiao Tong in the detection, treatment, management, Structured population models University, China; David Cai, Courant and prevention of the disease. The Institute of Mathematical Sciences, New are ubiquitous in many areas of interface of applied mathematical York University, USA mathematical biology including modeling and simulations with clinical microbial bioreactors, amyloid diseases, oncology are beginning to play a critical and cellular proliferation assays. In role in synthesizing and comprehending these populations, individual aggregates some of the dynamics underlying the can combine, fragment, and/or grow. behavior of disease and simultaneously Each of these phenomena impact the integrating across different spatial and model in substantially different ways. temporal scales. This minisymposium Accordingly, significant research has will present in the context of clinical focused on the development of correct oncology recent advances in applied models as well as accurate estimation of mathematical models and simulations kernels and rates. This minisymposium that will explore the dynamics of cancer will showcase current directions of progression and therapeutic response research in advanced simulation, treatment. estimation, and validation techniques to Organizer: Larry Nagahara better understand structured populations. National Cancer Institute, USA Organizer: David M. Bortz 9:30-9:55 Random Walks, Markov University of Colorado Boulder, USA Chains, and Cancer Progression Organizer: John G. Younger Models from Longitudinal and University of Michigan, USA Autopsy Data Paul Newton, University of Southern 9:30-9:55 Applied Particle California, USA Aggregation for Cell Isolation in the Life Sciences 10:00-10:25 Bayesian Support Vector John G. Younger, University of Michigan, Machines and Supervised Factor USA Modeling for General Omic Data Larry Carin, Duke University, USA 10:00-10:25 Flocculation Dynamics and Cell Sorting 10:30-10:55 Perfusion Heterogeneity David M. Bortz, University of Colorado in Tumors As a Challenge for Optimal Boulder, USA Nanotherapeutics Delivery Hermann Frieboes, University of 10:30-10:55 Modeling and Inverse Louisville, USA Problems in Environmental Toxicity H. Thomas Banks and Kevin Flores, North 11:00-11:25 Dynamics of Living Carolina State University, USA Systems: Wave-Based Mechanisms for Contact Guidance and Collective 11:00-11:25 Estimating the Division Migration Rate for a Growth-fragmentation Wolfgang Losert, University of Maryland, Equation with Self-similar Kernel College Park, USA; John Fourkas, Meghan Thibault Bourgeron, UPMC and Inria Driscoll, Xiaoyu Sun, Can Guven, and Paris-Rocquencourt, France Chenlu Wang, University of Maryland, USA; Carole Parent, National Cancer Institute, USA Lunch Break 11:30 AM-1:00 PM Attendees on their own 16 2014 SIAM Conference on the Life Sciences

Monday, August 4 Monday, August 4 Monday, August 4 IP2 MS9 MS10 Patient-Specific Recent Advances in Applications of Dynamical Mathematical Mathematical Epidemiology Systems to Biology and Neuro-Oncology: of Infectious Diseases - Part Medicine - Part II of II Every Patient Deserves Their II of II 2:00 PM-4:00 PM Own Equation 2:00 PM-4:00 PM Room:Symphony II 1:00 PM-1:45 PM Room:Symphony I For Part 1 see MS2 Room:Symphony I, II & III For Part 1 see MS1 Over the last decades mathematical models have been used to identify Chair: Katarzyna Rejniak, H. Lee Moffit This minisymposium will bring important features of immune responses Cancer Center Research Institute, USA researchers who are actively involved in development of mathematical approaches during disease. In this minisymposium Glioblastoma are notoriously in mathematical biology. The purpose of we bring together experts in modeling aggressive, malignant brain tumors that the minisymposium is to address recent immune responses and infectious disease have variable response to treatment. advances of mathematical methods dynamics. Our sessions will focus on Mathematical neuro-oncology (MNO) used to study dynamics of infectious challenges and new directions in the is a young and burgeoning field that diseases and discuss a wide range of study of viral kinetic dynamics, immune leverages mathematical models to topics: computational, mathematical responses, drug and vaccine efficacy, and predict and quantify response to and statistical techniques to study the the best strategies to use the available therapies. These mathematical models infectious diseases. biological data to identify parameters and can form the basis of modern “precision propose new designs for experiments. medicine” approaches to tailor therapy Organizer: Necibe Tuncer Organizer: Stanca Ciupe in a patient-specific manner. Patient- University of Tulsa, USA Virginia Tech, USA specific models (PSMs) can be used to Organizer: Maia Martcheva overcome imaging limitations, improve University of Florida, USA Organizer: Matthias Chung prognostic predictions, stratify patients, 2:00-2:25 Dynamics of Low and High Virginia Tech, USA and assess treatment response in silico. Pathogenic Avian Influenza in Wild 2:00-2:25 Within-Host Virus Model with The information gleaned from such and Domestic Bird Populations Immune Response and Infected Cell models can aid in the construction and Necibe Tuncer, University of Tulsa, USA Age Structure Cameron Browne, Vanderbilt University, efficacy of clinical trials and treatment 2:30-2:55 Modeling Hiv Latency and USA protocols, accelerating the pace of Viral Blips clinical research in the war on cancer. Libin Rong, Oakland University, USA 2:30-2:55 Modeling Human Papilloma Virus and the Onset of Cervical This talk will focus on the growing 3:00-3:25 A Model for the Spatial Cancer translation of PSM to clinical neuro- Transmission of Dengue with Daily Jonathan Forde, Hobart and William Smith oncology. It will also provide a forward- Movement between Villages and a Colleges, USA looking view on a new era of patient- City specific MNO. Andrew Nevai, University of Central 3:00-3:25 A Basic Model for In-Host TB Kristin Rae Swanson Florida, USA; Edy Soewono, Institut Infection Teknologi Bandung, Indonesia Jane Heffernan, Yimin Du, and Jianhong Northwestern University, USA Wu, York University, Canada 3:30-3:55 Disease Invasion of Community Networks with 3:30-3:55 Mechanism Elucidation in Environmental Pathogen Movement Intracellular Signaling Models Via Intermission Joseph Tien, The Ohio State University, Sensitivity Functions 1:45 PM-2:00 PM USA; Zhisheng Shuai, University of Karyn L. Sutton, University of Louisiana, Central Florida, USA; Marisa Eisenberg, USA University of Michigan, USA; P. van Den Driessche, University of Victoria, Canada 2014 SIAM Conference on the Life Sciences 17

Monday, August 4 Monday, August 4 Monday, August 4 MS11 MS12 MS13 Biomechanics in Medicine Recent Developments in Biofluids: Biological and 2:00 PM-4:00 PM Modeling and Analysis Physical Complexity in Room:Symphony III of Bacterial Motion and Fluid Structure Interaction Chemotaxis Problems - Part II of II Mathematics and biomechanics can bring a quantitative understanding to 2:00 PM-4:00 PM 2:00 PM-4:00 PM many questions that arise in medicine. Room:Symphony V Room:Symphony VI This minisymposium brings together For Part 1 see MS5 a diverse group of researchers that Chemotaxis is the active movement of Fluids are the natural environment use mathematical and engineering cells or organisms in response to external of virtually every organism and fluid perspectives to better understand medical chemical signals. It is critical in many structure interaction problems are questions pertaining to atherosclerosis, multicellular processes such as wound ubiquitous in biology. While Newtonian tumor growth and aortic valve disease. healing, cancer metastasis, and embryonic fluids and linearly elastic structures are A range of topics will be presented, development. In this minisymposium, found in nature, many important fluids from basic theoretical issues to more we bring together experts in and materials exhibit nonlinearities experimentally-driven approaches. modeling and analysis of chemotactic movement of cells and present recent or other complex properties. The aim Organizer: Rebecca Vandiver developments in this area. The topics of this minisymposium is to present St. Olaf College, USA of this minisymposium include new examples of such behavior in biological Organizer: Pak-Wing Fok mathematical modeling and analytical systems and the techniques used to University of Delaware, USA methods of chemotaxis at both single cell address these problems. The first half 2:00-2:25 A Mechanical and and cell population levels, and methods focuses on complex fluids and other Biochemical Model of Intimal that bridge these two scales. environmental considerations while the Hyperplastic Lesions Organizer: Chuan Xue second half focuses on properties of the Rebecca Vandiver, St. Olaf College, USA; The Ohio State University, USA immersed structures. The systems vary Pak-Wing Fok, University of Delaware, across multiple scales and present a USA 2:00-2:25 Remarks on Modeling and range of biofluids problems. Identification in Bacterial Chemotaxis 2:30-2:55 Understanding the Role of Zahra Aminzare, Maja Skataric, and Eduardo Organizer: Christina Hamlet Cell-substrate Interaction in Cell and Sontag, Rutgers University, USA Tulane University, USA Focal Adhesion Shapes Magdalena Stolarska, University of St. 2:30-2:55 Global Asymptotic Stability Organizer: Jacek K. Wrobel Thomas, USA of Constant Equilibrium States of a Tulane University, USA Repulsive Chemotaxis Model with 2:00-2:25 Hydrodynamic 3:00-3:25 Quantification of Iliac Artery Logarithmic Sensitivity Tortuosity and Its Implication for Contributions to Amoeboid Cell Kun Zhao, Tulane University, USA Rotation of Fenestrated Aortic Stent Motility Grafts 3:00-3:25 Collective Effects and Owen Lewis and Robert D. Guy, University Matthew G. Doyle and Cristina Amon, Correlations in Semidilute Bacterial of California, Davis, USA; Juan Carlos University of Toronto, Canada; Leonard Suspensions del Alamo and Shun Zhang, University of Tse, Toronto General Hospital, Canada Shawn Ryan, Pennsylvania State University, California, San Diego, USA USA; Igor Aranson, Argonne National 3:30-3:55 Modeling the Growth of an 2:30-2:55 Flow Through a Two- Laboratory, USA; Leonid Berlyand, Atherosclerotic Lesion Chambered Zebrafish Heart with Pennsylvania State University, USA; Trabeculae Jay R. Walton, Texas A&M University, USA Andrey Sokolov, Argonne National Nicholas A. Battista, Andrea Lane, and Laboratory, USA Laura A. Miller, University of North 3:30-3:55 Relating the Chemotactic Carolina, Chapel Hill, USA Sensitivity with Intracellular Signaling 3:00-3:25 The Effects of Perturbations and Cell Movement on Lamprey Swimming Chuan Xue, The Ohio State University, USA Christina Hamlet, Tulane University, USA; Eric Tytell, Tufts University, USA; Lisa J. Fauci, Tulane University, USA 3:30-3:55 Population Scale Effects of Macrophytes on Plankton Mobility Virginia B. Pasour, U.S. Army Research Office, USA; Laura Miller, University of North Carolina, Chapel Hill, USA 18 2014 SIAM Conference on the Life Sciences

Monday, August 4 Monday, August 4 Monday, August 4 MS14 MS15 MS16 Dynamics and Connectivity Algebraic Aspects of Structured Population of Complex Networks in the Biochemical Reaction Dynamics: Modeling, Brain - Part II of II Networks - Part I of II Estimation, and Validation - 2:00 PM-4:00 PM 2:00 PM-4:00 PM Part II of II Room:Symphony VII Room:Mecklenburg II 2:00 PM-4:00 PM For Part 1 see MS6 For Part 2 see MS22 Room:Mecklenburg III The dynamics of model neuronal Nonlinear, high-dimensional dynamical For Part 1 see MS8 networks have helped to explain systems with many unknown Structured population models many aspects of cognitive function. parameters are usually used as models are ubiquitous in many areas of As more realism is incorporated into of biochemical reaction networks. The mathematical biology including these models, novel dynamical features nonlinearities and the high number of microbial bioreactors, amyloid diseases, often arise which further enrich our parameters and variables make the direct and cellular proliferation assays. In understanding of the brain. This mathematical analysis of the networks’ these populations, individual aggregates minisymposium explores this theme by behavior difficult. This minisymposium can combine, fragment, and/or grow. discussing recent work in the modeling focuses on recent progress towards Each of these phenomena impact the of both individual neuron dynamics understanding the mathematical model in substantially different ways. and network topology, focusing upon aspects of reaction networks using Accordingly, significant research has implications on network behavior techniques from algebraic geometry and focused on the development of correct and information coding. The speakers computational algebra. The progress models as well as accurate estimation of will draw particular attention to new bypasses the need for simulation and kernels and rates. This minisymposium mathematical approaches in explaining highlights the rich algebraic structure will showcase current directions of sensory processing and information that underlies reaction networks. research in advanced simulation, propagation. Topics that will be covered include estimation, and validation techniques to Organizer: Victor Barranca multistationarity, qualitative properties, better understand structured populations. New York University, USA model comparison, and identifiability, Organizer: David M. Bortz with special focus on mass-action Organizer: Douglas Zhou University of Colorado Boulder, USA kinetics. Shanghai Jiao Tong University, China Organizer: John G. Younger Organizer: Elisenda Feliu 2:00-2:25 Path-integrals and Large University of Michigan, USA University of Copenhagen, Denmark Deviations in a Stochastic Hybrid 2:00-2:25 Limited Measurement Neural Network Organizer: Carsten Wiuf Domains: Robustness of Parameter Paul C. Bressloff, University of Utah, University of Copenhagen, Denmark Estimation in Flocculation Dynamics USA and University of Oxford, United 2:00-2:25 A Global Convergence Dustin Keck, University of Colorado, Kingdom; Jay Newby, The Ohio State Result for Processive Multisite Boulder & US Air Force, USA University, USA Phosphorylation Systems 2:30-2:55 A General Structured 2:30-2:55 Theoretical Modeling of Anne Shiu, University of Chicago, USA; Population Model with the Nonlinear Dendritic Integration Carsten Conradi, Max Planck Institute for Application to Amphibians Infected Songting Li and Douglas Zhou, Shanghai Dynamics of Complex Systems, Germany with Chytridiomycosis Jiao Tong University, China; David Cai, 2:30-2:55 Structural Identifiability of Baoling Ma and Azmy S. Ackleh, Shanghai Jiao Tong University, China Biological Models University of Louisiana, Lafayette, and Courant Institute of Mathematical Nicolette Meshkat and Seth Sullivant, USA; Jacoby Carter, USGS National Sciences, New York University, USA North Carolina State University, USA Wetlands Research Center, USA; Vinodh 3:00-3:25 Analytical Evaluation of Challamuthu, University of Louisiana, 3:00-3:25 Degree Two Polynomials Targeting Performances at Short and Lafayette, USA for Saddle Node Bifurcations in Mass Long Distances in a Stochastic Model Action Networks 3:00-3:25 Data Assimilation Methods for Neural Arborization Carsten Conradi, Max Planck Institute for and Inverse Problem for Protein Remus Osan and Jun Xia, Georgia State Dynamics of Complex Systems, Germany Polymerization University, USA; Emily Su, Rutgers Aurora Armiento and Marie Doumic, University, USA 3:30-3:55 The Dependence of the INRIA Rocquencourt, France Existence of Positive Steady States on 3:30-3:55 Vasculature Adaptation and the Rate Coefficients for Deficiency- 3:30-3:55 Impact of Ellipsoid Optimization in Embryonic Zebrafish One Mass Action Systems Geometry and Deformation on Brain Balázs Boros, Eötvös Loránd University, Flocculation Dynamics Dan Hu, Shanghai Jiao Tong University, Hungary Eric Kightley, University of Colorado, China USA 2014 SIAM Conference on the Life Sciences 19

Monday, August 4 Monday, August 4 5:30-5:55 Merging Population Genetics, Mosquito Behaviour and CP1 MS17 Epidemiology to Predicting the Success of the Use of GM Mosquitoes Cancer New Interventions and for Malaria Control 2:00 PM-4:00 PM Recent Progress on Christophe Boëte, Aix-Marseille Université, France Room:Mecklenburg I Modeling Malaria 6:00-6:25 Application of P. Chair: Hermann Frieboes, University of 4:30 PM-6:30 PM Falcipalrum Gametocyte Sex Louisville, USA Room:Symphony I Ratios Via Competitive and Non-Competitive Strategies: The 2:00-2:25 A Mathematical Model of New intervention techniques are Intermittent Androgen Suppression Evolutionary Implications being considered or currently being Miranda I. Teboh-Ewungkem, Lehigh Therapy for Treatment of Advanced employed as tools to control malaria Prostate Cancer University, USA; Thomas Yuster, in endemic malaria regions. Some of John G. Alford, Edward Swim, and Alacia Lafayette College, USA these include the use of Intermittent M. Voth, Sam Houston State University, USA Preventive Treatment (IPT), where at risk individuals receive a full curative dose 2:30-2:55 Can Mathematical Models of an antimalarial medication, or the use/ Predict the Outcomes of Prostate consideration of genetically modified Cancer Patients Undergoing Intermittent Androgen Suppression mosquitoes. The benefits and/or impact Therapy? of these intervention methods are still Rebecca A. Everett, Aaron Packer, and emerging and not fully understood, and Yang Kuang, Arizona State University, it will require some time to be fully USA evaluated in the field. Mathematical 3:00-3:25 Variance Reduced Model models can shed some light on these. for Tumor Growth This minisymposium aims to do that. Annelies Lejon, Giovanni Samaey, and Dirk Organizer: Miranda I. Teboh- Roose, Katholieke Universiteit Leuven, Ewungkem Belgium Lehigh University, USA 3:30-3:55 On the Accumulation of Organizer: Zhilan Feng Mutations in Cancer Purdue University, USA Cristian Tomasetti, Johns Hopkins University, USA 4:30-4:55 Ipt and the Spread of Drug Resistant Malaria Zhilan Feng, Purdue University, USA; Miranda Teboh-Ewungkem, Lehigh Coffee Break University, USA; Katharine Gurski, Howard University, USA; Carrie A. 4:00 PM-4:30 PM Manore, Tulane University, USA; Angela Room:Symphony Preconvene Area Peace, Arizona State University, USA; Olivia Prosper, Dartmouth College, USA 5:00-5:25 The Effect of IPT on the Spread of Drug Resistant Malaria Parasite When Regions are Connected Scott Duke-Sylvester, University of Louisiana, Lafayette, USA; Jemal Mohammed-Awel, Valdosta State University, USA; Frederick Baliraine, LeTourneau University, USA; Miranda Teboh-Ewungkem, Lehigh University, USA

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Monday, August 4 Monday, August 4 Monday, August 4 MS18 MS19 MS20 Modeling Biological Cell Mechanics and Motility Mechanisms and Phenomena Through the Use 4:30 PM-6:30 PM Computation in Neuronal of Diffusion Models Room:Symphony V Networks 4:30 PM-6:30 PM Cell migration is important in 4:30 PM-6:30 PM Room:Symphony III many processes, such as embryonic Room:Symphony VII The role of mathematical diffusion development, tissue repair, obtaining Our speakers address a range of neural has become an increasingly important nutrients, and cancer metastasis. networks mechanisms in order to tool as developing an understanding of Intracellular forces necessary for understand their impact on specific diffusion will help us explain natural migration are generated by cytoskeletal computations. processes. Diffusion is imperative in rearrangement, which is a dynamic process that effects the mechanical Organizer: Andrea K. Barreiro modeling processes where spatial factors Southern Methodist University, USA are essential. In addition to the standard properties of the cell. The appropriate heat equation, recent studies consider rheological description of the cell is Organizer: Katherine Newhall nonlinear reaction-diffusion models that generally unknown and depends on the Courant Institute of Mathematical give rise to traveling wave solutions timescale, cell type, environment, and Sciences, New York University, USA while investigating heterogeneous migration mode. This minisymposium 4:30-4:55 Impact of Single-Neuron environments. This session will highlight will present recent work on modeling Dynamics on Transfer of Correlations a variety of biological phenomena that the cytoplasm in migrating cells and from Common Input can be modeled with diffusion ranging elucidating the role of mechanics in Andrea K. Barreiro, Southern Methodist University, USA from epidemiology, physiology and single and collective cell migration. inflammation, and population ecology Organizer: Wanda Strychalski 5:00-5:25 Reduction Methods for utilizing theoretical and simulation Case Western Reserve University, USA Spiking Networks Cheng Ly, Virginia Commonwealth results. 4:30-4:55 The Physics of Collective University, USA; Wilten Nicola and Sue Cell Migration in Wound Healing and Organizer: Kamuela E. Yong Ann Campbell, University of Waterloo, Cancer Metastasis Arizona State University, USA Canada Charles Wolgemuth, University of Arizona, Organizer: Tracy L. Stepien USA 5:30-5:55 Integrate-and-Fire Model of Arizona State University, USA Insect Olfaction 5:00-5:25 Exploring Motility of Breast Pamela B. Fuller, Rensselaer Polytechnic 4:30-4:55 Modeling and Analysis of Cancer Cells Using a 3D Individual Institute, USA Glioma Tumor Growth Cell Based Model Tracy L. Stepien, Erica Rutter, and Yang Hildur Knutsdottir, University of British 6:00-6:25 The Essential Role of Phase Kuang, Arizona State University, USA Columbia, Canada Delayed Inhibition in Decoding 5:00-5:25 An Application of Synchronized Oscillations within the 5:30-5:55 Insights into Cytoplasmic Brain Mathematics to Osteoarthritis Related Rheology Gained from Modeling Mainak Patel, Duke University, USA; Badal Inflammation Cellular Blebbing Jason Graham, University of Scranton, USA Joshi, California State University, San Wanda Strychalski, Case Western Reserve Marcos, USA 5:30-5:55 The Effects of Cross-diffusion University, USA on an SIR Model 6:00-6:25 Actin-myosin Spatial Patterns Kamuela E. Yong, Arizona State University, from a Simplified Isotropic Viscoelastic USA Model 6:00-6:25 Success, Failure, and Jun Allard, Owen Lewis, and Robert D. Guy, Spreading Speeds for Invasions on University of California, Davis, USA Spatial Gradients Bingtuan Li, University of Louisville, USA 2014 SIAM Conference on the Life Sciences 21

Monday, August 4 Monday, August 4 Monday, August 4 MS21 MS22 MS23 Modeling Endocrine Algebraic Aspects of Heterogeneity in Electrically Regulation of Female Biochemical Reaction Excitable Cells and Networks Reproduction Networks - Part II of II - Part I of II 4:30 PM-6:30 PM 4:30 PM-6:30 PM 4:30 PM-6:30 PM Room:Mecklenburg I Room:Mecklenburg II Room:Mecklenburg III The complex interplay between For Part 1 see MS15 For Part 2 see MS31 hormones produced by the brain and Nonlinear, high-dimensional dynamical Electrically excitable cells include the ovaries is a key ingredient for systems with many unknown neurons, muscle and cardiac cells, and regulating and maintaining the female parameters are usually used as models many endocrine cells. Such cells typically reproductive system. Abnormal levels of biochemical reaction networks. The exhibit a great deal of heterogeneity, both of these hormones often result in cycle nonlinearities and the high number of among interacting cell types and within irregularities and infertility in humans parameters and variables make the direct populations of single cell types. In this and animals. Minisymposium speakers mathematical analysis of the networks’ minisymposium we focus on examples in will describe physiological mechanisms behavior difficult. This minisymposium which heterogeneity is a crucial element and mathematical models of various focuses on recent progress towards of the system, ways in which one can aspects of cycle regulation. Data analysis, understanding the mathematical use mathematical models to understand modeling and simulation may be helpful aspects of reaction networks using the basis of heterogeneity and overcome in understanding the roles of the many techniques from algebraic geometry and the challenges it presents, and methods components of the sexual endocrine computational algebra. The progress for extracting network connectivity system, in predicting successful bypasses the need for simulation and using data on a heterogeneous cellular hormone therapies for young and aging highlights the rich algebraic structure that population. women, and in studying methods of underlies reaction networks. Topics that Organizer: Richard Bertram contraception. will be covered include multistationarity, Florida State University, USA qualitative properties, model comparison, Organizer: James F. Selgrade Organizer: Duncan J. MacGregor and identifiability, with special focus on North Carolina State University, USA University of Edinburgh, United Kingdom mass-action kinetics. 4:30-4:55 Multiple Cycles and 4:30-4:55 Paracrine Regulation of Bifurcation in Models of Hormonal Organizer: Elisenda Feliu Glucagon and Somatostain Secretion Control of the Menstrual Cycle University of Copenhagen, Denmark Margaret A. Watts, National Institutes James F. Selgrade, North Carolina State Organizer: Carsten Wiuf of Health, USA; Ofer Kimchi, Princeton University, USA University of Copenhagen, Denmark University, USA; Arthur Sherman, National Institutes of Health, USA 5:00-5:25 A Differential Equation Model 4:30-4:55 Atoms of Multistationarity in for the Bovine Estrous Cycle Chemical Reaction Networks 5:00-5:25 Hypothalamic Vasopressin Claudia Stoetzel, Julia Ploentzke, and Badal Joshi, California State University, San Neurons: Signal Processing in An Susanna Roeblitz, Zuse Institute Berlin, Marcos, USA; Anne Shiu, University of Asynchronous Bursting Population Germany Chicago, USA Duncan J. MacGregor and Gareth Leng, University of Edinburgh, United Kingdom 5:30-5:55 The Use of Physiological 5:00-5:25 An Algebraic Framework Model of Menstrual Cycle Regulation for Describing and Studying Binary 5:30-5:55 Real-Time Model Calibration in Women’s Health: Fertility and Enzymatic Networks and Prediction Testing with the GPU Contraception Gilles Gnacadja, Amgen Inc., USA and Dynamic Clamp Anna Kondic and Craig Fancourt, Merck Patrick A. Fletcher, Joël Tabak, and Richard 5:30-5:55 Exploiting Reaction Network & Co., Inc., USA Bertram, Florida State University, USA Structure for Parameter Identification 6:00-6:25 The Role of Insulin and of Biochemical Switches 6:00-6:25 Leveraging Mathematical Androgen Dynamics in Female Irene Otero-Muras, IIM-CSIC, Vigo, Models to Understand Population Hormone Dysregulation Spain; Pencho Yordanov, ETH Zürich, Variability in Response to Cardiac Erica J. Graham and James Selgrade, North Switzerland; Attila Gabor, CSIC, Madrid, Drugs Carolina State University, USA Spain; Julio R. Banga, IIM-CSIC, Vigo, Eric Sobie, Icahn School of Medicine at Spain Mount Sinai, USA 6:00-6:25 Correspondence of Regular and Generalized Mass Action Systems Matthew Johnston, University of Wisconsin, Madison, USA 22 2014 SIAM Conference on the Life Sciences

Monday, August 4 Monday, August 4 Tuesday, August 5 CP2 Funding Agency Panel Epidemiology I 8:45 PM-9:30 PM Registration 4:30 PM-6:00 PM Room:Symphony II 7:30 AM-5:00 PM Room:Symphony II Chair: Mette Sofie Olufsen, North Room:Symphony Preconvene Area Chair: Andrew Nevai, University of Carolina State University, USA Central Florida, USA Panelists: 4:30-4:55 An SIRS Epidemic Model Mary Ann Horn, with Non-Exponential Probability for National Science Foundation, USA Remarks Temparary Immunity Larry Nagahara, 8:10 AM-8:15 AM Thomas W. Carr, Southern Methodist National Cancer Institute, USA Room:Symphony I, II & III University, USA Virginia Pasour, 5:00-5:25 A Simple Model U.S. Army Research Office, USA Incorporating Demographic and Epidemiological Processes in a Spatially Heterogeneous IP3 Yongli Cai and Shangbin Cui, Sun Yat- Modelling Plant Cell and Sen University, China; Weiming Wang, Tissue Growth Wenzhou University, China 8:15 AM-9:00 AM Room:Symphony I, II & III Dinner Break Chair: Laura A. Miller, University of 6:30 PM-8:00 PM North Carolina, Chapel Hill, USA Plant growth typically occurs through Attendees on their own the coordinated anisotropic expansion of plant cells. Growth is regulated by hormones and is driven by high PD1 intracellular pressures generated by osmosis. This machinery allows a Forward Looking Session plant primary root, for example, to 8:00 PM – 8:45 PM penetrate soil in a direction guided by gravity, while seeking out nutrients and Room: Symphony II avoiding obstacles. I will describe the Chair: Mette Sofie Olufsen, North Carolina biomechanical aspects of a multiscale State University, USA model for root gravitropism recently Panelists: developed with colleagues at the Martin Golubitsky Mathematical Biosciences Institute, Ohio Centre for Plant Integrative Biology State University, USA at the University of Nottingham, UK. This incorporates descriptions of cell Nicholas Hill walls as fibre-reinforced viscoelastic University of Glasgow, United Kingdom polymer networks and adopts upscaling Norman A. Mazer approaches to efficiently describe the F. Hoffmann-La Roche Ltd, Switzerland growth of multicellular tissues. John Rinzel Oliver E. Jensen New York University, USA University of Manchester, United Timothy W. Secomb Kingdom University of Arizona, USA Kristin Rae Swanson Northwestern University, USA Coffee Break 9:00 AM-9:30 AM Room:Symphony Preconvene Area 2014 SIAM Conference on the Life Sciences 23

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS24 MS25 MS26 Mathematical Modeling Mathematical Modeling of Molecular Biosciences: of Infectious Diseases - Oxygen Transport in Various Macromolecular Structures Part I of II Tissues - Part I of II and Interactions - Part I of II 9:30 AM-11:30 AM 9:30 AM-11:30 AM 9:30 AM-11:30 AM Room:Symphony I Room:Symphony III Room:Symphony V For Part 2 see MS32 For Part 2 see MS34 For Part 2 see MS35 Mathematical modeling has played an The efficient transport of oxygen along Molecular based mathematical biology important role in understanding the the entire vascular pathway is essential has been emerging as one of the most spread and control of infectious diseases to maintaining homeostasis, as improper promising interdisciplinary research in populations. Mathematical models oxygen transport is a leading cause of areas in the interface of mathematics have been increasingly used to guide disease in many tissues. This session and biology, driven by the fact that public health policy decisions and presents theoretical models that are used most experimental researches in life explore questions in infectious disease to quantitatively assess solute transport sciences are based on molecular biology control. This minisymposium will gather processes for which experiments can or molecular level understanding. This researchers employing a variety of merely provide qualitative observations. minisymposium will focus on recent mathematical techniques to study relevant These modeling studies integrate advances on a variety of modeling phenomena of infectious diseases. structural and functional experimental and computation developments for Organizer: Zhisheng Shuai data about oxygen-consuming tissues and studying macromolecular structures and University of Central Florida, USA the non-uniform vasculature that delivers interactions. Example topics include oxygen to them, providing insights into molecular mechanics and dynamics, Organizer: Isaac Chun-Hai Fung the behavior and regulation of a variety implicit solvent models, molecular Georgia Southern University, USA of tissues, including the kidney, skeletal docking, protein folding, protein-protein 9:30-9:55 A Simple Epidemic Model muscle, eye, and brain. interaction, biomolecular solvation, with Nosocomial Transmission Organizer: Brendan C. Fry membrane, ion-channels, etc. Emphasis Fred Brauer, University of British Columbia, Duke University, USA will be placed not only on mathematical Canada theories and methods, but also on 9:30-9:55 Assessing the Impact of 10:00-10:25 Epidemiological and Structural Organization of the Renal biomolecular simulations and software Economic Benefits of Targeted Medulla on Oxygen Distribution Using developments. Tuberculosis Screening in a a Mathematical Model Correctional Facility of New River Organizer: Shan Zhao Brendan C. Fry, Duke University, USA Health District University of Alabama, USA Kaja Abbas, Virginia Polytechnic Institute 10:00-10:25 Can Pre-Glomerular Organizer: Benzhuo Lu and State University, USA Oxygen Transport Be Used to Institute of Computational Mathematics, Investigate Renal Anatomy? 10:30-10:55 Demographic Transition China Bruce S. Gardiner, Saptarshi Kar, and and the Dynamics of Measles in China David Smith, University of Western 9:30-9:55 Computational Design of Sheng Li, Pennsylvania State University, Australia, Australia; Roger Evans, Monash Megadalton-Scale Nucleic Acid USA University, Australia Nanoassemblies 11:00-11:25 Modeling SIS Disease Mark Bathe, Massachusetts Institute of 10:30-10:55 Development of Hypoxia Dynamics on Random Contact Technology, USA in a Model of Renal Blood Flow Networks Control and Oxygen Consumption 10:00-10:25 The Structural Junling Ma, University of Victoria, Canada Ioannis Sgouralis, Duke University, USA Glycobiology of HIV: Insights from Molecular Simulations and 11:00-11:25 Models of Neurovascular Implications for the Design of Virucidal Coupling and Cerebral Autoreglation Lectins Tim David, University of Canterbury, New David F. Green, State University of New Zealand York, Stony Brook, USA

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Tuesday, August 5 Tuesday, August 5 10:30-10:55 Near Wall Motion of a Model Swimmer in a Viscoelastic Fluid MS26 MS27 Gaojin Li, Alireza Karimi, and Arezoo Ardekani, University of Notre Dame, USA Molecular Biosciences: Low Reynolds Number 11:00-11:25 Lyme Disease and Macromolecular Structures Locomotion in Viscoelastic Microorganism Swimming in Complex and Interactions - Part I of II and Heterogeneous Fluids - Fluids 9:30 AM-11:30 AM Part I of II Charles Wolgemuth, University of Arizona, USA continued 9:30 AM-11:30 AM Room:Symphony VI For Part 2 see MS36 10:30-10:55 3D Continuum Modeling Locomotion at low Reynolds number of Ion Permeation in Ion Channel in Newtonian fluids is a classical well- Systems studied problem. Many biological Benzhuo Lu, Bin Tu, and Yan Xie, Institute systems involve heterogeneous of Computational Mathematics, China; viscoelastic materials, such as the Linbo Zhang, Chinese Academy of mucus in the reproductive, digestive, Sciences, China and respiratory systems. The basic 11:00-11:25 Monte Carlo Solution of physics of viscoelastic fluids is Biochemical Electrostatics Problems not fully understood, and different Michael Mascagni, Florida State modeling assumptions have led to University, USA conflicting predictions about the effect of viscoelasticity on swimming speed. Simulations of these types of complex systems must address the nonlinear coupling between elastic stresses from the fluid and active complex structures. In this session we present recent work on locomotion in low Reynolds number viscoelastic fluids and in heterogeneous media. Organizer: Becca Thomases University of California, Davis, USA Organizer: Robert D. Guy University of California, Davis, USA 9:30-9:55 Finite Length Undulatory Swimmers: Whether to Kick or to Burrow in a Viscoelastic Fluid Becca Thomases and Robert D. Guy, University of California, Davis, USA 10:00-10:25 Flagellar Kinematics in Complex Fluids: Viscous and Elastic Effects Arvind Gopinath, Max Planck Institute for Dynamics and Self-Organization, Germany; Boyang Qin, University of Pennsylvania, USA; Jing Yang and Jerry P. Gollub, Haverford College, USA; Paulo E. Arratia, University of Pennsylvania, USA

continued in next column 2014 SIAM Conference on the Life Sciences 25

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS28 MS29 MS30 Modeling and Analysis of Dynamics of Thrombus Developments in Rhythm Generation and Development: Formation, the Mathematics of Control: CPGs - Part I of II Degradation, and Biochemical Reaction 9:30 AM-11:30 AM Therapeutic Design Networks - Part I of II Room:Symphony VII 9:30 AM-11:30 AM 9:30 AM-11:30 AM For Part 2 see MS37 Room:Mecklenburg I Room:Mecklenburg II Neural circuits produce rhythmic outputs Blood clot (thrombus) regulation is For Part 2 see MS39 that underlie a variety of behaviors. a complex process coordinated by Mathematical models of biochemical How these activity patterns arise and biochemistry, biomechanics, and fluid networks usually consist of intricate are modulated represent fundamental flow. Thrombus dysregulation can result systems of deterministic or stochastic questions in neuronal dynamics. An ideal in severe medical problems. Current nonlinear differential equations. setting in which to study these issues of research explores various aspects of Despite this great level of complexity, rhythm generation and control is provided thrombus development (structural important properties of biochemical by central pattern generators (CPGs), formation of fibrin, interaction of network models may depend only on relatively accessible circuits that produce blood components and flow, clot the structure of the network and not on the repetitive, multi-phasic outputs critical dissolution) and employs a wide range the specific values of the parameters to fundamental rhythmic behaviors such of mathematical tools (differential involved. In this minisymposium, as breathing, chewing, swimming, and equations, stochastic processes, speakers will describe current efforts to walking. This minisymposium will explore numerics, multiscale modeling). This (1) relate dynamical properties of these a variety of interesting topics that arise in minisymposium will highlight advances models (e.g. existence and uniqueness of the theoretical study of CPGs, including in thrombus modeling and discuss equilibria, stability, long-term behavior) the nonlinear dynamics of emergent implications for designing effective with the topology of the underlying rhythmicity, dynamics involving multiple therapies for clotting defects. network; (2) identify functional modules time scales and stochasticity, and closed of biochemical networks; and (3) use loop feedback control of neural systems. Organizer: Erica J. Graham North Carolina State University, USA recently obtained theoretical advances in Organizer: Jonathan E. Rubin modeling specific biochemical networks. University of Pittsburgh, USA Organizer: Brittany Bannish University of Central Oklahoma, USA Organizer: Casian Pantea Organizer: Lucy Spardy West Virginia University, USA 9:30-9:55 A Model-Based University of Pittsburgh, USA Comparison of Clinical and Organizer: Maya Mincheva 9:30-9:55 Multiple Rhythms from One Biological Determinants for Northern Illinois University, USA Network: Phase Plane and Stochastic Anticoagulation Therapy 9:30-9:55 Recent Developments, Analyses of Rhythmic Activity in Turtle Lisette G. dePillis, Harvey Mudd College, Connections and Open Problems in Motor Circuits USA; Erica J. Graham, North Carolina Chemical Reaction Network Theory Abigail Snyder and Jon Rubin, University of State University, USA; Yanping Ma, Murad Banaji, University of Portsmouth, Pittsburgh, USA Loyola Marymount University, USA; Ami United Kingdom 10:00-10:25 Using Experimental Phase Radunskaya, Pomona College, USA; Julie Simons, Tulane University, USA 10:00-10:25 Monotonicity of Response Curves to Characterize Inter- Chemical Reaction Networks with Leg Coupling 10:00-10:25 Structural Hierarchy Respect to Non-Simplicial Cones Silvia Daun-Gruhn, Nils Rosjat, and Tibor I. Governs Nonlinear Mechanics of Pete Donnell and Murad Banaji, University Toth, University of Cologne, Germany Fibrin Networks and Transport of of Portsmouth, United Kingdom Blood Clotting Factors 10:30-10:55 Shilnikov Cornerstone Oleg Kim, University of Notre Dame, USA 10:30-10:55 Sign Vectors in Chemical Bifurcation Generates a Family of Reaction Network Theory Mechanisms Governing Dynamics of 10:30-10:55 Fibrin Polymerization in Stefan Mueller, RICAM, Austrian Central Pattern Generators Flow: Gelation and Post Gelation Academy of Sciences, Austria William H. Barnett, Georgia State University, Dynamics USA Cheryl Zapata-Allegro, North Carolina 11:00-11:25 Persistence and the Global Attractor Conjecture 11:00-11:25 Dynamical Architectures for State University, USA Gheorghe Craciun, University of Control of Rhythmic Behavior 11:00-11:25 Therapeutic Implications Wisconsin, Madison, USA Peter J. Thomas, Hillel Chiel, and Jeffrey from a Multiscale Model of Blood Clot Gill, Case Western Reserve University, Degradation USA; David Lyttle, University of Arizona, Brittany Bannish, University of Central USA; Kendrick Shaw, Case Western Reserve Oklahoma, USA; Aaron L. Fogelson and University, USA James P. Keener, University of Utah, USA 26 2014 SIAM Conference on the Life Sciences

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS31 CP3 IP4 Heterogeneity in Electrically Epidemiology II Robustness, Control, and Excitable Cells and 9:30 AM-11:30 AM the Organization of Cell Networks - Part II of II Room:Symphony II Lineages 9:30 AM-11:30 AM Chair: Yun Kang, Arizona State 1:00 PM-1:45 PM Room:Mecklenburg III University, USA Room:Symphony I, II & III For Part 1 see MS23 9:30-9:55 Comparison of a Chair: Qing Nie, University of Electrically excitable cells include Deterministic and Stochastic Model California, Irvine, USA neurons, muscle and cardiac cells, for the Transmission Dynamics of Influenza In the wake of a deluge of phenotypic, and many endocrine cells. Such Adnan Khan, Lahore Univeristy of molecular, genomic and genetic data, cells typically exhibit a great deal of Management Sciences (Pakistan) biologists are increasingly returning to heterogeneity, both among interacting questions of biological organization: 10:00-10:25 Analysis of Labour cell types and within populations of Why are biological systems built single cell types. In this minisymposium Productivity in the Presence of Substance Abuse the way they are? Why are they so we focus on examples in which Isaac Takaidza, Vaal University of complex? How much is chance, and how heterogeneity is a crucial element of Technology, South Africa much is necessity? Systems Biologists the system, ways in which one can use 10:30-10:55 A Mixed-Strategy Game maintain that “design principles” are mathematical models to understand the drivers of biological organization, but basis of heterogeneity and overcome Theoretical Approach for Infectious Disease Prevention by Social given a biological system, how does the challenges it presents, and methods Distancing one identify the design principles that for extracting network connectivity Jing Li, California State University, (presumably) shaped it? The study of using data on a heterogeneous cellular Northridge, USA; Timothy Reluga, embryonic development—especially population. Pennsylvania State University, USA the elaboration of spatial pattern, the Organizer: Richard Bertram 11:00-11:25 Abms for Infectious determination of organ size, and the Florida State University, USA Diseases Spreading and Ill-Posed control of tissue growth—provides Organizer: Duncan J. MacGregor Problems fertile ground for investigating such University of Edinburgh, United Valeriy D. Perminov, BioTeckFarm Ltd., questions, in part because developmental Russia Kingdom systems are highly complex, highly conserved, and likely to have been 9:30-9:55 Estimating the Functional selected for high performance. In this Connectivity in Networks of Neurons talk, I will discuss how requirements for Henry D. Abarbanel, University of Lunch Break California, San Diego, USA stability, speed and robustness can be 11:30 AM-1:00 PM used to understand some of the complex 10:00-10:25 Inference of Network intra- and intercellular interactions that Structure from Spikes and Time Series Attendees on their own take place within animal cell lineage Timothy Sauer, George Mason University, USA pathways. 10:30-10:55 Using Mathematical Arthur Lander Models to Determine the Source of University of California, Irvine, USA Heterogeneity in Cellular Calcium Dynamics Richard Bertram, Florida State University, Intermission USA; Maurizio Tomaiuolo, University of Pennsylvania, USA; Arturo Gonzalez- 1:45 PM-2:00 PM Iglesias and Joël Tabak, Florida State University, USA; Henry D. Abarbanel, University of California, San Diego, USA 11:00-11:25 Heterogeneity As a Consequence of Homeostasis Timothy O’Leary, Brandeis University, USA 2014 SIAM Conference on the Life Sciences 27

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS32 MS33 MS34 Mathematical Modeling Parameter Estimation for Mathematical Modeling of of Infectious Diseases - Biological Systems Oxygen Transport in Various Part II of II 2:00 PM-4:00 PM Tissues - Part II of II 2:00 PM-4:00 PM Room:Symphony II 2:00 PM-3:30 PM Room:Symphony I Parameter estimation techniques Room:Symphony III For Part 1 see MS24 are a key tool to analyze biological For Part 1 see MS25 Mathematical modeling has played systems by comparing mathematical The efficient transport of oxygen along an important role in understanding models with available data. With these the entire vascular pathway is essential the spread and control of infectious methods researchers are able to validate to maintaining homeostasis, as improper diseases in populations. Mathematical models and predict the behavior of oxygen transport is a leading cause of models have been increasingly used to the underlying system. Parameter disease in many tissues. This session guide public health policy decisions estimation faces various challenges, presents theoretical models that are used and explore questions in infectious such as robustness of the estimates, ill- to quantitatively assess solute transport disease control. This minisymposium posedness of the problem, and efficiency processes for which experiments can will gather researchers employing a of the numerical methods. Without merely provide qualitative observations. variety of mathematical techniques to properly addressing these questions These modeling studies integrate study relevant phenomena of infectious results of the parameter estimation structural and functional experimental diseases. problem may be meaningless. In this data about oxygen-consuming tissues Organizer: Zhisheng Shuai minisymposium we will discuss these and the non-uniform vasculature that University of Central Florida, USA challenges and provide new directions delivers oxygen to them, providing and results for parameter estimation insights into the behavior and regulation Organizer: Isaac Chun-Hai Fung techniques for biological systems. of a variety of tissues, including the Georgia Southern University, USA Organizer: Matthias Chung kidney, skeletal muscle, eye, and brain. 2:00-2:25 Economic Evaluation of the Virginia Tech, USA Organizer: Brendan C. Fry Fungal Meningitis Outbreak Response in New River Valley: Local Health 2:00-2:25 Parameter Estimation for Duke University, USA Department and Clinical Perspectives Large-Scale Biological Systems 2:00-2:25 Effect of Intraocular Nargesalsadat Dorratoltaj and Kaja Justin Krueger, Virginia Tech, USA Pressure and Arterial Blood Pressure Abbas, Virginia Tech, USA 2:30-2:55 Beyond Acceptable on Oxygen Saturation Levels in the Retina: a Theoretical Model 2:30-2:55 Contact and Transmission in Parameter Fits Julia Arciero and Giovanna Guidoboni, Epidemiological Models Eberhard O. Voit, Georgia Institute of Indiana University - Purdue University Lydia Bourouiba, Massachusetts Institute Technology, USA Indianapolis, USA; Brent Siesky and of Technology, USA 3:00-3:25 Removing Irrelevant Alon Harris, Indiana University School of 3:00-3:25 Modeling Cholera in Parameters from Complex Biological Medicine, USA Heterogeneous Environments Models 2:30-2:55 Computational Modeling of Jin Wang, Old Dominion University, USA Mark K. Transtrum, Brigham Young University, USA Oxygen and ATP Transport in Skeletal 3:30-3:55 Mathematical Modeling of Muscle Capillary Networks of Normal Cholera 3:30-3:55 Convergence Properties and Pre-Diabetic Rats Zhisheng Shuai, University of Central of Gauss-Newton Methods, Well- Daniel Goldman, University of Western Florida, USA Posedness of Parameter Estimation Ontario, Canada Problems and the Reliability of Parameter Estimates 3:00-3:25 Green’s Function Methods Ekaterina Kostina, Fachbereich for Simulating Solute Transport in the Mathematik und Informatik, Philipps- Microcirculation Universität Marburg, Germany Timothy W. Secomb, University of Arizona, USA 28 2014 SIAM Conference on the Life Sciences

Tuesday, August 5 2:30-2:55 New Effective Finite Tuesday, August 5 Element Algorithms for Solving Local MS35 and Nonlocal Poisson-Boltzmann MS36 Molecular Biosciences: Equations for Biomolecules in Ionic Solvent Low Reynolds Number Macromolecular Structures Dexuan Xie, University of Wisconsin, Locomotion in Viscoelastic and Interactions - Part II of II Milwaukee, USA and Heterogeneous Fluids - 2:00 PM-4:00 PM 3:00-3:25 Fluctuation and Fidelity Part II of II Control of Single Transcriptional Room:Symphony V Machine 2:00 PM-4:00 PM For Part 1 see MS26 Jin Yu, Beijing Computational Science Room:Symphony VI Molecular based mathematical biology Research Center, China has been emerging as one of the most For Part 1 see MS27 3:30-3:55 Fast Pseudo-Time Locomotion at low Reynolds number promising interdisciplinary research Simulations of the Nonlinear Poisson- in Newtonian fluids is a classical well- areas in the interface of mathematics Boltzmann (NPB) Equation studied problem. Many biological and biology, driven by the fact that Shan Zhao, University of Alabama, USA systems involve heterogeneous most experimental researches in life viscoelastic materials, such as the mucus sciences are based on molecular biology in the reproductive, digestive, and or molecular level understanding. This respiratory systems. The basic physics of minisymposium will focus on recent viscoelastic fluids is not fully understood, advances on a variety of modeling and different modeling assumptions and computation developments for have led to conflicting predictions studying macromolecular structures and about the effect of viscoelasticity on interactions. Example topics include swimming speed. Simulations of these molecular mechanics and dynamics, types of complex systems must address implicit solvent models, molecular the nonlinear coupling between elastic docking, protein folding, protein-protein stresses from the fluid and active interaction, biomolecular solvation, complex structures. In this session we membrane, ion-channels, etc. Emphasis present recent work on locomotion in will be placed not only on mathematical low Reynolds number viscoelastic fluids theories and methods, but also on and in heterogeneous media. biomolecular simulations and software developments. Organizer: Becca Thomases University of California, Davis, USA Organizer: Shan Zhao University of Alabama, USA Organizer: Robert D. Guy University of California, Davis, USA Organizer: Benzhuo Lu Institute of Computational Mathematics, 2:00-2:25 Computational Models of China Cilia and Flagella in a Brinkman Fluid Karin Leiderman, University of California, 2:00-2:25 Nonlinear Poisson-Nernst- Merced, USA; Sarah D. Olson, Worcester Planck Equations for Ion Flux Through Polytechnic Institute, USA Confined Geometries Marie-Therese Wolfram, Johann Radon 2:30-2:55 An Immersed Boundary Institute for Computational and Applied Method for Two-fluid Mixtures Mathematics, Austria Robert D. Guy, University of California, Davis, USA; Jian Du, Florida Institute of Technology, USA; Aaron L. Fogelson, University of Utah, USA 3:00-3:25 Swimming Through Heterogeneous Networks Henry Fu, University of Nevada, Reno, USA 3:30-3:55 An Active Polar Nematic Model of Microtubule/motor-Protein Assemblies continued in next column Tony Gao and Michael J. Shelley, Courant Institute of Mathematical Sciences, New York University, USA; Robert Blackwell, Matthew Glaser, and Meredith Betterton, University of Colorado, USA 2014 SIAM Conference on the Life Sciences 29

Tuesday, August 5 Tuesday, August 5 2:30-2:55 Translational Modeling and Optimal Concurrent Treatment in MS37 MS38 Oncology Morgan Craig, Université de Montréal, Modeling and Analysis of Mathematical Problems Canada; Anthony Humphries, McGill Rhythm Generation and in Pharmacology: University, Canada; Jacques Bélair and Control: CPGs - Part II of II Perspectives and Jun Li, Université de Montréal, Canada; Michael Mackey, McGill University, 2:00 PM-4:00 PM Challenges Canada; Fahima Nekka, Universite de Montreal, Canada Room:Symphony VII 2:00 PM-4:00 PM 3:00-3:25 Systems Pharmacology: For Part 1 see MS28 Room:Mecklenburg I Revolutionizing Health Care One Neural circuits produce rhythmic Pharmacology has recently been Equation at a Time outputs that underlie a variety of submitted to increasing mathematical Angelean O. Hendrix, North Carolina State behaviors. How these activity patterns influences, to the extent that University, USA arise and are modulated represent “quantitative pharmacology” and fundamental questions in neuronal 3:30-3:55 Nonlinear Pharmacokinetic- “systems pharmacology” are shaping Modeling: A Real Example dynamics. An ideal setting in which to identities of their own. In this Carolyn Cho, Merck & Co., Inc., USA study these issues of rhythm generation minisymposium, we present some of and control is provided by central the central topics in these developing pattern generators (CPGs), relatively fields, emphasizing where mathematical accessible circuits that produce the challenges arise. Mathematical repetitive, multi-phasic outputs critical analysis and closed forms of newly to fundamental rhythmic behaviors reported pharmacokinetics phenomena, such as breathing, chewing, swimming, identification of drug disposition and walking. This minisymposium will characteristics in clinical conditions, explore a variety of interesting topics knowledge translation from in vitro to that arise in the theoretical study of in vivo conditions for drug design, as CPGs, including the nonlinear dynamics well as signal transduction modeling in of emergent rhythmicity, dynamics hematopoietic diseases are some of the involving multiple time scales and examples that will be highlighted. stochasticity, and closed loop feedback control of neural systems. Organizer: Fahima Nekka Universite de Montreal, Canada Organizer: Jonathan E. Rubin University of Pittsburgh, USA Organizer: Jacques Belair Université de Montréal, Canada Organizer: Lucy Spardy University of Pittsburgh, USA Organizer: Jun Li Université de Montréal, Canada 2:00-2:25 Identifying and Explaining Three Time Scale Oscillations 2:00-2:25 Old Problems, New Solutions: Variability and Nonlinearity Yangyang Wang and Jon Rubin, University in Biopharmaceutical Processes and of Pittsburgh, USA; Vivien Kirk and Mathematical Model-Based Problem Pingyu Nan, University of Auckland, New Solving Zealand Fahima Nekka, Universite de Montreal, 2:30-2:55 Robustness and Canada Multifunctionality of Reduced CPG Models Aaron Kelley, Justus T. Schwabedal, and Andrey Shilnikov, Georgia State University, USA 3:00-3:25 Differential Effects of Conductances on Pyloric CPG Output Wafa Soofi, Georgia Institute of Technology, USA 3:30-3:55 Linear Currents Can Be continued in next column Pacemaker Currents Jorge Golowasch, New Jersey Institute of Technology and Rutgers University, USA 30 2014 SIAM Conference on the Life Sciences

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS39 CP4 MS40 Developments in Neuroscience I Mathematical Models in the Mathematics of 2:00 PM-4:00 PM Biology and Epidemiology - Biochemical Reaction Room:Mecklenburg III Part I of II Networks - Part II of II Chair: To Be Determined 4:30 PM-6:30 PM 2:00 PM-4:00 PM 2:00-2:25 Fast-Slow Analysis of Neural Room:Symphony I Room:Mecklenburg II Excitability with Synaptic Noise For Part 2 see MS46 Xueying Wang, Washington State University, For Part 1 see MS30 Mathematical modeling and analysis USA; James P. Keener, University of Utah, are powerful tools to gain important Mathematical models of biochemical USA networks usually consist of intricate insights on the complicated biological systems of deterministic or stochastic 2:30-2:55 Nonlinear Stochastic and epidemiological processes by Dynamics of Sensory Hair Cells nonlinear differential equations. formulating, analyzing, simulating, Rami M. Amro and Alexander Neiman, Ohio and interpreting mathematical models. Despite this great level of complexity, University, USA important properties of biochemical In the proposed minisymposium, we network models may depend only on 3:00-3:25 Large Deviations of An bring together a group of distinguished the structure of the network and not on Ergodic System of Hebbian Neurons researchers who have particular James Maclaurin and Olivier Faugeras, the specific values of the parameters expertise in applying mathematical INRIA Sophia Antipolis, France involved. In this minisymposium, models and theory to study the speakers will describe current efforts to 3:30-3:55 Stationary Solutions for challenging problems arising from the (1) relate dynamical properties of these Neural Field Equations with Periodic field of biology and epidemiology. The Microstructures models (e.g. existence and uniqueness of invited speakers will present the most Elena Malyuting, Arcady Ponosov and John equilibria, stability, long-term behavior) cutting-edge studies in the filed, which Wyller, Norwegian University of Life may provide valuable opportunities with the topology of the underlying Sciences network; (2) identify functional modules for future modeling improvement and of biochemical networks; and (3) use practical applications. The diversity of recently obtained theoretical advances in our speakers may spur new interests modeling specific biochemical networks. Coffee Break and promote participation among 4:00 PM-4:30 PM underrepresented groups including Organizer: Casian Pantea women in this exciting field. West Virginia University, USA Room:Symphony Preconvene Area Organizer: Yun Kang Organizer: Maya Mincheva Arizona State University, USA Northern Illinois University, USA Organizer: Sophia Jang 2:00-2:25 Perturbations of the Lotka- Texas Tech University, USA Volterra System Manoj Gopalkrishnan, Tata Institute of 4:30-4:55 On a Diffusive Predator- Fundamental Research, India; Gheorghe prey Model with Nonlinear Harvesting Craciun, University of Wisconsin, Peng Feng, Florida Gulf Coast University, Madison, USA USA 2:30-2:55 Reaction-Diffusion 5:00-5:25 Qualitative Beavior of Equations With Periodic Behavior Tumor—CD4+ Cytokine System David Siegel, University of Waterloo, Sophia Jang, Texas Tech University, USA Canada; Blair Davey, University of 5:30-5:55 An Application of Optimal Minnesota, USA Control Theory to a Simple Age-of- 3:00-3:25 Elimination of Intermediate Infection Sir Model Species in the Stochastic Reaction Sunmi Lee, KyungHee University, South Networks Korea Daniele Cappelletti and Carsten Wiuf, 6:00-6:25 Evolutionary Dynamics of University of Copenhagen, Denmark a Population Model with Component 3:30-3:55 Bistability in the Dual Futile Allee Effects Cyle Yun Kang, Arizona State University, USA Alan Rendall, Johannes Gutenberg- Universität, Mainz, Germany 2014 SIAM Conference on the Life Sciences 31

Tuesday, August 5 Tuesday, August 5 5:30-5:55 Surface-Tension Molecular Surfaces for Deployment in Boundary MS41 MS42 Element Electrostatic Calculations Randy Zauhar, University of the Sciences, Probability Inverse Problems Molecular Biosciences: USA in Biophysics Boundary Elements 6:00-6:25 A Treecode-Accelerated 4:30 PM-6:30 PM Computing and Boundary Integral Poisson–Boltzmann Applications Solver for Electrostatics of Solvated Room:Symphony II Biomolecules Data collected across biology is noisy 4:30 PM-6:30 PM Weihua Geng, Southern Methodist and incomplete. This is especially Room:Symphony V University, USA; Robert Krasny, University of Michigan, Ann Arbor, USA true of data collected on small Electrostatics, as long rang interactions systems such as single molecules with abundant presence, are critical in where conformational and dynamical determining biological functions and fluctuations are strong. Inferring models structures at both the molecular and from such data poses fundamental cellular levels. Structural biologists challenges. What physical models are inevitably consider the effect of consistent with data? How should the electrostatics in studying protein model search be refined? What level of folding, protein-protein interactions, model detail is appropriate given data? ion-channels, cell-cell interactions, etc. A quantitative understanding of biology Meanwhile, attracted by electrostatics and biomedicine critically depends on related scientific significances and how these questions are answered. This computational challenges, numerical minisymposium will illustrate inference analysts actively seek numerical methods used to answer such questions methods for accurate and efficient across biophysics. computing. Among these methods, Organizer: Steve Presse boundary integral methods together with Indiana University - Purdue University N-body fast algorithms stand themselves Indianapolis, USA out at the combination of both accuracy 4:30-4:55 Estimating Velocity for and efficiency. We bring together experts Processive Motor Proteins with in addressing different aspects of these Random Detachment problems, methods, and applications. John Hughes, University of Minnesota, Organizer: Weihua Geng USA Southern Methodist University, USA 5:00-5:25 From Single Molecule 4:30-4:55 A Computational Method Experiments to Coupled Molecules for Nearly Singular Integrals John Fricks, Pennsylvania State University, J. Thomas Beale, Duke University, USA USA 5:00-5:25 On a Parallel Adaptive Fast 5:30-5:55 Superresolution Microscopy Multipole Poisson-Boltzmann Solver As a Quantitative Tool Bo Zhang, Duke University, USA; Xiaolin Steve Presse, Indiana University - Purdue Cheng, Oak Ridge National Laboratory, University Indianapolis, USA USA; Jingfang Huang, University of 6:00-6:25 Form-Function Relationship North Carolina at Chapel Hill, USA; in E. coli Chemotaxis Benzhuo Lu, Institute of Computational Jayajit Das, The Ohio State University, Mathematics, China; J Andrew USA McCammon, University of California, San Diego, USA; Nikos Pitsianis, Aristotle University of Thessaloniki, Greece; Xiaobai Sun, Duke University, USA

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Tuesday, August 5 Tuesday, August 5 6:00-6:25 Spiking Neuron Vs. Neural Mass Models in the Context of Sleep- MS43 MS44 Regulatory Circuits Andrew Phillips, Brigham and Women’s Blood Flow Propagation in Mathematical Modeling of Hospital and Harvard Medical School, Vessel Networks Sleep Patterns in Humans USA; Victoria Booth, University of Michigan, USA; Elizabeth B. Klerman, 4:30 PM-6:30 PM 4:30 PM-6:30 PM Brigham and Women’s Hospital and Room:Symphony VI Room:Symphony VII Harvard Medical School, USA During the last decades numerous Sleep is a behavioral state in which we models have been put forward analyzing spend nearly one third of our lives. This wave propagation in cardiovascular biological phenomenon clearly serves networks, yet numerous questions an important role in the lives of most still remain, in particular related to species. While much effort has been model validation. This minisymposium put forth in understanding the nature addresses new developments in of sleep, many aspects of sleep are still cardiovascular modeling and not well understood. Modeling can methodologies for validation of help to uncover some of the complex these models, in particular seen in underlying dynamics associated with the light of sparse data available for sleep cycles and their regulation. In this rendering models patient specific. minisymposium, speakers will discuss Another question is that of fluid sleep regulation considered at different dynamics models coupled with system spatio-temporal scales using various level models enabling analysis of modeling approaches. the complete system, this question Organizer: Shelby Wilson is important in studies were models Morehouse College, USA are applied for analysis of changes Organizer: Pamela B. Fuller associated with the cardiovascular Rensselaer Polytechnic Institute, USA control system, where the model input is changed as downstream properties are 4:30-4:55 Modeling Interindividual controlled. Differences in Spontaneous Internal Desynchrony Patterns Organizer: Mette S. Olufsen Victoria Booth, University of Michigan, North Carolina State University, USA USA; Cecilia Diniz Behn, Gettysburg Organizer: Mansoor A. Haider College, USA North Carolina State University, USA 5:00-5:25 A Mathematical Model of 4:30-4:55 A Coupled Model of the the Wake/NonREM/REM States Left Ventricle and the Systemic Selenne Garcia-Torres, University of Arteries Southern California, USA; Janet Best, Nicholas A. Hill, University of Glasgow, The Ohio State University, USA; Gemma Scotland, UK; Weiwei Chen and Hao Gao, Huguet, Universitat Politecnica de University of Glasgow, Scotland, United Catalunya, Spain; Alicia Prieto Langarica, Kingdom; Boyce Griffith, New York Youngstown State University, USA; University, USA; Xiaoyu Luo, University Shelby Wilson, Morehouse College, USA; of Glasgow, Scotland, United Kingdom Pamela B. Fuller, Rensselaer Polytechnic Institute, USA 5:00-5:25 Comparison of Inflow Boundary Conditions for Ventriculo- 5:30-5:55 Modeling the Effects of Arterial Coupling in 3D and 1D Fluid- Temperature on Sleep Patterns Structure Interaction Models Alicia Prieto Langarica, University of Kevin D. Lau, Jordi Alastruey, and C. Texas at Arlington, USA; Janet Best, The Alberto Figueroa, King’s College London, Ohio State University, USA; Gemma United Kingdom Huguet, Universitat Politecnica de Catalunya, Spain; Selenne Garcia-Torres, 5:30-5:55 Pulsatile Flow in the Entire University of Southern California, USA; Coronary Arterial Tree Shelby Wilson, Morehouse College, USA; Huo Yunlong, Peking University, China Pamela B. Fuller, Rensselaer Polytechnic 6:00-6:25 Physiological Modeling in Institute, USA Hypertension and Heart Failure Karim Azer, Merck & Co., Inc., USA continued in next column 2014 SIAM Conference on the Life Sciences 33

Tuesday, August 5 Tuesday, August 5 Tuesday, August 5 MS45 CP5 CP6 Change and Robustness in Biophysics Immunology and Diseases I the Evolution of Biological 4:30 PM-6:00 PM 4:30 PM-6:30 PM Systems Room:Symphony III Room:Mecklenburg I 4:30 PM-6:30 PM Chair: To Be Determined Chair: Lydia Bourouiba, Massachusetts Room:Mecklenburg III 4:30-4:55 Parameter Inference Using Institute of Technology, USA Diversity in biology contributes greatly Variance Fitting for Markov Models of 4:30-4:55 Modeling Effects of Drugs of to the adaptivity of living organisms, Voltage Gated Ion Channels Abuse on Hiv-1 Dynamics both enabling survival in a changing Philipp Kuegler, University of Hohenheim, Naveen K. Vaidya, University of Missouri, Germany environment and underlying the Kansas City, USA evolution of new phenotypes. We 5:00-5:25 A Fractional Order Model of 5:00-5:25 Sensitivity Analysis and will discuss the relationship between Electroporation Treatment of Hepatitis C Virus diversity and evolution at various Md Mehedi M. Hasan and Corina Infection levels of biology within a cell. How Drapaca, Pennsylvania State University, Ariel Cintron-Arias, East Tennessee State USA selection works at multiple levels, University, USA from the function of proteins through 5:30-5:55 Compatibility of Slender 5:30-5:55 The Effect of Systemic genes to cellular architecture, remains Bodies and Surface Traction at Low Estrogen and Cortisol on the an open question, and approaches Reynolds Number Inflammatory Phase of Wound Eva M. Strawbridge, James Madison in mathematical modeling and Healing University, USA; Charles Wolgemuth, Angela M. Reynolds, Racheal Cooper, optimization will be used to address University of Arizona, USA Rebecca Segal, and Robert Diegelmann, it. These applications enable us to Virginia Commonwealth University, USA understand mechanisms contributing to robustness within a biological system, 6:00-6:25 The Role of Interleukin-2 in Immune Response Regulation and their role in evolution. Ryan S. Waters and Tomas Gedeon, Organizer: Loretta Au Montana State University, USA State University of New York, Stony Brook, USA 4:30-4:55 Disentangling Protein Fitness Requirements Using Computational Mutagenesis Loretta Au, State University of New York, Stony Brook, USA 5:00-5:25 Conserved Enhancer Function When Sequence Is Not Conserved: Adventures with Cis- Regulatory Logic John Reinitz, University of Chicago, USA 5:30-5:55 Decoding Information in Cell Shape Padmini Rangamani, University of California, Berkeley, USA 6:00-6:25 A Mechanistic Model of the Bacterial Flagellar Motor Kranthi Mandadapu, Jasmine Nirody, and George Oster, University of California, Berkeley, USA 34 2014 SIAM Conference on the Life Sciences

Tuesday, August 5 Tuesday, August 5 Modeling the Dynamics of Opioid Abuse CP7 PP1 William Consagra, Rochester Institute of Technology, USA Genetic and Biochemical Poster Session A Computational Model for a Porous Networks 8:00 PM-10:00 PM Viscoelastic Cytoskeleton with 4:30 PM-6:30 PM Room:Symphony IV Applications to Cell Mechanics Calina A. Copos and Robert D. Guy, Room:Mecklenburg II University of California, Davis, USA Chair: Eduardo Sontag, Rutgers Network Bursting in Inhibitory Neural Predicting Severity and Periodicity of University, USA Circuits Mountain Pine Beetle Outbreaks Deniz Alacam and Andrey Shilnikov, 4:30-4:55 On the Perfect Jacob P. Duncan, James Powell, and Luis Georgia State University, USA Reconstruction of the Topology of Gordillo, Utah State University, USA; Joe Gene Regulatory Networks Test Criterion for Finding the Global Eason, University of Utah, USA Alan Veliz-Cuba, University of Houston, Minimum of a Function Using Temperature Effects on REM/Non-REM USA Exclusion Algorithm Sleep Dynamics Ibraheem Alolyan, King Saud University, 5:00-5:25 Spatial Uniformity of Pamela B. Fuller, Rensselaer Polytechnic Saudia Arabia Solutions of Reaction-Diffusion Pde’s Institute, USA; Janet Best, The Ohio Zahra Aminzare and Eduardo Sontag, Staying in Shape: Patterns in Radial State University, USA; Gemma Huguet, Rutgers University, USA Symmetry Provide Protein Structural Universitat Politecnica de Catalunya, Stability and Functionality Spain; Shelby Wilson, Morehouse 5:30-5:55 Scale-Invariant Sensing of Loretta Au, State University of New York, College, USA; Alicia Prieto Langarica, Singularly Perturbed Biomolecular Stony Brook, USA Youngstown State University, USA; Models Selenne Garcia-Torres, University of Maja Skataric, Evgeni Nikolaev, and Modeling the Deformation of Proteins: Southern California, USA Eduardo Sontag, Rutgers University, USA from Coarse-Grained to Continuum George Borleske, Colorado State How Robust Is the Zero-Lag 6:00-6:25 Simulation-Based University, USA Synchrony When Two Neurons Simplification of Non-Linear Feed- Interact Via a Third Relay Neuron Forward Models Demographics and Modeling Zahra Ghasemi Esfahani and Alireza Richard Allen and Cynthia Musante, Pfizer of Multisite HPV Infection and Valizadeh, Institute of Advanced Studies Inc., USA Transmission in Basic Science, Iran Andrew Brouwer, Rafael Meza, and Marisa Eisenberg, University of Michigan, USA Investigating the Effect of Atropine on Baroreceptor Heart Rate Regulation Dinner Break Binocular Rivalry Waves in Christian H. Haargaard Olsen and Directionally Selective Neural Fields Mette S. Olufsen, North Carolina State 6:30 PM-8:00 PM Sam R. Carroll, University of Utah, USA; University, USA; Johnny T. Ottesen, Paul C. Bressloff, University of Utah, Attendees on their own Roskilde University, Denmark; Jesper USA and University of Oxford, United Mehlsen, Frederiksberg Hospital, Kingdom Denmark; Hien T. Tran, North Carolina Modeling Interactions Between Two State University, USA Major Southeastern U.S. Sea Turtle Accelerated Uzawa Iteration for the Nest Predators and Their Effects on Stokes Equations Nest Depredation Rates Nguyenho Ho, Sarah D. Olson, and Homer Joshua Castro, John Weishampel, Andrew F. Walker, Worcester Polytechnic Institute, Nevai, and Pedro Quintana-Ascencio, USA University of Central Florida, USA Determining An Optimal Intrinsic Mechanisms for Pattern Mathematical Model for Tumor Generation in Three-Node Networks Growth Jarod Collens, Aaron Kelley, Deniz Hana Jaafari, Michael Ellis, and Hana Alacam, Tingli Xing, Justus T. Dobrovolny, Texas Christian University, Schwabedal, and Andrey Shilnikov, USA Georgia State University, USA

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Synchrony in Metapopulations with Distribution of Correlated Spiking Identifiability of Linear Dynamical on-off Stochastic Dispersal Events in Integrate-and-Fire Networks Systems from a Single Trajectory Russell Jeter and Igor Belykh, Georgia Katherine Newhall, Jiwei Zhang, and Adi Shelby R. Stanhope, Jonathan Rubin, and State University, USA Rangan, Courant Institute of Mathematical David Swigon, University of Pittsburgh, Sciences, New York University, USA; USA Two-Theta Neuron: Phase Models for Douglas Zhou, Shanghai Jiao Tong Bursting Networks From Chaos to Periodicity: Revisiting University, China Aaron Kelley, Georgia State University, the Logistic Map with an Ecologically USA Modeling Dynamics of Mosquito Realistic Spatial Structure and Populations and Assessing Dispersal Mechanism A Linear Analysis of a Straight Rod Abatement Strategies for West Nile Laura Storch and James Pringle, University under Tension Both With and Without Virus of New Hampshire, USA Drag Kasia A. Pawelek, Patrick R. Niehaus, Victoria Kelley, James Madison University, Identifying Physiological Origins of and Cristian Salmeron, University of USA Baroreceptor Firing Characteristics South Carolina, Beaufort, USA; Elizabeth Through a Conductance Based Conserved NPZ Models with Time J. Hager and Gregg J. Hunt, Beaufort Neural Model Delay County Mosquito Control, USA Jacob Sturdy, North Carolina State Matt Kloosterman, Sue Ann Campbell, and Activity Patterns of Neuronal Network University, USA; Johnny T. Ottesen, Francis Poulin, University of Waterloo, with Voltage-Sensitive Piecewise Roskilde University, Denmark; Mette S. Canada Smooth Coupling Olufsen, North Carolina State University, Prediction of Biphasic Mitogenic Choongseok Park, North Carolina A&T USA Activity by Hgf, a Cancer-Associated State University, USA; Jonathan Rubin, Leaf Inclination Angle Regulates the Stroma-Derived Growth Factor, Using University of Pittsburgh, USA Distribution of Light in the Sorghum a Multi-Species Continuum Model Modeling the Effects of Canopy Anna Konstorum, University of California, Craniosynostosis on Intracranial Sandra K. Truong, Ryan F. McCormick, Irvine, USA Pressure and John Mullet, Texas A&M University, The Role of CD200-CD200R in Cancer Jackson Penning, Madeline Anderson, USA Suppression and Promotion Emily Van Heel, and Magda Stolarska, Modeling the Effect of Antiarrhythmic University of St. Thomas, USA Kang-Ling Liao, Xue-Feng Bai, and Avner Agents on the Action Potential of Friedman, The Ohio State University, Investigation of Dual Virus Infection of Human Ventricular Cells USA Human Respiratory Tract Binaya Tuladhar and Hana Dobrovolny, Patient-Specific Modeling of Lubna Pinky and Hana Dovrobolny, Texas Texas Christian University, USA Average Cerebral Blood Flow During Christian University, USA Understanding and Distinguishing Orthostatic Stress Synchronization of Bursting Neurons: Three Time Scale Oscillations Gregory C. Mader, Mette S. Olufsen, a Synergetic Effect of Excitation and Yangyang Wang, University of Pittsburgh, and Adam Mahdi, North Carolina State Inhibition USA; Pingyu Nan and Vivien Kirk, University, USA Reimbay Reimbayev and Igor Belykh, University of Auckland, New Zealand; Periodic Accumulation of Genetic Georgia State University, USA Jonathan Rubin, University of Pittsburgh, Variation in the Genome of the Plant USA Determining Mechanism of Action Sorghum Bicolor and Efficacy of Novel Influenza Coupling-Induced Synchronization of Ryan F. McCormick, Sandra K. Truong, Antivirals Mexican Jumping Beans and John Mullet, Texas A&M University, Thalia Rodriguez and Hana Dobrovolny, Andrea J. Welsh, Flavio Fenton, and Ilija USA Texas Christian University, USA Uzelac, Georgia Institute of Technology, Gene Regulatory Network Based USA Within-Host Models of Influenza Virus on a Novel Evolvable Partially Infection: The Role of Macrophages Phenotypic Modulation of Virulence Connected Artificial Neural Network Cristian Salmeron and Kasia A. Pawelek, Facilitates Pathogen Invasion of the Mina Moradi Kordmahalleh, Mohammad University of South Carolina, Beaufort, Gut Gorji Sefidmazgi, and Abdollah Homaifar, USA Glenn S. Young, Bard Ermentrout, and North Carolina A&T State University, Jonathan Rubin, University of Pittsburgh, USA Bursting in the Pituitary Corticotroph: USA The Role of Bk Ion Channels Accumulation Behavior Sevgi Sengul and Joel Tabak, Florida State Thomas Morrisey, Infosys, USA University, USA; Peter Duncan and Mike Shipston, University of Edinburgh, United Kingdom; Richard Bertram, Florida State University, USA

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Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 MT2 MS46 Registration Modelling Arterial Wall Mathematical Models in Mechanics and Adaption Biology and Epidemiology - 7:30 AM-5:00 PM using Structurally Based Part II of II Room:Symphony Preconvene Area Constitutive Laws 9:30 AM-11:30 AM 9:30 AM-11:30 AM Room:Symphony I Remarks Room:Symphony VI For Part 1 see MS40 Mathematical modeling and analysis 8:10 AM-8:15 AM Chair: Xiaoyu Luo, University of Glasgow, Scotland, United Kingdom are powerful tools to gain important Room:Symphony I, II & III insights on the complicated biological This mini-tutorial will introduce the four and epidemiological processes by different aspects of modelling in arterial formulating, analyzing, simulating, wall mechanics. and interpreting mathematical models. IP5 Constitutive Laws for Artery Wall with In the proposed minisymposium, we Application to Optimal Fibre Angle in Deterministic and Stochastic bring together a group of distinguished Iliac Artery researchers who have particular Thresholds for Disease Xiaoyu Luo, University of Glasgow, expertise in applying mathematical Scotland, United Kingdom Extinction in Infectious models and theory to study the Disease Models Arterial Wall Remodelling in challenging problems arising from the Abdominal Aortic Aneurysm field of biology and epidemiology. The 8:15 AM-9:00 AM Nicholas A. Hill, University of Glasgow, invited speakers will present the most Room:Symphony I, II & III Scotland, UK cutting-edge studies in the filed, which Chair: Maia Martcheva, University of Stability of Arterial Wall with Case may provide valuable opportunities Study on Acute Aneurysm Initiation Florida, USA for future modeling improvement and as a Bifurcation Phenomenon practical applications. The diversity of Thresholds for disease extinction Yibin Fu, Keele University, United our speakers may spur new interests provide essential information for Kingdom and promote participation among control, eradication or management of Assessment of Statistical Variability in underrepresented groups including diseases. Relations between branching Wall Model Material Parameters for women in this exciting field. process theory and corresponding 1d Arterial Network Simulations deterministic models show that Leif Hellevik, Norwegian University of Organizer: Yun Kang deterministic and stochastic thresholds Science and Technology, Norway Arizona State University, USA are in agreement for discrete-time and Organizer: Sophia Jang continuous-time infectious disease Texas Tech University, USA models with multiple infectious groups. 9:30-9:55 Modeling Drug Resistance Markovian branching process theory in in Metastatic Cancers conjunction with deterministic models Doron Levy, University of Maryland, USA provide additional information about the 10:00-10:25 Vector Dynamics and Its probability of disease extinction. These Impact on the Vector Borne Disease- relations are illustrated in discrete- Malaria time and continuous-time models of Miranda I. Teboh-Ewungkem, Lehigh infectious diseases. University, USA Linda J. Allen Texas Tech University, USA

Coffee Break 9:00 AM-9:30 AM Room:Symphony Preconvene Area continued on next page 2014 SIAM Conference on the Life Sciences 37

10:30-10:55 From Within-Host to Wednesday, August 6 Wednesday, August 6 Between-Host Dynamics. Systems Biology of Epidemiology MS47 MS48 Juan B. Gutierrez, University of Georgia, USA Modeling and Inverse Recent Advances of 11:00-11:25 The Impact of Decay in Problems of Complex Membrane Modeling and BedNet Efficacy over Time on Malaria Biological Systems Computation - Part I of II Transmission 9:30 AM-11:30 AM 9:30 AM-11:30 AM Jemal Mohammed-Awel, Valdosta State University, USA; Calistus Ngonghalaa, Room:Symphony II Room:Symphony III National Institute for Mathematical and The analysis of complex hierarchical For Part 2 see MS55 Biological Synthesis, USA; Sara Del Val, Dynamics of lipid bilayer in vivo Los Alamos National Laboratory, USA; biological systems represents one of the Ruijun Zhao, Minnesota State University most important open areas in biology. involves multiscale interactions Mankato, USA At the molecular and cellular levels, with surrounding fluid and other detailed components of biological macromolecular complexes. To date, systems are being uncovered by grand challenges remain in high-fidelity powerful and modern experimental modeling and efficient computation methodologies. The coordination of the composition variations, large and integration of these details into deformation and topological changes functional biological systems require of membrane induced by multiscale insights that come from mathematical electrostatic, entropic, hydrodynamics, abstraction as well as experimental and mechanical interactions. This data from biologists. In this minisymposium will (1) address some of minisymposium, invited speakers will the most interesting topics in modeling discuss mathematical development and of bilayer membranes, including methodologies that provide biological coupling of asymmetric bilayers, insights into a wide spectrum of protein insertion and pore formation, applications in life sciences including pattern formation, multicomponent infectious diseases, cancer biology, and coupling, fluid-vesicle coupling, fluid- kidney disease. electrostatics-vesicle coupling, and fast Organizer: Philip J. Aston algorithms; (2) nurture collaborations University of Surrey, United Kingdom among young scholars in applied and computational mathematics, Organizer: Hien T. Tran biophysics, and mechanical engineering North Carolina State University, USA internationally. 9:30-9:55 A New Mathematical Organizer: Shuwang Li Model for Hepatitis C Infection: Illinois Institute of Technology, USA Derivation, Analysis and Implications Philip J. Aston, University of Surrey, Organizer: Yongcheng Zhou United Kingdom Colorado State University, USA 10:00-10:25 Mathematical Modeling 9:30-9:55 Continuum Models of of Malignant Brain Tumor with T11 Membrane Protein Insertion and Target Structure As a Potent Immune Stability Stimulator. Michael Grabe, University of California, Sandip Banerjee, Indian Institute of San Francisco, USA Technology Roorkee, India 10:00-10:25 Competitive Geometric 10:30-10:55 Parameter Subset Evolution of Lipid Bilayers and Pores Selection and Generalized Shibin Dai, New Mexico State University, Sensitivities for a Model of USA; Keith Promislow, Michigan State Erythropoiesis University, USA Franz Kappel, University of Graz, Austria 11:00-11:25 Deconvolution of Isotope Signals Mixed from Sampling Bundles of Multiple Hairs Christopher Remien, University of Tennessee, USA; Frederick Adler, Lesley continued on next page Chesson, Luciano Valenzuela, James Ehleringer, and Thure Cerling, University of Utah, USA 38 2014 SIAM Conference on the Life Sciences

Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 MS48 MS49 MS50 Recent Advances of Molecular Biosciences: Dynamics of Multistable Membrane Modeling and Topological Modeling of Perception and Decision Computation - Part I of II Biomolecules - Part I of II Making - Part I of II 9:30 AM-11:30 AM 9:30 AM-11:30 AM 9:30 AM-11:30 AM continued Room:Symphony V Room:Symphony VII For Part 2 see MS56 For Part 2 see MS58 In the past two decades,molecular Multi-stable perception (spontaneous 10:30-10:55 Periodic Migration based mathematical biology has changes in subject’s perception when in a Physical Model of Cells on emerged as one of the most promising confronted with an ambiguous sensory Micropatterns interdisciplinary research areas in the stimulus) and decision making (selecting Yanxiang Zhao, University of California, interface of mathematics and biology. a course of action from several available San Diego, USA This minisymposium will focus on options) are two important cognitive 11:00-11:25 On Minimizers of the recent advances on topological modeling processes that have attracted a lot of Bending Energy of Two-Phase of the macromolecular structures attention from both experimentalists Biomembranes and interactions. The topics include and modelers. While several models Marco Veneroni, University of Pavia, topological states of DNA, DNA have been proposed, the exact Italy; Rustum Choksi, McGill University, Canada; Marco Morandotti, Carnegie knots and links, neural data analysis, mechanisms underlying the dynamics Mellon University, USA flexibility and rigidity analysis of of these processes remain unclear. biomolecule, elasticity modeling of This minisymposium brings together protein, etc. We will emphasize not only scientists studying different aspects of the topological theories, methods and these cognitive processes and sensory algorithms, but also their application in modalities. Through enhanced discussion, the real biomolecular systems. the minisymposium aims to gain insight Organizer: Kelin Xia into the mechanisms that operate in the Michigan State University, USA brain, and to inspire collaboration. Organizer: Yuanan Diao Organizer: Rodica Curtu University of North Carolina, Charlotte, University of Iowa, USA USA Organizer: Gemma Huguet 9:30-9:55 Topological Tools for Universitat Politecnica de Catalunya, Detecting Hidden Geometric Spain Structure in Neural Data 9:30-9:55 Build-Up and Neural Carina Curto, University of Nebraska, Competition in a Model of Auditory Lincoln, USA Streaming 10:00-10:25 Topological Distances on Rodica Curtu, University of Iowa, USA; DNA Knots and Links John M. Rinzel, Courant Institute of Isabel Darcy and Annette Honken, Mathematical Sciences, New York University of Iowa, USA University, USA 10:30-10:55 The Topological Structure 10:00-10:25 Modelling the Emergence of the Mitochondrial Dna from and Dynamics of Perceptual Trypanosomes Organisation in Auditory Streaming Yuanan Diao, University of North Carolina, Sue Denham, Plymouth University, United Charlotte, USA Kingdom 11:00-11:25 Modeling Dna Packing 10:30-10:55 Bistable Auditory with Confined Equilateral Random Perception: Neural Competition with Polygons Periodic Input Claus Ernst, Western Kentucky University, James Rankin and John Rinzel, New York USA University, USA 11:00-11:25 Diagnosing Excitation- inhibition Balance using Psychophysics Shashaank Vattikuti and Carson C. Chow, National Institutes of Health, USA 2014 SIAM Conference on the Life Sciences 39

Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 MS51 MS52 CP8 The Mathematics of Sudden Modeling and Numerical Evolution and Ecology I Cardiac Death - Part I of II Methods for Complex 9:30 AM-11:30 AM 9:30 AM-11:30 AM Systems in Developmental Room:Mecklenburg III and Cell Biology - Part I of II Room:Mecklenburg I Chair: Marc Harper, University of For Part 2 see MS59 9:30 AM-11:30 AM California, Los Angeles, USA Cardiac arrhythmias, in which Room:Mecklenburg II 9:30-9:55 Linear Algebra of the propagating electrical waves that trigger Quasispecies Model For Part 2 see MS60 cardiac contraction become localized This minisymposium aims to Artem S. Novozhilov, North Dakota State University, USA; Alexander Bratus, and uncoordinated, affect the lives of bring researchers to address recent Lomonosov Moscow State University, millions of people around the world and advances of mathematical modeling have serious health and economic costs. Russia; Yuri Semenov, Moscow State and numerical methods for complex University of Railway Engineering, Russia The most severe arrhythmias can lead to biological systems including (but not 10:00-10:25 Species Coexistence sudden cardiac death if normal electrical limited to) morphogenesis and stem Under Eco-evolutionary Dynamics wave patterns are not restored. This cells, cell signaling pathways, cell two-part minisymposium brings together Swati Patel and Sebastian Schreiber, polarization, cancer stem cells, tumor University of California, Davis, USA researchers studying cardiac arrhythmias growth, tissue patterning, etc. Many and sudden death from multiple such systems usually consist of multiple 10:30-10:55 Stationary Stability for Evolutionary Dynamics in Finite perspectives. The utility of different interacting components that exhibit modeling techniques, including PDEs, Populations complicated temporal and spatial Dashiell Fryer, Pomona College, USA; delay differential equations, stochastic dynamics with multiple scales and processes, and data assimilation, Marc Harper, University of California, Los high dimensions, which are extremely Angeles, USA as well as approaches to modeling difficult to describe, model or predict. cardiac structure, will be discussed. 11:00-11:25 Mutational History In this minisymposium, the challenges Dominates Clonal Selection Within Applications to arrhythmia development of modeling these complex systems will will be presented. Evolving Tumors be discussed, and more beyond, the new Scott T. Bickel, Joseph Juliano, and John Organizer: Elizabeth M. Cherry mathematical and numerical methods to D. Nagy, Arizona State University, USA Rochester Institute of Technology, USA analyze and simulate these models will 9:30-9:55 Delay-Differential Equations also be presented. in Cardiac Electrophysiology Models Organizer: Xinfeng Liu Lunch Break Elizabeth M. Cherry and Ryan Thompson, University of South Carolina, USA Rochester Institute of Technology, USA 11:30 AM-1:00 PM Organizer: Yongtao Zhang 10:00-10:25 The Role of Feedback University of Notre Dame, USA Attendees on their own and Heart Rate Variability on Cardiac Rhythm Stability Organizer: Lei Zhang Elena Tolkacheva, Stephen McIntyre, and Peking University, China Yoichiro Mori, University of Minnesota, 9:30-9:55 Stochastic Dynamics in USA Signal Transduction, Stem Cells, and 10:30-10:55 Experimentally-based Development Patterning Modified Cable Equation That Qing Nie, University of California, Irvine, Reproduces Alternans Measured in USA Cardiac Tissue 10:00-10:25 Mathematical Models for Flavio Fenton and Yanyan Ji, Georgia Stem Cell Interactions Institute of Technology, USA Jianjun Paul Tian, College of William & 11:00-11:25 Effects of Intracellular Mary, USA Sodium Accumulation on Cardiac 10:30-10:55 Computation of Transition Reentry Dynamics State and Its Applications in System Trine Krogh-Madsen and Margo Smith, Biology Cornell University, USA; David Christini, Lei Zhang, Peking University, China Weill Cornell Medical College, Cornell University, USA 11:00-11:25 Numerical Studies on Cell Lineage Models Yongtao Zhang, University of Notre Dame, USA 40 2014 SIAM Conference on the Life Sciences

Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 IP6 MS53 MS54 Is “Good Cholesterol” Advances in Mathematical Optimal Control and Always “Good”? New Modeling of Complex Optimization in Biological Insights about HDL from Aspects and Control of Models an In-Silico Model of Some Prevalent Infectious 2:00 PM-4:00 PM Lipoprotein Metabolism and Diseases - Part I of II Room:Symphony II Kinetics 2:00 PM-4:00 PM This minisymposium features talks by 1:00 PM-1:45 PM Room:Symphony I advanced students and recent postdocs Room:Symphony I, II & III For Part 2 see MS61 on optimal control and optimization This minisymposium will present recent techniques and numerical results on Chair: Dean Bottino, Takeda biological models. Ecological and Pharmaceuticals North America, USA efforts in understanding underlying mechanisms that drive patterns of epidemiological applications will be Individuals with higher endogenous infectious pathogens in the population and presented. The types of models include plasma levels of high-density in the host. The talks will discuss pressing systems of ODEs, PDEs, agent-based lipoprotein-cholesterol (HDL-C), the so issues relevant to control of infectious models and difference equations. called “good cholesterol”, have a lower diseases such as influenza, malaria, Organizer: Suzanne M. Lenhart risk of developing cardiovascular disease Hepatitis-C, HIV. Amidst active research University of Tennessee, USA (CVD) – an effect that is generally in controlling them through optimal attributed to the role of HDL particles in Organizer: Eric Numfor public health planning (vaccination) University of Tennessee, USA the reverse cholesterol transport process. and/or therapeutic strategies, discerning 2:00-2:25 The Impact of Spatial Nevertheless recent efforts to increase complimentary aspects like immunity, HDL-C levels pharmacologically have Arrangements on Intervention nosocomial input, drug resistance will Strategies in Epidemic Models failed to lower CVD risk in patients. be indispensible in developing ways to To understand this apparent paradox, Michael Kelly, University of Tennessee, eliminate them for good. The sessions Knoxville, USA we developed a novel in-silico model promote several women and minorities, 2:30-2:55 Optimal Control and of lipoprotein metabolism and kinetics and can be of interest to students and Analysis of a Coupled Ode/pde [1.Lu J, Hübner K, Nanjee MN, Brinton researchers in infectious diseases, applied EA, Mazer NA. An in-silico model of Immuno-Epidemiological Model mathematics including public health. Eric Numfor, University of Tennessee, USA lipoprotein metabolism and kinetics for the evaluation of targets and biomarkers Organizer: Swati Debroy 3:00-3:25 Optimizing Hiv Treatment In in the reverse cholesterol transport University of South Carolina, Beaufort, a Resource Limited Settings pathway.] USA Gordon Akudibillah and Jan Medlock, Oregon State University, USA Our model highlights the geometrical Organizer: Anuj Mubayi aspects of HDL structure and dynamics, Northeastern Illinois University, USA 3:30-3:55 Inferring Equation Models from Agent-Based Model Data and suggests why certain HDL-C raising 2:00-2:25 Optimizing Vaccine Matthew Oremland, Virginia Tech, USA therapies have not been successful to Allocation for Influenza date. 1.Lu J, Hübner K, Nanjee MN, Jan Medlock, Oregon State University, USA Brinton EA, Mazer NA. An in-silico 2:30-2:55 Malaria Vaccine Efficacy model of lipoprotein metabolism and in a Region with Naturally Acquired kinetics for the evaluation of targets and Immunity biomarkers in the reverse cholesterol Olivia Prosper, Dartmouth College, USA; transport pathway. Nick Ruktanonchai and Maia Martcheva, University of Florida, USA Norman Mazer 3:00-3:25 A Two-Patch Avian Influenza F. Hoffmann-La Roche Ltd., Switzerland Model Omar Saucedo, University of Florida, USA 3:30-3:55 Mathematical Model of Intermission Community-Acquired and Hospital- Acquired Methicillin-Resistant 1:45 PM-2:00 PM Staphylococcus Aureus Transmission in Hospital Settings Folashade Agusto, Austin Peay State University, USA 2014 SIAM Conference on the Life Sciences 41

Wednesday, August 6 2:30-2:55 Three Dimensional Vesicle Wednesday, August 6 Electrohydrodynamics: A Numerical MS55 Investigation MS56 David Salac and Ebrahim M. Kolahdouz, Recent Advances of State University of New York at Buffalo, Molecular Biosciences: Membrane Modeling and USA Topological Modeling of Computation - Part II of II 3:00-3:25 A Continuum Model Biomolecules - Part II of II for Simulating Bilipid Membrane 2:00 PM-4:00 PM Deformation During Vesicle Drying 2:00 PM-4:00 PM Room:Symphony III Chris Vogl, University of Washington, USA Room:Symphony V For Part 1 see MS48 3:30-3:55 Numerical Simulations of For Part 1 see MS49 Dynamics of lipid bilayer in vivo Fluctuating Vesicles in Linear Flow In the past two decades,molecular involves multiscale interactions Shuwang Li and Kai Liu, Illinois Institute based mathematical biology has with surrounding fluid and other of Technology, USA emerged as one of the most promising macromolecular complexes. To date, interdisciplinary research areas in the grand challenges remain in high-fidelity interface of mathematics and biology. modeling and efficient computation This minisymposium will focus on of the composition variations, large recent advances on topological modeling deformation and topological changes of the macromolecular structures of membrane induced by multiscale and interactions. The topics include electrostatic, entropic, hydrodynamics, topological states of DNA, DNA and mechanical interactions. This knots and links, neural data analysis, minisymposium will (1) address some of flexibility and rigidity analysis of the most interesting topics in modeling biomolecule, elasticity modeling of of bilayer membranes, including protein, etc. We will emphasize not only coupling of asymmetric bilayers, the topological theories, methods and protein insertion and pore formation, algorithms, but also their application in pattern formation, multicomponent the real biomolecular systems. coupling, fluid-vesicle coupling, fluid- Organizer: Kelin Xia electrostatics-vesicle coupling, and fast Michigan State University, USA algorithms; (2) nurture collaborations among young scholars in applied Organizer: Yuanan Diao and computational mathematics, University of North Carolina, Charlotte, biophysics, and mechanical engineering USA internationally. 2:00-2:25 Flexibility-Rigidity Index for Protein Flexibility Analysis Organizer: Shuwang Li Kristopher Opron, Michigan State Illinois Institute of Technology, USA University, USA Organizer: Yongcheng Zhou 2:30-2:55 Knotting in Open Chains, Colorado State University, USA Closed Chains, and Proteins 2:00-2:25 Electromechanics of Eric Rawdon, University of St. Thomas, Bilayer Membrane: Forces and Fast USA Algorithms 3:00-3:25 Unlinking of Supercoiled Michael Mikucki, Colorado State DNA Catenanes by Type IIA University, USA Topoisomerases Alexander Vologodskii, New York University, USA 3:30-3:55 Invariant Manifold and Persistent Homology for Biomolecules. Guo-Wei Wei and Kelin Xia, Michigan State University, USA continued in next column 42 2014 SIAM Conference on the Life Sciences

Wednesday, August 6 Wednesday, August 6 2:30-2:55 Network Symmetry and Binocular Rivalry Experiments MS57 MS58 Martin Golubitsky, The Ohio State University, USA; Casey Diekman, New Cellular, Tissue, and Organ Dynamics of Multistable Jersey Institute of Technology, USA Level Biofluid Dynamics - Perception and Decision 3:00-3:25 Networks That Learn the Part I of II Making - Part II of II Timing of Event Sequences 2:00 PM-4:00 PM 2:00 PM-4:00 PM Alan Veliz-Cuba, Kresimir Josic, and Zachary Kilpatrick, University of Room:Symphony VI Room:Symphony VII Houston, USA For Part 2 see MS64 For Part 1 see MS50 3:30-3:55 Integration of Information Fluid flows play an important role in Multi-stable perception (spontaneous over Multiple Timescales in a Large- animal and plant physiology, from the changes in subject’s perception scale Model of the Cortex level of single cells up to the level of when confronted with an ambiguous Rishidev Chaudhuri, Jorge F. Mejias, and organs and organisms. In the first part sensory stimulus) and decision making Xiao-Jing Wang, New York University, of this minisymposium, we begin by (selecting a course of action from USA highlighting the role of fluids at the several available options) are two tissue and organ level by considering the important cognitive processes that have importance of flow to the development attracted a lot of attention from both of embryonic lung. We then consider the experimentalists and modelers. While role of structures such as the pericardium several models have been proposed, in the transport of fluids within the the exact mechanisms underlying the body. In the next session, we consider dynamics of these processes remain the importance of non-Newtonian and unclear. This minisymposium brings multiphase flows in biological processes together scientists studying different such as biofilm formation, cellular aspects of these cognitive processes and motility, and the tracks of tears. sensory modalities. Through enhanced Organizer: Laura A. Miller discussion, the minisymposium aims University of North Carolina, Chapel to gain insight into the mechanisms Hill, USA that operate in the brain, and to inspire collaboration. 2:00-2:25 Transport in the Embryonic Lung I Organizer: Rodica Curtu Kishore Krishna Bokka and Sharon Lubkin, University of Iowa, USA North Carolina State University, USA Organizer: Gemma Huguet 2:30-2:55 Transport in the Embryonic Universitat Politecnica de Catalunya, Lung II Spain Uduak Z. George, Kishore Krishna Bokka, 2:00-2:25 Noise and Adaptation in and Sharon Lubkin, North Carolina State Multistable Perception: A Case Study University, USA with Tristable Visual Plaids 3:00-3:25 Role of the Pericardium in Gemma Huguet, Universitat Politecnica the Tubular Hearts of Tunicates de Catalunya, Spain; John M. Rinzel, Lindsay Waldrop, University of North Courant Institute of Mathematical Carolina, Chapel Hill, USA Sciences, New York University, USA; Jean-Michel Hupé, Toulouse University & 3:30-3:55 Fluid-Composite Structure CNRS, France Interaction in Hemodynamics Suncica Canic, University of Houston, USA; Martina Bukac, University of Pittsburgh, USA; Boris Muha, University of Zagreb, Croatia

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Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 MS59 MS60 CP9 The Mathematics of Sudden Modeling and Numerical Evolution and Ecology II Cardiac Death - Part II of II Methods for Complex 2:00 PM-4:00 PM 2:00 PM-4:00 PM Systems in Developmental Room:Mecklenburg III and Cell Biology - Part II of II Room:Mecklenburg I Chair: Dashiell Fryer, Pomona College, For Part 1 see MS51 2:00 PM-4:00 PM USA Cardiac arrhythmias, in which Room:Mecklenburg II 2:00-2:25 The Information Player: propagating electrical waves that trigger a Novel Strategy That Dominates For Part 1 see MS52 cardiac contraction become localized Zero Determinant and Other Known This minisymposium aims to and uncoordinated, affect the lives of Strategies in Multiplayer Evolutionary bring researchers to address recent millions of people around the world and Games advances of mathematical modeling have serious health and economic costs. Christopher Lee and Marc Harper, and numerical methods for complex The most severe arrhythmias can lead to University of California, Los Angeles, biological systems including (but not sudden cardiac death if normal electrical USA; Dashiell Fryer, Pomona College, limited to) morphogenesis and stem USA wave patterns are not restored. This two- cells, cell signaling pathways, cell part minisymposium brings together 2:30-2:55 Quantifying the polarization, cancer stem cells, tumor researchers studying cardiac arrhythmias Relationships among Natural growth, tissue patterning, etc. Many and sudden death from multiple Selection, Mutation, and Stochastic such systems usually consist of multiple Drift in Multidimensional Finite perspectives. The utility of different interacting components that exhibit Populations modeling techniques, including PDEs, complicated temporal and spatial Marc Harper, University of California, Los delay differential equations, stochastic dynamics with multiple scales and Angeles, USA processes, and data assimilation, as high dimensions, which are extremely well as approaches to modeling cardiac 3:00-3:25 Pest Persistence and difficult to describe, model or predict. Eradication in a Deterministic Model structure, will be discussed. Applications In this minisymposium, the challenges for Sterile Insect Release to arrhythmia development will be of modeling these complex systems will Luis Gordillo, Utah State University, USA presented. be discussed, and more beyond, the new 3:30-3:55 Quantifying the Impact Organizer: Elizabeth M. Cherry mathematical and numerical methods to of the Recent Invasive Species, Rochester Institute of Technology, USA analyze and simulate these models will Pomacea insularam 2:00-2:25 Predicting Arrhythmias with a also be presented. Lihong Zhao, University of Louisiana, Lafayette, USA Nonlinear Cardiac Fiber Model Organizer: Xinfeng Liu Laura Munoz and Niels Otani, Rochester University of South Carolina, USA Institute of Technology, USA; Anna Gelzer, Cornell University, USA; Flavio M. Fenton, Organizer: Yongtao Zhang Georgia Institute of Technology, USA; University of Notre Dame, USA Coffee Break Weiye Lin and Min Chul Shin, Cornell Organizer: Lei Zhang 4:00 PM-4:30 PM University, USA; Robert Gilmour, Jr., University of Prince Edward Island, Canada Peking University, China Room:Symphony Preconvene Area 2:00-2:25 Time to Mutation Acquisition 2:30-2:55 Compositionality Results for in Stem Cell Driven Cancers Cardiac Cell Dynamics Alexandra Jilkine, University of Notre Md. Ariful Islam and Abhishek Murthy, Dame, USA Stony Brook University, USA; Antoine Girard, Université Joseph Fourier, France; 2:30-2:55 Analysis and Simulations of Scott Smolka, Stony Brook University, a Three Dimensional Model of Cell USA; Radu Grosu, Vienna University of Signal Transduction Technology, Austria David Iron, Dalhousie University, Canada 3:00-3:25 Microscale Modeling of 3:00-3:25 Spatial-Temporal Regulation Cardiac Tissue of the First Embryonic Development Letitia Hubbard and Craig Henriquez, Duke Decision University, USA William Holmes, University of California, Irvine, USA 3:30-3:55 Intramural Forecasting of Cardiac Electrical Dynamics Using 3:30-3:55 Mathematical Modeling of Data Assimilation Proliferation Kinetics of Cancer Stem Matthew J. Hoffman, Stephen Scorse, and Cells Elizabeth M. Cherry, Rochester Institute of Xinfeng Liu, University of South Carolina, Technology, USA USA 44 2014 SIAM Conference on the Life Sciences

Wednesday, August 6 5:00-5:25 Silibinin As a Drug Wednesday, August 6 for Hepatitis C in Patients with MS61 Compromised Liver MS62 Swati Debroy, University of South Advances in Mathematical Carolina, Beaufort, USA; Harel Dahari, Uncertainty, Complexity, Modeling of Complex Loyola University, USA; Laetitia Canini, and Model Qualification for Los Alamos National Laboratory, USA; Life Sciences Aspects and Control of Zoe Marino, Gonzalo Crespo, and Miquel Some Prevalent Infectious Navasa, CIBERehd, Spain; Massimo 4:30 PM-6:30 PM D’Amato, Rottapharm Spa, Italy; Xavier Diseases - Part II of II Room:Symphony II Forns, CIBERehd, Spain; Scott Cotler, 4:30 PM-6:00 PM Loyola University, USA; Alan S. Perelson, How do modelers in life sciences Room:Symphony I Los Alamos National Laboratory, USA responsibly support decision-making given the potential impact versus the For Part 1 see MS53 5:30-5:55 Role of Methamphetamine This minisymposium will present recent in Transmission Dynamics of HIV in number and complexity of unknowns? efforts in understanding underlying MSM Population Many life science applications have mechanisms that drive patterns of Aprillya Lanz, Norfolk State University, significant consequences: dosing in USA infectious pathogens in the population clinical drug trials, interpretation of and in the host. The talks will discuss data to inform decisions on new drugs pressing issues relevant to control of or devices, etc. Speakers will balance infectious diseases such as influenza, complexity, uncertainty, and impact malaria, Hepatitis-C, HIV. Amidst via visualization and intentional active research in controlling them communication as well as mathematics, through optimal public health planning statistics, and computation. Examples (vaccination) and/or therapeutic will include qualifying physiological strategies, discerning complimentary models in pharmaceutical applications, aspects like immunity, nosocomial input, leveraging visualization and probability drug resistance will be indispensible to obtain a critical cancer-drug threshold, in developing ways to eliminate them statistical perspectives on assessing the for good. The sessions promote several impact of knowns and unknowns, and women and minorities, and can be of incorporating in physiologically-based interest to students and researchers in pharmacokinetic models variability and infectious diseases, applied mathematics changes between species. including public health. Organizer: Jeff Sachs Organizer: Swati Debroy Merck Research Laboratories, USA University of South Carolina, Beaufort, Organizer: Karim Azer USA Merck & Co., Inc., USA Organizer: Anuj Mubayi 4:30-4:55 Developing Fit-for- Northeastern Illinois University, USA purpose Physiological Models in Drug Discovery and Development 4:30-4:55 Detailed Viral Kinetics - A Framework for Qualification Best During Liver Transplantation Indicates Practices that the Liver Plays a Role in HCV Karim Azer, Merck & Co., Inc., USA; Jeff Clearance Sachs, Merck Research Laboratories, Harel Dahari, Loyola University, USA USA; Stefan Willmann, Bayer Technology Services, Germany; Carolyn Cho, Merck & Co., Inc., USA; Thomas Kerbusch, Antonio Cabal, Christopher Gibson, and Sandra Sandra Allerheiligen, Merck Research Laboratories, USA

continued in next column continued on next page 2014 SIAM Conference on the Life Sciences 45

5:00-5:25 Leveraging Visualization Wednesday, August 6 Wednesday, August 6 and Probabilistic Thinking to Get Consensus on an Assay Level Target MS63 MS64 for a Cancer Drug Jeff Sachs, Jos Lommerse, Jeroen Elassaiss Molecular Biosciences: Cellular, Tissue, and Organ - Schaap, and Yali Zhu, Merck Research Geometric Modeling in Level Biofluid Dynamics - Laboratories, USA Biomolecular Systems Part II of II 5:30-5:55 A Sensitivity Based Statistical Approach to Parameter 4:30 PM-6:30 PM 4:30 PM-6:30 PM Selection and Uncertainty Room:Symphony V Room:Symphony VI Quantification Large biological systems such as For Part 1 see MS57 H. T. Banks, North Carolina State Fluid flows play an important role in University, USA molecular motors and viruses are of great importance to the processes of life, animal and plant physiology, from the 6:00-6:25 Application of and now also to biologically inspired level of single cells up to the level of Modelling and Simulation in engineering. However, the complex organs and organisms. In the first part Oncology: Physiologically-based of this minisymposium, we begin by Pharmacokinetics and Dynamics interactions between these systems Examples and their aquatic environment pose highlighting the role of fluids at the Michael Block, Bayer Technology Services, enormous challenges for theoretical tissue and organ level by considering the Germany understanding and design, particularly importance of flow to the development in offering accurate predictions of of embryonic lung. We then consider experimental data. This minisymposium the role of structures such as the will address how advances in geometric pericardium in the transport of fluids modeling and computation are within the body. In the next session, advancing our understanding of these we consider the importance of non- interactions. Topics include multiscale Newtonian and multiphase flows in continuum models, new bio-medical biological processes such as biofilm imaging methods, and the interplay formation, cellular motility, and the between chemical and mathematical tracks of tears. approximations. Speakers will address Organizer: Laura A. Miller mathematical theories and methods, as University of North Carolina, Chapel well as simulation and software. Hill, USA Organizer: Jaydeep P. Bardhan 4:30-4:55 Plant Leaves Reconfigure Northeastern University, USA into Cone Shapes to Reduce Drag Organizer: Zhan Chen and Flutter University of Minnesota, USA Laura A. Miller, University of North Carolina, Chapel Hill, USA 4:30-4:55 Chemical Insights, Matrix Approximations, and Boundary- 5:00-5:25 Modeling and Simulation of Integral Equations Biofilm Flows Jaydeep P. Bardhan, Northeastern Qi Wang, University of South Carolina, University, USA USA; Jia Zhao, University of South Carolina, USA 5:00-5:25 Geometry of Surfaces in the Protein Images and the Graph 5:30-5:55 Surface Tension in Human Algorithms Lungs: Modeling and Experiments Jing He, New Mexico State University, Rachel Levy, Harvey Mudd College, USA; USA Karen Daniels, North Carolina State University, USA; Ellen Swanson, Centre 5:30-5:55 Accurate Electrostatics in College, USA; Stephen Strickland, North 3D Classical Dft Carolina State University, USA; Peter Matthew G. Knepley, University of Megson and Shreyas Kumar, Harvey Chicago, USA Mudd College, USA 6:00-6:25 Protein Modeling from 6:00-6:25 Biofilm Pattern Formation Intermediate-Resolution Density Within Microfluidic Chambers Maps Using Geometric Skeletons Mark E. Whidden, Nick Cogan, and Matt Tao Ju, Washington University, St. Louis, Donahue, Florida State University, USA; USA Fernando Navarrete and Leonardo de La Fuente, Auburn University, USA 46 2014 SIAM Conference on the Life Sciences

Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 MS65 CP10 CP11 Recent Advances in Neuroscience II Circadian Rhythms Ecosystems and Disease 4:30 PM-6:00 PM 4:30 PM - 6:30 PM Models Room:Symphony VII Room: Mecklenburg I 4:30 PM-6:30 PM Chair: Janet Best, The Ohio State Chair: To Be Determined Room:Mecklenburg III University, USA 4:30-4:55 Glucose and Temperature 4:30-4:55 Robust Design of Mathematical models have been playing Compensation in the Neurospora Polyrhythmic Neural Circuits significant roles in life sciences to Circadian Clock: Mathematical capture the complex relationship among Justus T. Schwabedal, Georgia State Modeling and Experimental University, USA; Alexander Neiman, humans, animals, microorganisms, and Validation Ohio University, USA; Andrey Shilnikov, Andrey A. Dovzhenok and Mokryun Baek, infectious diseases. This minisymposium Georgia State University, USA will focus on recent advances in University of Cincinnati, USA; Arun Mehra, Jennifer Loros, and Jay Dunlap, ecosystems and disease models. The 5:00-5:25 Relating Spiking Neural Network to Partial Differential Dartmouth College, USA; Sookkyung purpose of this minisymposium is to Equations Lim and Christian Hong, University of bring together researchers from different Li Yang, Olivier Faugeras, and Pierre Cincinnati, USA backgrounds to work together and Kornprobst, INRIA Sophia Antipolis, contribute to the study of biological France 5:00-5:25 Molecular Mechanisms That processes. It will serve as a platform 5:30-5:55 Characterization of Regulate the Coupled Period of the to report on recent progresses, Transient and Spatially Distributed Mammalian Circadian Clock exchange ideas, propose questions High-Frequency Oscillations in the Jae Kyoung Kim, The Ohio State University, for discussion, extend networks, and Brain with Quasi-Periodic Time Scales USA; Zachary Kilpatrick, University seek further collaborations. Topics of Catherine Stamoulis, Harvard Medical of Houston, USA; Matthew Bennett, talks are carefully selected to make School, USA; Bernard Chang, Harvard Rice University, USA; Krešimir Josic, the minisymposium interesting and Medical School, Beth Israel Medical University of Houston, USA attractive to a diverse audience. Center, USA Organizer: Guihong Fan 5:30-5:55 Mathematical Modeling of the Hypothalamic-Pituitary-Adrenal Columbus State University, USA Axis in Relation to Major Depression Organizer: Xiang-Sheng Wang Johanne Gudmand-Høyer and Johnny T. Southeast Missouri State University, Ottesen, Roskilde University, Denmark USA 4:30-4:55 Basic Reproductive Ratios in Ecosystems and Disease Models Xiang-Sheng Wang, Southeast Missouri State University, USA 5:00-5:25 Parameter Estimation and Model Discrepancy with Application to the Life Sciences John A. Burns and Eugene Cliff, Virginia Tech, USA 5:30-5:55 Habitat and Abundance Modeling of West Nile Virus Vector Heidi Brown, University of Arizona, USA 6:00-6:25 Optimal Control in PDE/DE Model for an Anthrax Epizootic Buddhi Pantha, University of Tennessee, Knoxville, USA; Suzanne M. Lenhart, University of Tennessee, USA 2014 SIAM Conference on the Life Sciences 47

Wednesday, August 6 Wednesday, August 6 Wednesday, August 6 CP12 CP15 PD3 Cell Biology Systems Physiology Lee Segel Forum 4:30 PM-6:00 PM 4:30 PM-6:00 PM 8:45 PM-9:30 PM Room:Mecklenburg II Room:Symplony III Room:Symphony II Chair: To Be Determined Chair: To Be Determined Chair: Robert D. Guy University of California, Davis, USA 4:30-4:55 Modeling the Spatio- 4:30-4:55 Spatial Modelling Temporal Dynamics of Small Gtpase of Cytokine Dynamics Within The focus of this year’s Lee Segel Activity at Dendritic Spines Osteoarthritic Articular Cartilage Forum is on careers in mathematical Samuel A. Ramirez and Sridhar Michelle Baker, University of Nottingham, biology with panelists representing Ragavachari, Duke University, USA United Kingdom different career types including industry, 5:00-5:25 In Vitro Assay Geometry medicine, research and teaching. The Affects Estimates of the Cell Diffusivity 5:00-5:25 In Vivo Volume and Forum will start with brief presentations and Cell Proliferation Rate Hemoglobin Dynamics in Red Blood by panelists, which will be followed by Katrina Treloar, Matthew Simpson, and Cells an open question and answer session. Sean McElwain, Queensland University Roy Malka, Harvard Medical School, USA The Forum will provide and integrate of Technology, Australia; Ruth E. Baker, 5:30-5:55 Fractional Model for recommendations for undergraduate, University of Oxford, United Kingdom Neurovascular Coupling graduate, and postdoctoral training in 5:30-5:55 Unravelling the Impact of Zehor Belkhatir, King Abdullah University mathematical biology. The audience Obstacles in Diffusion and Kinetics of of Science & Technology (KAUST), Saudi for the Forum will likely include many An Enzyme Catalysed Reaction Arabia; Taous-Meriem Laleg, INRIA students seeking advice for career Marcio Duarte Albasini Mourao, The Rocquencourt, France directions as well as faculty interested Ohio State University, USA; Doree in updating the training that their own Kreitmann and Santiago Schnell, University of Michigan, USA institutions provide. This Forum is in Dinner Break memory of Lee Segel. Panelists: 6:30 PM-8:00 PM Timothy David Attendees on their own University of Canterbury, New Zealand Timothy C. Elston University of North Carolina at Chapel Hill, SIAG/LS Business Meeting USA Oliver E. Jensen 8:00 PM-8:45 PM University of Manchester, United Kingdom Room:Symphony II Suzanne M. Lenhart University of Tennessee, USA (Open to all SIAG/LS members.) Rachel Levy Complimentary wine and beer will be Harvey Mudd College, USA served. Jeff Sachs Merck Research Laboratories, USA 48 2014 SIAM Conference on the Life Sciences

Thursday, August 7 10:30-10:55 Optimal Control of Thursday, August 7 Continuous Systems with Impulse MS66 Controls Rachel Leander, Middle Tennessee Registration Mathematical Modeling State University, USA; S.M. Lenhart, and Control of Ecological University of Tennessee, USA; Vladimir 7:30 AM-3:00 PM and Epidemiological A. Protopopescu, Oak Ridge National Laboratory, USA Room:Symphony Preconvene Area Problems - Part I of II 11:00-11:25 How Fish Ecology Affects 9:30 AM-11:30 AM the Effectiveness of Marine Protected Room:Symphony I Areas Closing Remarks Patrick DeLeenheer, Oregon State For Part 2 see MS74 University, USA 8:10 AM-8:15 AM The management of ecological Room:Symphony I, II & III and epidemiological systems is of importance to agriculture, public health and biodiversity. The complexity of IP7 these systems, however, makes it difficult to develop tractable models Early Warning Signs and that can produce actionable control Critical Transitions in policies, and model validation remains Ecology: Corals, Theory, a fundamental difficulty. This session Pitfalls, and Advances will bring together a diverse group of researchers to discuss innovative 8:15 AM-9:00 AM methods of modeling and control. Room:Symphony I, II & III Challenges and open questions will be discussed in the context of both Chair: Robert D. Guy, University of application-specific and theoretical California, Davis, USA presentations. In the process, we will I will start by describing specific explore the roles of space, time and ecological systems that have multiple stochasticity in the modeling, analysis, stable states, lakes and coral algal and management of ecological and grazer systems giving models of the epidemiological systems. latter. I will then discuss approaches for predicting sudden shifts in the face of Organizer: Wandi Ding Middle Tennessee State University, USA slow parameter change. The approach will depend on developing a simple Organizer: Rachel Leander stochastic model and using this model Middle Tennessee State University, USA to describe the data. A key element in 9:30-9:55 Probability of Extinction in describing the results will be the use of Stochastic Models of Populations and receiver-operator curves. This part of the Infectious Diseases: Importance of talk will include both possibilities and Time and Location pitfalls. I will then discuss how the use Linda J. Allen, Texas Tech University, USA of data can both help and be misleading 10:00-10:25 Optimal Control in judging the efficacy of warning Applied to Hospital-Acquired and signals. Community-Acquired Methicillin- Resistant Staphylococcus Aureus Alan M. Hastings Strains in Hospitals University of California, Davis, USA Wandi Ding, Middle Tennessee State University, USA; Glenn Webb, Vanderbilt University, USA Coffee Break 9:00 AM-9:30 AM Room:Symphony Preconvene Area continued in next column 2014 SIAM Conference on the Life Sciences 49

Thursday, August 7 Thursday, August 7 Thursday, August 7 MS67 MS68 MS69 Practical Parameter Modeling and Simulation of Molecular Biosciences: Ion Estimation and Uncertainty Complex Biological Systems Channels and their Roles in Quantification Methods for - Part I of II Cell Biology - Part I of II Physiological Models 9:30 AM-11:30 AM 9:30 AM-11:30 AM 9:30 AM-11:30 AM Room:Symphony III Room:Symphony V Room:Symphony II For Part 2 see MS76 For Part 2 see MS77 Numerous physiological models has been Mathematical modeling and simulation Ion channels are special proteins developed to gain insight into the system is a powerful approach for understanding embedded in cell membranes and dynamics, though few has been combined complex biological systems. conduct ionic flux from extracellular with data enabling patient specific Development of novel mathematical to intracellular environment or vice analysis. One obstacle is the lack of models and simulation algorithms is versa. Thus, they are among the adequate inverse methods for parameter critical for studying these systems. most fundamental building blocks identification and estimation. Two groups Recently, several successful attempts to understand behaviors (e.g. action of methods exist: methods that rely on have been made for simulating complex potential) of individual cells or their linearization around given parameter biological processes like metabolic interactions with microenvironment (e.g. values and global methods, frequently pathways, gene regulatory networks, cell angiogenesis, chemotaxis). However, based on Monte Carlo simulations, signaling pathways, cell dynamics, tissue studies of functions of ion channels predicting a global sensitivity matrix engineering and biofabrication, etc. require molecular scales. The purpose by sampling. Global methods are These models have not only generated of the proposed minisymposium is to computationally intensive and are thus experimentally verifiable hypothesis promote multiscale modeling, analysis, less suitable for practical parameter but also provided valuable insights into and simulations of ion channels and identifiability and estimation. On the the behavior of the complex biological their roles in cellular or developmental other hand they also provide uncertainty systems. This minisymposium will biology. The invited speakers include quantification as a part of the method. showcase some new progresses made in biophysicists, computational biologists, developing mathematical and efficient and mathematicians working in areas Organizer: Mette S. Olufsen computational approaches for a set of of modeling, analysis, and scientific North Carolina State University, USA biological systems. computing. Organizer: Johnny T. Ottesen Organizer: Qi Wang Organizer: Duan Chen Roskilde University, Denmark University of South Carolina, USA University of North Carolina, Charlotte, 9:30-9:55 Patient Specific Modelling Organizer: Yi Sun USA of the Endocrine HPA-Axis and Its Relation to Depression: Ultradian and University of South Carolina, USA Organizer: Wei Cai Circadian Oscillations 9:30-9:55 Diffusion in Soft Matter: University of North Carolina, Charlotte, Johnny T. Ottesen, Stine Timmerman, Theory, Modeling, and Simulations USA and johanne Gudmand-Hoeyer, Roskilde M. Gregory Forest and John Mellnik, 9:30-9:55 Ions in Channels: Natural University, Denmark University of North Carolina at Chapel Nanovalves Hill, USA; Paula Vasquez, University of 10:00-10:25 Uncertainty Quantification Bob Eisenberg, Rush University Medical South Carolina, USA; Scott McKinley, in ODE Modeling of Immune Response Center, USA University of Florida, USA; David Hill, David Swigon, Ericka Mochan, Jonathan University of North Carolina at Chapel 10:00-10:25 Title Not Available at Time Rubin, and Gilles Clermont, University of Hill, USA of Publication Pittsburgh, USA Tai-Chia Lin, National Taiwan University, 10:00-10:25 A Multicell Model to 10:30-10:55 Model Calibration in Taiwan, ROC Investigate How Vasculogenesis Is Systems Biology: Making the Most of Disrupted in Cerebral Cavernous 10:30-10:55 A Energy-Preserving Limited Data Malformations Scheme for Pnp Equations Brian P. Ingalls and Rahul Rahul, Timothy Elston, University of North Xiaofan Li, Illinois Institute of Technology, University of Waterloo, Canada Carolina, Chapel Hill, USA USA 11:00-11:25 Combined Parameter and 10:30-10:55 Homeostatic Mechanisms 11:00-11:25 The Way Cells Talk: State Estimation in Ensemble Kalman in Biochemical Systems Modeling and Simulations of Ion Filters Michael C. Reed, Duke University, USA Transport Daniela Calvetti, Andrea N. Arnold, and Duan Chen, University of North Carolina, Erkki Somersalo, Case Western Reserve 11:00-11:25 Mathematical Charlotte, USA University, USA Understanding of Cancer Virotherapy Jianjun Paul Tian, College of William & Mary, USA 50 2014 SIAM Conference on the Life Sciences

Thursday, August 7 10:30-10:55 The Effects of In Phase Thursday, August 7 and Out of Phase Pulsations in Groups MS70 of Upside-down Jellyfish, Cassiopea MS71 sp Fluid Dynamics of Julia E. Samson, University of North Mathematical Questions Propulsion and Transport - Carolina, Chapel Hill, USA; Arvind in Neuronal and Neural Santhanakrishnan, Oklahoma State Network Dynamics - Part I of II University, USA; Laura A. Miller, 9:30 AM-11:30 AM University of North Carolina, Chapel Hill, Part I of II USA Room:Symphony VI 9:30 AM-11:30 AM 11:00-11:25 Experiments and For Part 2 see MS78 Room:Symphony VII Modeling Study of Low Reynolds The surrounding fluid environment plays Number Flows Generated by a For Part 2 see MS79 an important in both propulsion and Processing Nodal Cilia Understanding the brain and the transport in the biological world. In the Longhua Zhao, Case Western Reserve physiological control mechanisms first part of this minisymposium, we will University, USA; Roberto Camassa, James of neurons is difficult. It begin focus on a hydrodynamic level, D. Martindale and Richard McLaughlin, necessarily requires understanding by first exploring the role of neuronal University of North Carolina at Chapel electrophysiology, the biochemistry of control mechanisms in swimming Hill, USA; Leandra Vicci, University of neurons, the behavior of large-scale organisms. We will then examine North Carolina, USA neural networks and how neural control transport mechanisms found on an is coordinated with other physiological organismal level and in complex fluid systems. This is a daunting task because environments. In our second session, these aspects of neural function are we will shift our focus to movement related to behavior, to changing levels of and through air. We will begin by of gene regulation, and to the endocrine examining scaling effects in insect system. The mathematical techniques flight and respiration, before moving used to gain understanding range on to mechanisms found for pathogen from dynamical systems and partial transmission through air. differential equations to probability Organizer: Alexander Hoover theory and stochastic processes. The University of North Carolina, Chapel talks in this minisymposium will Hill, USA illustrate a diversity of biological systems and mathematical techniques. Organizer: Laura Miller University of North Carolina at Chapel Organizer: Janet Best Hill, USA The Ohio State University, USA 9:30-9:55 Neuromuscular Pumping in Organizer: Michael C. Reed Jellyfish Bells Duke University, USA Alexander Hoover and Laura A. Miller, 9:30-9:55 The Influence of University of North Carolina, Chapel Hill, Neurochemistry USA Janet Best, The Ohio State University, 10:00-10:25 The Metachronal USA; Michael C. Reed and H Frederik Limb Stroke Pattern in Crustacean Nijhout, Duke University, USA Swimming 10:00-10:25 Interaction of Two Distinct Calvin Zhang, Courant Institute of Timescales in Computational a Mathematical Sciences, New York Model of in-Vitro Sigh Generation University, USA; Robert D. Guy and Natalia Toporikova, Washington and Lee Timothy Lewis, University of California, University, USA; Muriel Thoby-Brisson, Davis, USA; Boyce Griffith, New York Universite de Bordeaux I, France University, USA; Charles S. Peskin, Courant Institute of Mathematical 10:30-10:55 How Precise Can Sciences, New York University, USA We Make a Biophysical Neural Integrator? Michael Schwemmer, The Ohio State University, USA continued in next column 11:00-11:25 The Effects of Long-Range Coupling on Neural Activity in the Crayfish Swimmeret System Lucy Spardy, University of Pittsburgh, USA; Brian Mulloney and Tim Lewis, University of California, Davis, USA 2014 SIAM Conference on the Life Sciences 51

Thursday, August 7 Thursday, August 7 Thursday, August 7 MS72 MS73 CP13 Mechanisms for Probabilistic Methods in Cell Evolution and Ecology III Defibrillation and Control of Biology - Part I of II 9:30 AM-11:30 AM Cardiac Tissue 9:30 AM-11:00 AM Room:Mecklenburg III 9:30 AM-11:00 AM Room:Mecklenburg II Chair: To Be Determined Room:Mecklenburg I For Part 2 see MS81 9:30-9:55 The Dynamics of Foraging When spiral waves of electrical With the increasing availability of Activity in Harvester Ants activity form in the heart, they drive single-cell experimental data, increasing Oyita Udiani, Arizona State University, USA it to a spatiotemporally complex state attention is being focused on the 10:00-10:25 A Continuous Model of Ant that prevents contraction. Currently, sources and effects of stochasticity Foraging with Pheromones and Trail the only reliable way to eliminate in the dynamics of cells. Although Formation these “reentrant” waves is to apply deterministic models provide “on Paulo V. Amorim, Universidade Federal de a strong electric field that activate average” information, they cannot Rio de Janeiro, Brazil the whole heart and reset it. In this explain variability key to understanding 10:30-10:55 Using Homogenization minisymposium, different alternative properties such as robustness and to Estimate Random-Walk Motility methods for defibrillation or control of synchronization. Classical probabilistic from Gps Collar Data in Variable waves before they become arrhythmic approaches ranging from stochastic Landscapes will be presented. These newer methods simulations to Langevin approximations Martha J. Garlick, South Dakota School of Mines & Technology, USA; James Powell aim to use lower energies to reduce the have previously been used to study such and Luis Gordillo, Utah State University, risk of damage and pain. variability; some newer approaches have focussed on additional sources USA Organizer: Flavio Fenton such as delay and genetic variation. 11:00-11:25 Respect Versus Disrespect Georgia Institute of Technology, USA This minisymposium will bring together for Ownership: An Iterated Hawk-Dove 9:30-9:55 Local Termination of theorists and experimentalists to Game with Relocation Costs Cardiac Alternans Using Isostable discuss different approaches to study Tugba Karabiyik, Florida State University, Response Curve Techniques stochasticity in biology. USA Dan D. Wilson and Jeff Moehlis, University of California, Santa Barbara, Organizer: Alan Veliz-Cuba USA University of Houston, USA Lunch Break 10:00-10:25 Large Reduction of Organizer: Chinmaya Gupta Defibrillation Threshold Using a Four- University of Houston, USA 11:30 AM-1:00 PM Electrode System 9:30-9:55 Extrinsic Noise and Cell- Attendees on their own Jean Bragard, Universidad de Navarra, Cycle Dependence of Genetic Spain; Ana Simic and Jorge Elorza, Oscillators University of Navarra, Spain Alan Veliz-Cuba, University of Houston, 10:30-10:55 Unification of Electrical USA Restitution Dynamics and Ion 10:00-10:25 An Optimal Control Channel Dynamics in the Control of Framework for Stochastic Gene Cardiac Rhythm - An Eigenmode Regulatory Networks Approach David Murrugarra, Georgia Institute of Niels Otani, Rochester Institute of Technology, USA Technology, USA 10:30-10:55 Exact Protein Distributions for Stochastic Models of Gene Expression Rahul Kulkarni and Niraj Kumar, University of Massachusetts, Boston, USA; Hodjat Pendar, Virginia Tech, USA; Thierry Platini, Coventry University, United Kingdom 52 2014 SIAM Conference on the Life Sciences

Thursday, August 7 Thursday, August 7 Thursday, August 7 IP8 MS74 MS75 Synthetic Biology and Mathematical Modeling and Identifiability and Parameter Biocomputation: Life Control of Ecological and Estimation in Mathematical Redesigned Epidemiological Problems - Models of Biological 1:00 PM-1:45 PM Part II of II Phenomena Room:Symphony I, II & III 2:15 PM-4:15 PM 2:15 PM-4:15 PM Chair: Eduardo Sontag, Rutgers Room:Symphony I Room:Symphony II University, USA For Part 1 see MS66 Mathematical modeling of biological Synthetic biology is bringing together The management of ecological and phenomena is a very fast growing area engineers, computational scientists epidemiological systems is of importance of research. It is a common situation and biologists to design and construct to agriculture, public health and that some of the model’s parameters are biological circuits out of proteins, genes biodiversity. The complexity of these unknown and have to be inferred from and other bits of DNA, and to use systems, however, makes it difficult the available data. An important question these circuits to rewire and reprogram to develop tractable models that can is: Can all, or at least some, of the organisms. These re-engineered produce actionable control policies, and model’s parameters be estimated uniquely organisms are going to change our lives model validation remains a fundamental from system’s input and output? This is in the coming years, leading to cheaper difficulty. This session will bring together the problem of structural identifiability. drugs, “green” means to fuel our car a diverse group of researchers to discuss This minisymposium will focus on both and clean our environment, and targeted innovative methods of modeling and the current research areas related to therapies to attack “superbugs” and control. Challenges and open questions structural and practical identifiability as diseases such as cancer. In this talk, we will be discussed in the context of both well as parameter estimation techniques highlight recent efforts to create synthetic application-specific and theoretical in models arising in biology. gene networks and programmable presentations. In the process, we will Organizer: Adam Mahdi cells, and discuss a variety of synthetic explore the roles of space, time and North Carolina State University, USA stochasticity in the modeling, analysis, biology applications in biocomputing, Organizer: Nicolette Meshkat biotechnology and biomedicine. and management of ecological and epidemiological systems. North Carolina State University, USA James J. Collins Organizer: Wandi Ding 2:15-2:40 Identifiability and Parameter Boston University, USA Estimation in Modeling Disease Middle Tennessee State University, USA Dynamics Organizer: Rachel Leander Marisa Eisenberg, University of Michigan, Middle Tennessee State University, USA USA 2:15-2:40 Optimal Control in Models 2:45-3:10 Identifiability of High- Coffee Break of Management Involving Trees and Dimensional Models Forest Resources Hongyu Miao, University of Rochester, USA 1:45 PM-2:15 PM Suzanne M. Lenhart, University of 3:15-3:40 Identifiability and Parameter Tennessee, USA Room: Symphony Preconvene Area Estimation in Systems Biology and 2:45-3:10 Modeling of Transgenic Or Drug Development Sterile Mosquitoes in Fighting Vertor- Andreas Raue, University of Freiburg, Borne Diseases Germany Jia Li, University of Alabama, Huntsville, 3:45-4:10 Identifiability of Linear State USA Space Models 3:15-3:40 An Ecological Model for Seth Sullivant, North Carolina State Producers and Scroungers in a Spatial University, USA Habitat Chris Cosner, University of Miami, USA; Andrew Nevai, University of Central Florida, USA 3:45-4:10 The Role of Avian Stage- structure in the Transmission and Control of West Nile Virus Suzanne Robertson, Virginia Commonwealth University, USA; Kevin Caillouet, St. Tammany Parish Mosquito Abatement District, USA 2014 SIAM Conference on the Life Sciences 53

Thursday, August 7 Thursday, August 7 Thursday, August 7 MS76 MS77 MS78 Modeling and Simulation of Molecular Biosciences: Ion Fluid Dynamics of Propulsion Complex Biological Systems Channels and their Roles in and Transport - Part II of II - Part II of II Cell Biology - Part II of II 2:15 PM-4:15 PM 2:15 PM-4:15 PM 2:15 PM-4:15 PM Room:Symphony VI Room:Symphony III Room:Symphony V For Part 1 see MS70 For Part 1 see MS68 For Part 1 see MS69 The surrounding fluid environment plays Mathematical modeling and Ion channels are special proteins an important in both propulsion and simulation is a powerful approach embedded in cell membranes and transport in the biological world. In the for understanding complex biological conduct ionic flux from extracellular first part of this minisymposium, we will systems. Development of novel to intracellular environment or vice begin focus on a hydrodynamic level, by mathematical models and simulation versa. Thus, they are among the first exploring the role of neuronal control algorithms is critical for studying these most fundamental building blocks mechanisms in swimming organisms. We systems. Recently, several successful to understand behaviors (e.g. action will then examine transport mechanisms attempts have been made for simulating potential) of individual cells or their found on an organismal level and in complex biological processes like interactions with microenvironment (e.g. complex fluid environments. In our metabolic pathways, gene regulatory angiogenesis, chemotaxis). However, second session, we will shift our focus networks, cell signaling pathways, studies of functions of ion channels to movement of and through air. We cell dynamics, tissue engineering and require molecular scales. The purpose will begin by examining scaling effects biofabrication, etc. These models have of the proposed minisymposium is to in insect flight and respiration, before not only generated experimentally promote multiscale modeling, analysis, moving on to mechanisms found for verifiable hypothesis but also provided and simulations of ion channels and pathogen transmission through air. valuable insights into the behavior their roles in cellular or developmental Organizer: Alexander Hoover of the complex biological systems. biology. The invited speakers include University of North Carolina, Chapel This minisymposium will showcase biophysicists, computational biologists, Hill, USA some new progresses made in and mathematicians working in areas Organizer: Laura Miller developing mathematical and efficient of modeling, analysis, and scientific University of North Carolina at Chapel computational approaches for a set of computing. Hill, USA biological systems. Organizer: Duan Chen 2:15-2:40 Clap and Fling Interaction of Organizer: Qi Wang University of North Carolina, Charlotte, Bristled Wings in Tiny Insect Flight University of South Carolina, USA USA Arvind Santhanakrishnan, Oklahoma Organizer: Yi Sun Organizer: Wei Cai State University, USA; Alice Robinson, University of South Carolina, USA University of North Carolina, Charlotte, University of California, Davis, USA; USA Tyson Hedrick and Laura A. Miller, 2:15-2:40 Modeling Cartilage Tissue University of North Carolina, Chapel Hill, Engineering in Cell-Seeded Scaffolds 2:15-2:40 Title Not Available at Time USA Mansoor A. Haider, North Carolina State of Publication 2:45-3:10 Fluid Flow Through Many University, USA Chun Liu, Pennsylvania State University, Bristled Wings USA 2:45-3:10 Mathematical Modeling of Shannon Jones and Laura Miller, University Renal Hemodynamics 2:45-3:10 A Model of Tissue of North Carolina, Chapel Hill, USA Anita T. Layton, Duke University, USA Electrodiffusion and Osmosis and Its 3:15-3:40 Microscale Gas Transport in 3:15-3:40 Let There be Force: Application to Cortical Spreading Depression Insect Respiratory Systems Modeling Cell-ECM Interactions Anne Staples, Virginia Tech, USA Yi Jiang, Georgia State University, USA Yoichiro Mori, University of Minnesota, USA 3:45-4:10 Roles of Droplets and 3:45-4:10 Kinetic Monte Carlo 3:15-3:40 Pnp Equations with Steric Bubbles in Pathogen Transmission Simulations of Multicellular Effects: A Model of Ion Flow Through Through Air Aggregate Self-Assembly in Channels Lydia Bourouiba, Massachusetts Institute of Biofabrication Technology, USA Yi Sun, University of South Carolina, USA Tzyy-Leng Horng, Feng Chia University, Taichung, Taiwan 3:45-4:10 Computer Simulation of Voltage Sensitive Calcium Ion Channels in a Dendritic Spine Pilhwa Lee, University of Connecticut Health Center, USA 54 2014 SIAM Conference on the Life Sciences

Thursday, August 7 Thursday, August 7 Thursday, August 7 MS79 MS80 MS81 Mathematical Questions Mathematical Modeling Probabilistic Methods in Cell in Neuronal and Neural and Experiments Toward Biology - Part II of II Network Dynamics - Mechanisms of Pulmonary 2:15 PM-4:15 PM Part II of II Hypertension Room:Mecklenburg II 2:15 PM-4:15 PM 2:15 PM-3:45 PM For Part 1 see MS73 Room:Symphony VII Room:Mecklenburg I With the increasing availability of single-cell experimental data, increasing For Part 1 see MS71 Pulmonary hypertension is a attention is being focused on the Understanding the brain and the pathophysiological condition of sustained sources and effects of stochasticity physiological control mechanisms of mean pulmonary arterial pressure greater in the dynamics of cells. Although neurons is difficult. It necessarily requires than 25 mmHg at rest. It is a syndrome deterministic models provide “on understanding electrophysiology, the in which remodeling of pulmonary average” information, they cannot biochemistry of neurons, the behavior vasculature leads to increased pulmonary explain variability key to understanding of large-scale neural networks and vasculature resistance leading to right properties such as robustness and how neural control is coordinated with ventricular hypertrophy and heart failure. synchronization. Classical probabilistic other physiological systems. This is a This minisymposium would highlight approaches ranging from stochastic daunting task because these aspects of the current state of our understanding of simulations to Langevin approximations neural function are related to behavior, to the mechanisms underlying pulmonary have previously been used to study such changing levels of gene regulation, and to hypertension such as dysfunction of variability; some newer approaches the endocrine system. The mathematical endothelium and arterial stiffening. The have focussed on additional sources techniques used to gain understanding discourse goes together with multiscale such as delay and genetic variation. range from dynamical systems and partial modeling of the pulmonary blood flow This minisymposium will bring together differential equations to probability theory circulation and prediction of right theorists and experimentalists to and stochastic processes. The talks in this ventricular heart failure. discuss different approaches to study minisymposium will illustrate a diversity Organizer: Pilhwa Lee stochasticity in biology. of biological systems and mathematical University of Michigan, Ann Arbor, USA techniques. Organizer: Chinmaya Gupta 2:15-2:40 Individualized Pulmonary University of Houston, USA Organizer: Janet Best Arterial Blood Flow Analysis The Ohio State University, USA Pilhwa Lee, Shivendra Tewari, and Daniel Organizer: Alan Veliz-Cuba University of Houston, USA Organizer: Michael C. Reed Beard, University of Michigan, Ann Arbor, Duke University, USA USA 2:15-2:40 Rare Events for Genetic 2:45-3:10 A Mathematical and Networks: Studying Interactions 2:15-2:40 Multi-Motor Transport in Between Meta-Stability and Time- Neurons: Moving Beyond Tug-of-War Computational Structured-Tree Model of the Pulmonary Circulation Delays Scott McKinley, University of Florida, USA Nicholas A. Hill, University of Glasgow, Chinmaya Gupta, Manuel Lopez, and 2:45-3:10 Measuring Edge Importance Scotland, UK; M. Umar Qureshi, Robert Azencott, University of Houston, for Random Processes on Networks International Islamic University, Pakistan USA; Matthew Bennett, Rice University, Deena Schmidt, Case Western Reserve and University of Glasgow, United USA; Kresimir Josic and William Ott, University, USA Kingdom; Gareth D.A. Vaughan and University of Houston, USA 3:15-3:40 Stochastic Switching: Christopher Sainsbury, University of 2:45-3:10 Queueing Approaches to Mathematical Surprises and Biological Glasgow, Scotland, United Kingdom; Multisite Enzyme Kinetics Insight Martin Johnson, Western Infirmary, William H. Mather, Virginia Tech, USA Sean D. Lawley, Duke University, USA Glasgow, United Kingdom; Charles S. Peskin, Courant Institute of Mathematical 3:15-3:40 First-Passage Time 3:45-4:10 Spontaneous Neural Activity Sciences, New York University, USA; Mette Calculations for Gene Networks: Caused by Ion Channel Fluctuations S. Olufsen, North Carolina State University, Implications for Phage Lambda Lysis Jay Newby, The Ohio State University, USA USA Time Abhyudai Singh, University of Delaware, 3:15-3:40 Analysis of Cardiovascular USA; John Dennehy, City University Dynamics in Pulmonary Hypertensive of New York, USA; Khem Ghusinga, C57BL6/J Mice University of Delaware, USA Shivendra Tewari, University of Michigan, Ann Arbor, USA; Naomi Chesler, 3:45-4:10 Impact of Stochastic University of Wisconsin, Madison, USA; Transcriptional Delay on Gene Daniel Beard, University of Michigan, Ann Networks Arbor, USA Manuel Lopez, University of Houston, USA 2014 SIAM Conference on the Life Sciences 55

Thursday, August 7 CP14 Immunology and Diseases II 2:15 PM-3:15 PM Room:Mecklenburg III Chair: Martha J. Garlick, South Dakota School of Mines & Technology, USA 2:15-2:40 The Virus of My Virus Is My Friend: Modeling the Ecological Effect of Virophages Bradford Taylor, Michael H. Cortez, and Joshua Weitz, Georgia Institute of Technology, USA 2:45-3:10 Analyzing the Effects of a Non-Host Worm Population on the Spread of Whirling Disease in Trout Tamra Heberling, Lisa G. Davis, Ryan Lamb, and Billie Karens, Montana State University, USA 56 2014 SIAM Conference on the Life Sciences

Notes 2014 SIAM Conference on the Life Sciences 57

LS14 Abstracts

Abstracts are printed as submitted. 58 LS14 Abstracts

IP1 Department of Epidemiology and Public Health Perceptual Dynamics in an Ambiguous World Yale University School of Medicine [email protected] When experiencing an ambiguous sensory stimulus (e.g., the vase-faces image), subjects may report haphazard alternations (time scale, seconds) between the possi- IP6 ble interpretations. I will describe dynamical mod- Is Good Cholesterol Always Good? New Insights els for neuronal populations that compete through mu- about HDL from an In-Silico Model of Lipoprotein tual inhibition for dominance - showing alternations, be- Metabolism and Kinetics having as noisy oscillators or as multistable systems subject to noise-driven switching. In highly idealized Individuals with higher endogenous plasma levels of high- formulations networks are percept specific without di- density lipoprotein-cholesterol (HDL-C), the so called good rect representation of stimulus features. Our recent cholesterol, have a lower risk of developing cardiovascular work involves perception of ambiguous auditory stimuli disease (CVD) an effect that is generally attributed to (e.g., http://auditoryneuroscience.com/topics/streaming- the role of HDL particles in the reverse cholesterol trans- galloping-rhythm-paradigm ); the models incorporate fea- port process. Nevertheless recent efforts to increase HDL- ture specificity, tonotopy, so that perceptual selectivity is C levels pharmacologically have failed to lower CVD risk emergent rather than built-in. in patients. To understand this apparent paradox, we de- veloped a novel in-silico model of lipoprotein metabolism John Rinzel and kinetics [1]. Our model highlights the geometrical as- New York University pects of HDL structure and dynamics, and suggests why [email protected] certain HDL-C raising therapies have not been success- ful to date. 1.Lu J, Hbner K, Nanjee MN, Brinton EA, IP2 Mazer NA. An in-silico model of lipoprotein metabolism and kinetics for the evaluation of targets and biomarkers Invited Plenary Speaker - Title Tbd - Swanson in the reverse cholesterol transport pathway. PLoS Com- put Biol. 2014 Mar 13;10(3):e1003509. doi: 10.1371/jour- TBD nal.pcbi.1003509. eCollection 2014 Mar. Kristin Rae Swanson Northwestern University, USA Norman Mazer [email protected] F. Hoffmann-La Roche Ltd, Switzerland [email protected]

IP3 IP7 Modelling Plant Cell and Tissue Growth Early Warning Signs and Critical Transitions in Plant growth typically occurs through the coordinated Ecology: Corals, Theory, Pitfalls, and Advances anisotropic expansion of plant cells. Growth is regulated by hormones and is driven by high intracellular pressures gen- I will start by describing specific ecological systems that erated by osmosis. This machinery allows a plant primary have multiple stable states, lakes and coral algal grazer root, for example, to penetrate soil in a direction guided by systems giving models of the latter. I will then discuss gravity, while seeking out nutrients and avoiding obstacles. approaches for predicting sudden shifts in the face of slow I will describe the biomechanical aspects of a multiscale parameter change. The approach will depend on devel- model for root gravitropism recently developed with col- oping a simple stochastic model and using this model to leagues at the Centre for Plant Integrative Biology at the describe the data. A key element in describing the results University of Nottingham, UK. This incorporates descrip- will be the use of receiver-operator curves. This part of tions of cell walls as fibre-reinforced viscoelastic polymer the talk will include both possibilities and pitfalls. I will networks and adopts upscaling approaches to efficiently de- then discuss how the use of data can both help and be scribe the growth of multicellular tissues. misleading in judging the efficacy of warning signals.

Oliver E. Jensen Alan M. Hastings University of Manchester, United Kingdom UC Davis [email protected] [email protected]

IP4 IP8 Invited Speaker - Title Tbd - Lander Synthetic Biology and Biocomputation: Life Re- TBD designed

Arthur Lander Synthetic biology is bringing together engineers, compu- University of California, Irvine tational scientists and biologists to design and construct [email protected] biological circuits out of proteins, genes and other bits of DNA, and to use these circuits to rewire and reprogram organisms. These re-engineered organisms are going to IP5 change our lives in the coming years, leading to cheaper Invited Plenary Speaker - Title Tbd - Galvani drugs, ”green” means to fuel our car and clean our envi- ronment, and targeted therapies to attack ”superbugs” and TBD diseases such as cancer. In this talk, we highlight recent ef- forts to create synthetic gene networks and programmable Alison Galvani cells, and discuss a variety of synthetic biology applications LS14 Abstracts 59

in biocomputing, biotechnology and biomedicine. Giovanni Samaey Department of Computer Science, K. U. Leuven James J. Collins [email protected] Boston University Department of Biomedical Engineering Dirk Roose [email protected] KU Leuven Dept. of Computer Science [email protected] CP1 A Mathematical Model of Intermittent Androgen Suppression Therapy for Treatment of Advanced CP1 Prostate Cancer On the Accumulation of Mutations in Cancer

Advanced prostate cancer is often treated with andro- In this work we consider the problem of modeling the gen deprivation therapy (ADT) which facilitates the death stochastic accumulation of somatic mutations in cancer. of androgen-dependent (AD) cancer cells. Androgen- The integration of mathematical modeling and statistical independent (AI) cancer cells may increase with continu- analysis with sequencing and clinical data represents a new ous ADT so that intermittent androgen suppression (IAS) powerful approach for better understanding the evolution- therapy is utilized to delay the onset of AI cells. We model ary dynamics of cancer, and for implementing quantita- the dynamics of IAS therapy with a system of ordinary tive approaches to cancer classification and treatment. By differential equations and determine the optimal times to considering, for the first time, all relevant phases of a tis- collect data relative to model parameters in order to de- sues history - the model makes unexpected predictions, velop better treatment protocols. validated by the analysis of sequencing data: what is the number of somatic mutations that occur prior to the on- John G. Alford, Edward Swim, Alacia M. Voth set of neoplasia? How many rate-limiting mutations are Sam Houston State University needed for cancer to occur? The talk is partially based on: [email protected], [email protected], [email protected] Tomasetti C, Vogelstein B, Parmigiani G. Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci CP1 USA 2013, 110(6):1999-2004. Can Mathematical Models Predict the Outcomes of Cristian Tomasetti Prostate Cancer Patients Undergoing Intermittent Johns Hopkins University Androgen Suppression Therapy? [email protected] Prostate cancer is often treated by intermittent androgen deprivation therapy since prostate cells depend on andro- CP2 gens for proliferation and survival. We extend an existing A Simple Model Incorporating Demographic and prostate cancer model and test the model’s predictive ac- Epidemiological Processes in a Spatially Heteroge- curacy when only a subset of the data is used to find pa- neous rameter values. The results are compared with those of an existing linear model. We also develop a second method In this talk, we explore an epidemic model incorporating for testing the accuracy in predicting the duration of off- demographic processes in a spatially heterogeneous envi- treatment periods. ronment in which the individuals are subject to a random movement. Our analytical and numerical results reveal Rebecca A. Everett, Aaron Packer that the persistence of the population and disease outbreak Arizona State University be ignited by both individuals mobility and environmental [email protected], [email protected] heterogeneity.

Yang Kuang Yongli Cai Arizona State University Department of Mathematics School of Mathematical and Statistical Sciences Sun Yat-Sen University [email protected] [email protected]

Shangbin Cui CP1 Department of Mathematics, Sun Yat-Sen University Variance Reduced Model for Tumor Growth [email protected]

One of the major challenges when using individual-based Weiming Wang models for tumor growth is to reduce the computational College of Mathematics and Information Science cost. We consider an individual-based model for tumor Wenzhou University, Wenzhou, 325035 P.R.China growth, which is continuous in space and time and coupled [email protected] with a set of reaction diffusion equations to model the envi- ronment. We propose a novel variance reduction scheme to reduce the computational cost, based on a control variate CP2 that is obtained from a kinetic description. An SIRS Epidemic Model with Non-Exponential Probability for Temparary Immunity Annelies Lejon KU Leuven We consider an SIRS model for disease dynamics that ac- Dept. Computer Science counts for temporary immunity whereby recovered individ- [email protected] uals return to the susceptible class. We allow for a general 60 LS14 Abstracts

probability function of remaining immune such that the of these data. In my talk I will illustrate that for a model model is a system of integro-differential equations (IDE). of influenza epidemic spreading in a city. We show how the IDEs can be approximated by a system of delay-differential equations. We then show that different Valeriy D. Perminov probabilities, whose parameters have been chosen such that BioTeckFarm Ltd. they have equal moments, generate equivalent dynamical [email protected] output. For the case of a linear function we can derive bi- furcation equations that determine how the moments affect the intensity and duration of epidemics. CP3

Thomas W. Carr Analysis of Labour Productivity in the Presence of Southern Methodist University Substance Abuse Department of Mathematics [email protected] Substance abuse impedes the productivity of employees and reduces economic growth. Efficient management of an organizations workforce must involve eradicating drug CP3 use. In this paper, we formulate and analyse a mathemat- ical model for labour productivity in the presence of sub- Comparison of a Deterministic and Stochastic stance abuse transmission dynamics that includes interven- Model for the Transmission Dynamics of Influenza tion strategies. We investigate the existence and stability We consider an extension of the SEIR model for the trans- of equilibria and use Pontryagin’s Maximum Principle to mission dynamics of influenza. We describe two stages of derive necessary conditions for the optimal control of the the infection, an early and a late stage, in the later stage disease. Numerical simulations are performed to illustrate the infected may or may not take medicine, in addition a the analytical results. fraction from both these groups may be hospitalized. We perform rigorous analysis of the system. It is shown that for Isaac Takaidza Vaal University of Technology the basic reproductive number R0 the disease free equilib- rium is stable and the system has an endemic equilibrium [email protected] for R0. We next consider an analogous Continuous Time Markov Chain (CTMC) based model. Numerical simula- tions are used to estimate the mean, variance and proba- CP4 bility distributions for the various states and are compared Nonlinear Stochastic Dynamics of Sensory Hair to the steady state solutions of the deterministic model. Cells The expected time to extinction in the CTMC model is also estimated. Hair cells are mechano-receptors in vertebrate senses of hearing and balance. In lower vertebrates sensory hair cell Adnan Khan exhibits spontaneous oscillations of hair bundle and mem- Lahore Univeristy of Management Sciences brane potential. We use modelling to study how mechan- Department of Mathematics ical and electrical oscillations emerge, interact and con- [email protected] tribute to the overall sensitivity and selectivity of the hair cell. We show that oscillatory regimes result in enhanced sensitivity to harmonic stimuli. Irregular spontaneous dy- CP3 namics is best suited for sensing broad-band slowly chang- A Mixed-Strategy Game Theoretical Approach for ing external stimuli. Infectious Disease Prevention by Social Distancing Rami M. Amro, Alexander Neiman We describe a population game in which individuals are al- Department of Physics and Astronomy lowed to decide between adopting different social distanc- Ohio University ing strategies in order to lower infection risk and maximize [email protected], [email protected] payoffs. When the reduction in infection risk is a convex function of the cost of social-distancing, there is a unique pure-strategy game equilibrium. When the reduction in CP4 infection risk is not convex, the existence of equilibria be- comes more complicated. We will discuss three cases vis-- Large Deviations of An Ergodic System of Hebbian vis different costs of infection. Neurons

Jing Li, Timothy Reluga We investigate finite-size effects in a system of neurons in- Pennsylvanian State University teracting ergodically. Our model consists of N Hodgkin- [email protected], [email protected] Huxley neurons, with external noise. The noise is corre- lated in an ergodic manner, meaning that its probability law is invariant under a uniform translation of the neurons. CP3 We asymptote N to infinity and apply the theory of Large Abms for Infectious Diseases Spreading and Ill- Deviations to determine in which direction the system is Posed Problems most likely to deviate from its limit equation.

Usually rules and behavior of agents in ABMs are not James Maclaurin known exactly. In the general case a problem of ABMs INRIA SOPHIA ANTIPOLIS parameters evaluation is so called ill-posed one and there- [email protected] fore it can have no unique solution for available data de- scribing emergent patterns under consideration or can have Olivier Faugeras unique but unstable solution with respect to small changes INRIA Sophia-Antipolis LS14 Abstracts 61

[email protected] [email protected]

CP4 CP5 Fast-Slow Analysis of Neural Excitability with Compatibility of Slender Bodies and Surface Trac- Synaptic Noise tion at Low Reynolds Number

By considering a stochastic Morris-Lecar model with the The past forty years have witnessed an ever-increasing in- inclusion of synaptic noise, we study neural excitability terest in applications of slender-body dynamics (such as using a systematic perturbation analysis. In this presen- Kirchhoff rod theory), in particular with regard to the tation, I will talk about our understanding and findings of shape, movement, or material parameters of biomolecules synaptic noise on neural excitability. or materials. In most applications, hydrodynamic inter- actions (i.e. surface traction often approximated by resis- Xueying Wang tive force theory) have been of utmost importance since Washington State University the biologically relevant scales usually result in very small [email protected] Reynolds number. However, the formulation of classical Kirchhoff slender-body assumes no surface traction in the development of the constitutive relation. We will discuss James P. Keener an asymptotic approach to reconciling this apparent incon- University of Utah sistency and provide velocity bounds for which the compat- [email protected] ibility of Kirchhoff rod and resistive force theory hold.

Eva M. Strawbridge CP5 University of Chicago A Fractional Order Model of Electroporation Department of Mathematics [email protected] Electro-chemotherapy and gene electro-transfer have re- cently emerged as promising new cancer therapies that use Eva M. Strawbridge locally applied electric fields to facilitate the transport of James Madison University either chemotherapeutic drugs or genes into tumor cells Department of Mathematics and Statistics using the cell membrane electroporation. The continuous [email protected] evolving microstructure of tissues and tumors affect the distribution of the applied electric field. To account for Charles Wolgemuth such complex and mostly unknown dynamics, we propose University of Arizona a novel fractional order model for the local electric field Department of Physics distribution. [email protected] Md Mehedi M. Hasan The Pennsylvania State University CP6 [email protected] Sensitivity Analysis and Treatment of Hepatitis C Virus Infection Corina Drapaca Department of Engineering Science and Mechanics The interplay between two types of immune responses, an- Pennsylvania State University tibodies and CTL cells, is explored in the context of hepati- [email protected] tis C virus (HCV) infection. The competition for HCV is explored with sensitivity analyses, considered under three main steady states: co-existence, dominant CTL response, CP5 and dominant antibody response. Sensitivity functions al- Parameter Inference Using Variance Fitting for low temporal ranking of parameters, in relation to their Markov Models of Voltage Gated Ion Channels degree of influence in viral load. Comparisons between steady states with and without treatment are discussed. Voltage gated ion channels play a central role in neuronal and electric signaling and are experimentally studied by Ariel Cintron-Arias the voltage clamp technique with single channel or whole Department of Mathematics and Statistics cell current recordings. In this talk we address the inverse East Tennessee State University problem of identifying rate parameters in Markov chain [email protected] models that describe the transition between the conforma- tional states the channel can sojourn in. Assuming that single channel data from repeated observations is available CP6 we utilize model predictions of the current variance and The Effect of Systemic Estrogen and Cortisol on directly compare it with the sample variance derived from the Inflammatory Phase of Wound Healing the data. Cost functions that account for variance fitting may feature landscapes in the parameter space with more A complex combination of interactions initiates and regu- pronounced curvatures than mean based approaches such late the inflammatory phase of the wound healing response. that parameter unidentifiability or model ambiguity may Many chronic wounds arise due to an improper transition be weakened or even overcome. out of this phase. To understand regulation of this transi- tion, we developed a model for key inflammatory cells dur- Philipp Kuegler ing wound healing that accounts for the effects of cortisol RICAM, Austrian Academy of Sciences and estrogen. Latin Hypercube sampling was performed to Austria determine feasible parameters for the model. Experimental 62 LS14 Abstracts

data was used to validate this model. Feed-Forward Models

Angela M. Reynolds Mechanistic modeling of signaling or metabolic pathways Department of Mathematics and Applied Mathematics is highly valuable for understanding and predicting basic Virginia Commonwealth University (VCU) biology, disease, and therapy. However, due to the com- [email protected] plexity of biological systems it is necessary to make simpli- fying assumptions to reduce the degrees of freedom of any Racheal Cooper model. Here we demonstrate in a simple, yet biologically Virginia Commonwealth University relevant, case an approach using simulation and data to [email protected] simplify non-linear feed-forward models. We apply this to a model of hepatic de novo-lipogenesis.

Rebecca Segal Richard Allen Virginia Commonwealth University University of North Carolina, Chapel Hill Department of Mathematics and Applied Mathematics richard.allen@pfizer.com [email protected] Cynthia Musante Robert Diegelmann Pfizer. Inc Virginia Commonwealth University cynthia.j.musante@pfizer.com [email protected]

CP7 CP6 Spatial Uniformity of Solutions of Reaction- Modeling Effects of Drugs of Abuse on Hiv-1 Dy- Diffusion Pde’s namics Motivated by the question of pattern formation, we study Complications of HIV-1 infection with simultaneous drugs the behavior of the solutions of reaction-diffusion PDE’s. of abuse are an emergent problem. I will present a within- Applying some techniques from modern functional analy- host viral dynamics model that incorporates effects of sis, such as logarithmic Lipchitz constants and logarithmic drugs of abuse on HIV-1 infection. Our model agrees well norms, we provide conditions for global convergence to uni- with experimental data from Simian Immunodeficiency form solutions. We then illustrate the result by a simple Virus infections in morphine-addicted macaques (animal biomolecular model. model of HIV). I will discuss how our model helps evalu- ate morphine-induced alterations in viral dynamics, steady Zahra Aminzare, Eduardo Sontag state viral load, and basic reproduction number. Rutgers University [email protected], [email protected] Naveen K. Vaidya Dept of Applied Maths, University of Western Ontario London, Ontario, Canada CP7 [email protected] Scale-Invariant Sensing of Singularly Perturbed Biomolecular Models

CP6 Feedforward motifs such as a simple incoherent feedfor- ward loop have been the subject of extensive research in The Role of Interleukin-2 in Immune Response systems biology, and they are inherent in cellular systems Regulation ranging from bacteria to mammalian cells. Additionally, it was observed that multiple time scales are typically inher- The immune system has many adaptive and dynamic com- ent in such motifs. Experimentally, it has been shown that ponents that are delicately regulated to ensure appropri- certain incoherent feedforward molecular circuits can (ap- ate, precise, and rapid response to a pathogen. Inadequate proximately) exhibit a scale invariance property, namely, immune response can lead to prolonged disease, while an scale invariance of the complete output trajectory with re- excessive or under-regulated response can lead to autoim- spect to a rescaling of input magnitudes. Even though munity. We are interested in the role cytokines play in they may not exhibit the perfect scale invariance property, maintaining this balance. Through the use of mathemat- such circuits can often possess an approximate scale in- ical models, we attempt to understand cytokine signaling variance property, and we study conditions under which including problems leading to autoimmunity and MS treat- systems with different time scales can possess the approxi- ment by Daclizumab. mate scale invariance property, estimate the accuracy with which this property can be established, and illustrate our Ryan S. Waters theoretical predictions on three examples. Department of Mathematical Sciences Montana State University Maja Skataric [email protected] Graduate Student [email protected] Tomas Gedeon Montana State University Evgeni Nikolaev, Eduardo Sontag Dept of Mathematical Sciences Rutgers University [email protected] [email protected], [email protected]

CP7 CP7 Simulation-Based Simplification of Non-Linear On the Perfect Reconstruction of the Topology of LS14 Abstracts 63

Gene Regulatory Networks describe extensions to populations evolving on graphs.

The network inference problem consists in reconstruct- Dashiell Fryer ing the topology or wiring diagram of a dynamic network Pomona College from data. Solving this problem is specially important for [email protected] gene regulatory networks, because in many cases regulation mechanisms are unknown or cannot be detected directly. Marc Harper Even though this problem has been studied in the past, UCLA there is no algorithm that guarantees perfect reconstruc- [email protected] tion of the topology of a dynamic network. In this talk we will present a framework and algorithm to solve the net- work inference problem for discrete networks that, given CP8 enough data, is guaranteed to reconstruct the topology of Linear Algebra of the Quasispecies Model a dynamic network perfectly. The framework uses tools from algebraic geometry. Eigen’s quasispecies model is a famous ’almost linear’ sys- tem of ODEs, for analysis of which intricate methods of Alan Veliz-Cuba classical and quantum mechanics, statistical physics, and University of Houston elaborate numerical algorithms were applied. In a nutshell, Rice University the analysis boils down to studying the leading eigenvalue [email protected] and the corresponding eigenvector of the matrix describing mutation–selection process. Our approach to this problem is to use the methods of linear algebra. Using the fact that CP8 the mutation matrix has a special form, a change of the Mutational History Dominates Clonal Selection basis is suggested such that in new coordinates a number Within Evolving Tumors of exact results can be obtained.

Natural selection acting on clonal diversity within tumors Artem S. Novozhilov is thought to drive tumor progression, but details remain North Dakota State University obscure. Evolutionary mathematical models of the angio- [email protected] genic switch predict the emergence of hypovascular necro- sis caused by hypertumors—“cheating” clones that free- Alexander Bratus ride on vasculature organized by cooperative clones. Here Lomonosov Moscow State University we show that hypertumors should rarely evolve because [email protected] the deterministic evolutionary trajectory is overwhelmed by stochastic mutational history. These results highlight Yuri Semenov mutation pressure as a significant evolutionary force in can- Moscow State University of Railway Engineering cer. yuri semenoff@mail.ru Scott T. Bickel Arizona State University CP8 Scottsdale Community College [email protected] Species coexistence under eco-evolutionary dynam- ics

Joseph Juliano Ecological mechanisms for coexistence of interacting Arizona State University species have been studied extensively. In light of recent [email protected] evidence that feedbacks between ecological and evolution- ary processes are more common and substantial than orig- John D. Nagy inally thought, we examine how these feedbacks mediate Scottsdale Community College coexistence in a three-species interaction. We model these Arizona State University processes using a Lotka-Volterra and quantitative genetics [email protected] framework and use singular perturbation theory to analyze coexistence for this model.

CP8 Swati Patel Stationary Stability for Evolutionary Dynamics in Department of Mathematics Finite Populations University of California Davis [email protected] We extend the theory of evolutionary stability to multidi- mensional finite populations with mutation, connecting the Sebastian Schreiber theory of the stationary distribution of the Moran process University of California, Davis with the Lyapunov theory of evolutionary stability for the [email protected] replicator dynamic. We show essentially that the local ex- trema of the stationary distribution minimize the relative entropy of the current population state and the ”expected CP9 next state” computed by weighting the adjacent states by Pest Persistence and Eradication in a Deterministic the appropriate transition probabilities. This holds for Model for Sterile Insect Release a variety of selection processes including the increasingly popular Fermi selection. We present several complete com- The release of sterile insects is an environment friendly pest putational examples for illustration and we show that the control method used in integrated pest management pro- classical stability theory of the replicator dynamic is re- grams. New deterministic population models that include covered in the large population limit. If time allows, we sterile male release are derived and explored numerically. 64 LS14 Abstracts

The differential equations account separately the effects of ing in significant vegetation consumption. In collaboration mating failure due to sterile release and the frequency of with the National Wetlands Research Center, we present mating encounters. When insects spatial spread is incor- the estimation of vital rates in a size-structured mathe- porated through diffusion terms, computations reveal the matical model from a population observed in a laboratory possibility of steady pest persistence in finite size patches. setting. We compare these results and estimates of popula- tion sizes and growth dynamics with the calibrated model to preliminary field data, highlighting necessary modifica- Luis Gordillo tions necessary to adapt the model to this natural setting, Utah State University such as the incorporation of predation. We discuss the [email protected] possible impact of this species and potential for its control.

CP9 Lihong Zhao Quantifying the Relationships among Natural Se- Mathematics Department lection, Mutation, and Stochastic Drift in Multidi- University of Louisiana at Lafayette mensional Finite Populations [email protected] The interrelationships of the fundamental biological pro- cesses natural selection, mutation, and stochastic drift are CP10 quantified by the entropy rate of Moran processes with mu- tation, measuring the long-run variation of a Markov pro- Bursting in Networks of Integrate and Fire Neu- cess. The entropy rate is shown to behave intuitively with rons respect to evolutionary parameters such as monotonicity with respect to mutation probability (for the neutral land- We use mean field analysis to study bursting in networks scape), relative fitness, and strength of selection. of identical, pulse-coupled neurons. The individual neu- rons are represented using a class of two-dimensional inte- Marc Harper grate and fire model. The mean field model is a system of UCLA switching ordinary differential equations and the transition [email protected] to bursting involves both standard and nonsmooth bifurca- tions. The results of the mean field analysis are compared with numerical simulations of large networks. CP9 The Information Player: a Novel Strategy That Sue Ann Campbell Dominates Zero Determinant and Other Known University of Waterloo Strategies in Multiplayer Evolutionary Games Dept of Applied Mathematics We present a long-history strategy capable of quickly infer- [email protected] ring opponent strategies and building coalitions in popula- tion games using statistical inference and machine learning Wilten Nicola techniques. These ”information players” very effectively University of Waterloo invade existing strategies including tit-for-tat, win-stay- [email protected] lose-shift, and zero determinant strategies, and conversely block invasion by these strategies, even in the presence of substantial ambient noise (errors in play). Crucially, infor- CP10 mation players initially seek not to maximize their score, Robust Design of Polyrhythmic Neural Circuits but rather their information about the opponent’s strategy.

Christopher Lee Neural circuit motifs showing multiple coexistent rhythms Depts. of Chemistry & Biochemistry, and Computer are building blocks of neural networks. We study ro- Science bustness of such circuitry to sustain rhythms by revealing University of California, Los Angeles statistics of their switches due to random perturbations. [email protected] We find a threshold of coupling strength beyond which ac- cidental switching between rhythms occurs frequently. We Marc Harper elucidate mechanisms underlying this stochastic arrhyth- Institute for Genomics & Proteomics mia, and show how the type of coupling enhance rhythm UCLA robustness. Our findings are applicable to a broad class of [email protected] oscillator systems.

Dashiell Fryer Justus T. Schwabedal Pomona College Division of Sleep Medicine, Brigham & Women’s Hospital [email protected] Harvard Medical School [email protected]

CP9 Alexander Neiman Quantifying the Impact of the Recent Invasive Department of Physics and Astronomy Species, Pomacea insularam Ohio University [email protected] Pomacea insularam, or applesnail, is a relatively new species to the Gulf Coast region and threatens local sugar Andrey Shilnikov and rice crops, due to their relatively low predation rates Neuroscience Institute and Department of Mathematics at high sizes and seemingly fast population growth, result- Georgia State University LS14 Abstracts 65

[email protected] Taous-Meriem Laleg INRIA Rocquencourt [email protected] CP10 Characterization of Transient and Spatially Dis- tributed High-Frequency Oscillations in the Brain CP11 with Quasi-Periodic Time Scales Glucose and Temperature Compensation in the Neurospora Circadian Clock: Mathematical Mod- Spatially distributed neural oscillations with characteristic eling and Experimental Validation frequencies ≥80 Hz have recently been identified in non- invasive electroencephalograms. These high-frequency os- Circadian rhythms play a vital role in an organisms func- cillations (HFO) are transient and are thought to be mod- tions anticipating daily changes in its environment. The ulated by abnormal and dynamic neurophysiological pro- period of circadian oscillator is relatively insensitive to cessses. In continuous multi-day recordings, it is possible changes in physiological temperature and nutrients (e.g. to estimate HFO dynamics and their corresponding time glucose), which are referred to as temperature and glucose scales. In this study we show that transient HFO dynamics compensation, respectively. In this study, we constructed a have quasi-periodic time scales, with periods of occurrence mathematical model of the Neurospora circadian clock, and that are modulated by relatively rare electrophysiological investigated molecular mechanisms of glucose and temper- events. ature compensation. Our model shows that temperature compensation is achieved by an intricate balance of synthe- Catherine Stamoulis sis and degradation of FRQ and WC-1. We experimentally Massachusetts Institute of Technology validated loss of glucose compensation in wc-1 overexpres- Department of Ocean Engineering sion mutant and maintenance of nuclear abundance of FRQ [email protected] as predicted in the model.

Bernard Chang Andrey A. Dovzhenok Harvard Medical School, Beth Israel Deaconess Medical University of Cincinnati Center Department of Mathematical Sciences Department of Neurology [email protected] [email protected] Mokryun Baek University of Cincinnati College of Medicine CP10 Department of Molecular and Cellular Physiology Relating Spiking Neural Network to Partial Differ- [email protected] ential Equations Arun Mehra In this talk we show that a spiking neural network without Geisel School of Medicine at Dartmouth the constraint of symmetry can be approximated by the Department of Genetics FitzHugh-Nagumo equations. The well-known FitzHugh- n/a Nagumo equations are much easier to analyze than an enor- mous system of differential equations, describing the activ- Jennifer Loros ity of each spiking neuron. Geisel School of Medicine at Dartmouth Department of Biochemistry Li Yang [email protected] Inria at Sophia-Antipolis, France [email protected] Jay Dunlap Geisel School of Medicine at Dartmouth Olivier Faugeras, Pierre Kornprobst Department of Genetics INRIA Sophia-Antipolis [email protected] [email protected], [email protected] Sookkyung Lim CP11 University of Cincinnati Fractional Model for Neurovascular Coupling Department of Mathematical Sciences [email protected] Functional magnetic resonance imaging (fMRI) is an indi- rect measure of brain activity. To describe the chain from Christian Hong neural activity to the measured fMRI signal namely the University of Cincinnati College of Medicine Blood Oxygen Level Dependent (BOLD) signal, we pro- Department of Molecular and Cellular Physiology pose to use a system of fractional differential equation in- [email protected] spired from the dynamical Balloon Model [K. J. Friston et al, 2000. Nonlinear responses in fMRI: the Balloon model, Volterra kernels, and other hemodynamics. NeuroImage CP11 12, 466 477]. We show that thanks to its non-locality and Molecular Mechanisms That Regulate the Coupled memory properties, fractional derivatives constitute a pow- Period of the Mammalian Circadian Clock erful tool for the neurovascular coupling. In the mammalian circadian clock, intercellular coupling Zehor Belkhatir synchronizes rhythms with the period close to the popula- Computer, Electrical and Mathematical Sciences and tion mean of individual periods. With the theory of weekly Engineering, KAUST coupled oscillators, we found that the coupled period stays [email protected] near the population mean if transcriptional repression oc- 66 LS14 Abstracts

curs with piecewise-linear protein sequestration, but not [email protected], [email protected] highly non-linear Hill-type regulation in individual cells. This shows that the behavior of coupled oscillator with the same topology changes depending on the mechanisms un- CP12 derlying individual oscillator. Mathematical Modeling of the Hypothalamic- Pituitary-Adrenal Axis in Relation to Major De- Jae Kyoung Kim pression Department of Mathematics University of Michigan, Ann Arbor, Michigan 48109, USA Both circadian and ultradian oscillations are seen in the [email protected] levels of the hormones of the Hypothalamic-Pituitary- Adrenal axis, including cortisol. With a model consisting Zachary Kilpatrick of non-linear ordinary differential equations, we investigate University of Houston enzyme reactions taking place inside the cortisol-producing [email protected] adrenal cortex cell to see, whether the presence of potential Goldbeter-Koshland switches is instrumental in generating the ultradian oscillations. The performances in model re- Matthew Bennett duction of the standard quasi-steady-state approximation Department of Biochemistry & Cell Biology, Rice (sQSSA) and the total QSSA are compared. University [email protected]¿ Johanne Gudmand-Høyer Roskilde University Kreimir Josic [email protected] Department of Mathematics, University of Houston [email protected] Johnny T. Ottesen Roskilde University Department of Mathematics CP11 [email protected] In Vivo Volume and Hemoglobin Dynamics in Red Blood Cells CP12 Human red blood cells (RBCs) lose ∼30% of their volume Modeling the Spatio-Temporal Dynamics of Small and ∼20% of their protein during their ∼100-day lifespan Gtpase Activity at Dendritic Spines in the bloodstream. We use measurements of RBC size and protein concentration to derive a model for the physi- Signaling through small GTPases at dendritic spines is cru- cal processes controlling RBC volume and hemoglobin. We cial for synaptic plasticity, a cellular correlate for learning show that common models of vesicle shedding alone are suf- and memory. We implement a computational method in ficient to explain surface area lost but insufficient to explain order to model the spatio-temporal dynamics of GTPase the lost volume and hemoglobin mass. We use single-cell activity accounting explicitly for the spine geometry. A measurements of human RBCs to validate the models and question that motivates our research is how does the ac- to define requirements for alternative explanations. tivity of the GTPase Cdc42 localize persistently to spine membranes despite its rapid lateral diffusion. Roy Malka Systems Biology, Harvard Medical School Samuel A. Ramirez Center for Systems Biology, Massachusetts General Duke University Hospital [email protected] Roy [email protected] Sridhar Ragavachari Duke University Medical Center CP12 [email protected] Unravelling the Impact of Obstacles in Diffusion and Kinetics of An Enzyme Catalysed Reaction CP12 In Vitro Assay Geometry Affects Estimates of the We develop a two-dimensional lattice-based Monte Cell Diffusivity and Cell Proliferation Rate Carlo simulation to model enzyme-catalyzed reactions in diffusion-limited conditions to investigate effects of obsta- Cells respond to biochemical and physical cues during cle density and size on reactant diffusion and rate coeffi- wound-healing and tumour progression. In vitro assays cients. Our results show that these factors affect first- and used to study these processes are typically conducted in second-order rates. We also find that particle rotations and one geometry. In this work, we investigate the capacity weak force interactions affect rate coefficients. Our simu- of cell populations to spread in two different in vitro as- lations suggest that the anomalous kinetic observed in cel- say geometries by comparing estimates of the effective cell lular crowded environments can appear in less restricted diffusivity and effective cell proliferation rate. conditions than previously reported. Katrina Treloar, Matthew Simpson Marcio Duarte Albasini Mourao Queensland University of Technology Mathematical Biosciences Institute [email protected], [email protected] The Ohio State University [email protected] Sean McElwain School of Mathematical Sciences Doree Kreitmann, Santiago Schnell Queensland University of Technology University of Michigan [email protected] LS14 Abstracts 67

Ruth E. Baker interaction. Centre for Mathematical Biology University of Oxford Tugba Karabiyik [email protected] Florida State University [email protected]

CP13 CP13 A Continuous Model of Ant Foraging with Pheromones and Trail Formation The Dynamics of Foraging Activity in Harvester Ants We propose and numerically analyze a PDE model of ant Collective foraging is ubiquitous in social animals. Its util- foraging behavior. Ant foraging is among the most interest- ity is largely dependent on the efficient use of social in- ing behaviors in the animal kingdom, and a prime example formation to communicate changes in environmental prof- of individuals following simple behavioral rules based on itability and coordinate the actions of individual group local information producing complex, organized and “intel- members. Here, we develop a simple compartmental model ligent’ strategies at the population level. One of its main of foraging activity in harvester ant colonies based on aspects is the widespread use of pheromones, which are non-spatial, interaction-mediated worker recruitment. Our chemical compounds laid by the ants used to attract other analysis indicate that adaptive changes in worker availabil- ants to a food source. We consider a continuous descrip- ity relative to the frequency of contacts with successful tion of a population of ants and simulate numerically the foragers can allow colonies to sustain activity when worker foraging behavior using a system of PDEs of chemotaxis activation rates are low. Simulated forager removals ex- type. We show that, numerically, this system accurately ploring the effects of short-term reductions in forager re- reproduces observed foraging behavior, such as trail forma- turn rates (e.g. due to elevated predation on the trail) tion, optimization of routes, and efficient removal of food show good fits with empirical data. We discuss the bio- sources. Furthermore, we present a preliminary mathemat- logical interpretation of our results and motivate further ical analysis of a simplified version of the model. improvements to the model.

Paulo V. Amorim Oyita Udiani Instituto de Matem´atica Applied Mathematics for the Life & Social Sciences Universidade Federal do Rio de Janeiro College of Liberal Arts and Sciences ASU [email protected] [email protected]

CP13 CP14 Using Homogenization to Estimate Random-Walk Analyzing the Effects of a Non-Host Worm Popu- Motility from Gps Collar Data in Variable Land- lation on the Spread of Whirling Disease in Trout scapes We present a mathematical model of the Host/Parasite sys- We compute the probability of an animal passing through tem describing the Myxobolus Cerebralis parasite and the various habitat patches between known GPS collar loca- Tubifex worms that cause Whirling Disease in trout. A tions using solutions of a homogenized ecological diffusion Non-Host worm is incorporated which competes with the model. From these probabilities we can obtain the time Host producing a negative effect but also eliminates the an animal spends in a particular habitat type to use in parasite spores causing a positive, indirect effect. System estimating motility coefficients. We apply this method to dynamics, parameters and bifurcation analysis will be dis- parameterize a model of the spread of chronic wasting dis- cussed. ease in mule deer in Utah. Tamra Heberling, Lisa G. Davis, Ryan Lamb, Billie Martha J. Garlick Karens Dept. of Mathmatics and Statistics Montana State University Utah State University [email protected], [email protected], [email protected] [email protected], [email protected]

James Powell, Luis Gordillo CP14 Utah State University [email protected], [email protected] The Virus of My Virus Is My Friend: Modeling the Ecological Effect of Virophages

CP13 Virophages are viruses that rely on the replication machin- ery of other viruses for reproduction. We construct two Respect Versus Disrespect for Ownership: An It- mean field models of population dynamics between hosts, erated Hawk-Dove Game with Relocation Costs viruses and virophage to address how different modes of coinfection affect the ecological dynamics. We prove that The classic Hawk-Dove game predicts that when ”Bour- virophage reduce the viral population and increase the host geois” respect for ownership arises as a pure convention, population at equilibrium. We also identify differences in so does ”anti-Bourgeois” disrespect. Why is the former so the frequency and nature of coexistence within the two common in nature, the latter so rare? An iterated model models. can yield stable strategy mixtures with any degree of par- tial respect between 0 and 1. This poster describes how Bradford Taylor their basins of attraction depend on both the relocation Georgia Tech costs of ”infinite regress” and the probability of further [email protected] 68 LS14 Abstracts

Michael H. Cortez, Joshua Weitz human influenza is introduced to better understand the Georgia Institute of Technology complex epidemiology of avian influenza. The model is [email protected], [email protected] used to rank the efficacy of the current control measures used to prevent the emergence of a pandemic strain. We find that culling without re-population and vaccination are MS1 the two most efficient control measures. Control measures A Structured Model for the Transmission Dynam- applied to humans, such as wearing protective gear, are ics of Mycobacterium Marinum Between Aquatic not very efficient. Furthermore, we find that should a Animals pandemic strain emerge, it will invade, possibly displac- ing the human influenza virus in circulation at that time. Abstract: Mycobacterium marinum (Mm), a genetically Moreover, higher prevalence levels of human influenza will similar bacterium to Mycobacterium tuberculosis, affects obstruct the invasion capabilities of the pandemic H5N1 a number of fish industries (fisheries, aquaculture, aquari- strain. This effect is not very pronounced, as 1% increase ums and research stocks) on a comparable scale to tuber- in human influenza prevalence will decrease the invasion culosis (TB) in humans. Because of this, and the practical capabilities of the pandemic strain with 0.006%. advantages of working with animal models as opposed to humans, Mm infections in recently established fish models Maia Martcheva provide a unique opportunity for the study of mycobac- University of Florida terial infections. We derive a model of transmission dy- maia@ufl.edu namics of Mm in fish, which either involves consumption of an infected host or a source of bacteria to ensure acti- vation into a highly infectious state. We derive a model MS2 of transmission within a food web, in which infected fish Parameter Identifiability in Virus Infection Models behavior is structured by infection severity. This is a key component as chronic (seemingly asymptomatic) infection Confidence in the accuracy of estimated parameters is es- is prominent in both fish and human TB. We develop a fi- sential for the development of successful treatment proto- nite difference method to compute solutions of this model. cols. Guidance when designing the experiment is needed We illustrate, via this numerical scheme, that this model for recovery of accurate parameters and identifiability. can be used to reproduce experimental settings. Noise associated with data collection affects that design. Here, we establish a computational method that investi- Azmy S. Ackleh gates the effect of noise on the design of the experiment Department of Mathematics and the identifiability of parameters. Our method is ap- University of Louisiana at Lafayette plied to a model of hepatitis B infection. [email protected] Matthias Chung,StancaCiupe Virginia Tech MS1 [email protected], [email protected] Mathematics of Anti-Hpv Vaccines

Human papilloma virus (HPV) is a major sexually- MS2 transmitted disease that inflicts a significant public health Early HIV Infection Predictions: Role of Viral burden globally. HPV causes various cancers and warts in Replication Errors females and males, notably cervical cancer in females (the second highest malignancy in women globally, accounting Less than 0.1% of circulating virus in any HIV+ individ- for over 250,000 deaths annually). The talk is based on ual is infectious. Non-infectious virus may arise from errors the use of mathematical models to gain insight into the in viral replication or other processes; the specific mecha- population-level impact of the two currently-available anti- nism does not affect deterministic modeling predictions. HPV vaccines (Cervarix (by GlaxoSmithKline) and Gar- However, during the earliest stages of infection, viral loads dasil (by Merck Inc.)). are small and more appropriately modeled stochastically. We model viral dynamics using continuous-time branching Abba Gumel processes to investigate how viral replication error assump- University of Manitoba tions change predictions on risk of infection and time to Department of Mathematics infection clearance/detection. [email protected] Jessica M. Conway Los Alamos National Laboratory MS1 [email protected] Transient Periodic Oscillations and the Dynamics of CTL Response to Viral Infections Alan S. Perelson Abstract not available at time of publication. Theoretical Biology and Biophysics LosAlamosNationalLab Michael Li n/a University of Alberta [email protected] MS2 Coping with Model Uncertainty in the Analysis of MS1 Acute Hiv Infection Datasets Modeling Avian Influenza and Implications for Control HIV datasets are sparse. For example, sampling occurs infrequently relative to the pace of the infection, sampled A mathematical model of avian influenza which involves viral sequences are few in number or lack linkage informa- LS14 Abstracts 69

tion, and data for the immune response is sparse relative [email protected], [email protected] to the complexity of the immune system. I will describe an approach for dealing with this uncertainty in the context of estimating CTL escape rates. CTLs are immune system MS3 cells that kill HIV infected cells depending on the viral Bio-Mechanical Modeling of Tracheal Angioedema genotype, thereby mediating selective pressure from which by Nonlinear Finite Elasticity HIV escapes through mutation. Quantifying the rate of this escape is valuable in understanding the role of CTL Tracheal angioedema refers to the rapid swelling of tra- response in HIV infection. cheal tissue by excess accumulation of fluid from vascular leakage, which can be life threatening if it narrows air- Sivan Leviyang way rapidly. We present a bio-mechanical analysis with Georgetown University a swelling dependent natural configuration to reflect the [email protected] altered tissue volume increment under angioedema. Var- ious localized swelling and far field boundary conditions are studied in order to assess how the interaction between MS2 swelling, anisotropy and large deformation affects airway constriction. Multi-Scale Modeling of Immune Response to In- fluenza Infection Kun Gou Texas A&M University Many systems in engineering and physics such as a rocket Department of Mathematics system can be represented by differential equations, which [email protected] can be derived from well-established physics laws and the- ories. It is unclear whether the biological systems follow a Thomas Pence mathematical representation such as differential equations. Michigan State University Fortunately, recent advances in cutting-edge biomedical Department of Mechanical Engineering technologies allow us to generate intensive high-throughput [email protected] data to gain insights into biological systems. It is badly needed to develop mathematical models and statistical methods to test whether a biological system follows a math- MS3 ematical representation based on experimental data. In A Continuum Mechanics Model of Stress Mediated this talk, I will present our recent work in developing sta- Arterial Growth During Hypertension Using An tistical methods to identify high-dimensional ordinary dif- Eulerian Frame. ferential equation (HD-ODE) models and solve the asso- ciated inverse problems for HD-ODE models in modeling In the classical approach to continuum mechanics, one as- immune responses to influenza infection. The time course sumes that a material body is deformed from a ”stress free” high-throughput data from both mice and human experi- reference configuration into a loaded current configuration. ments will be used to illustrate our methodologies. However, a reference configuration is merely a mathemat- ical construct and cannot actually be determined, espe- Hulin Wu cially for dynamic physiological processes. We introduce a University of Rochester framework that is formulated entirely in the current con- hulin [email protected] figuration and test its effectiveness by showing how well it predicts arterial growth during instantaneous hyperten- sion. MS3 Maya E. Johnson Mechanical Forces Drive Morphogenesis: How the Texas A&M University Embryonic Brain Twists Dept. of Mathematics [email protected] The embryonic chick brain undergoes progressive, right- ward torsion, one of the earliest organ-level symmetry- breaking events. Researchers speculated that heart loop- Jay R. Walton ing affects the brain torsion direction, but direct evidence Department of Mathematics rarely exists. Our experiments show that the vitelline Texas A&M membrane exerts loads necessary for torsion and that direc- [email protected] tion of heart looping determines brain torsion direction. A computational model and a physical model are built to in- MS3 terpret these findings, together classifying mechanical ori- gins of brain torsion. Estimating Residual Stresses in Soft Tissues by An Inverse Spectral Technique

Zi Chen A mathematical model is studied to estimate residual Washington University stresses in the arterial wall using intravascular ultrasound Department of Bimedical Engineering (IVUS) techniques. A BVP is formulated for the nonlinear, [email protected] slightly compressible elastic wall, the boundary of which is subjected to a quasi-static blood pressure, and then an Qiaohang Guo idealized model for IVUS is constructed by superimpos- Fuzhou University ing small amplitude time harmonic vibrations on large de- [email protected] formations. Using the classical theory of inverse Sturm- Liouville problems and optimization techniques, an inverse Eric Dai, Larry Taber spectral algorithm is developed to approximate the resid- Washington University ual stresses, given the first few eigenfrequencies of several 70 LS14 Abstracts

induced pressures. the biochemical pathways that mediate the intrinsic light responses of ipRGCs and mediate its adaptation to light Sunnie Joshi and dopamine. Temple University [email protected] Phyllis R. Robinson Dept. of Biological Sciences Jay R. Walton UMBC Department of Mathematics [email protected] Texas A&M [email protected] MS4 MS4 Genetic Regulation of Cell Motility Modeling the Melanopsin Phototransduction Cas- Morphogens generate distinct cell fates by differences in cade concentrations. The release, diffusion, uptake, and decay Melanopsin is a recently discovered photopigment found in rates of these molecules impact concentration and thereby intrinsically photosensitive retinal ganglion cells (ipRGCs) cellular responses. We propose that the irregular domains and is involved in non-image forming vision, such as cir- of adjacent tissue also alter the local concentration. To cadian rhythm entrainment and the pupillary light reflex. examine this, we utilize the well-studied development of the We model the activation and inactivation of the melanopsin Drosophila ovary. We are characterizing a genetic pathway phototransduction cascade, and compare the model simu- that promotes cell motility in response to a morphogen and lations to experimental data. The research was conducted relate pathway activation to tissue architecture. by undergraduates at UMBC and funded by an NSF un- dergraduate training grant. Michelle Starz-Gaiano Dept. of Biological Sciences Kathleen A. Hoffman UMBC University of Maryland, Balt. Co. [email protected] Deapartment of Math. and Stat. khoff[email protected] Lathiena Manning UMBC Biological Sciences [email protected] MS4 Collective Cell Migration: Modeling from Initia- tion to Destination MS5 Marine Invertebrate Sperm Chemotaxis: Search Collective cell migration is critical in development and Trajectories pathology. We consider the Drosophila ovary as an ex- perimental system for transition to cell. We use a force balance dynamical system approach to capture cell adhe- In marine invertebrate sperm, chemotaxis guides the sperm sion, repulsion, chemotaxis, and stochastic motion in the towards the egg. The chemoattractant causes changes in migration. We show that basic forces in 3-dimensions can intracellular calcium, associated with changes in flagellar account for observed apparent rotation of the cluster, as waveforms and curvature of path trajectories. We use a well as reduced migration speed in mutants that reduce fluid-structure interaction model where the calcium con- the number of migrating cells. centration is coupled to the forces in the flagellum. Results will be presented to show how trajectories can be modu- David Stonko lated by calcium parameters as well as elastic properties of UMBC the flagellum. [email protected] Sarah D. Olson Bradford E. Peercy Worcester Polytechnic Institute Department of Mathematics and Statistics [email protected] University of Maryland, Baltimore County [email protected] MS5 Michelle Starz-Gaiano Modeling Tumor and Microenvironment Interac- Dept. of Biological Sciences tions under Treatment: the Role of the Interstitial UMBC Fluid [email protected] The interactions between tumor cells and their microen- vironment are complex, and this complexity is leveraged MS4 when both tumor and stromal cells are exposed to anti- Phototransduction in Melanopsin Expressing Reti- cancer therapeutic agents. We use fluid-structure inter- nal Ganglion Cells action methods to systematically explore the role of the interstitial fluid flow and tumor tissue architecture on the Intrinsically photosensitive retinal ganglion cells (ipRGCs) extent of drug and biomarker molecule penetration into the in the mammalian retina express the photopigment tissue. melanopsin and constitute a third class of photoreceptors. The ipRGCs contribute primarily to non-image forming vi- Katarzyna A. Rejniak sion and the melanopsin-based signaling cascade generates Moffitt Cancer Research Center a depolarizing light response. Our goal is to characterize Integrated Mathematical Oncology LS14 Abstracts 71

Kasia.Rejniak@moffitt.org

Victor Barranca MS5 Rensselaer Polytechnic Institute Sperm Altruism and Motility Near Surfaces [email protected]

As mammalian sperm traverse the oviduct, they undergo Douglas Zhou significant changes in motility. During this process, sperm Shanghai Jiao Tong University are known to bind to the oviductal epithelium and their [email protected] ability to detach is dependent upon contractions that occur near the time of ovulation. Thus, the impact that surfaces David Cai and their motion have upon sperm fertility is significant. New York University Using the method of regularized Stokeslets, we investigate Courant institute surface interactions and sperm cooperativity to elucidate [email protected] how epithelial detachment occurs.

Julie Simons,LisaJ.Fauci MS6 Tulane University Improved Estimation of Neural Correlations Sug- Department of Mathematics gests Detailed Interactions in Visual Cortex [email protected], [email protected] How does connectivity impact network dynamics? We ad- Ricardo Cortez dress this question by linking network characteristics on Tulane University two scales. On the global scale we consider the coherence Mathematics Department of overall network dynamics. We show that such global [email protected] coherence in activity can often be predicted from the lo- cal structure of the network. To characterize local network structure we use motif cumulants, a measure of the devia- MS5 tion of pathway counts from those expected in a minimal Swimming Through Highly Heterogeneous, Vis- probabilistic network model. coelastic Media Kresimir Josic We present a simple model of a free microswimmer in a University of Houston highly heterogeneous, viscoelastic medium. An effect of Department of Mathematics viscoelasticity is modeled by immersing viscoelastic struc- [email protected] tures into a viscous environment. Varying complexity of those structures allows medium to exhibit different vis- Yu Hu coelastic properties. Several tests are performed show- Department of Applied Mathematics ing that the model agrees with rheological properties of University of Washington a medium. Regions of higher structural density can sig- [email protected] nificantly affect a swimming pattern of a microorganism. James Trousdale University of Houston Jacek K. Wrobel Department of Mathematics Tulane University [email protected] [email protected] Eric Shea-Brown Ricardo Cortez Department of Applied Mathematics Tulane University University of Washington Mathematics Department [email protected] [email protected]

Lisa J. Fauci MS6 Tulane University Sparsity and Compressed Coding in Sensory Sys- Department of Mathematics tems [email protected] Considering many natural stimuli are sparse, can a sensory system evolve to take advantage of sparsity? We show sig- MS6 nificant downstream reductions in the numbers of neurons Novel Characterization of Brain Networks Through transmitting stimuli in early sensory pathways might be a Low-Rank Network Decomposition consequence of sparsity. Our work points to a potential mechanism for transmitting stimuli related to compressed- Small-world networks occur naturally throughout the brain sensing (CS) data acquisition. Through simulation, we ex- on multiple scales. In this work, we develop a new formal- amine the characteristics of networks that optimally en- ism using a low-rank decomposition of network adjacency code sparsity and the role of receptive fields in stimulus matrices to classify neuronal networks. This new procedure sampling. scales well with network size and connection density, yield- ing stable results independent of node indexing. We apply Gregor Kovacic our methodology to recent experimental data on cerebral Rensselaer Polytechnic Inst cortex connectivity, proposing such a network may be cate- Dept of Mathematical Sciences gorized into a broader class of networks than small-worlds. [email protected] 72 LS14 Abstracts

Victor Barranca of heterogeneities in vascular perfusion within solid tumors. Rensselaer Polytechnic Institute Using intravital microscopy data previously obtained, we [email protected] develop a machine-learning framework to determine which perfusion features most affect nanoparticle transport. Fur- Douglas Zhou ther, nanoparticle surface modifications can provide for in- Shanghai Jiao Tong University creased targeting and uptake within tumor tissue. To guide [email protected] nanoparticle design, we apply computational modeling to simulate tumor perfusion heterogeneity in order to evalu- David Cai ate uptake and distribution as functions of nanoparticle- Courant Institute for Mathematical Sciences, NYU and tumor-specific characteristics. Shanghai Jiao-Tong University Hermann Frieboes [email protected] University of Louisville [email protected] MS6 Spatiotemporal Dynamics of Neuronal Population MS7 Response in the Primary Visual Cortex Dynamics of Living Systems: Wave-Based Mecha- We use a large-scale computational model of the primary nisms for Contact Guidance and Collective Migra- visual cortex (V1) to study the population responses in V1 tion as observed in experiments in which monkeys performed visual detection tasks. Our model can well capture spa- Guided cell migration is a key aspect of many physiological tiotemporal activities measured by voltage-sensitive-dye- processes from the immune response to cancer metastasis. based optical imaging in V1. Our computational modeling I will describe how simple physical measurements of shape approach allows us to reveal intrinsic cortical dynamics, dynamics and motion reveal an underlying wave-like pro- separating it from those statistical effects arising from av- cess of the cellular scaffolding that drives persistent migra- eraging procedures in experiment. tion. We find that wave-like dynamics of the scaffolding also contributes to the ability of cells to recognize and fol- Douglas Zhou low surface nanotopography, and allows cells to couple to Shanghai Jiao Tong University each other during collective motion. [email protected] Wolfgang Losert Department of Physics Aaditya Rangan, David McLaughlin University of Maryland, College Park Courant Institute of Mathematical Sciences [email protected] New York University [email protected], [email protected] John Fourkas, Meghan Driscoll, Xiaoyu Sun, Can Guven, Chenlu Wang David Cai University of Maryland New York University [email protected], [email protected], Courant institute [email protected], [email protected], [email protected] [email protected]

MS7 Carole Parent Bayesian Support Vector Machines and Supervised National Cancer Institute Factor Modeling for General Omic Data [email protected]

A new Bayesian formulation is developed for nonlinear sup- port vector machines (SVMs), based on a Gaussian process MS7 and with the SVM hinge loss expressed as a scaled mixture Random Walks, Markov Chains, and Cancer Pro- of normals. We then integrate the Bayesian SVM into a fac- gression Models from Longitudinal and Autopsy tor model, in which feature learning and nonlinear classifier Data design are performed jointly. Inference is performed with expectation conditional maximization (ECM) and Markov We will describe our models of metastatic cancer progres- Chain Monte Carlo (MCMC). An extensive set of experi- sion using Markov chain modeling on a directed graph ments on multiple types of omics data demonstrate the util- of nodes that are the various anatomical sites where ity of using a nonlinear Bayesian SVM within supervised metastatic tumors can form for a given type of primary feature learning and factor modeling, from the standpoints cancer. We use metastatic tumor distributions gathered of prediction accuracy and physiological interpretability. from historical autopsy data, as well as current longitudi- nal data sets to estimate the transition probabilities from Larry Carin site to site. This creates a systemic network diagram from Electrical & Computer Engineering which we can calculate reduced two-step diagrams using Duke University the fact that the systems converge to their steady-state dis- [email protected] tribution after roughly two steps. The diagrams are used to categorize metastatic sites as ‘sponges’ or ‘spreaders’, as well as to run hypothetical therapeutic scenarios based on MS7 Monte Carlo simulations of progression. A useful metric Perfusion Heterogeneity in Tumors As a Challenge which we describe is the notion of metastatic entropy. for Optimal Nanotherapeutics Delivery Paul Newton Optimal nanotherapeutics delivery remains elusive because Univ Southern California LS14 Abstracts 73

Dept of Aerospace and Mechanical Engineering ing cells is of particular industrial, life science, and there- [email protected] fore commercial interest. By fabricating beads with high affinity for cell surface markers, methods for achieving re- markable levels of enrichment from mixed populations are MS8 possible. In this presentation, Ill present current and pro- Modeling and Inverse Problems in Environmental posed methods for exploiting aggregative physics towards Toxicity real world applications, and consider where mathematics will play a large role. Daphnia magna is a vital species in ongoing investigations into the synergistic toxicity of chemicals. D. magna is a John G. Younger species with a complex life history; females are partheno- University of Michigan genetic and males are only produced in response to envi- [email protected] ronmental stressors. Males can fertilize the females’ eggs, transforming them into diapause eggs which are capable of withstanding extreme conditions and hatch when condi- MS9 tions improve. We model D. magna population growth A Model for the Spatial Transmission of Dengue by combining a two-sex age structured partial differen- with Daily Movement between Villages and a City tial equation model with an ordinary differential equation model to describe their food environment. We then val- Dengue is a re-emergent vector-borne disease affecting idate this model by performing parameter estimation us- large portions of the worlds population living in the tropics ing structured population data collected from experiments. and subtropics. A discrete-time multi-patch model which This work is joint with K. Adoteye (Math), Karissa Cross takes into account the mobility of people as well as pro- (Biological Sciences) and a group of toxicologists lead by cesses of infection, recovery, recruitment, and mortality is Gerald LeBlanc. considered here. One patch (the city) is connected to all other patches (the villages) in a spoke-like network. Vector H. Thomas Banks control, human treatment and vaccination, and different North Carolina State Univ kinds of mobility are studied. Dept of Math & Ctr for Rsch in [email protected] Andrew Nevai Department of Mathematics Kevin Flores University of Central Florida Mathematics [email protected] North Carolina State University kbfl[email protected] Edy Soewono Department of Mathematics, Institut Teknologi Bandung Bandung 40132, Indonesia MS8 [email protected] Flocculation Dynamics and Cell Sorting

Flocculation is the process whereby particles in suspension MS9 aggregate and fragment and size-structured models are the Modeling Hiv Latency and Viral Blips best framework for modeling and simulation. It arises in many natural, environmental, and medical settings such HIV cannot be eliminated by combination therapy because as wastewater treatment and algal dyanmics. In this talk, of latent infection. The latent reservoir consisting of la- we will present recent results in how size-structured mod- tently infected CD4+ T cells is relatively stable. Many els of cell sorting devices can be used to improve sorting patients also experience transient viral load measurements efficiency. above the detection limit (the so-called ”viral blips”) even with suppressive treatment for many years. The mecha- David M. Bortz nisms underlying the emergence of intermittent viral blips University of Colorado and stability of the latent reservoir are not fully under- Department of Applied Mathematics stood. In this talk, I will introduce a new model based [email protected] on the establishment of HIV latency to address this issue. Both deterministic and stochastic simulations of the model MS8 show that it is able to generate a stable latent reservoir, intermittent viral blips, as well as low-level viremia per- Estimating the Division Rate for a Growth- sistence. The results provide more insights into the latent fragmentation Equation with Self-similar Kernel reservoir replenishment and long-term HIV dynamics in Abstract not available at time of publication. patients on suppressive combination therapy. Thibault Bourgeron Libin Rong UPMC and Inria Paris-Rocquencourt Oakland University Paris, France [email protected] [email protected] MS9 MS8 Disease Invasion of Community Networks with En- Applied Particle Aggregation for Cell Isolation in vironmental Pathogen Movement the Life Sciences Consider a set of communities (patches), connected to one Among the many applications for particle aggregation, con- another by a network. When can disease invade this net- trolled assembly of synthetic beads onto the surface of liv- work? Intuitively, this should depend upon both the prop- 74 LS14 Abstracts

erties of the communities, as well as on the network struc- [email protected] ture. Here we make this dependence explicit for a broad class of disease models with environmental pathogen move- ment. In particular, the rooted spanning trees of the net- MS10 work and a generalization of the group inverse of the graph Laplacian play fundamental roles in determining the ability Modeling Human Papilloma Virus and the Onset of disease to invade. of Cervical Cancer

Joseph Tien High-risk strains of Human Papillomavirus are the dom- Ohio State University inant cause of cervical cancers. Incorporating the known [email protected] biology of viral persistence and the generation of cancerous and pre-cancerous cells, we develop and analyze a model Zhisheng Shuai the connection between HPV infection and cervical cancer University of Central Florida onset. The model provides a framework for understanding [email protected] the factors relevant to reducing cancer risk and the role of suppressive drug therapies in long-term treatment. Marisa Eisenberg University of Michigan Jonathan Forde [email protected] Hobart and William Smith Colleges [email protected] P. van Den Driessche U. Victoria MS10 [email protected] A Basic Model for In-Host TB Infection

MS9 Tuberculosis (TB) infection can result in clearance, latent Dynamics of Low and High Pathogenic Avian In- infection or active disease. Mathematical models have been fluenza in Wild and Domestic Bird Populations used to provide insight into TB infection and progression. The models to date, however, have been very complex or An earlier infection with low pathogenic avian influenza have not been able to produce all disease outcomes. We (LPAI) provides a partial immunity towards infection with present a simple 4-dimensional mathematical model of TB high pathogenic avian influenza (HPAI). We consider a infection in-host. The model includes macrophages, T lym- time-since recovery structured model to study the dynam- phocytes, TB bacteria and their interactions. The model ics of LPAI and HPAI in wild and domestic bird popula- provides a foundation for future studies on the pathogene- tions. The system has a unique disease-free equilibrium sis of drug resistant TB and HIV-TB co-infection. which is locally and globally stable when the reproduc- tion number is less than one. There are unique LPAI-only Jane Heffernan, Yimin Du and HPAI-only equlibria, which are locally asymptotically York University stable as long as the other pathogen can not invade the jmheff[email protected], [email protected] equilibrium. There exist a coexistence equilibirum when the invasion number of both pathogens are greater than one. We show that both pathogen can coexist in the form Jianhong Wu of sustained oscillations. York University, Canada [email protected] Necibe Tuncer University of Tulsa [email protected] MS10 Mechanism Elucidation in Intracellular Signaling MS10 Models Via Sensitivity Functions Within-Host Virus Model with Immune Response Many physiological and cellular processes, from G-protein and Infected Cell Age Structure coupled receptor (GPCR) signaling to circadian rhythms, There is substantial evidence that the CTL (Cytotoxic are regulated by oscillatory signals. Although an actively T Lymphocyte) immune response plays a crucial role in studied area, even the most well-known and commonly controlling HIV in infected patients. CTLs recognize studied pathways can have controversy and lack of clarity pathogen-derived proteins (epitopes) presented on the sur- on circuit architecture. Time-dependent stimulation, using face of infected cells to mediate their killing. Recent studies microfluidics technology, has proven valuable in eliciting have demonstrated the heterogeneity of epitope presenta- previously unseen cellular responses, thereby potentially tion and recognition with respect to the infected cell lifecy- allowing researchers to glean new insights. We discuss the cle, which may impact the efficacy of the immune response. use of sensitivity functions as tools to decipher the un- This talk concerns modeling the coupled within-host pop- derlying mechanisms driving the responses, and to under- ulation dynamics of virus and CTL immune response, pay- stand the differences in circuitry under constant and time- ing special attention to the cellular infection-age kinetics of dependent stimulation patterns. We further discuss the recognition and killing of infected cells by CTLs. In partic- possible information gained from observing other species ular, we extend a cellular infection-age structured within- in the pathway, and offer suggestions to improve future host virus model to include immune response and analyze experimental design. the resulting dynamics. Karyn L. Sutton Cameron Browne University of Louisiana Vanderbilt University Lafayette LS14 Abstracts 75

[email protected] eled as a collection of discrete elastic springs, which can be dynamically added and removed. We use this model to investigate how substrate elasticity, cell elasticity, FA MS11 strength, and FA spacing affect cell shapes during spread- Quantification of Iliac Artery Tortuosity and Its ing. We also investigate how cellular active deformation Implication for Rotation of Fenestrated Aortic must be coupled to FA forces and intracellular stresses in Stent Grafts order to obtain experimentally observed cell spread areas and observed tractions exerted by the cell onto the sub- Tortuosity is a measure of the deviation of an artery from a strate. straight line, and is an indicator of potential problems dur- ing deployment of fenestrated aortic stent grafts, which can Magdalena Stolarska have unwanted rotation in severely tortuous arteries. We University of St. Thomas will present mathematical techniques for tortuosity assess- Department of Mathematics ment and iliac artery tortuosity values for typical patients [email protected] and those for which rotation was an issue, with the goal of establishing criteria to predict when tortuosity will cause graft rotation. MS11 Matthew G. Doyle,CristinaAmon Modeling the Growth of an Atherosclerotic Lesion University of Toronto [email protected], [email protected] Atherosclerosis is a vascular disease driven by inflamma- tory processes. Atherogenesis can be viewed as an in- Leonard Tse flammatory instability of a reaction-diffusion-chemotactic Toronto General Hospital (RDC) system on a fixed domain while modeling [email protected] atherosclerotic lesion growth requires coupling the RDC system to the momentum balance system for the mechan- MS11 ical response of the affected tissue. This talk presents a model of this process and presents numerical simulations A Mechanical and Biochemical Model of Intimal of a free-boundary problem modeling lesion growth. Hyperplastic Lesions

We investigate an axisymmetric model of intimal hyper- Jay R. Walton plasia using hyperelasticity theory. Our model incorpo- Department of Mathematics rates growth of the intima due to cell proliferation which is Texas A&M driven by the release of cytokines. The growth rate is tied [email protected] to local stresses and concentration of cytokine. We find that rapid intimal thickening coupled to a quiescent me- dia puts the intima in a state of compression. Our results MS12 are compared with intima-media thickness measurements of carotid arteries from clinical studies. Collective Effects and Correlations in Semidilute Bacterial Suspensions Rebecca Vandiver St. Olaf College To understand the non-trivial correlations emerging from Department of Mathematics, Statistics and Computer collective swimming, a simple model is introduced where a Science bacterium is represented as a force dipole subject to two [email protected] types of interactions: hydrodynamic and excluded volume (collisions). This model allows for efficient direct simula- Pak-Wing Fok tions confirming a striking experimental observation: cor- University of Delaware relations are independent of concentration and swimming [email protected] speed, past the concentration threshold for collective mo- tion. The effects of the particle shape, size, and dipole moment will also be presented. MS11 Understanding the Role of Cell-substrate Interac- Shawn Ryan tion in Cell and Focal Adhesion Shapes Department of Mathematics Penn State University Mechanical interaction between a cell and its underlying [email protected] substrate have important implications in many contexts, and it has been shown experimentally that that the mate- rial properties of the substrate affect cellular response. We Igor Aranson present a two-dimensional mathematical model and finite Argonne National Laboratory element simulations of a biological cell interacting with a Materials Science Division deformable substrate and use this model to gain a better [email protected] understanding of how the mechanical interaction between the cell and substrate affects cell shape and focal adhesion Leonid Berlyand (FA) dynamics during cell spreading. The cell is treated as Penn State University a hypoelastic actively-deforming continuum and the sub- Department of Mathematics strate is modeled as a linearly elastic continuum. The ac- [email protected] tive deformation, captured by the addition of an active rate of deformation tensor, models local cytoskeletal reorgani- Andrey Sokolov zation. FAs connecting the cell and the substrate are mod- Argonne National Laboratory 76 LS14 Abstracts

[email protected] The former often refers to the attractive chemotaxis and latter to the repulsive chemotaxis. Chemotaxis has been advocated as a leading mechanism to account for the mor- MS12 phogenesis and self-organization of a variety of biologi- Remarks on Modeling and Identification in Bacte- cal coherent structures such as aggregates, fruiting bod- rial Chemotaxis ies, clusters, spirals, spots, rings, labyrinthine patterns and stripes, which have been observed in experiments. In this We discuss various topics related to the modeling talk, I will present recent results on the rigorous analysis of and identification of bacterial chemotaxis, including the a partial differential equation model arising from repulsive use of advection-diffusion and other PDE’s to match chemotaxis, which is a system of hyperbolic balance laws microfluidics-generated population behavior, and the in- consisting of nonlinear and coupled parabolic and hyper- ference of signaling dynamics to match single-cell tracking bolic type PDEs. In particular, global wellposedness, large- data. Mathematically, the first topic involves the care- time asymptotic behavior of classical solutions to such a ful modeling of pathways and shallow gradient approxima- model are obtained. The long-time behavior result shows tions (following work of Grunbaum, Othmer, and Erban), that constant equilibrium states are globally stable, which and the second topic requires the development of tools for indicates that chemorepulsion problem with non-diffusible the identification of time-varying parameters in nonhomo- chemical signal and logarithmic chemotactic sensitivity ex- geneous Poisson processes that model motor events (such hibits strong tendency against pattern formation. The re- as tumbling) as a function of the phosphorylation states sults are consistent with general results for classical repul- of certain enzymes. We present new results on these top- sive chemotaxis models. ics, including a model-based approach to the latter iden- tification problem, and discuss our results in view of new Kun Zhao experimental data. Department of Mathematics Tulane University Zahra Aminzare ”Zhao, Kun” ¡[email protected]¿ Rutgers University [email protected] MS13 Maja Skataric Flow Through a Two-Chambered Zebrafish Heart Graduate Student with Trabeculae [email protected] Trabeculae form in developing zebrafish hearts for Re on Eduardo Sontag the order of 0.1; effects of trabeculae in this flow is not well Rutgers University understood. Dynamic processes, such as vortex formation, [email protected] are important in the generation of shear at the endothelial surface layer and strains at the epithelial layer, which aid in proper morphology and functionality. In this study, CFD is MS12 used to quantify the effects of Re and idealized trabeculae Relating the Chemotactic Sensitivity with Intracel- height on the resulting flows. lular Signaling and Cell Movement Nicholas A. Battista Chemotaxis of single cells has been extensively studied and University of North Carolina at Chapel Hill a great deal on intracellular signaling and cell movement is [email protected] known. However, systematic methods to embed such infor- mation into continuum PDE models for cell population dy- Andrea Lane namics are still in their infancy. In this talk, I will present UNC at Chapel Hill our recent results on relating the chemotaxis sensitivity [email protected] in the PatlakKellerSegel (PKS) model with the detailed biochemistry of intracellular signaling for run-and-tumble Laura A. Miller bacteria. Our general formulas are useful in explaining re- University of North Carolina - Chapel Hill lations of single cell behavior and population dynamics. We Department of Mathematics show that the PKS model is valid when the external sig- [email protected] nal changes slowly, but inadequate when the signal changes fast. The general theory can also be applied to collective behavior of other individuals that move using a similar MS13 strategy. The Effects of Perturbations on Lamprey Swim- ming Chuan Xue Ohio State University The lamprey is a basal vertebrate and a model organism [email protected] for neurophysiology and locomotion studies. Here a 2D, in- tegrative, multi-scale model of the lamprey’s anguilliform (eel-like) swimming is driven by neural activation and mus- MS12 cle kinematics coupled to body interactions with fluid sur- Global Asymptotic Stability of Constant Equilib- roundings and implemented using the immersed boundary rium States of a Repulsive Chemotaxis Model with method. Effects on swimming speed and cost (metabolic Logarithmic Sensitivity work) by nonlinear dependencies associated with muscle force development combined with perturbations to the neu- In contrast to diffusion (random diffusion without orienta- ral activation are presented. tion), chemotaxis is the biased movement of cells/particles toward the region that contains higher concentration of Christina Hamlet beneficial or lower concentration of unfavorable chemicals. Tulane University LS14 Abstracts 77

New Orleans LA hybrid neural network [email protected] We construct a path-integral representation of solutions Eric Tytell to a stochastic hybrid system describing the dynamics of Tufts University synaptically coupled neuronal populations. The state of Department of Biology each local population is described in terms of two stochas- [email protected] tic variables, a continuous synaptic variable and a discrete activity variable. The spike-driven dynamical equations Lisa J. Fauci for the synaptic currents are only valid between stochas- Tulane University tic jumps in spiking activity, which are described by a Department of Mathematics neural master equation. We use the path-integral repre- [email protected] sentation to derive a large deviation variational principle for a stochastic hybrid neural network. We illustrate the theory by considering the optimal paths of escape from a MS13 metastable state in a bistable neural network. Hydrodynamic Contributions to Amoeboid Cell Motility Paul C. Bressloff University of Utah and University of Oxford, UK In this research, we develop a computational model of Department of Mathematics crawling Physarum polycephalum based on the Immersed bressloff@math.utah.edu Boundary Method. Our model incorporates the effects of cell cytoplasm, the internal cytoskeleton and adhesions to Jay Newby the substrate. Of particular interest are stresses generated Mathematical Biosciences Institute by flow and how transmission of stresses to the substrate The Ohio State University is coordinated. We attempt to characterize conditions nec- [email protected] essary to generate directed motion. Cytoplasmic flows and traction stresses are compared to experimentally measured values in Physarum. MS14

Owen Lewis Vasculature Adaptation and Optimization in Em- University of California, Davis bryonic Zebrafish Brain [email protected] During the development of vasculature in the midbrain of Robert D. Guy embryonic zebrafishes, both angiogenesis and vessel prun- Mathematics Department ing are observed. The vessel pruning occurred preferen- University of California Davis tially at loop-forming segments, leading to gradual reduc- [email protected] tion in the vasculature complexity. An shear-stress-driven adaptation model of blood vessels, which naturally opti- mizesthevesselnetwork,isemployedtopredicttheves- Juan Carlos del Alamo, Shun Zhang sel pruning. The successful prediction suggests that vessel University of California, San Diego pruning is a consequence of the adaptation process and [email protected], [email protected] makes the vasculature more efficient.

MS13 Dan Hu Shanghai Jiao Tong University Population Scale Effects of Macrophytes on Plank- [email protected] ton Mobility

Small-scale interactions between water and vegetation can MS14 have a significant, complex effect on water flow. Us- ing a two-dimensional hydrodynamic model, we represent Theoretical Modeling of Nonlinear Dendritic Inte- macrophytes as a simple, flexible and deforming porous gration layer, varying the bending stiffnesses and porosities of the plants, as well as background flow speeds and type of flow. We address the question of how a neuron integrates excita- Studying velocities, shear stress, and mixing, we show that tory (E) and inhibitory (I) inputs from different dendritic small-scale physical-biological interactions can have major sites. For an idealized neuron with an unbranched den- and important implications for plankton patchiness, move- drite, a conductance-based cable model is derived and its ment, and ultimate destiny. asymptotic solutions are constructed. The solutions reveal the underlying mechanisms of a dendritic integration rule Virginia B. Pasour discovered in a recent experiment. We then extend our U.S. Army Research Office analysis to the multi-branch case and confirm our analysis [email protected] through numerical simulation of a realistic neuron.

Laura Miller Songting Li, Douglas Zhou UNC-Chapel Hill Shanghai Jiao Tong University [email protected] [email protected], [email protected]

David Cai MS14 Courant Institute for Mathematical Sciences, NYU Path-integrals and large deviations in a stochastic Shanghai Jiao-Tong University 78 LS14 Abstracts

[email protected] [email protected]

MS14 MS15 Analytical Evaluation of Targeting Performances at Structural Identifiability of Biological Models Short and Long Distances in a Stochastic Model for Neural Arborization Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. We investigate the behavior of a simplified neural growth Many biological models are unidentifiable, which means model that branches with uniform probability and is sub- that parameters can take on an infinite number of values ject to a total length constraint. Treating all possible tree and yet yield the same input-output data. We study the instantiations as outcomes drawn from a discrete probabil- identifiability properties of several types of models, arising ity distribution, we compute the expected number of active in Systems Biology and Chemical Reaction Networks, and tree branches as a function of distance. We show analyti- demonstrate how to obtain identifiable reparametrizations cally that both the rising and decaying part of the resulting of these models when they are unidentifiable. curve are respectively described exactly and approximated by geometrical series. Nicolette Meshkat, Seth Sullivant North Carolina State University Remus Osan [email protected], [email protected] Georgia State University Department of Mathematics and Statistics MS15 [email protected] A Global Convergence Result for Processive Mul- Jun Xia tisite Phosphorylation Systems Georgia State University Multisite phosphorylation plays an important role in in- [email protected] tracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when Emily Su the phosphorylation/dephosphorylation mechanism is dis- Rutgers University tributive, that is, when the binding of a substrate and an [email protected] enzyme molecule results in addition or removal of a single phosphate group and repeated binding therefore is required for multisite phosphorylation. In particular, such systems MS15 admit bistability. Here we analyze a different class of multi- The Dependence of the Existence of Positive site systems, in which the binding of a substrate and an en- Steady States on the Rate Coefficients for zyme molecule results in addition or removal of phosphate Deficiency-One Mass Action Systems groups at all phosphorylation sites. That is, we consider systems in which the mechanism is processive, rather than It is well-known that there exists a unique positive steady distributive. We show that in contrast with distributive state in each of the positive stoichiometric classes for single systems, processive systems modeled with mass-action ki- linkage class weakly reversible (WR) deficiency-one mass netics do not admit bistability and, moreover, exhibit rigid action systems. The existence result does not remain valid dynamics: each invariant set contains a unique equilib- in general if we omit the weak reversibility assumption. In rium, which is a global attractor. Additionally, we obtain a this talk, we charaterise those single linkage class non-WR monomial parametrization of the steady states. Our proofs defeiciency-one mass action systems for which the existence rely on a technique of Johnston for using ”translated” net- of positive steady states does not depend on the rate coef- works to study systems with ”toric steady states”, recently ficients. given sign conditions for injectivity of polynomial maps, and a result from monotone systems theory due to Angeli Bal´azs Boros and Sontag. E¨otv¨os Lor´and University [email protected] Anne Shiu University of Chicago [email protected] MS15 Degree Two Polynomials for Saddle Node Bifurca- Carsten Conradi tions in Mass Action Networks Max-Planck-Institut Dynamik komplexer technischer Systeme Bistability has been recognized an important feature of dy- [email protected] namical systems originating in Biology and it is often estab- lished numerically (via a saddle-node bifurcation). How- ever, parameter uncertainty complicates numerical analy- MS16 sis. Hence techniques allowing the analytic computation Data Assimilation Methods and Inverse Problem of parameters where a given system exhibits bistability are for Protein Polymerization desirable. We present a condition involving only polyno- mials of degree ≤ 2 that allows to determine state and Data assimilation methods are particular methods that ex- parameter vectors where a mass action system generically ploiting some available data give us an estimation of pa- undergoes a saddle-node bifurcation. rameters or state variables. In this presentation, we will introduce several data assimilation methods and their ap- Carsten Conradi plication to protein aggregation, a chain reaction which is Max-Planck-Institut Dynamik komplexer technischer one of the causes of neurodegenerative diseases called amy- Systeme loid diseases (among which are Alzheimers, Huntingtons, LS14 Abstracts 79

Parkinsons etc). Moving from Lifshitz-Slyozov equation, range of application including amphibian dynamics and as- we define a model for protein polymerization. We cou- sociated diseases. This modeling approach is then extended ple the model and observations to define an inverse prob- to investigate amphibians to understand the effect of the lem. The aim is to apply data assimilation methods on this disease Bd and the symbiont Jl on their population dynam- inverse problem to obtain an estimation of kinetic coeffi- ics and provide useful insights to biologists in the control cients and/or cluster concentrations, with application on of Chytridiomycosis under various scenarios. real data. Baoling Ma Aurora Armiento University of Louisiana - Lafayette Inria, Rocquencourt [email protected] France [email protected] Azmy S. Ackleh Department of Mathematics Marie Doumic University of Louisiana at Lafayette INRIA Rocquencourt, France [email protected] marie.doumic-jauff[email protected] Jacoby Carter USGS National Wetlands Research Center MS16 [email protected] Limited Measurement Domains: Robustness of Pa- rameter Estimation in Flocculation Dynamics Vinodh Challamuthu University of Louisiana at Lafayette While incorporating the Smoluchowski coagulation equa- [email protected] tion to model aggregation in size structured populations, the actual physical structures we study can exist in clus- ters smaller than the lower limit and larger than the up- MS17 per limit of experimental devices. With the motivation of identifying an aggregation kernel under real-world experi- Merging Population Genetics, Mosquito Behaviour mental limitations, we aim to rigorously study the impact and Epidemiology to Predicting the Success of the of the limited measurement domain on the robustness of Use of GM Mosquitoes for Malaria Control our parameter estimation inverse problem. Transgenic mosquitoes are a potential tool for the con- Dustin Keck trol or eradication of insect-vectored diseases. For malaria, Applied Mathematics one possible strategy relies on the introduction of malaria- University of Colorado, Boulder refractory transgenes into wild Anopheles mosquito pop- [email protected] ulations that would limit their capacity to transmit the disease. This could be done with or without a gene-drive that could facilitate the spread of the allele of interest. By MS16 merging population genetics, epidemiology and mosquito Impact of Ellipsoid Geometry and Deformation on life-history traits, it is possible to explore the importance Flocculation Dynamics of the gene-drive, the eventual role of mosquito mating preferences as well as the impact of the cost and efficacy Fragmentation is an important yet poorly understood as- of refractoriness on its spread in the mosquito population. pect of flocculation dynamics. Simulations of fragmenta- As the aim of such approach is not only a modification tion events can be simplified by approximating the floc as of the mosquito population but a significant decrease of a solid ellipsoid. The force on the surface of such an ellip- malaria prevalence in the human population, it is essential soid can have a strong dependence on its geometry, further to determine how such releases could affect the long-term compounded by deformation due to the flow. We present prevalence of malaria in humans. Those different aspects results on the deformation of ellipsoidal flocs in laminar are going to be discussed in the current context of the fight flow. against malaria.

Eric Kightley Christophe Bo¨ete Interdisciplinary Quantitative Biology Aix Marseille Universit´e, IRD (Institut de Recherche pour University of Colorado le [email protected] EHESP (Ecole des Hautes Etudes en Sant´e Publique) [email protected]

MS16 A General Structured Population Model with the MS17 Application to Amphibians Infected with Chytrid- The Effect of IPT on the Spread of Drug Resistant iomycosis Malaria Parasite When Regions are Connected

The disease Chytridiomycosis occurs when the skin of The use of IPT is an increasingly popular preventive strat- an amphibian is infected by the chytrid fungus Batra- egy aimed at reducing malaria incidence in vulnerable in- chochytrium dendrobatidi (Bd). The rapid and widespread dividuals. We seek to understand how IPT can affect the growth of Chytridiomycosis has been associated with major spread of antimalarial drug resistance when there is move- population declines and extinctions in many frog species. ment between neighboring low and high transmission ar- Studies show that the inoculation of anti-Bd bacterial eas. We expanded a previously published model to include species Janthinobacterium lividum (Jl) could reduce Bd movement between neighboring high and low transmission infection on amphibians. We first develop a new and gen- areas. Our results suggest that population movement re- eral class of structured metapopulation models with wide sults in resistance spreading fastest in high transmission 80 LS14 Abstracts

areas. The more complete the antimalarial resistance, the [email protected] faster the resistance spread through a population.

MS17 Scott Duke-Sylvester Department of Biology Application of P. Falcipalrum Gametocyte Sex Ra- University of Louisiana at Lafayette tios Via Competitive and Non-Competitive Strate- [email protected] gies: The Evolutionary Implications A mathematical model that simulates the within-mosquito Jemal Mohammed-Awel dynamics of Plasmodium falciparum in an Anopheles Valdosta State University mosquito is used to investigate optimal gametocyte sex [email protected] ratios under varying fecundity. Gametocytes are the sex- ual forms of the Plasmodium malaria parasite and under- Frederick Baliraine standing mechanisms that determine the ratio of male ga- Department of Biology, metocytes to female gametocytes has engendered consid- LeTourneau University, Longview, TX erable interest among researchers. Under unbiased ran- [email protected] dom mating and incomplete fertilization the model illus- trate that optimal gametocyte sex ratios vary from a highly Miranda Teboh-Ewungkem female-biased to a slight male-biased sex ratio under a non- Lehigh University competitive strategy. When two distinct fitness optimiza- Bethlehem, PA, 18020 tion strategies for for P. falciparum with varying fecun- [email protected] dity was analyzed, initial results indicate that the non- competitive strategy is the winning strategy.

Miranda I. Teboh-Ewungkem MS17 Lafayette College [email protected] Ipt and the Spread of Drug Resistant Malaria Thomas Yuster Intermittent Preventive Treatment (IPT) is a malaria con- Lafayette College trol strategy in which vulnerable asymptomatic individuals Easton, PA, 18042 are given a full curative dose of an antimalarial medication [email protected] at specified intervals, regardless of whether they are in- fected with malaria or not. A mathematical model is devel- oped to explore the effect of IPT use on the malaria preva- MS18 lence and control under different scenarios. The model An Application of Mathematics to Osteoarthritis includes both drug-sensitive and drug-resistant strains of Related Inflammation the parasite as well as interactions between human hosts and mosquitoes. The basic reproduction numbers for both The degenerative joint disease osteoarthritis (OA) has tra- strains as well as the invasion reproduction number by the ditionally been viewed as a consequence of aging and “wear resistant strain are computed and used to examine the role and tear.” However, the most recent research indicates of IPT in the development of resistant infections. Sensitiv- that inflammation, as related to the innate immune re- ity and uncertainty analysis is carried out to examine the sponse, is fundamental in the development and progression influence of model parameters in the model outcomes. of OA. The goal of this talk is to describe mathematical approaches to developing a theoretical foundation for re- cent discoveries in this area of biological research, and for Zhilan Feng understanding the connections between OA and inflamma- Department of Mathematics tion. Purdue University [email protected] Jason Graham Department of Mathematics Miranda Teboh-Ewungkem University of Scranton Lehigh University [email protected] Bethlehem, PA, 18020 [email protected] MS18 Katharine Gurski Success, Failure, and Spreading Speeds for Inva- Howard University sions on Spatial Gradients [email protected] We present a model that describes the spatial spread of a species along a habitat gradient. We demonstrate that the Carrie A. Manore species may succeed or fail in local invasion depending on Tulane University the species’ growth function and dispersal kernel. We show [email protected] how a species can escape a region of poor quality habitat by climbing a resource gradient to good quality habitat where Angela Peace it spreads at a constant spreading speed. Joint work with Arizona State University William Fagan and Kimberly Meyer. [email protected] Bingtuan Li Olivia Prosper Department of Mathematics Dartmouth University University of Louisville LS14 Abstracts 81

[email protected] Robert D. Guy Mathematics Department University of California Davis MS18 [email protected] Modeling and Analysis of Glioma Tumor Growth

Glioblastoma multiforme is the most common and most MS19 deadly primary brain tumor in adults. Gliomas are charac- terized by highly diffusive growth patterns, thus reaction- Exploring Motility of Breast Cancer Cells Using a diffusion equations are often used in modeling. To give in- 3D Individual Cell Based Model sight on the mechanisms most responsible for tumor growth and the difficult task of forecasting future tumor behav- Experiments have demonstrated that white blood cells ior, numerical and analytical results from various models, are directly involved in the invasion of breast tumor including ones with density-dependent diffusion, are com- cells into surrounding tissues and blood vessels. The pared to experimental data. white blood cells interact with tumor cells via a short- ranged chemical signaling loop involving two signalling Tracy L. Stepien, Erica Rutter molecules. We developed a 3D individual cell based com- School of Mathematical and Statistical Sciences putational model to study these interactions and to under- Arizona State University stand the observed streaming motility pattern. The cells [email protected], [email protected] are simulated as freely moving deformable ellipsoids and the signalling molecule concentrations are estimated using Yang Kuang reaction-diffusion equations. The movement and deforma- Arizona State University tion of cells are calculated from equations of motion ac- School of Mathematical and Statistical Sciences counting for all forces acting on each cell. This simplified [email protected] model is able to reproduce results from both in vitro and in vivo experiments. The model suggests that the removal of the signalling molecules is essential to produce the observed MS18 ratio of 3 invasive tumor cells per 1 invasive white blood The Effects of Cross-diffusion on an SIR Model cell. A preliminary exploration of the parameter space in- dicates that the ratio between tumor cells and iwhite blood During the outbreak of infectious diseases, susceptible in- cells is robust to changes in most model parameters, sup- dividuals naturally tend to avoid infective individuals. We porting the experimental results. An exception to this ro- use a two-dimensional reaction-diffusion model, adapted bustness is that changes in the decay and secretion rates of from the Shigesada-Kawasaki-Teramoto (1979) model, to the signalling molecules can alter and even eliminate the describe the effects of cross-diffusion on an SIR model. invasion of tumor cells.

Kamuela E. Yong Hildur Knutsdottir Arizona State University Department of Mathematics [email protected] The University of British Columbia [email protected]

MS19 Actin-myosin Spatial Patterns from a Simplified MS19 Isotropic Viscoelastic Model Insights into Cytoplasmic Rheology Gained from F-actin networks are involved in cell mechanical processes Modeling Cellular Blebbing ranging from motility to endocytosis. The mesoscale ar- chitecture of assemblies of individual F-actin polymers Blebbing occurs when the cytoskeleton detaches from the that gives rise to micrometer-scale rheological properties cell membrane, resulting in the pressure-driven flow of cy- is poorly understood, despite numerous in vivo and vitro tosol towards the area of detachment and local expansion studies. In vitro networks have been shown to organize into of the cell membrane. Recent experiments involving bleb- spatial patterns when spatially confined, including dense bing cells have led to conflicting hypotheses regarding the spherical shells inside spherical emulsion droplets. Here we timescale of intracellular pressure propagation. The inter- develop a simplified model of an isotropic, compressible, pretation of one set of experiments supports a poroelastic viscoelastic material continually assembling and disassem- cytoplasmic model which leads to slow pressure equilibra- bling. We demonstrate that spherical shells emerge nat- tion when compared to the timescale of bleb expansion. A urally when the strain relaxation rate (corresponding to different study concludes that pressure equilibrates faster internal network reorganization) is slower than the disas- than the timescale of bleb expansion. To address this, a sembly rate (corresponding to F-actin depolymerization). dynamic computational model of the cell was developed These patterns are consistent with recent experiments, in- that includes mechanics of and the interactions between cluding a collapse of shells to a central high-density fo- the intracellular fluid, the actin cortex, the cell membrane, cus of F-actin when either assembly or disassembly is re- and the cytoskeleton. The model results quantify the rela- duced with drugs. Our results demonstrate how complex tive importance of cytoskeletal elasticity and drag in bleb spatio-temporal patterns can emerge without spatially- expansion dynamics. This study also shows that recent distributed force generation, polar alignment of F-actin multi-bleb experimental results can be explained by the polymers, or spatially non-uniform regulation of F-actin combination of cytoskeletal poroelasticity with either dy- by upstream biochemical networks. namic membrane-cortex adhesion or cortical reformation.

Jun Allard,OwenLewis Wanda Strychalski University of California, Davis Department of Mathematics [email protected], [email protected] University of California, Davis 82 LS14 Abstracts

[email protected] [email protected]

MS19 MS20 The Physics of Collective Cell Migration in Wound Reduction Methods for Spiking Networks Healing and Cancer Metastasis

Multicellular organisms require groups of cells to function We consider a simple spiking LIF neuron model driven together as a unit. A common scenario involves the collec- by excitatory conductance input, and highlight a dimen- tive movement of cells. For example, when your skin gets sion reduction method to capture the firing rate dynamics. cut, one of the first processes is re-epithelialization where We further consider a QIF population with adaptation and epidermal cells crawl over the wounded region. And, in recurrent (all-to-all) excitatory coupling, where an analo- cancer, tumor cells will often move as a group to detach gous reduction method can be applied with augmentation. from the primary tumor and invade distal regions of the Based on the reduction, a linear stability analysis method body. In this presentation, I will describe the work that is applied to capture some of the features of the simula- we have been doing to develop a multiscale model for collec- tions. tive cell migration. This model is based in the fundamental biophysics of a single cell. We show that a combination of Cheng Ly directed cell motility, dipole-distributed forces, and adhe- University of Pittsburgh sion to neighboring cells and the environment is sufficient Department of Mathematics to explain in vitro wound healing dynamics and gives in- [email protected] sight into the biophysical changes that occur when cancer cells become metastatic. This model provides testable pre- Wilten Nicola dictions that we are now testing with experiments. University of Waterloo [email protected] Charles Wolgemuth University of Arizona Sue Ann Campbell Department of Physics University of Waterloo [email protected] Dept of Applied Mathematics [email protected] MS20 Impact of Single-Neuron Dynamics on Transfer of MS20 Correlations from Common Input The Essential Role of Phase Delayed Inhibition One source of spike train correlations in the nervous system in Decoding Synchronized Oscillations within the is common input, an inevitable consequence of the ubiquity Brain of coding by populations. The details of how input corre- lations map onto output spike correlations is surprisingly The widespread presence of synchronized neuronal oscil- complex, depending on single-neuron dynamics in subtle lations within the brain suggests that a mechanism must ways. Much progress has been made in untangling this re- exist that is capable of decoding such activity. Two re- lationship in Type I and Type II excitable neurons, in both alistic designs for such a decoder include: 1) a read-out simplified phase oscillator and conductance-based models. neuron with a high spike threshold, or 2) a phase-delayed In this talk, we apply these techniques to novel patterns of inhibition network motif. Despite requiring a more elab- excitability that arise in the presence of calcium currents. orate network architecture, phase-delayed inhibition has been observed in multiple systems, suggesting that it may Andrea K. Barreiro provide inherent advantages over simply imposing a high Department of Mathematics spike threshold. We use a computational and mathematical Southern Methodist University approach to investigate the efficacy of the phase-delayed in- [email protected] hibition motif in detecting synchronized oscillations, show- ing that phase-delayed inhibition is capable of detecting synchrony far more robustly than a high spike threshold MS20 detector. Furthermore, we show that in a system with Integrate-and-Fire Model of Insect Olfaction noisy encoders where stimuli are encoded through syn- chrony, phase-delayed inhibition enables the creation of a When a locust detects an odor, the stimulus triggers a decoder that can respond both reliably and specifically to series of synchronous oscillations of the neurons in the an- a stimulus, while a high spike threshold does not. tenna lobe. These oscillations are followed by slow dy- namical modulation of the firing rates which continue after Mainak Patel the stimulus has been turned off. I model this behavior Duke University by using an Integrate-and-Fire neuronal network with ex- Department of Mathematics citatory and inhibitory neurons. The inhibitory response [email protected] of both types of neurons contains a fast and slow compo- nent. The fast component, together with the excitation, Badal Joshi creates the initial oscillations while the slow component California State University, San Marcos suppresses them and aids in the creation of the slow pat- [email protected] ters that follow. During the initial oscillations the stimulus can be identified by determining which excitatory neurons participate consistently in every cycle of the oscillations. MS21 Pamela B. Fuller The Use of Physiological Model of Menstrual Cy- Rensselaer Polytechnic Institute cle Regulation in Women’s Health: Fertility and LS14 Abstracts 83

Contraception we will present the model and its dynamical properties. Open questions such as the administration of GnRH and The biology of female menstrual cycle hormonal regulation an improved modeling of follicular development will be dis- is complex and not completely understood. The system cussed. makes an excellent case study for mathematical modeling due to intrinsic nonlinearities, feedback mechanisms and Claudia Stoetzel, Julia Ploentzke, Susanna Roeblitz delays. Several dynamical models with varying complexity Zuse Institute Berlin and biological plausibility have been proposed. We provide [email protected], [email protected], su- an industrial perspective for how these models can and [email protected] should be used to inform clinical decisions for therapies targeting contraception, fertility, and endometriosis. MS22 Anna Kondic, Craig Fancourt An Algebraic Framework for Describing and Study- Merck & Co., Inc. ing Binary Enzymatic Networks [email protected], craig [email protected] We present a framework to describe and reason about en- MS21 zymatic networks. The initial motivation for this construct was to extend examples from the literature into the follow- The Role of Insulin and Androgen Dynamics in Fe- ing theorem: a binary enzymatic network that is futile and male Hormone Dysregulation cascaded is persistent, i.e. molecular species do not tend to Although the physiological role of insulin and androgens extinction. The framework provides mathematically sound in follicle development remains unclear, excess concentra- and biochemically applicable definitions for the notions of tions are commonly associated with ovulatory defects. We futile enzymatic cycles and enzymatic cascades, and sev- incorporate insulin and androgen dynamics into a mathe- eral prerequisite concepts. The framework could be used matical model of folliculogenesis, which describes hormone to prove more results, or even to help assess the plausibility production and pituitary-ovarian feedback through succes- of models of enzymatic networks during their design. sive growth stages. Changes in model periodicity and go- Gilles Gnacadja nadotropin/hormone profiles under various biological cir- Amgen cumstances are used to characterize the physiological ver- [email protected] sus pathological influences of insulin and androgens on ovu- lation. Erica J. Graham MS22 North Carolina State University Correspondence of Regular and Generalized Mass Department of Mathematics Action Systems [email protected] In this talk, we investigate systems where graph-based cor- respondence of dynamics for mass action systems may not James Selgrade be made directly, but for which correspondence may be North Carolina State University made to a ”generalized” mass action system. The con- [email protected] structed generalized mass action system contains different monomials than implied by the chemistry of the system, MS21 but has a ”well-structured” reaction graph. We will dis- cuss some of the newest results regarding the algorithmic Multiple Cycles and Bifurcation in Models of Hor- construction of such generalized mass action systems. monal Control of the Menstrual Cycle

Two models for hormonal control of the menstrual cycle are Matthew Johnston presented using the same system of differential equations University of Wisconsin Madison but based on different data sets . For the best-fit param- [email protected] eter sets, simulations for the two models agree well with the data but one model also has a stable periodic solution MS22 representing an abnormal, nonovulatory menstrual cycle. Differences in model behavior are explained by studying Atoms of Multistationarity in Chemical Reaction hysteresis curves in bifurcation diagrams with respect to Networks sensitive model parameters. Multistationarity is a prerequisite for a reaction network James F. Selgrade to act as a biochemical switch. Theoretical tools that help Department of Mathematics and Biomathematics rule out multistationarity include the Jacobian criterion of Program Craciun and Feinberg. We provide results that are helpful [email protected] in establishing multistationarity of certain networks. The key result is that if a multistationary network N is “embed- ded” in a larger network G then G is also multistationary. MS21 The partial ordering resulting from the embedding prop- A Differential Equation Model for the Bovine Es- erty yields minimal (with respect to number of chemical trous Cycle species and reactions) multistationary networks. We also provide results which identify the smallest such minimal Based on the models for the human menstrual cycle by networks. Selgrade and coworkers, a fully coupled feedback model for the bovine estrous cycle has been developed. It has Badal Joshi been used for an analysis of follicular wave patterns and California State University, San Marcos for the simulation of synchronization studies. In this talk, [email protected] 84 LS14 Abstracts

Anne Shiu cessing in An Asynchronous Bursting Population University of Chicago [email protected] Vasopressin acts as an antidiuretic hormone, as part of the homeostatic system that maintains osmotic pressure. Experiments show a robust linear relationship between os- MS22 motic pressure and vasopressin secretion despite very non- Exploiting Reaction Network Structure for Param- linear properties of spike generation and secretion in the eter Identification of Biochemical Switches neurons, and highly heterogeneous spiking activity. Here we develop a previous model of the spiking and secretion One key challenge in Systems Biology is the identification mechanisms to examine how the heterogeneous population of kinetic models from limited quantitative data. In this might coordinate a robust signal response using local inter- work we illustrate the potential of Chemical Reaction Net- neuronal (dendritic) communication. work Theory (CRNT) for the parameter identification of kinetic models. We introduce a method for inverse bifur- Duncan J. MacGregor, Gareth Leng cation of bistable biochemical reaction networks, that ex- Centre for Integrative Physiology ploits inherent structural properties of bistable switches University of Edinburgh to infer the kinetic parameters from dose response curves. [email protected], [email protected] Uniqueness and identifiability properties of the associated inverse problem are analyzed. MS23 Irene Otero-Muras Leveraging Mathematical Models to Understand CSIC Population Variability in Response to Cardiac [email protected] Drugs

Pencho Yordanov Mathematical models of heart cells and tissues are suffi- ETH Zurich ciently advanced that the models can predict mechanisms [email protected] underlying pro-arrhythmic or anti-arrhythmic effects of drugs. However, these models are not presently adequate for understanding variability across a population, i.e. why Attila Gabor a drug my be effective in one patient but ineffective in CSIC another patient. I will discuss novel computational ap- [email protected] proaches my laboratory has developed that can quantify and predict differences between individuals in the response Julio R. Banga to cardiac drugs IIM-CSIC Vigo, Spain Eric Sobie [email protected] Mount Sinai Hospital [email protected]

MS23 Real-Time Model Calibration and Prediction Test- MS23 ing with the GPU and Dynamic Clamp Paracrine Regulation of Glucagon and Somatostain Secretion Electrical activity of anterior pituitary cells is heteroge- neous, motivating model fitting to individual cells. We use Pancreatic islets are composed of α-, β-, and δ-cells. These the parallel computational power of the GPU to find pa- cells secrete the hormones glucagon, insulin, and somato- rameters of a biophysical model with similar bifurcation statin, respectively. Together, these hormones regulate glu- structure to live individual cells. The optimization is iter- cose homeostasis in the body. While β-cells are coupled atively improved by making model predictions that induce through gap junctions, individual α-andδ-cells are het- a qualitative changes in electrical activity, testing the pre- erogenous. We investigate the paracrine interacts between dictions with dynamic clamp on the same cell, then adding these cells, which gives synchronous oscillations of insulin the results to the set of optimization constraints. and somatostain, and anti-synchronous oscillations of in- sulin and glucagon at high glucose levels. Patrick A. Fletcher Department of Mathematics Margaret A. Watts Florida State University Laboratory of Biological Modeling pfl[email protected] National Institutes of Health [email protected] Jo¨el Tabak Department of Biological Science Ofer Kimchi Florida State University Princeton University [email protected] [email protected]

Richard Bertram Arthur Sherman Department of Mathematics Laboratory of Biological Modeling Florida State University National Institutes of Health [email protected] [email protected]

MS23 MS24 Hypothalamic Vasopressin Neurons: Signal Pro- Epidemiological and Economic Benefits of Targeted LS14 Abstracts 85

Tuberculosis Screening in a Correctional Facility of sistent with endemic persistence. New River Health District Sheng Li Objective: The objective of this study is to conduct cost- Pennsylvania State University effectiveness analysis of pre-screening inmates for tubercu- [email protected] losis compared to no pre-screening in a correctional facility in Southwest Virginia. Background: Correctional facilities represent a relatively higher risk for tuberculosis transmis- MS24 sion in the United States because they have close living Modeling SIS Disease Dynamics on Random Con- quarters, overcrowding, and poor ventilation, thereby en- tact Networks hancing the risk of tuberculosis acquisition and transmis- sion. Methods: We conducted cost effectiveness analysis to Contact networks represent persons by nodes and contacts evaluate pre-screening measures for tuberculosis compared by edges. It is a more realistic model of disease related to the baseline scenario of no pre-screening. We developed human contacts than the random mixing model, which as- a dynamic model to understand and analyze the transmis- sumes that every pair of individuals have identical con- sion dynamics of tuberculosis in a correctional facility and tact rate. An effective degree SIS epidemic model was de- its associated costs over a time horizon of 5 years, from the veloped before, and was shown to have different disease perspective of the correctional facility and the local health thresholds than an SIR model. This contradicts with the department. Data from a tuberculosis outbreak in 2011 prediction of classic disease models that SIR and SIS mod- at a correctional facility located in Southwest Virginia is els should have the same disease threshold. But this effec- incorporated to calibrate the dynamic model. Results: We tive degree model is too complex to derive a closed formula used the ratio of 68 to 200 out of 100,000 inmates will de- for the disease threshold. In this talk, I will introduce a velop active tuberculosis while incarcerated when conduct- simplified SIS model on random contact networks, which ing analysis for the baseline of no pre-screening. Based on agrees with stochastic simulations and is mathematically preliminary results, the incremental cost-effectiveness ratio tractable. The model yields a disease threshold formula of tuberculosis pre-screening is estimated at $-15,461 per that bears a clear biological meaning: for the disease to disability adjusted life year averted (cost saving) from the spread, the average number of transmissible neighbours perspective of the correctional facility and the local health times the average number of times a neighbour can be in- department. Conclusion: Our findings indicate that tuber- fected must be greater than unity. The threshold converges culosis pre-screening is a cost-saving intervention; thereby, to that of the SIR model under the homogeneous mixing we recommend adoption of tuberculosis pre-screening pro- limit. grams in correctional facilities. Junling Ma Kaja Abbas University of Victoria, Canada Virginia Polytechnic Institute and State University [email protected] [email protected] MS25 MS24 Models of Neurovascular Coupling and Cerebral A Simple Epidemic Model with Nosocomial Trans- Autoreglation mission Our research group has developed a parallel numerical model describing neurovascular coupling. NVUs are cou- The SARS epidemic of 2002-3 drew attention to nosoco- pled through a space filling H-tree simulating a vascular mial disease transmission, as many of the disease cases tree and spatially embedded in cerebral tissue. The model were transmitted through hospital staff and visitors. Var- regulates bloodflow in response to neuronal activity in a ious types of models have been proposed to describe this, 2-dimensional tissue slice of width and depth of the order including metapopulation models. We formulate and an- of millimetres culminating in the dynamic simulation of alyze a simple compartmental model with heterogeneous several million cells. The model thus allows us to study a mixing to describe nosocomial transmission and determine number of important pathological scenarios. its reproduction number and the final size relations. Tim David Fred Brauer Centre for Bioengineering University of British Columbia University of Canterbury, New Zealand Department of Mathematics [email protected] [email protected]

MS25 MS24 Assessing the Impact of Structural Organization of Demographic Transition and the Dynamics of the Renal Medulla on Oxygen Distribution Using Measles in China aMathematicalModel

Industrialization and demographic transition generate non- A theoretical model is presented to analyze the impact on stationary dynamics in human populations that can impact oxygen distribution of the heterogeneous organization of the transmission and persistence of infectious disease. By the rat medulla revealed in anatomical studies. Model catalytic transmission model, we show that demographic equations are based on transmural transport and conser- transition and reduced prevalence has driven a shift in vation of water and solutes (NaCl, urea, O2,HbO2,Hb), the age distribution of susceptibility to measles in China. and are solved to steady state. Results suggest that the The force of infection of measles has declined dramatically structural organization of the renal medulla produces sig- in the industrialized eastern provinces in the last decade; nificant axial and radial PO2 gradients, and impacts the while central and western provinces exhibit dynamics con- effectiveness of the medullary urine concentrating mecha- 86 LS14 Abstracts

nism. tively predicts the 3D solution structure of megadalton- scale DNA-based assemblies based on underlying DNA se- Brendan C. Fry quence, as well as their emergent light-harvesting proper- Duke University ties when decorated with dyes and porphyrins. Department of Mathematics [email protected] Mark Bathe MIT [email protected] MS25 Can Pre-Glomerular Oxygen Transport Be Used to Investigate Renal Anatomy? MS26 There is a close spatial association of arteries and veins The Structural Glycobiology of HIV: Insights from in the pre-glomerular vasculature, which facilitates oxygen Molecular Simulations and Implications for the De- shunting and protects the kidney from hyperoxia. However sign of Virucidal Lectins this anatomical structure may lead to hypoxia. We have developed a mathematical model of oxygen transport in The HIV envelope-glycoproteins are heavily glycosylated the paired pre-glomerular branched vasculature. Here we to avoid immune recognition, creating both challenges to demonstrate how differences in transit times and shapes of the effective inhibition of viral-cell recognition and unique pulses of oxygen and labelled haemoglobin, due to shunt- opportunities; for example, carbohydrate-binding proteins ing, could be used to explore this pre-glomerular anatomy. have been shown to have the potential to act as potent viru- cides. The development of detailed computational models that explain the relative affinities of distinct oligosaccha- Bruce S. Gardiner rides, provide insight into mechanisms of multi-valent bind- University of Western Australia ing, and provide a foundation for the rational design of [email protected] improved inhibitors will be presented.

Saptarshi Kar, David Smith David F. Green The University of Western Australia Department of Applied Mathematics and Statistics [email protected], [email protected] Stony Brook University [email protected] Roger Evans Monash University [email protected] MS26 3D Continuum Modeling of Ion Permeation in Ion Channel Systems MS25 Development of Hypoxia in a Model of Renal Blood As it is hard to apply all-atomic model to simulate the Flow Control and Oxygen Consumption whole process of ion permeation in ion channel, we use continuum electrodiffusion description for ion flow in the Hypoxia is an important pathway in the development channel system. Electrodiffusion process exists in many ap- of acute kidney injury during cardiopulmonary bypass parently different physical objects such as electrolyte cell, surgery. Using a model of renal hemodynamics we assess nanofluidic device, charged porous media, and ion chan- the degree to which hypoxia develops under reduced hema- nel in biology. Real 3D ion channel is particularly difficult tocrit, temperature, and systemic pressure that are com- to simulate due to the multiscale nature of the transport monly induced in such surgery. Oxygenation is determined process and the complex geometry/boundary of the chan- by renal blood flow and the metabolic work of sodium re- nel protein system. For this reason, there are so far only absorption. Results suggest that although oxygen supply a few software publicly available in this important area of and consumption both decrease bellow physiologic levels, biology. We will present a software platform for ion chan- fractional extraction increases significantly. nel simulations. The platform includes three parts: (1) Ioannis Sgouralis finite element solver for the Poisson-Nernst-Planck equa- Duke University tions and their improved forms, (2) molecular meshing that [email protected] is required for finite element method. We recently devel- oped a novel and robust molecular surface mesh generation tool TMSmesh that can handle complex and arbitrarily MS26 large biomolecular system. (3) a visual system, VCMM, Computational Design of Megadalton-Scale Nu- for molecule, mesh and simulation data visualization and cleic Acid Nanoassemblies analysis. The platform is applied to compute properties such as current-voltage characteristics (curves) and con- Programmed self-assembly of nucleic acids offers the ductance of a few channel systems, and the calculations unique opportunity to engineer complex megadalton-scale are compared with Brownian Dynamics simulation and ex- macromolecular architectures with atomic-level accuracy. perimental results. The sequence specificity of DNA additionally renders these nanoassemblies spatially addressable structural scaffolds Benzhuo Lu,BinTu,YanXie to host secondary molecules such as light-harvesting dyes Institute of Computational Mathematics, China and chemically active compounds. These properties may [email protected], [email protected], be exploited to rationally design, for example, biomimetic [email protected] light-harvesting constructs to replicate aspects of bacterial photosynthesis. Here, I present our computational design Linbo Zhang tool CanDo (http://cando-dna-origami.org) that quantita- LSEC, Chinese Academy of Sciences LS14 Abstracts 87

[email protected] ticity on the swimming behavior of the microscopic alga Chlamydomonas reinhardtii and on the kinematics of its flagella. We find that the flagellar beating frequency and MS26 wave speed are both enhanced by fluid elasticity. Interest- Monte Carlo Solution of Biochemical Electrostatics ingly, the swimming speeds during the alga power and re- Problems covery strokes are enhanced by fluid elasticity for Deborah numbers larger than unity, De > 1. Despite such enhance- Electrostatic forces and the electrostatic properties of ments, however, the alga net forward speed is hindered by molecules in solution are among the most important is- fluid elasticity by as much as 30% compared to Newtonian sues in understanding the structure and function of large fluids of similar shear viscosities. We use slender body the- biomolecules. The use of implicit-solvent models, such as ory and Principal Component Analysis (PCA) to analyse the Poisson-Boltzmann equation (PBE), have been used ciliary waveforms and elucidate the role of fluid elasticity with great success as a way of computationally deriv- and viscous dissipation in regulating the kinematics of the ing electrostatics properties such molecules. We discuss swimming process. how to solve an elliptic system of partial differential equa- tions (PDEs) involving the Poisson and the PBEs using Arvind Gopinath path-integral based probabilistic, Feynman-Kac, represen- MIT tations. This leads to a Monte Carlo method for the so- Mechanical Engineering lution of this system which is specified with a stochastic [email protected] process, and a score function. We use several techniques to simplify the Monte Carlo method and the stochastic pro- Boyang Qin cess used in the simulation, such as the walk-on-spheres Mechanica Engineering and Applied Mechanics (WOS) algorithm, and an auxiliary sphere technique to University of Pennsylvania, Philadelphia. handle internal boundary conditions. We then specify some [email protected] optimizations using the error (bias) and variance to balance the CPU time. We show that our approach is as accurate as widely used deterministic codes, but has many desirable Jing Yang properties that these methods do not. In addition, the cur- Department of Physics and Astronomy rently optimized codes consume comparable CPU times to Haverford College, Haverford, PA 19041 the widely used deterministic codes. Thus, we have an [email protected] very clear example where a Monte Carlo calculation of a low-dimensional PDE is as fast or faster than deterministic Jerry P. Gollub techniques at similar accuracy levels. Haverford College Department of Physics Michael Mascagni [email protected] Computer Science/Computational Science Florida State University, Tallahassee Paulo E. Arratia [email protected] Mechanical Engineering and Applied Mechanics University of Pennsylvania, Philadelphia. [email protected] MS27 Near Wall Motion of a Model Swimmer in a Vis- coelastic Fluid MS27 Microorganisms interacting in viscoelastic fluids are ubiq- Finite Length Undulatory Swimmers: Whether to uitous in nature; this includes bacteria colonizing in vis- Kick or to Burrow in a Viscoelastic Fluid coelastic mucus in human and animal bodies, bacteria in biofilms grown on natural and manmade surfaces. Here We explore finite length undulatory swimmers in viscoelas- is this work, we perform a three-dimensional direct nu- tic fluids. The worm is modeled as an inextensible infinitely merical simulation of an archetypal low-Reynolds-number thin sheet in 2 dimensions and the swimming is driven us- swimmer, squirmer, near a surface and investigate the role ing a prescribed target curvature. We look at front-back of viscoelasticity of the background fluid on the swimming asymmetries in the prescribed stroke pattern and consider speed and trajectory of the swimmer near the surface. the effect on swimming speed and efficiency. The impor- tance of passive dynamics, where swimmers are given pre- Gaojin Li, Alireza Karimi scribed torques rather than prescribed shapes, is explored. University of Notre Dame We show that kickers can get a larger boost from viscoelas- [email protected], [email protected] ticity than burrowers.

Arezoo Ardekani Becca Thomases NotreDameUniversity University of California at Davis Department of Aerospace and Mechanical Engineering [email protected] [email protected] Robert D. Guy Mathematics Department MS27 University of California Davis Flagellar Kinematics in Complex Fluids: Viscous [email protected] and Elastic Effects

The motility behavior of microorganisms can be signifi- MS27 cantly affected by the rheology of their fluidic environment. Here, we experimentally investigate the effects of fluid elas- Lyme Disease and Microorganism Swimming in 88 LS14 Abstracts

Complex Fluids rently, we use a combined experimental and computational approach to investigate the effect of specific front leg sen- Lyme disease is caused by infection of the mammalian sors onto the middle leg CPGs to gain a deeper insight into host by the highly invasive spirochete, Borrelia burgdor- the inter-connection of the CPGs of all legs and into the feri. These bacteria easily invade and colonize the dermis, processing of inter-leg sensory signals. joints, connective tissue, heart, and central nervous sys- tem. The motility of this organism is, therefore, crucial to Silvia Daun-Gruhn the pathogenesis of the disease. I will describe experiments Emmy-Noether Research Group, Department of Animal that we have been doing to measure the biophysical param- Physiology eters of motility of these bacteria in realistic environments, Zoological Institute, University of Cologne such as matrices that mimic the ECM. These experiments [email protected] show a number of interesting behaviors that are not pre- dicted by recent theories of swimming in non-Newtonian Nils Rosjat, Tibor I. Toth environments. I will then describe the models and simu- Emmy-Noether Research Group lations that we have been sing to describe the motility of University of Cologne this fascinating organism in complex environments. Using [email protected], [email protected] our data, we have also developed a mathematical model to elucidate pathogen-host interactions during early Lyme disease, which explains the spatiotemporal dynamics of the MS28 characteristic first sign of the disease, a large (5 cm di- Multiple Rhythms from One Network: Phase ameter) rash, known as an erythema migrans (or EM). Plane and Stochastic Analyses of Rhythmic Activ- The model predicts that the bacterial replication and dis- ity in Turtle Motor Circuits semination rates are the primary factors controlling the speed that the rash spreads, whereas the rate that active We analyze a central pattern generators ability to produce macrophages are cleared from the dermis is the principle differing motor patterns from a single pool of neurons under determinant of rash morphology. In addition, the model different tonic drives, focusing on a particular motoneurons supports the clinical observations that antibiotic treatment response to different phasic synaptic inputs. We study the quickly clears spirochetes from the dermis and that the rash impact of these phasic inputs on motoneuron phase space, appearance is not indicative of the efficacy of the treat- associated trajectories and show how these yield sufficient ment. The quantitative agreement between our results and conditions for reproduction of observed rhythms. We also clinical data suggest that this model could be used to de- present preliminary results from stochastic analysis to ex- velop more efficient drug treatments and may form a basis amine the role of strong synaptic conductances. for modelling pathogen-host interactions in other emerging infectious diseases. Abigail Snyder University of Pittsburgh Charles Wolgemuth [email protected] University of Arizona Department of Physics [email protected] Jon Rubin University of Pittsburgh Department of Mathematics MS28 [email protected] Shilnikov Cornerstone Bifurcation Generates a Family of Mechanisms Governing Dynamics of MS28 Central Pattern Generators Dynamical Architectures for Control of Rhythmic The cornerstone Shilnikov bifurcation generates a family Behavior of mechanisms that determines temporal characteristics of endogenously bursting, spiking, and silent neurons. We How do rhythmic motor systems achieve both robustness to described a model of insect locomotion. The model gait perturbations and sensitivity to variable operating condi- is controlled by the burst duration and interburst interval tions? Do limit cycle (LC) oscillators and chain reflexes of protractor and retractor interneurons. The transition (CR) capture two extremes along a continuum of cen- from tetrapod to tripod gait is governed by the duty cycle tral pattern generation models? We investigate the con- of endogenously silent retractor interneurons, which fire in sequences of different dynamical architectures for incorpo- response to endogenously bursting protractor interneurons. rating sensory input in motor control, and quantitatively evaluate the advantages of intermediate architectures, such as stable heteroclinic channels, which combine features of William H. Barnett both LC and CR dynamics. Neuroscience Institute Georgia State University Peter J. Thomas, Hillel Chiel, Jeffrey Gill [email protected] Case Western Reserve University [email protected], [email protected], [email protected]

MS28 David Lyttle Using Experimental Phase Response Curves to University of Arizona Characterize Inter-Leg Coupling Program in Applied Mathematics [email protected] Walking movements result from a complex interplay of central pattern generating networks (CPGs), local sensory Kendrick Shaw feedback about movements and forces generated in the legs Case Western Reserve University and coordinating signals from neighboring limbs. Cur- Department of Biology LS14 Abstracts 89

[email protected] Clotting Factors

When a blood vessel ruptures, a hemostatic clot, consisting MS29 mainly of platelets and fibrin, is formed to restrict the loss Therapeutic Implications from a Multiscale Model of blood. Salutary blood clotting is highly regulated, but a of Blood Clot Degradation pathological clot (thrombus) may form within a vessel and restrict blood flow to organs or clot pieces (emboli) can de- tach and be carried to the lungs, causing a life-threatening We develop a multiscale model of blood clot degradation to complication called pulmonary embolism. Fibrin network study safer, more effective treatments for stroke patients. plays an important role in determining thrombus mechani- With a microscale model of a single fibrin fiber, we study cal properties. It is responsible for thrombus integrity and how individual activator and inhibitor molecules affect the redistribution of various mechanical loads acting on the degradation of the fiber. Data from this microscale model thrombus due to blood flow and vessel deformations. Ad- are used in a macroscale model of a full blood clot, where ditionally, the structure of the network affects movement of we study the effect of different treatment strategies on clot blood clotting factors through the clot. This study demon- degradation. strates that structural changes in fibrin networks exposed to external load strongly correlate with networks mechan- Brittany Bannish ics. It is also shown that permeability of the fibrin network Department of Mathematics and protein diffusivity are important factors determining University of Central Oklahoma the transport of blood proteins inside the thrombus. The [email protected] obtained results combining microfluidic experiments and thrombus hemodynamics model suggests that a fibrin net- Aaron L. Fogelson, James P. Keener work formed at early stages of thrombus initiation can pre- University of Utah vent normally asymptomatic thrombi from developing into [email protected], [email protected] pathological clots.

Oleg Kim MS29 University of Notre Dame A Model-Based Comparison of Clinical and Biolog- Dept of Applied and Computational Mathematics and ical Determinants for Anticoagulation Therapy Statistics [email protected] We combine temporal models of coagulation and fib- rinolytic pathways with warfarin pharmacokinetics and pharmacodynamics to study anticoagulation therapy. We MS29 compare two modeling frameworks to determine treat- Fibrin Polymerization in Flow: Gelation and Post ment efficacy: a traditional clinical assessment based on Gelation Dynamics a simulated prothrombin time test and a biological assess- ment influenced by platelet activation and simplified chem- Blood clots are composed of platelets and a gel of fibrin ical/cellular transport dynamics. We then discuss the roles fibers. The amount and structure of the fibrin fibers de- of these assessment methods in the development and suc- pend on conditions during their formation. In this pre- cess of individualized treatment strategies. sentation, I will discuss a 2-D advection-diffusion model for fibrin polymerization in flow that includes gelation Lisette G. dePillis and post gelation dynamics. Hindered diffusion and a Harvey Mudd College Brinkman resistance term dependent on fiber properties, [email protected] including branch point density and volume faction, supply feedback in the system. Erica J. Graham North Carolina State University Cheryl Zapata-Allegro Department of Mathematics North Carolina State University [email protected] [email protected]

Yanping Ma Loyola Marymount University MS30 [email protected] Recent Developments, Connections and Open Problems in Chemical Reaction Network Theory Ami Radunskaya Pomona College Mathematics Department I’ll give a brief overview of some recent developments in [email protected] chemical reaction network theory, namely the study of the structure-dynamics relationship for chemical reaction net- works (CRNs). The talk will outline the nature of conclu- Julie Simons sions which may be drawn about a CRN based primarily on Tulane University network structure, and some of the challenges remaining: Department of Mathematics these include theoretical challenges, but also questions re- [email protected] garding the implementation of theory as algorithms. I will also discuss some connections between claims for mass ac- tion kinetics and for more general kinetics. MS29 Structural Hierarchy Governs Nonlinear Mechan- Murad Banaji ics of Fibrin Networks and Transport of Blood University of Portsmouth 90 LS14 Abstracts

[email protected] Neither voltage data nor Calcium concentration data alone suffices to estimate properties of the model; two measure- ments are required. We show that both voltage and Ca MS30 measurements suffice or measurements based on the wave- Persistence and the Global Attractor Conjecture form of the time course of voltage will suffice. This has strong implications for experiment on neurons where both A positive trajectory of a dynamical system is called persis- types of dynamics are present. tent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the per- Henry D. Abarbanel sistence property is critical in deciding if a species in an Physics Depratment ecosystem will become extinct, an infection will die off, or Univ of California, San Diego a chemical species will be completely consumed by a re- [email protected] action network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the global attractor con- MS31 jecture, which says that a large class of mass-action systems Using Mathematical Models to Determine the (called complex balanced or toric dynamical systems) have Source of Heterogeneity in Cellular Calcium Dy- a global attractor within any invariant subspace. namics

Gheorghe Craciun Cell responses to stimuli are commonly heterogeneous. Department of Mathematics, University of We describe a model-based technique for determining the Wisconsin-Madison source of the heterogeneity in the calcium response of pi- [email protected] tuitary lactotrophs to a calcium-mobilizing agonist. This method samples specific parameters to produce various re- MS30 sponses, and then compares scatter plots of features of the response to features from experimental traces to determine Monotonicity of Chemical Reaction Networks with the likely sources of response variability. This technique is Respect to Non-Simplicial Cones applicable to any situation in which the heterogeneous bi- ological response is described by a mathematical model. The theory of monotone flows has been applied to numer- ous chemical reaction networks in recent years. A dynami- cal system is said to be monotone if states preserve a partial Richard Bertram ordering as they evolve with time. Monotonicity restricts Department of Mathematics the possible asymptotics of dynamical systems: stable pe- Florida State University riodic orbits cannot exist in a monotone dynamical system, [email protected] and it is frequently possible to draw stronger conclusions, such as generic convergence to equilibria. To date, most applications of the theory of monotone flows to chemical Maurizio Tomaiuolo reaction networks focus on networks that are either coop- University of Pennsylvania erative, or can be made cooperative by applying a simi- [email protected] larity transform to the state space. This talk will explore networks that cannot be made cooperative, yet are still Arturo Gonzalez-Iglesias monotone with respect to an ordering defined by a non- Department of Biological Science simplicial cone. The problem of identifying a suitable cone Florida State University for a given network will be discussed, along with the con- [email protected] sequences for the dynamics. Jo¨el Tabak Pete Donnell, Murad Banaji Florida State University University of Portsmouth [email protected] [email protected], [email protected] Henry D. Abarbanel MS30 Physics Depratment Univ of California, San Diego Sign Vectors in Chemical Reaction Network The- [email protected] ory

Abstract not available at time of publication. MS31 Stefan Mueller Heterogeneity As a Consequence of Homeostasis RICAM, Austrian Academy of Sciences [email protected] A fundamental question in neuroscience is how neurons develop, control, and maintain their electrical signaling properties in spite of ongoing protein turnover and activ- MS31 ity perturbations. I will introduce some recent modelling Estimating the Functional Connectivity in Net- work that has tied together experimental data with long- works of Neurons standing questions about the inherent variability of neu- ronal properties. Interestingly, the model predicts patho- We will discuss the role of chaotic interplay among voltage logical behavior that can arise as a consequence of home- gated neural dynamics and intracellular Calcium dynam- ostasis rather than a failure of it. ics. In particular we have analyzed the issues that arise in determining unknown parameters in the dynamical equa- Timothy O’Leary tions of such models when presented with observed data. Brandeis University LS14 Abstracts 91

[email protected] health department to prioritize and allocate limited public health resources. We are currently extending the analysis to include the clinical perspective. MS31 Inference of Network Structure from Spikes and Nargesalsadat Dorratoltaj Time Series Virginia Tech [email protected] We discuss recent usage of data assimilation techniques to track and infer structure from networks of excitable cells. Kaja Abbas We emphasize methods that are statistical in nature in Virginia Tech the sense of avoiding arbitrary thresholds, and that can be Department of Population Health Sciences applied in real time to deal with nonstationary systems. [email protected]

Timothy Sauer Department of Mathematical Sciences MS32 George Mason University Mathematical Modeling of Cholera [email protected] Cholera was one of the most feared diseases in the 19th century, and remains a serious public health concern to- MS32 day. It can be transmitted to humans directly by person- Contact and Transmission in Epidemiological Mod- to-person contact or indirectly through ingestion of con- els taminated water. Basic cholera models that include both direct and indirect transmission and assume homogeneous The mechanisms of contact leading to the transmission of mixing in the host population will be reviewed. Detailed pathogens from one host to another in a population shape models that incorporate spatial heterogeneity will be ap- the dynamics of an epidemic. Despite major modeling ef- plied to understand cholera transmission and to evaluate forts at the population level in epidemiology; the mech- disease control strategies. anisms of contact and transmission remain poorly under- stood and their modeling remain typically rooted in models Zhisheng Shuai describing mixing of particles in homogeneous baths. Here, University of Central Florida we discuss how a combination of theoretical and experi- [email protected] mental approaches can be used to start reformulating the fundamental definitions and formulations of contact and transmission between hosts in a population. MS32 Modeling Cholera in Heterogeneous Environments Lydia Bourouiba Massachusetts Institute of Technology We present some recent work in mathematical modeling of [email protected] cholera, a severe water-borne infectious disease. Particu- larly, we discuss the impacts of spatial heterogeneity and seasonal variation on the transmission dynamics of cholera, MS32 using both mathematical analysis and numerical simula- Economic Evaluation of the Fungal Meningitis Out- tion. Based on a deterministic modeling framework that break Response in New River Valley: Local Health involves systems of ODEs and PDEs, we establish results Department and Clinical Perspectives of disease extinction and persistence for each model, and compare the threshold dynamics in homogeneous and het- The objective of this study is to conduct an economic eval- erogeneous settings. uation of the fungal meningitis outbreak response in New River Valley of Virginia from the local public health de- Jin Wang partment and clinical perspectives. The multi-state fungal Old Dominion University meningitis outbreak started during September 2012 in Ten- [email protected] nessee. The immediate cause of the outbreak was injection of contaminated lots of methylprednisolone acetate used in epidural steroid injections. Roanoke and New River Valley MS33 were the epicenter of this outbreak in Virginia, with two Convergence Properties of Gauss-Newton Meth- clinical centers having administered the contaminated in- ods, Well-Posedness of Parameter Estimation jections to their patients. New River Health District and Problems and the Reliability of Parameter Esti- local hospitals deployed their resources to control the re- mates gional impact of the outbreak, starting in October 2012. Public health personnel, in collaboration with clinicians Parameter estimation from measurement data is crucial in local hospitals, followed up the exposed patients for 6 for model validation. After computing of the estimates months, and provided treatment including lab tests and the question arises about their reliability. It appears that hospitalizations. The health department continued the reliability of the estimates is connected to a convergence outbreak investigation until March 2013 to ascertain that rate of Gauss-Newton methods which present good local all possible cases were identified and treated. None of the convergence in so-called small residual problems. We show followed-up patients met the case definition, as defined by that bad performance of Gauss-Newton in large residual CDC. Based on preliminary analysis, the local health de- problems is an advantage rather than a disadvantage of partment expenditure is estimated to be $30,493 and 73.5 the method, since it indicates ill-posedness of problems. years of disability adjusted life years are averted among the patients, for an incremental cost-effectiveness ratio of Ekaterina Kostina $415 per disability adjusted life year averted. The esti- Fachbereich Mathematik und Informatik mated incremental cost effectiveness ratio assists the local Philipps-Universitaet Marburg 92 LS14 Abstracts

[email protected] arterial pressure (MAP) are varied. Model predictions sug- gest that oximetry data from patients are not sufficient for distinguishing between the factors that alter saturation MS33 levels, since nearly identical venous saturation levels are Parameter Estimation for Large-Scale Biological predicted for various combinations of MAP and IOP. Systems Julia Arciero As scientists continue to make discoveries in the biologi- Department of Mathematical Sciences cal sciences, the dynamical systems they are studying con- Indiana University-Purdue University Indianapolis tinue to grow in size and complexity. These increases [email protected] make model fitting and parameter estimation more diffi- cult. Hence, the effectiveness and efficiency of such tech- Giovanna Guidoboni niques are crucial. This presentation shares a new param- Indiana University-Purdue University at Indianapolis eter estimation technique designed to address some of the Department of Mathematical Sciences issues presented by large-scale biological systems by taking [email protected] advantage of the sparsity often present in such systems.

Justin Krueger Brent Siesky, Alon Harris Department of Mathematics Indiana University School of Medicine Virginia Tech [email protected], [email protected] [email protected] MS34 MS33 Computational Modeling of Oxygen and ATP Removing Irrelevant Parameters from Complex Bi- Transport in Skeletal Muscle Capillary Networks ological Models of Normal and Pre-Diabetic Rats

Parameter inference in biological sytems often results in In skeletal muscle, capillaries are responsible for delivering estimates with huge uncertainties. I discuss how these ir- oxygen and are involved in regulating the oxygen supply relevant parameter combinations can be systematically re- to meet tissue needs. A key mechanism in this regula- moved to reveal relevant combinations that govern the col- tion is oxygen-dependent release by red blood cells of the lective system behavior and can be accurately inferred from signaling molecule ATP, leading to changes in upstream data. Using an information geometric approach, I recast arteriolar resistance and hence blood flow. We present an the model reduction problem as a manifold approximation experiment-based model of oxygen and ATP transport in problem. The coarse-grained models vividly illustrate the 3D capillary networks showing how oxygen delivery and emergent control mechanisms (e.g. feedback loops) that RBC ATP-based regulation are disturbed in pre-diabetes. govern the system’s behavior. Daniel Goldman Mark K. Transtrum University of Western Ontario Department of Physics and Astronomy Department of Medical Biophysics Brigham Young University [email protected] [email protected] MS34 MS33 Green’s Function Methods for Simulating Solute Beyond Acceptable Parameter Fits Transport in the Microcirculation

Biological time series contain enormous, but hidden in- Delivery of oxygen and other solutes to tissue is an es- formation that needs to be extracted with computational sential function of the microcirculation, and is critically means. This extraction is difficult, due to noise, large dependent on the spatial arrangement of microvessels. For numbers of parameters, and computational issues. Fur- numerical simulations involving realistic three-dimensional thermore, the typical criterion of squared residual errors vascular network geometries, Greens function methods is often insufficient, especially if the best-suited functional are more computationally efficient than finite-difference or forms for describing the biological system are not known. finite-element methods, and are also advantageous with re- The structural uncertainty complicates any estimation, but gard to the imposition of appropriate boundary conditions. can be ameliorated if the right types of time series data are Steady-state and time-dependent formulations will be pre- available. sented and applications to several tissue types will be dis- cussed. Eberhard O. Voit Georgia Institute of Technology Timothy W. Secomb [email protected] University of Arizona [email protected]

MS34 Effect of Intraocular Pressure and Arterial Blood MS35 Pressure on Oxygen Saturation Levels in the Nonlinear Poisson-Nernst-Planck Equations for Retina: a Theoretical Model Ion Flux Through Confined Geometries

Impaired oxygen delivery to the retina has been shown to The mathematical modelling and simulation of ion trans- contribute to the retinal cell death characteristic of glau- port trough biological and synthetic channels is a challeng- coma. A mathematical model is used to predict retinal ing problem since at least two major effects have to be oxygen saturation as intraocular pressure (IOP) and mean taken into account: the electrostatic interaction of ions and LS14 Abstracts 93

the effects due to size exclusion in narrow regions. We in- [email protected] vestigate an important modification of the Poisson-Nernst- Planck (PNP) equations due to size exclusion, which is de- rived from a self-consisted random walk. Next we discuss MS35 the stationary solutions as well as the computation of con- Fast Pseudo-Time Simulations of the Nonlinear ductance. The need of incorporating nonlinear mobilities Poisson-Boltzmann (NPB) Equation in high density situations is demonstrated in an investiga- tion of conductance as a function of bath concentrations, Recently, we have developed a pseudo-time approach for which does not lead to obvious saturation effects in the solving the NPB equation. In the operator splitting frame- case of linear mobility. work, an analytical integration is conducted to suppress the nonlinear instability, and central differences are designed Marie-Therese Wolfram for both sharp and diffused molecular surfaces. Various Department of Mathematics, University of Vienna time splitting schemes that reduce 3D linear systems into [email protected] 1D ones, such as ADI, LOD, and AOS, have been examined for unconditional stability, accuracy, and efficiency so that a fast NPB solver can be built for biomolecular simulations of large proteins. MS35 New Effective Finite Element Algorithms for Solv- Shan Zhao ing Local and Nonlocal Poisson-Boltzmann Equa- Department of Mathematics tions for Biomolecules in Ionic Solvent University of Alabama [email protected] Calculation of electrostatic potential energy for biomolecule (such as protein and DNA) in ionic sol- MS36 vent is a fundamental task in computational biology. To reflect the polarization correlations among water Swimming Through Heterogeneous Networks molecules, nonlocal dielectric models were studied in the I will present results for swimmers moving near similar- last thirty years, but only limited to the case of pure size microstructural heterogeneities. First, spherical ob- water solvent due to modeling and algorithmic difficulties. structions are used to deduce physical principles linking We recently overcome such difficulties and proposed a the swimmer flow field, forces on obstructions, and changes new nonlocal dielectric model for protein in ionic solvent, in swimming velocities. Then single rod-like obstructions together with a fast finite element solver and an effective are studied which are similar to the filaments of networks. program package. In this talk, I will give these new Using these results, we deduce the effect of a network of fil- progresses a short review. Specifically, a new nonlocal aments. Notably, swimming properties such as the variance and nonlinear Poisson-Boltzmann Equation (PBE) model of the swimming speed reflect the density and orientation will be discussed in details. Since our nonlocal PBE correlations of the microstructure, and hence swimming model includes the classic local PBE model as a special properties can be used as probes of microstructure. case, our new finite element program package works efficiently and effectively not only for our nonlocal PBE Henry Fu model but also for the local PBE model. This project University of Nevada, Reno is a joined work with Prof. L. Ridgway Scott at the Dept. Mechanical Engineering University of Chicago under the support by NSF grants [email protected] (DMS-0921004, DMS-1226259, and DMS-1226019) and the UWM Research Growth Initiative. MS36 Dexuan Xie An Active Polar Nematic Model of Department of Mathematical Sciences Microtubule/motor-Protein Assemblies University of Wisconsin-Milwaukee [email protected] We develop a multiscale theory for a class of “bioactive’ materials consisting of microtubules and motor-proteins. Brownian dynamics simulations are used to study micro- MS35 scopic organization and identifies two sources of active destabilizing stress: polarity-sorting and crosslink relax- Fluctuation and Fidelity Control of Single Tran- ation. A Doi-Onsager theory captures polarity sorting, and scriptional Machine the hydrodynamic flows generated by active stresses. In simulating experiments of active flows on immersed sur- Polymerases catalyze gene replication and transcription. faces, the model exhibits turbulent-like flows and genera- We investigated how polymerases achieve high fidelity ef- tion and annihilation of disclination defects. ficiently by stepwise nucleotide selection. We noticed that early selections outperform the late ones in error reduction, Tony Gao while initial screening seems indispensable for maintain- Courant Institute of Mathematical Sciences ing speed. We studied T7 RNA polymerase in atomistic New York University simulations, and found that substantial nucleotide selec- [email protected] tion happens prior to full insertion of the nucleotide for Watson-Crick base pairing. Our studies provide a kinetic Michael J. Shelley framework along with molecular mechanisms. New York University Courant Inst of Math Sciences Jin Yu [email protected] Beijing Computational Science Research Center, China Robert Blackwell, Matthew Glaser, Meredith Betterton 94 LS14 Abstracts

University of Colorado will provide biological examples of oscillations generated [email protected], by such linear inward currents. The stabilizing role that [email protected], mered- hyperpolarization-activated inward currents may play will [email protected] also be discussed.

Jorge Golowasch MS36 Dept of math sciences at NJIT and An Immersed Boundary Method for Two-fluid Dept of biological sciences at Rutgers-Newark Mixtures [email protected]

We present an Immersed Boundary method for interactions between elastic boundaries and mixtures of two fluids. A MS37 penalty method is used to enforce the condition that both Robustness and Multifunctionality of Reduced fluids’ velocities agree with that of the elastic boundaries. CPG Models The method is applied to several problems: Taylor’s swim- ming sheet problem for a mixture of two viscous fluids, CPGs stably produce bursting patterns underling vital peristaltic pumping of a mixture of two viscous fluids, with rhythmic behaviors. We developed analytical and com- and without immersed particles, and peristaltic pumping putational tools reducing the problem of robustness and of a mixture of a viscous fluid and a viscoelastic fluid. Nu- existence of rhythmic patterns to analysis of attractors in merical results demonstrate that the method converges and return maps for phase lags between bursters. We identify show its capability to handle a number of flow problems of organizing centers determining CPG outputs and analyze substantial current interest. their bifurcations as network circuitry varies. We study sustainability of networks by revealing statistics of rhythms Robert D. Guy switching due to random perturbations. Our findings are Mathematics Department applicable for most oscillatory networks. University of California Davis [email protected] Aaron Kelley GSU Jian Du [email protected] Department of Mathematics Florida Institute of Technology Justus T. Schwabedal jdu@fit.edu Division of Sleep Medicine, Brigham & Women’s Hospital Harvard Medical School Aaron L. Fogelson [email protected] University of Utah [email protected] Andrey Shilnikov Neuroscience Institute and Department of Mathematics Georgia State University MS36 [email protected] Computational Models of Cilia and Flagella in a Brinkman Fluid MS37 The interaction between dynamic elastic structures and Differential Effects of Conductances on Pyloric their surrounding fluid is important for sperm navigation CPG Output and cilia beating within airways. We study a generalized Euler elastica immersed in a Brinkman fluid, a viscous fluid Central pattern generators are neuronal circuits that con- filled with a network of proteins. Regularized Greens func- trol rhythmic activities such as breathing and chewing. tions for Brinkman flow are used to investigate emergent The output of such circuits can be characterized with rel- dynamics with preferred kinematics. Results are presented ative ease, making them good candidates for studying reg- for swimming speeds, synchronization, and efficiency of ulation of neuronal activity at the network and single-cell flagella with planar waveforms in a Brinkman fluid. levels. Our recent work characterizes the effect of specific conductances on the activity of the pacemaker kernel in the Karin Leiderman pyloric circuit of the crustacean stomatogastric ganglion Applied Mathematics through a series of computational and electrophysiological UC Merced studies. [email protected] Wafa Soofi Sarah D. Olson Georgia Institute of Technology and Emory University Worcester Polytechnic Institute wsoofi@gmail.com [email protected] MS37 MS37 Identifying and Explaining Three Time Scale Os- Linear Currents Can Be Pacemaker Currents cillations

Regenerative currents necessary for production of oscilla- CPGs may exhibit behavior, including bursting, involving tory activity are inward voltage-gated currents. I will show multiple distinct time scales. Our goal is to understand that voltage-dependence is not required. A linear current bursting dynamics in three-time-scale systems, motivated with negative conductance plus a voltage-gated recovery by a model from respiratory CPG neuron. Using geometric current are sufficient. We will discuss conditions that these singular perturbation theory, we explain the mechanisms currents need to satisfy for oscillations to be produced, and underlying some forms of bursting dynamics in a three- LS14 Abstracts 95

time-scale model. To elucidate which characteristics truly mon goal: Improving the health and well being of patients. represent three-time-scale features, we investigate certain This talk will discuss opportunities within the developmen- reductions to two time scales and the parameter depen- tal pipeline where significant contributions can be made dence of solution features in the three-time-scale frame- by classically trained mathematicians. We will address work. the unique challenges that pharmaceutical companies face within a highly regulated world and specific areas of great- Yangyang Wang est need. Novel and symbiotic research opportunities await University of Pittsburgh those with the tools and vision for exploration in this in- [email protected] terface where a systems approach to pharmacology is in- creasingly necessary. Jon Rubin University of Pittsburgh Angelean O. Hendrix Department of Mathematics North Carolina State University [email protected] [email protected]

Vivien Kirk, Pingyu Nan University of Auckland MS39 [email protected], [email protected] Elimination of Intermediate Species in the Stochas- tic Reaction Networks MS38 Translational Modeling and Optimal Concurrent Biochemical reactions often proceed through the forma- Treatment in Oncology tion of intermediate species. These species are transient species, such as the substrate-enzyme complex appearing Neutropenia caused by the indiscriminate nature of anti- in Michaelis-Menten kinetics. For the sake of simplicity cancer drugs is a dose-limiting consequence of chemother- the intermediates are often ignored in the description of a apy which necessitates treatment adaptation. To avoid reaction network, especially when they happen to be more therapy interruption, granulocyte colony-stimulating fac- unstable than the other species and they are degraded at a tor (G-CSF) is administered during chemotherapy. This fast rate. It is not clear, however, whether this simplifica- talk will outline the development of physiologically-based tion can have consequences on the reliability of the model. mathematical models of myelopoiesis in conjunction with We focus on stochastically modeled reaction networks and pharmacokinetic and pharmacodynamic models of zalypsis provide a rigorous asymptotic result for the elimination of and filgrastim, and address their use in the optimisation of the eventual intermediate species from the model. In our chemotherapeutic regimens with G-CSF. settings the intermediate species can only appear alone and with unitary stoichiometric coefficient in any reaction in- Morgan Craig volving them. We define a suitable reduced system and we Facult´edePharmacie prove that the complete system tends to the reduced one in Universit´edeMontr´eal finite dimensional distribution when the rates of consump- [email protected] tion of the intermediate species tend to zero. Further we show that our reduced system coincide with one obtained Anthony Humphries before in the deterministic settings, where the the num- McGill University ber of equilibrium points were studied. Moreover, we ex- [email protected] tend our results to the situation when the non-intermediate species are described by a single scaled system. We only Jacques B´elair add the assumption that the rates of the intermediate con- Universit´edeMontr´eal sumption tend to infinity fast enough compared to the rates D´epartement de Math´ematiques of their production. [email protected] Daniele Cappelletti,CarstenWiuf Jun Li University of Copenhagen Unievrsit´edeMontr´eal [email protected], [email protected] [email protected]

Michael Mackey MS39 McGill University, Canada Perturbations of the Lotka-Volterra System [email protected] We explore certain large perturbations of the Lotka- Fahima Nekka Volterra system, and show that they retain persistence, and Universit´edeMontr´eal, Facult´edePharmacie even periodicity. This is an exploration of how persistence Centre de Recherches Math´ematiques is affected by a reaction network not being endotactic. [email protected] Manoj Gopalkrishnan MS38 Tata Institute of Fundamental Research Systems Pharmacology: Revolutionizing Health Mumbai, India Care One Equation at a Time [email protected]

Similar challenges and questions arise in both the mathe- Gheorghe Craciun matical and pharmaceutical sciences. Unfortunately, dif- Department of Mathematics, University of ferences in culture and approach sometime blur our com- Wisconsin-Madison 96 LS14 Abstracts

[email protected] Component Allee Effects

We investigate the evolutionary outcomes of a single MS39 species prey population subject to component Allee effects Bistability in the Dual Futile Cyle within the framework of a continuous strategy evolutionary game theory (EGT) model. Our model assumes a single The idea has been around for some years that trait creates a phenotypic trade-off between carrying capac- the system consisting of two successive phosphoryla- ity and predator evasion ability following a Gaussian distri- tion/dephosphorylation loops exhibits bistability and on bution. This assumption contributes to one of our interest- the level of heuristic and numerical investigations this can ing findings that evolution prevents extinction even when be seen as well-established. After surveying the existing the population is subject to strong Allee effects. However, results I will present a purely analytical proof (obtained to- the extinction equilibrium can be an ESS under some spe- gether with Juliette Hell) that there exist parameter values cial distributions of anti-predation phenotypes. The ratio for which this system has two stable stationary solutions. of variation in competition and anti-predation phenotypes The methods used are bifurcation theory and geometric play an important role in determining the global dynamics singular perturbation theory. I will then go on to discuss of our EGT model: (a) evolution may suppress strong Allee possible generalizations to a larger number of loops and effects for large values of this ratio; (b) evolution may pre- to more complicated systems such as those modelling the serve strong Allee effects for small values of this ratio; and MAP kinase cascade. (c) intermediate values of this ratio can result in multiple ESSs. Alan Rendall Johannes Gutenberg-Universit¨at Mainz Yun Kang [email protected] Applied Sciences and Mathematics, Arizona State [email protected]

MS39 MS40 Reaction-Diffusion Equations With Periodic Be- havior An Application of Optimal Control Theory to a Simple Age-of-Infection Sir Model We consider the Lotka-Volterra model and the Ivanova re- action. The ODE equations have explicit periodic solutions Abstract not available at time of publication. and equilibrium points. With equal diffusion rates, we give Sunmi Lee conditions for a solution to converge to a spatially homo- Department of Applied Mathematics geneous periodic solution. Yongin, Kyung Hee University, South Korea. David Siegel [email protected] University of Waterloo Department of Applied Math MS41 [email protected] Form-Function Relationship in E. coli Chemotaxis Blair Davey Cell-to-cell variations in protein abundance in clonal cell University of Minnesota populations are ubiquitous in living systems. Because pro- [email protected] tein composition determines responses in individual cells, it stands to reason that the variations themselves are subject to selective pressures. However, the functional role of these MS40 cell-to-cell differences is not well understood. One way to On a Diffusive Predator-prey Model with Nonlin- tackle questions regarding relationships between form and ear Harvesting function is to perturb the form (e.g., change the protein abundances) and observe the resulting changes in some In this talk, we study the dynamics of a diffusive Leslie- function. We take on the form-function relationship from Gower model with a nonlinear harvesting term on the prey. the inverse perspective, asking instead what specific con- We analyze the existence of positive equilibria and their straints on cell-to-cell variations in protein abundance are dynamical behaviors. In particular, we consider the model imposed by a given functional phenotype [1]. We develop with a weak harvesting term and find the conditions for a maximum entropy based approach to posing questions the local and global asymptotic stability of the interior of this type and illustrate the method by application to equilibrium. The global stability is established by consid- the well-characterized chemotactic response in Escherichia ering a proper Lyapunov function. In contrast, the model coli. We find that full determination of observed cell-to-cell with strong harvesting term has two interior equilibriums variations in protein abundances is not inherent in chemo- and bistability may occur for this system. We also give taxis itself but, in fact, appears to be jointly imposed by the conditions of Turing instability and perform a series the chemotaxis program in conjunction with other factors of numerical simulations and find that the model exhibits (e.g., the protein synthesis machinery and/or additional complex patterns. non-chemotactic cell functions, such as cell metabolism). These results illustrate the power of maximum entropy as Peng Feng a tool for the investigation of relationships between biolog- Florida Gulf Coast University ical form and function. [1] Sayak Mukherjee, Sang-Cheol [email protected] Seok, Veronica J. Vieland, and Jayajit Das, Proceedings of National Academy of Sciences 110 18531 (2013).

MS40 Jayajit Das Evolutionary Dynamics of a Population Model with Ohio State University LS14 Abstracts 97

[email protected] inference regarding motor velocity in the one-sample case, and (2) can significantly reduce power in the two-sample case. These results should be of interest to experimentalists MS41 who wish to engineer motors possessing specific functional From Single Molecule Experiments to Coupled characteristics. Molecules John Hughes Molecular motors convert chemical energy, often stored in University of Minnesota the form of ATP, into mechanical energy, a vital activity [email protected] for living cells. In particular, kinesin and dynein are two molecular motors that convey cargo, such as vesicles and organelles, along microtubules to where they are needed MS41 in the cell. This is especially important in neurons which Superresolution Microscopy As a Quantitative Tool canbeuptoameterinlengthandwhereabreakdownin motor function has been implicated as a factor in neurode- Protein-protein interaction is the basis for all of commu- generative diseases. Since the early 1990’s, experimental- nication and information transfer in biology. Nonetheless, ists have been manipulating single motor molecules in vitro protein complexes –the basic interaction subunit– are dif- using laser traps. This has allowed detailed mechanical in- ficult to image in living cells because of their size (tens of formation to be gathered from isolated motors, at least nm). Superresolution imaging methods are now commonly in these non-physiological experimental conditions. In liv- used to generate high resolution images of biological fea- ing cells, however, a single motor does not move a single tures about 10-100nm in size. We describe a strategy for cargo. Multiple motors, possibly both kinesin and dynein turning superresolution imaging data into a quantitative each biased towards opposite directions, are attached to tool to enumerate proteins in a complex. a single cargo transporting it along the microtubule. A number of questions arise. How do different motors with Steve Presse opposing biases transport the cargo? How are cargos trans- Indiana University Purdue University Indianapolis ported to the appropriate locations within the cells? Are [email protected] there important regulatory proteins which affect this trans- port process? In this talk, we will discuss data emerging from these multi-motor/single cargo experiments and how MS42 information from single molecule experiments can be in- A Computational Method for Nearly Singular In- corporated into the multi-motor analysis. In addition, we tegrals will discuss how these experiments can inform us about the underlying mechanisms which drive this multi-motor trans- We will describe a realtively simple method for computing port phenomena using a combination of stochastic models singular or nearly singular integrals on a closed curve in and statistical inference. 2D or a closed surface in 3D. This method can be used for Stokes flow, e.g., if values of velocity and pressure are John Fricks needed at regular grid points. In work with Anita Layton, Dept of Statistics we have used this approach for a moving elastic interface Pennsylvania State University in 2D Stokes flow. We have also devised a second-order [email protected] accurate method for Navier-Stokes flow coupled with an interface, in which the velocity is decomposed into a Stokes velocity and a more regular part. The advantage is that MS41 the interaction of the interface with Stokes flow is much Estimating Velocity for Processive Motor Proteins simpler to deal with than the full Navier-Stokes equations. with Random Detachment Partially implicit motion of the interface can be used in either case to improve the time step. Processive motor proteins are ATP-powered biological nanomachines that drive many forms of movement in living J. Thomas Beale organisms. For example, kinesin and cytoplasmic dynein Duke University motors transport payloads, such as organelles or vesicles, [email protected] through the cytoplasm of eukaryotic cells. The existence of eukaryotic organisms depends on these tiny motors because the passive process of diffusion is not sufficient to trans- MS42 port large and/or massive payloads through the crowded A Treecode-Accelerated Boundary Integral Pois- cytoplasm in a timely fashion. A motor protein overcomes sonBoltzmann Solver for Electrostatics of Solvated these difficulties by hydrolyzing ATP in order to tow a Biomolecules cargo rapidly and in a directed path along a suitable sub- strate. An understanding of these motors could lead to im- We present a treecode-accelerated boundary integral portant biomedical applications, e.g., anti-tumor technolo- (TABI) solver for electrostatics of solvated biomolecules gies; treatments for neurodegenerative diseases; devices for described by the linear Poisson-Boltzmann equation. The blood testing and genetic screening; and treatments for dis- method employs a well-conditioned boundary integral for- eases caused by motor protein defects. We show that, for a mulation for the electrostatic potential and its normal wide range of models, the empirical velocity of processive derivative on the molecular surface.. The surface is trian- motor proteins has a limiting Pearson type VII distribu- gulated and the integral equations are discretized by cen- tion with finite mean but infinite variance. We develop troid collocation. The linear system is solved by GMRES maximum likelihood inference for this Pearson type VII iteration and the matrix-vector product is carried out by distribution. In two simulation studies, we compare the a Cartesian treecode which reduces the cost from O(N 2) performance of our MLE with the performance of stan- to O(N log N), where N is the number of faces in the tri- dard Students t-based inference. The studies show that angulation. We find that the TABI solver exhibits good incorrectly assuming normality (1) can lead to imprecise serial and parallel performance combined with relatively 98 LS14 Abstracts

simple implementation, efficient memory usage, and geo- tation developed to handle large macromolecules. metric adaptability. Randy Zauhar Weihua Geng Department of Chemistry & Bioc Southern Methodist University University of the Sciences in Philadelphia [email protected] [email protected]

Robert Krasny MS43 University of Michigan Department of Mathematics Physiological Modeling in Hypertension and Heart [email protected] Failure In this talk, we present the application of a fluid mechanics MS42 model in drug development. The model is a cardiovascu- lar circulation model which has enabled decisions on com- On a Parallel Adaptive Fast Multipole Poisson- pounds in development. The circulation model integrates Boltzmann Solver systemic, pulmonary and cardiac function, and is fit for the purpose of assessing questions arising in heart failure and In this talk, I will present the mathematical analysis, hypertension drug development. In this presentation, we numerical algorithms, and parallel implementation de- provide a description of the circulation model, and demon- tails of the Adaptive Fast Multipole Poisson-Boltzmann strate its utility through some examples. (AFMPB) solver. The package is available under open source license agreement. Karim Azer Applied Computer Science and Mathematics Dept. Bo Zhang Merck & Co., Inc. Duke University Karim [email protected] [email protected]

Xiaolin Cheng MS43 Oak Ridge National Laboratory A Coupled Model of the Left Ventricle and the Sys- [email protected] temic Arteries

Jingfang Huang A three-dimensional finite-strain model of a human left Department of Mathematics ventricle is coupled with a one-dimensional physiologically- University of North Carolina, Chapel Hill based structured-tree model of the systemic arteries by [email protected] matching the pressure and flow rate at the aortic root. The governing equations, which also incorporate fluid- structure interaction and active contraction of the my- Benzhuo Lu ocardium, are solved using a combined immersed-boundary Institute of Computational Mathematics, China finite-element method, and a Lax–Wendroff scheme. The [email protected] effects of changes in vascular compliance and rarefaction on blood pressure and flow are studied. J Andrew McCammon University of California in San Diego Nicholas A. Hill Department of Chemistry and Biochemistry Department of Mathematics [email protected] University of Glasgow, UK [email protected] Nikos Pitsianis Department of Electrical & Computer Engineering Weiwei Chen, Hao Gao Aristotle University School of Mathematics and Statistics [email protected] University of Glasgow [email protected], [email protected] Xiaobai Sun Department of Computer Science Boyce Griffith Duke University Leon H. Charney Division of Cardiology [email protected] NYU Medical School [email protected]

MS42 Xiaoyu Luo Surface-Tension Molecular Surfaces for Deploy- School of Mathematics and Statistics ment in Boundary Element Electrostatic Calcula- University of Glasgow tions [email protected]

Molecular surface generators that define the surface by a rolling probe inevitably produce regions with cusps and MS43 points, and are not suitable for BEM applications. The Comparison of Inflow Boundary Conditions for SMART algorithm was developed in our laboratory to Ventriculo-Arterial Coupling in 3D and 1D Fluid- avoid these issues with a guaranteed continuous surface Structure Interaction Models normal. As an alternative to the rolling-probe approach, we have begun to explore physics-based surfaces whose re- Each cardiac cycle the heart contracts and ejects blood sults will be discussed, along with a new BEM implemen- into the systemic circulation. Coupled via the aortic LS14 Abstracts 99

root, cardiac output into the systemic circulation is gov- five REM bouts which become longer as the night pro- erned by both ventricular contractility and haemody- gresses. This model is motivated by one presented by namic impedance of the systemic vasculature. Following previous authors and is constructed using known neuronal a reduced-order coupling approach, a 0D model of cardiac groups involved with sleep and wake. contraction was implemented in 3D and 1D fluid-structure interaction frameworks. Using such models permits the Selenne Garcia-Torres examination of pressure wave propagation under altered University of Southern California physiological states of the heart. Department of Mathematics [email protected] Kevin D. Lau, Jordi Alastruey, C. Alberto Figueroa Department of Biomedical Engineering Janet Best Kings College London The Ohio State University [email protected], [email protected], al- Department of Mathematics berto.fi[email protected] [email protected]

Gemma Huguet MS43 Centre de Recerca Matematica Pulsatile Flow in the Entire Coronary Arterial Tree [email protected] The hemodynamic analysis, based on the experimental measurements, plays an important role in the study of coro- Alicia Prieto Langarica nary circulation given millions of blood vessels in the vas- Youngstown State University culature. Here, I will show a mathematical model of pul- [email protected] satile blood flow in the entire coronary arterial tree that is reconstructed from the measured morphometric data. The Shelby Wilson pathological states (i.e., left ventricular hypotrophy and Morehouse College congestive heart failure) are studied in relation to changes [email protected] in model parameters and tree structures. Pamela B. Fuller Huo Yunlong Rensselaer Polytechnic Institute Department of Mechanics and Engineering Science [email protected] Peking University, China [email protected] MS44 Spiking Neuron Vs. Neural Mass Models in the MS44 Context of Sleep-Regulatory Circuits Modeling Interindividual Differences in Sponta- neous Internal Desynchrony Patterns Neural populations can be abstracted in different ways. Neural mass models assign macroscopic state variables to Using a physiological model of a sleep-wake regulatory each neural population, whereas spiking neuron models network, we investigated the transition from typical hu- simulate the dynamics of individual neurons. Both types man sleep patterns to spontaneous internal desynchrony. of models are widely used, but it is not always clear under The model describes the neurotransmitter-mediated inter- what conditions the two agree when it comes to predicting actions among neuronal populations that promote wake, dynamics of real physiological systems. Here, we consider REM sleep and non-REM sleep, and the circadian pace- this problem in the context of sleep-regulatory circuits. maker in the SCN. Model analysis suggests that similar mechanisms underlie different desynchronized behaviors, Andrew Phillips and that synchronization of sleep and circadian rhythms Brigham & Womens Hospital, Harvard Medical School may depend on SCN modulation of REM sleep-promoting [email protected] centers. Victoria Booth Victoria Booth University of Michigan University of Michigan Depts of Mathematics and Anesthesiology Depts of Mathematics and Anesthesiology [email protected] [email protected] Elizabeth B. Klerman Cecilia Diniz Behn Brigham and Women’s Hospital & Harvard Medical Gettysburg College School Dept of Mathematics [email protected] [email protected]

MS44 MS44 Modeling the Effects of Temperature on Sleep Pat- AMathematicalModeloftheterns Wake/NonREM/REM States Several studies have been done on human patients that We propose a mathematical model for REM/NonREM dy- suggest that different temperatures, such as room temper- namics with sleep/wake cycling that illustrates several fea- ature, core body temperature, and distal skin temperature, tures observed in humans during sleep. These include first have an important effect on sleep patterns, such as length falling into the NonREM stage, oscillating between it and and frequency of REM cycles. A mathematical model is the REM stage during the sleep period, and having four or created to investigate the effects of temperature on the 100 LS14 Abstracts

REM/NonREM dynamics. Our model was based on previ- [email protected] ous well established and accepted models of sleep dynamics and thermoregulation models. Jasmine Nirody New York Medical College, NY Alicia Prieto Langarica [email protected] The University of Texas at Arlington [email protected] George Oster Molecular and Cellular Biology Janet Best University of California, Berkeley The Ohio State University [email protected] Department of Mathematics [email protected] MS45 Gemma Huguet Decoding Information in Cell Shape Centre de Recerca Matematica [email protected] Shape is an indicator of cell health. But how is the in- formation in shape decoded? We hypothesize that decod- Selenne Garcia-Torres ing occurs by modulation of signaling through changes in University of Southern California plasma membrane curvature. Using analytical approaches Department of Mathematics and numerical simulations, we studied how elongation of [email protected] cell shape affects plasma membrane signaling. Mathemat- ical analyses reveal transient accumulation of activated re- Shelby Wilson ceptors at regions of higher curvature with increasing cell Morehouse College eccentricity. In this talk, I will discuss the applicability of [email protected] reaction-diffusion formulations in understanding the role of cell shape. Pamela B. Fuller Rensselaer Polytechnic Institute Padmini Rangamani [email protected] University of California, Berkeley Department of Molecular and Cell Biology [email protected] MS45 Disentangling Protein Fitness Requirements Using Computational Mutagenesis MS45 Conserved Enhancer Function When Sequence Is Although methods in comparative sequence analysis can Not Conserved: Adventures with Cis-Regulatory measure conservation within a protein family, purely Logic sequence-based methods cannot elucidate the reasons un- derlying conservation. To deconvolve the multiple roles of The blastoderm stage of Drosophila development affords amino acids in protein fitness, we have adapted compu- unique advantages for the study of transcriptional control. tational protein design algorithms for efficient large-scale The embryo can be used as a microarray in which the re- mutagenesis, and compare this to alternative in silico mod- sponse of reporters to transcription factors can be quanti- eling approaches. Our method is applied to a G-protein tatively monitored at cellular resolution. With this data, heterotrimer, and provides insight on amino-acid involve- we have constructed quantitative and predictive models ment in structural stability, and ligand- or protein-binding of transcriptional control that shed light on the apparent interactions. paradox that conserved gene expression can be driven by highly diverged regulatory sequence. Loretta Au Department of Applied Mathematics & Statistics John Reinitz Stony Brook University Statistics Dept, Dept. of Ecology & Evolution [email protected] The University of Chicago [email protected] MS45 A Mechanistic Model of the Bacterial Flagellar Mo- MS46 tor From Within-Host to Between-Host Dynamics. The bacterial flagellar motor (BFM) drives swimming in Systems Biology of Epidemiology many bacterial species. Using structural information from recent experiments, we propose a mechanism for the BFMs This talk explores an alternate mechanistic formulation of conversion of transmembrane ion potential into torque. We epidemiological dynamics based upon studying the influ- also address how the motor reverses the torque direction, ence of within-host dynamics in environmental transmis- allowing bacteria to reorient during chemotaxis. Addi- sion. A basic propagation number is calculated from the tionally, we suggest a ”mechanical homology” between the host-pathogen interaction; such quantification takes into BFM and the only other known protein motor driven by a account antigenic diversity and antigenic variation, and transmembrane ion potential: the Fo motor of ATP syn- could guide public health policy. thase. Juan B. Gutierrez Kranthi Mandadapu University of Georgia University of California, Berkeley Department of Mathematics LS14 Abstracts 101

[email protected] population and the disease dynamics. Using a mathemati- cal model, I will highlight how the lifestyle of the Anopheles mosquito and the interaction between the mosquito and hu- MS46 mans affect malaria transmission dynamics and introduce Modeling Drug Resistance in Metastatic Cancers complexities not previously observed in unforced continu- ous time models. Implications for disease control will also The development of drug resistance is a major challenge be discussed. in the treatment of cancer. In this talk we will overview our recent results on studying the role of cell density and Miranda I. Teboh-Ewungkem mutations on the dynamics of drug resistance in metastatic Lafayette College cancers. This is a joint work with Jim Greene, Orit Lavi, [email protected] and Michael Gottesman.

Doron Levy MS47 University of Maryland A New Mathematical Model for Hepatitis C Infec- [email protected] tion: Derivation, Analysis and Implications

The hepatitis C virus was first identified in 1989 and MS46 mathematical models for HCV infection followed within The Impact of Decay in BedNet Efficacy over Time a decade. Since then, many models have been proposed. on Malaria Transmission Biological knowledge regarding HCV has also progressed recently and we use this to derive a new model of HCV Insecticide-treated nets (ITNs) are at the forefront of infection. We analyse the steady states and bifurcations in malaria control programs. The potential impact of ITNs this model and show how the solutions differ from those of on reducing malaria transmission is limited due to incon- other models. We then consider the implications for HCV sistent or improper use, as well as decay in effectiveness. treatment. We develop a mathematical model for malaria spread that captures the decrease in ITN effectiveness. We perform un- Philip J. Aston certainty and sensitivity analyses to identify and rank pa- University of Surrey rameters that play a critical role in malaria transmission. Department of Mathematics These analyses show that the basic reproduction number [email protected] R0, and the infectious human population are most sensi- tive to bed-net coverage and the biting rate of mosquitoes. We consider the case in which ITN efficacy is constant over MS47 time as well as the case in which ITN efficacy decays over Mathematical Modeling of Malignant Brain Tumor time. with T11 Target Structure As a Potent Immune Stimulator. Jemal Mohammed-Awel Valdosta State University T11 Target structure, a membrane glycoprotein isolated [email protected] from sheep erythrocytes, reverses the immune suppressed state of brain tumor induced animals by boosting the func- Calistus Ngonghalaa tional status of the immune cells. This study aims at aid- National Institute for Mathematical and Biological ing in the design of more efficacious brain tumor therapies Synthesis with T11 target structure as a potent immune stimula- [email protected] tor. We propose a mathematical model for brain tumor (glioma) and the immune system (microglial cells, cyto- Sara Del Val toxic T lymphocytes, TGF-β,IFN-γ) interactions, which Energy and Infrastructure Analysis, Los Alamos National aims in designing efficacious brain tumor therapy. The sys- Lab tem undergoes sensitivity analysis, that determines which [email protected] state variables are sensitive to the given parameters and the parameters are estimated from the published data. Com- Ruijun Zhao puter simulations were used for model verification, which Minnesota State University, Mankato highlight the importance of T11 target structure in brain [email protected] tumor therapy. Sandip Banerjee MS46 Indian Institute of Technology Roorkee (IITR) Vector Dynamics and Its Impact on the Vector [email protected] Borne Disease-Malaria

Mathematical models have extended our understanding of MS47 the biology and transmission dynamics of the vector borne Parameter Subset Selection and Generalized Sen- disease malaria, dating back to the models of Sir Ronald sitivities for a Model of Erythropoiesis Ross and George Macdonald. However, most models ei- ther treat the mosquito population density as a constant We present a model for erythropoiesis involving structured or do not model the reproductive gains that accrue to the population models for the various cell stages involved. mosquito’s population as a result of its lifestyle, feeding and Since the model involves around 30 parameters and only reproductive habits, as well as its interaction with the hu- limited data are available, it is necessary to investigate man population. The interaction between mosquitoes and which parameters can be estimated with reasonable ac- humans introduce high variability in the mosquito popula- curacy and how the collection of data can be improved tion density and this variability affects both the mosquito within the given limitations. We show how recently devel- 102 LS14 Abstracts

oped methods for parameter subset selection and general- analysis suggests that membrane bending helps to expose ized sensitivity analysis can be applied. charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to Franz Kappel identify membrane distortions that minimize the insertion Department of Mathematics and Scientific Computing of charged TM peptides into the membrane. Here, we ex- University of Graz tend our work to consider the energetics of ion and small [email protected] peptide penetration into the membrane as well as large protein complexes. First, we show that our continuum method accurately reproduces energy profiles and mem- MS47 brane shapes generated from molecular simulations of bare Deconvolution of Isotope Signals Mixed from Sam- ion permeation at a fraction of the computational cost. pling Bundles of Multiple Hairs Importantly, we find that the energetics of membrane de- formation strongly depend on membrane patch size both Hair records temporal information of body chemical sig- for ions and peptides. Finally, we present experimental nals, including stable isotopes. Multiple hairs are typically and theoretical analysis that suggests that the antibacterial combined into a bundle to obtain enough material for anal- protein RegIIIa, a C-type lectin, forms channel like com- ysis by segmentation. We developed a mathematical model plexes that disrupt cellular homeostasis by inserting into to describe signal averaging from combining multiple hairs membranes containing anionic lipids. We believe that our for analysis and an inverse method to estimate the original work presents a novel, computationally efficient method to signal from measurements. The inverse method provides a simulate the effects of small molecules, peptides and large refined interpretation of an oxygen stable isotope chronol- complexes with the membrane. ogy from hair of an unidentified murder victim. Michael Grabe Christopher Remien Department of Pharmaceutical Chemistry National Institute for Mathematical and Biological University of California, San Francisco Synthesis [email protected] University of Tennessee [email protected] MS48 Frederick Adler On Minimizers of the Bending Energy of Two- University of Utah Phase Biomembranes Mathematics Department & Biology Department [email protected] We consider the problem to find the shape of multiphase biomembranes, modeled as closed surfaces enclosing a fixed Lesley Chesson, Luciano Valenzuela, James Ehleringer, volume and having fixed surface area. The surface energy is Thure Cerling assumed to be the sum of two terms: the Canham-Helfrich Department of Biology energy, in which the bending rigidities and spontaneous University of Utah curvatures depend on the phase, and a line tension penal- [email protected], [email protected], ization for the phases interface. By restricting attention to [email protected], [email protected] axisymmetric surfaces and phase distributions, we prove existence of a global minimizer. This is a joint work with Rustum Choksi (McGill University, Montreal) and Marco MS48 Morandotti (Instituto Superior Tecnico, Lisbona). Competitive Geometric Evolution of Lipid Bilayers Marco Veneroni and Pores Department of Mathematics We discuss the competitive geometric evolution of co- University of Pavia existing complex structures in amphiphilic mixtures, mod- [email protected] eled by the functionalized Cahn-Hilliard (FCH) equation. The system supports lipid bilayers, filamentous pores, mi- Rustum Choksi celles, and complex network structures. We analyze the ge- Department of Mathematics ometric evolution laws of bilayers and pores, respectively, McGill University the mechanism under which they compete, and the possi- [email protected] bility of co-existence. Marco Morandotti Shibin Dai Carnegie Mellon University New Mexico State University [email protected] [email protected]

Keith Promislow MS48 Michigan State University Periodic Migration in a Physical Model of Cells on [email protected] Micropatterns

We extend a model for the morphology and dynamics of MS48 a crawling eukaryotic cell to describe cells on micropat- Continuum Models of Membrane Protein Insertion terned substrates. This model couples cell morphology, ad- and Stability hesion, and cytoskeletal flow in response to active stresses induced by actin and myosin. We propose that protrusive Experimental and computational studies have shown that stresses are only generated where the cell adheres, leading cellular membranes deform to stabilize the inclusion of to the cell’s effective confinement to the pattern. Consis- transmembrane (TM) proteins harboring charge. Recent tent with experimental results, simulated cells exhibit a LS14 Abstracts 103

broad range of behaviors, including steady motion, turn- [email protected], [email protected] ing, bipedal motion, and periodic migration, in which the cell crawls persistently in one direction before reversing periodically. We show that periodic motion emerges natu- MS49 rally from the coupling of cell polarization to cell shape by The Topological Structure of the Mitochondrial reducing the model to a simplified one-dimensional form Dna from Trypanosomes that can be understood analytically. Additionally, we will discuss a turning instability arising from our model apply- Trypanosomatid parasites are the cause of disease and ing onto a free moving cell without interaction with the death in many third world countries. One of the most micropatterned substrates. Some attempts have made to unusual features of these organisms is the 3 dimensional test how the instability depends on the parameters in the organization of their mitochondrial DNA into maxi and model numerically. For a much simplified model, we do minicircles. Here we investigate the effects of the confine- find that surface tension is a key factor to stabilize the cell ment on the topology of the network using a simplified turning. model where randomly oriented minicircles are placed on the plane with their centers on the vertices of the simple Yanxiang Zhao square lattice. Department of Mathematics University of California, San Diego Yuanan Diao [email protected] Department of Mathematics and Statistics University of North Carolina at Charlotte [email protected] MS49

Topological Tools for Detecting Hidden Geometric MS49 Structure in Neural Data Modeling Dna Packing with Confined Equilateral Random Polygons Experimental neuroscience is undergoing a period of rapid progress in the collection of neural activity and connec- We introduce and study a model of equilateral random tivity data. This promises to allow more direct testing of polygons confined in a sphere. DNA packed in a virus head a variety of theoretical ideas, and thus advance our un- motivates this model. The difference between the biolog- derstanding of ”how the brain works.” Detecting meaning- ically observed topological characteristics and benchmark ful structure in neural data, however, remains a signifi- data created by our model reveals the bias of DNA packed cant challenge. A major obstacle is that these data often in the viral capsids and possibly lead to a better under- measure quantities that are related to more ”fundamental” standing of the DNA packing mechanism. variables by an unknown nonlinear transformation. This transformation obscures the underlying structure, dimin- Claus Ernst ishing the power of traditional linear algebra-flavored tools. Department of Mathematics Methods from computational topology, however, are often Western Kentucky University capable of detecting the hidden structure. We adapt these [email protected] methods for the analysis of correlation matrices, and illus- trate their use for testing the ”coding space” hypothesis on neural data. MS50 Build-Up and Neural Competition in a Model of Carina Curto Auditory Streaming Department of Mathematics University of Nebraska-Lincoln A two-population rate model is built to study the percep- [email protected] tual organization of tones in the auditory cortex. When repetitive sequences of tones alternating between two fre- quencies are presented, the system’s dynamics switches be- MS49 tween two distinct states: (1) a coherent, galloping-like sin- Topological Distances on DNA Knots and Links gle stream (”integration”), and (2) two separate streams of constant pitch tones (”segregation”). The model accounts Topoisomerases and recombinases are two classes of pro- for the dynamics observed for such stimuli, in single unit teins which can knot circular DNA. Type II topoisomerases recordings in monkey primary auditory cortex. The under- are proteins which cut one double-stranded DNA segment, lying mechanism for the build-up of the stream segregation allowing a second DNA segment to pass through before is also investigated. resealing the break. This is mathematically modeled by changing a crossing. Recombinases break two segments Rodica Curtu of DNA, exchanging the DNA ends before resealing the University of Iowa breaks. This action can be mathematically modeled by Department of Mathematics smoothing a crossing. Distances between knots have been [email protected] defined based upon the minimum number of times these proteins must act to convert one knot into another knot. John M. Rinzel Methods for calculating these distances will be discussed. Courant Institute and Center for Neural Science Applications and ways to visualize and analyze these dis- New York University tances via graphs and KnotPlot will be discussed. [email protected]

Isabel Darcy, Annette Honken Department of Mathematics MS50 University of Iowa Modelling the Emergence and Dynamics of Percep- 104 LS14 Abstracts

tual Organisation in Auditory Streaming implications of our findings.

Auditory perception solves the problem of associating Elizabeth M. Cherry,RyanThompson causes with sound events by switching between alterna- Rochester Institute of Technology tive solutions. I present a model of auditory scene anal- School of Mathematical Sciences ysis at the core of which is a process that seeks to dis- [email protected], [email protected] cover predictable patterns in the ongoing sound sequence. Representations are created on the fly, and maintained, strengthened or weakened depending on predictive success MS51 and conflict with other representations. Auditory percep- Experimentally-based Modified Cable Equation tual organisation emerges spontaneously through the com- That Reproduces Alternans Measured in Cardiac petition between these representations. Tissue

Sue Denham We incorporate a data-based model to regulate gap junc- Plymouth University, UK tion conductance by transjunction potentials into the cable [email protected] equation. This modification results in a dynamic decrease of gap-junction conductance during the action potential (AP) plateau, which lowers coupling at high membrane po- MS50 tentials without altering AP restitution dynamics and con- Bistable Auditory Perception: Neural Competition duction velocities. Inclusion of a voltage-dependent gap- with Periodic Input junction conductance in the cable equation allows spatial alternans to develop in realistic tissue sizes without altering Spontaneous switches in perception occur for auditory other predictions from the cable equation. stimuli where high A and low B tones are repeated in ABA- sequences [van Noorden 1975, Pressnitzer and Hup´e 2006]. Flavio Fenton,YanyanJi We extend a classical neural competition model to include Georgia Institute of Technology periodic onset-like inputs and capture the parametric or- fl[email protected], [email protected] ganisation of percepts reported in the psychoacoustics lit- erature. We use the model to carry out a comparison study between bistability in auditory perception and other sen- MS51 sory modalities. Effects of Intracellular Sodium Accumulation on Cardiac Reentry Dynamics James Rankin,JohnRinzel New York University The morphology and duration of cardiac action potentials [email protected], [email protected] is controlled partly by ionic currents that depend on intra- cellular sodium concentration. We demonstrate how the dynamics of cardiac reentry vary with intracellular sodium MS50 accumulation and how this plays a special role in simulated Diagnosing Excitation-inhibition Balance using chronic atrial fibrillation. Psychophysics Trine Krogh-Madsen Excitation-inhibition imbalance is a potential cause of men- Cornell University - Weill Medical College tal illness such as Autism. It is useful to understand how [email protected] such a perturbation may be manifested in psychophysical tests, such as perceptual rivalry. Here, I will discuss recent Margo Smith experimental and theoretical work that makes this connec- Cornell University - Weill Medical College Division of tion explicit. Cardi [email protected] Shashaank Vattikuti National Institutes of Health, NIDDK David Christini [email protected] Cornell University - Weill Medical College Division of Cardiology Carson C. Chow [email protected] Laboratory of Biological Modeling NIDDK, NIH [email protected] MS51 The Role of Feedback and Heart Rate Variability on Cardiac Rhythm Stability MS51 Delay-Differential Equations in Cardiac Electro- Cardiac dynamics is usually analyzed under the assump- physiology Models tion of periodic stimulation, i.e. in the presence of feed- back. However, under physiological conditions, the heart In the heart, period-2 behavior of electrical responses, re- rate exhibits substantial variations in time, known as heart ferred to as alternans, often gives rise to more compli- rate variability (HRV), which introduces deviations from cated arrhythmias. To date, alternans has been gener- periodic stimulation. We incorporated HRV into pacing ated mathematically from coupled nonlinear ODE/PDE protocols, both with and without feedback, and investi- systems. We use the fact that delays arise naturally in non- gated the role of HRV and feedback on rhythm stability instantaneous cellular processes to suggest an alternative using numerical simulations of an ionic model of the car- approach using delay-differential equations (DDEs), which diac action potential. are known to promote complex dynamics. We analyze the dynamical behaviors of our DDE system and discuss the Elena Tolkacheva LS14 Abstracts 105

Department of Biomedical Engineering [email protected] University of Minnesota [email protected] MS53 Stephen McIntyre Mathematical Model of Community-Acquired and University of Minnesota Hospital-Acquired Methicillin-Resistant Staphylo- [email protected] coccus Aureus Transmission in Hospital Settings

Yoichiro Mori In this paper a deterministic model to quantifying the School of Mathematics interactions of community-acquired and hospital-acquired University of Minnesota methicillin-resistant staphylococcus aureus transmission in [email protected] a hospital settings is developed. The model include envi- ronmental contaminants and isolation of colonized and in- fected patients. The reproduction number is determined MS52 and sensitivity analysis is carried out to determine the im- Stochastic Dynamics in Signal Transduction, Stem pact of model parameters to various outputs. The results Cells, and Development Patterning of the stochastic version of the deterministic model is dis- cussed. Abstract not available at time of publication. Folashade Agusto Qing Nie Austin Peay State University University of California at Irvine [email protected] [email protected]

MS53 MS52 Optimizing Vaccine Allocation for Influenza Mathematical Models for Stem Cell Interactions The emergence of the 2009 H1N1 influenza A strain and Abstract not available at time of publication. delays in production of vaccine against it illustrate the im- portance of optimizing vaccine allocation. We have de- Jianjun Paul Tian veloped computational optimization models to determine Mathematics Department optimal vaccination strategies with regard to multiple ob- College of William and Mary jective functions: e.g. deaths, years of life lost, economic [email protected] costs. Looking at single objectives, we have found that vac- cinating children, who transmit most, is robustly selected as the optimal allocation. I will discuss ongoing extensions MS52 to this work to incorporate multiple objectives and uncer- Computation of Transition State and Its Applica- tainty. tions in System Biology Jan Medlock Abstract not available at time of publication. Oregon State University [email protected] Lei Zhang Department of Math University of California, Irvine, MS53 [email protected] Malaria Vaccine Efficacy in a Region with Natu- rally Acquired Immunity MS52 The advent of malaria vaccines raises the question of how Numerical Studies on Cell Lineage Models effective vaccination will be in regions with naturally ac- quired immunity (NAI). Our malaria model incorporat- Multistage cell lineages, typically comprising of a stem cell ing vaccination and NAI suggests that disproportionately stage and several subsequent progenitor cell stages (also treating non-immune individuals increases the likelihood referred to as transit-amplifying or TA cells), underlie the of subthreshold endemic equilibria, a dangerous scenario production of different terminally differentiated (TD) cell that increases the risk for malaria epidemics and renders types within a tissue. Genetic studies and tissue culture vaccination ineffective. Additionally, optimal control the- experiments have shown that control of stem and progen- ory suggests that efforts to vaccinate should increase as the itor cell proliferation and differentiation, which ultimately level of NAI in a population decreases. control the TD cell number, is mediated by secreted mor- phogens through feedback regulation. In this talk, I shall Olivia Prosper present our recent work on using numerical simulations of Dartmouth College advection-reaction-diffusion model to study the formation [email protected] and regeneration of intestinal crypts, which is based on our early model on tissue stratification patterning of the olfactory epithelium of the mouse. This is a joint work Nick Ruktanonchai with Tian Jiang (University of Notre Dame), Lei Zhang University of Florida (Peking University), and Qing Nie (University of Califor- Department of Biology nia, Irvine). [email protected]

Yongtao Zhang Maia Martcheva University of Notre Dame University of Florida 106 LS14 Abstracts

maia@ufl.edu model of coupled within-host model of ODEs and between- host model of ODE and PDE. Existence and uniqueness of solution to the between-host model is established, and an MS53 explicit expression for the basic reproduction number of A Two-Patch Avian Influenza Model the between-host model is derived. Stability of disease- free and endemic equilibria of the between-host model Abstract not available at time of publication. is investigated. An optimal control problem with drug- treatment control on the within-host system is formulated Omar Saucedo and analyzed. Numerical simulations based on the forward- University of Florida backward sweep method are obtained. Department of Mathematics osaucedo1987@ufl.edu Eric Numfor University of Tennessee [email protected] MS54 Optimizing Hiv Treatment In a Resource Limited Settings MS54 Antiretroviral drugs have a clinical benefit of substantially Inferring Equation Models from Agent-Based reducing infectiousness thus making them potentially an Model Data important strategy in the fight against AIDS. Recent ad- vances in drug therapy have seen the use of antiretroviral Abstract not available at time of publication. medications as a prophylaxis. In this study, we constructed a compartmental heterosexual transmission model based Matthew Oremland on the dynamics of HIV in heterosexual population in Sub- Virginia Tech University Sahara. The model classifies the male and female popula- [email protected] tions by risk (low, medium and high) according to their sexual preferences. Data from South Africa was used to parameterize the model. For a finite amount of drugs we MS55 implemented a numerical optimization algorithm to find Numerical Simulations of Fluctuating Vesicles in optimal allocation of the drugs that minimizes objective Linear Flow functions such as Total Number of Deaths and Total Num- ber of Infections. Preliminary results suggest that, the pri- In this talk, we present the fluctuation dynamics of a 2D ority should be given to the high-risk females during drug vesicle in extensional flow. In the quasi-circular limit, we allocations to minimize the number of deaths or infection derive a Langevin type SDEs. We then simulate a vesi- per year cle dynamics using an immersed boundary method, and achieve good agreement with the theoretical predictions Gordon Akudibillah,JanMedlock for the equilibrium deformation correlations. Preliminary Oregon State University results show that thermal noise can change the character- [email protected], istic wavelength of the wrinkles, and prevent the rotation [email protected] of a tilted vesicle in extensional flow.

Shuwang Li,KaiLiu MS54 Department of Applied Mathematics The Impact of Spatial Arrangements on Interven- Illinois Institute of Technology tion Strategies in Epidemic Models [email protected], [email protected]

The role of spatial arrangements in a metapopulation on the spread and optimal intervention strategies of a cholera MS55 epidemic is investigated. We consider how human and Electromechanics of Bilayer Membrane: Forces and pathogen movement affects the optimal vaccination strat- Fast Algorithms egy. For each patch, the model has an SIR system of dif- ferential equations coupled with an equation modeling the Lipid bilayers appear ubiquitously in living systems. Defin- concentration of Vibrio cholerae in an aquatic reservoir. ing and computing the forces on lipid membranes is critical The model will be used to compare two basic spatial ar- to understanding how these systems operate. In this talk, rangements of populations along a water source. The work the electrostatic potential energy for membrane-protein in- is motivated by the recent cholera outbreak in Haiti. Op- teractions is defined and used to compute the dielectric timal control results are found numerically. boundary force via the shape derivative. We then describe Michael Kelly a fast algorithm for minimizing the electromechanical en- University of Tennessee - Knoxville ergy of vesicles using a spherical harmonic parameteriza- [email protected] tion of the membrane surface. We conclude with examples and numerical results.

MS54 Michael Mikucki Department of Mathematics Optimal Control and Analysis of a Coupled Colorado State University Ode/pde Immuno-Epidemiological Model [email protected] Optimal control can be used to design intervention strate- gies for the management of infectious diseases, and has been applied in immunological and epidemiological mod- MS55 els separately. We formulate an immuno-epidemiological Three Dimensional Vesicle Electrohydrodynamics: LS14 Abstracts 107

A Numerical Investigation within knotted open chains, closed chains, and proteins. This is joint work with Ken Millett, Andrzej Stasiak, and The dynamics of three-dimensional vesicles when exposed Joanna Sulkowska. to electric fields is complex. There is a nonlinear relation- ship between the material parameters and the shape of Eric Rawdon the vesicle. This talk will present a numerical method de- Department of Mathematics veloped to investigate the electrohydrodynamics of three- University of St. Thomas dimensional vesicles is presented. This represents a first [email protected] step towards modeling the electroporation of vesicles in a general, fully three-dimensional framework. Here, the nu- merical method will be outlined and an investigation of MS56 vesicle dynamics will be shown. Unlinking of Supercoiled DNA Catenanes by Type David Salac IIA Topoisomerases University at Buffalo - SUNY davidsal@buffalo.edu It was found recently that DNA catenanes, formed dur- ing replication of circular plasmids, become positively (+) supercoiled, and the unlinking of such catenanes by type Ebrahim M. Kolahdouz IIA topoisomerases proceeds much more efficiently than SUNY Buffalo the unlinking of negatively (-) supercoiled catenanes. In mkolahdo@buffalo.edu an attempt to explain this striking finding we studied, by computer simulation, conformational properties of super- MS55 coiled DNA catenanes. Although the simulation showed that conformational properties of (+) and (-) supercoiled A Continuum Model for Simulating Bilipid Mem- replication catenanes are very different, these properties brane Deformation During Vesicle Drying per se do not give any advantage to (+) supercoiled over Bilipid membranes are of interest due to their similar dy- (-) supercoiled DNA catenanes for unlinking. An advan- namics to certain cells under flow and the ability to man- tage became evident, however, when we took into account ufacture them in a lab. Modeled as a homogeneous, con- the established features of the enzymatic reaction catalyzed tinuum material, the deformation of a vesicle undergoing by the topoisomerases. The enzymes create a sharp DNA drying is studied. The level set method is modified to ex- bend in the first bound DNA segment and allow for the plicitly capture the curvature in order to avoid stability transport of the second segment only from inside the bend issues when calculating curvature derivatives. The results to its outside. We showed that in (-) supercoiled DNA cate- will guide lyopreservation approaches, where cell drying is nanes this protein-bound bent segment becomes nearly in- used as a storage technique. accessible for segments of the other linked DNA molecule, inhibiting the unlinking. Chris Vogl Department of Applied Mathematics, University of Alexander Vologodskii Washington Department of Chemistry [email protected] [email protected]

MS56 MS56 Flexibility-Rigidity Index for Protein Flexibility Invariant Manifold and Persistent Homology for Analysis Biomolecules.

We introduce a simple method, flexibility-rigidity index We introduce molecular nonlinear dynamics (MND) as a (FRI), to analyze macromolecular flexibility and rigidity in theoretical framework for describing protein folding. We atomic detail. The FRI measures the topological connec- unveil the existence of intrinsically low dimensional mani- tivity of protein atoms or residues and characterizes the ge- folds (ILDMs) in the chaotic dynamics of folded proteins. ometric compactness of the protein structure. The FRI by- We reveal that the transition from disordered to ordered passes matrix diagonalization, which underpins most other conformations in protein folding increases the transverse flexibility analysis methods and FRIs computational com- stability of the ILDM, which yields some the best quan- plexity is of O(N2) at most, where N is the number of tification of protein uncertainty or protein thermal factors. atoms, in contrast to O(N3) for Hamiltonian based meth- Persistent homology is employed to characterize protein ods. folding pathways and protein flexibility. The predicted cut- off distance is highly consistent with the numerical results Kristopher Opron from our ILDM model and other state-of-art methods. Department of Biochemistry and Molecular Biology Michigan State University Guo-Wei Wei [email protected] Department of Mathematics Michigan State University [email protected] MS56 Knotting in Open Chains, Closed Chains, and Pro- Kelin Xia teins Department of Mathematics Michigan State University Some proteins are now classified as being knotted. How- [email protected] ever, proteins have free ends and knotting, mathematically, is only defined for closed curves. Defining knotting in open chains (like proteins) is tricky and ambiguous. We show MS57 one definition of open knotting and search for knotted arcs Fluid-Composite Structure Interaction in Hemody- 108 LS14 Abstracts

namics Tunicates

The speaker will talk about modeling and simulation of Tubular hearts of tunicates have a stiff, outer pericardium FSI between an incomprensible, viscous fluid and a com- that encloses a layer of myocardium which contracts to posite structure. Examples include FSI between blood flow drive fluid flow through the tube. Most models of heart and arterial walls, which are composed of several layers, function have not included the pericardium or its possi- each with different mechanical characteristics, and FSI be- ble contributions to the fluid flow produced by myocar- tween blood flow, arterial walls, and vascular devices called dial contractions. Here I present both experimental and stents. A stable loosely coupled scheme will be introduced, model evidence that the pericardium fulfills an important and numerical results, showing novel features of this class mechanical role in the tunicate hearts ability to produce of FSI problem, will be discussed. fluid flow through the circulatory system.

Suncica Canic Lindsay Waldrop Department of Mathematics University of North Carolina at Chapel Hill University of Houston [email protected] [email protected]

Martina Bukac MS58 University of Pittsburgh Integration of Information over Multiple Department of Mathematics Timescales in a Large-scale Model of the Cortex [email protected] Models of the neural mechanisms of decision-making typ- Boris Muha ically focus on local circuits operating within a single Department of Mathematics, Faculty of Science functionally-defined cortical area. To move beyond this, University of Zagreb we study the dynamics of distributed decision-making in an [email protected] anatomically-constrained model of multiple interacting ar- eas in the macaque cortex. The anatomical constraints pro- duce a hierarchical architecture where cortical areas are op- MS57 timized to integrate information over different timescales. We investigate how such dynamical heterogeneity can be Transport in the Embryonic Lung II combined to allow flexible decision-making.

Numerous studies have led to the identification of genes Rishidev Chaudhuri, Jorge F. Mejias, Xiao-Jing Wang and morphogens that play important roles in lung branch- New York University ing morphogenesis. However the mechanism by which [email protected], [email protected], these signaling molecules regulate lung branching is not [email protected] fully understood. It is also known that physical processes such as transport of morphogens could drive biological re- sponses during development. Thus, in this study, we uti- MS58 lize a computational model to investigate the role of solute Network Symmetry and Binocular Rivalry Exper- transport in lung morphogenesis. iments

Uduak Z. George This talk discusses a generalized network model for ri- University of Wisconsin valry proposed by Hugh Wilson. The application shows [email protected] how symmetry-breaking Hopf bifurcation can lead to rigid phase-shift synchrony in periodic solutions of coupled sys- Kishore Krishna Bokka, Sharon Lubkin tems of differential equations that in turn can predict per- North Carolina State University cepts in a variety of binocular rivalry experiments. [email protected], [email protected] Martin Golubitsky Ohio State University MS57 Mathematical Biosciences Institute Transport in the Embryonic Lung I [email protected]

Airway peristalsis (AP) begins as soon as the smooth mus- Casey Diekman cle forms, and persists until birth. We analyze a model Department of Mathematical Sciences of the fluid-structure interactions between embryonic tis- New Jersey Institute of Technology sues and lumen fluid resulting from peristaltic waves that [email protected] partially occlude the airway. We conclude that AP has a strong effect on flow sensing away from the tip and on transport of morphogens. These effects may be the in- MS58 termediate mechanisms for the enhancement of branching Noise and Adaptation in Multistable Perception: seen in occluded embryonic lungs. A Case Study with Tristable Visual Plaids

Kishore Krishna Bokka, Sharon Lubkin We study the dynamics of perceptual switching in ambigu- North Carolina State University ous visual scenes that admit more than two interpretations [email protected], [email protected] to gain insight into the dynamics of perceptual multistabil- ity and their underlying neural mechanisms. We focus on a classical paradigmatic stimulus, the visual plaids, consist- MS57 ing of two superimposed drifting gratings with transpar- Role of the Pericardium in the Tubular Hearts of ent intersections. For visual plaids, tristable perception is LS14 Abstracts 109

experienced: one coherent percept (the gratings move to- propagation and breakup of electrical waves, a data- gether as a single pattern) and two transparent percepts assimilation system is coupled to a simple model of car- (the gratings slide across one another) with alternating diac electrical dynamics. Data assimilation is a technique– depth order. In order to decipher the complex mechanisms common in numerical weather prediction–for combining of tristable perception, we gathered a large amount of psy- observations with a numerical model to derive an improved chophysical data on tristable plaids and developed a firing- estimate of the state of a dynamical system. Here an en- rate model based on mutual inhibition and adaptation that semble Kalman filter is used on synthetic data for both 1D involves stochastic dynamics of multiple-attractor systems. and 3D models. The model can account for the dynamical properties (tran- sition probabilities, distributions of percept durations, etc) Matthew J. Hoffman, Stephen Scorse observed in the experiments. Noise and adaptation have Rochester Institute of Technology been shown to both play a role in the dynamics of bistable [email protected], [email protected] perception. Here, tristable perception allows us to specify the role of noise and adaptation in our model. Noise is Elizabeth M. Cherry critical when considering the time of a switch. However, Rochester Institute of Technology adaptation mechanisms are critical when considering per- School of Mathematical Sciences ceptual choice (in tristable perception, each time a percept [email protected] ends, there is a possible choice between two new percepts).

MS59 Gemma Huguet Microscale Modeling of Cardiac Tissue Centre de Recerca Matematica [email protected] Focal activity in localized regions of cardiac tissue with poor, heterogeneous gap junction coupling can lead to long John M. Rinzel conduction delays, isolated wavefront breakthrough sites, Courant Institute and Center for Neural Science and reentry as the wavefront propagates into healthy sur- New York University rounding tissue. In this study we use two-dimensional, [email protected] microstructural computer models of ventricular monolay- ers (1 cm x 1 cm) to investigate the effect of modulating Jean-Michel Hup´e sodium and calcium currents on the formation of break- Toulouse University & CNRS through sites and the development of sustained reentry. [email protected] Letitia Hubbard Duke University MS58 [email protected] Networks That Learn the Timing of Event Se- quences Craig Henriquez Dept of Biomedical Engineering We discuss a neuronal network model capable of learning Duke University the timing of a sequence of events, each of which lasts mil- [email protected] liseconds to seconds. Short term facilitation is a second- timescale accumulation process that controls switching be- tween events. Long term plasticity allows the network to MS59 learn event timings quickly and accurately. Time scale sep- Predicting Arrhythmias with a Nonlinear Cardiac arations, between the plasticity processes and neuronal ac- Fiber Model tivity dynamics, allow us to describe how long term plas- ticity parameters should depend upon short term facilita- A dynamical model of a cardiac fiber was developed to help tion parameters for the network to be able to learn any investigate the relationship between premature beats and sequence of timings. ventricular fibrillation (VF), a lethal cardiac arrhythmia. When tested with canine ventricular data, the model was Alan Veliz-Cuba shown to predict which patterns of premature beats were University of Houston more likely to produce VF in vitro. In addition, model- Rice University predicted spatial changes in action potential duration were [email protected] positively correlated with the observed values.

Kresimir Josic Laura Munoz University of Houston Rochester Institute of Technology Department of Mathematics School of Mathematical Sciences [email protected] [email protected]

Zachary Kilpatrick Niels Otani University of Houston Rochester Institute of Technology [email protected] [email protected]

Anna Gelzer MS59 Department of Biomedical Sciences Intramural Forecasting of Cardiac Electrical Dy- Cornell University namics Using Data Assimilation [email protected]

As a first step in reconstructing the three-dimensional Flavio M. Fenton 110 LS14 Abstracts

Georgia Institute of Technology sider the effect of adding in a delay to the production of fl[email protected] signal molecules and analyze the resulting Hopf bifurca- tion. Weiye Lin, Min Chul Shin Department of Biomedical Sciences David Iron Cornell University Dalhousie University, Canada [email protected], [email protected] [email protected]

Robert Gilmour, Jr. MS60 University of Prince Edward Island Time to Mutation Acquisition in Stem Cell Driven [email protected] Cancers

Abstract not available at time of publication. MS59 Compositionality Results for Cardiac Cell Dynam- Alexandra Jilkine ics University of Notre Dame [email protected] We show that the 13-variable Markovian sodium-channel component of the 67-variable Iyer Mazhari Winslow cardiac cell model can be replaced by an approximately equivalent MS60 2-variable Hodgkin-Huxley-type abstraction. This substi- Mathematical Modeling of Proliferation Kinetics of tution of (approximately) equals for equals is safe in the Cancer Stem Cells sense that the approximation error between the sodium channel models does not get amplified by the feedback-loop Abstract not available at time of publication. context in which the components are placed. The proof entails automatic computation of Lyapunov-like functions Xinfeng Liu that characterize input-to-output stability of dynamical University of South Carolina systems. xfl[email protected]

Md. Ariful Islam, Abhishek Murthy Computer Science MS61 Stony Brook University Detailed Viral Kinetics During Liver Transplanta- [email protected], tion Indicates that the Liver Plays a Role in HCV [email protected] Clearance

Antoine Girard While the liver is widely accepted as the main site for Universit´e Joseph Fourier hepatitis C virus (HCV) production, its role in the clear- [email protected] ance of circulating HCV remains unknown. By analyzing and modeling HCV kinetics during liver transplantation we were able to shed light on the function of the liver in clear- Scott Smolka ing free virus from the circulation. In vitro experiments in Computer Science HCV-infected hepatocytes support in part our findings. Stony Brook University [email protected] Harel Dahari Loyola University Medical College Radu Grosu Chicago Vienna University of Technology [email protected] [email protected]

MS61 MS60 Silibinin As a Drug for Hepatitis C in Patients with Spatial-Temporal Regulation of the First Embry- Compromised Liver onic Development Decision Hepatitis C patients with compromised liver and those Abstract not available at time of publication. awaiting liver transplant rarely respond to standard ther- apy. Silibinin lowered viral load in such patients in two William Holmes pilot clinical trials. We use treatment data from these stud- Department of Mathematics ies to understand the mode of action, efficacy and compare University of California, Irvine these between the two cohorts. We also aim at describing [email protected] Hepatitis C viral kinetics in patients treated with Silibinin, according to severity of liver disease, from the two clinical trials. MS60 Analysis and Simulations of a Three Dimensional Swati Debroy Model of Cell Signal Transduction University of Missouri -Kansas City [email protected] We consider a model of cell singnal transduction in a spher- ical cell. Signal molecule production is restricted to specific Harel Dahari areas of the cell. We use asymptotic analysis to construct Loyola University Medical College an system of ordinary differential equations which approx- Chicago imate the full partial differential equation. We then con- [email protected] LS14 Abstracts 111

Laetitia Canini developed a framework for the qualification of physiolog- 5Theoretical Biology and Biophysics, Los Alamos ical models, which employ statistical or other techniques National Lab to explain variability from various sources. The adoption Los Alamos, NM 87545 and application of this framework will support the goals [email protected] of effective physiological model development, communica- tion, and increased acceptance of physiological models for Zoe Marino enabling critical decisions. 3Liver Unit, CIBERehd, IDIBAPS. Barcelona, Spain [email protected] Karim Azer Applied Computer Science and Mathematics Dept. Merck & Co., Inc. Gonzalo Crespo, Miquel Navasa Karim [email protected] Liver Unit, CIBERehd, IDIBAPS. Barcelona, Spain [email protected], [email protected] Jeff Sachs Merck Research Laboratories Massimo D’Amato Quantitative Pharmacology and Pharmacometrics Rottapharm SpA, Monza jeff [email protected] Italy [email protected] Stefan Willmann Bayer Technology Services xavier Forns [email protected] Liver Unit, CIBERehd, IDIBAPS. Barcelona, Spain [email protected] Carolyn Cho Merck & Co., New Jersey Scott Cotler [email protected] Loyola University Medical College [email protected] Thomas Kerbusch, Antonio Cabal Merck Research Laboratories Alan S. Perelson Quantitative Pharmacology and Pharmacometrics Los Alamos National Laboratory [email protected], [email protected] [email protected] Christopher Gibson MS61 Merck Research Laboratories PPDM Role of Methamphetamine in Transmission Dy- [email protected] namics of HIV in MSM Population

Methamphetamine is an addictive stimulant that releases Sandra Sandra Allerheiligen high levels of neurotransmitter dopamine. The use of Merck Research Laboratories methamphetamine have shown to increase libido and re- Quantitative Pharmacology and Pharmacometrics duces inhibition. As a result, methamphetamine is com- [email protected] monly used among men who have sex with men to to ini- tiate, enhance, and prolong sexual encounters. This, in turns, promotes high risk sexual behavior in this commu- MS62 nity of methamphetamine users which increases the risk A Sensitivity Based Statistical Approach to Param- of acquiring an STD. Furthermore, studies have shown eter Selection and Uncertainty Quantification that the use of methamphetamine is associated with more frequent risky sexual behaviors among HIV positive men We discuss both global and local sensitivity analysis in the when compared with HIV negative men. This study seeks context of statistical approaches (requiring a good statis- tical model as well an adequate mathematical model) to to evaluate the dynamics of the methamphetamine abuse assessing and quantifying the effect of known and unknown and HIV incidence through the stability analysis. The re- parameters in complex systems. We use recently developed production number of the system is identified. All parame- parameter subset techniques to investigate the impact of ters are approximated and the system is explored by simu- estimated parameters on the corresponding selection scores lations. The implications of preventative measures will be and uncertainty. These ideas are presented in the context discussed. of an in-host model for HIV-1 infection dynamics developed and validated with patient data. Aprillya Lanz Norfolk State University H. T. Banks 700 Park Avenue Norfolk, VA 23504 CRSC, NC State University [email protected] [email protected]

MS62 MS62 Developing Fit-for-purpose Physiological Models in Application of Modelling and Simulation in Oncol- Drug Discovery and Development - A Framework ogy: Physiologically-based Pharmacokinetics and for Qualification Best Practices Dynamics Examples

Physiological models are used in drug discovery and de- A physiologically-based model applicable for oncological velopment programs to enable decisions such as dose se- questions in drug development was developed by use of lection, risk assessment, or competitive strategy. We have the systems biology platform including PK-Sim and MoBi. 112 LS14 Abstracts

It includes representation of all relevant processes and its [email protected] typical variability for small molecules and biologics at a physiological level. MS63 By means of different examples it will be demon- Protein Modeling from Intermediate-Resolution strated that such models are able to represent the Density Maps Using Geometric Skeletons pharmacokinetics and related tumor growth dynamics in preclinical species and to provide useful insight into This talk will present our continuing work on protein mod- scenarios relevant for the clinic including exploration and eling from density maps that are captured at intermedi- separation of variability and uncertainty by the model ate resolutions (6-10A),˚ which have become increasingly process. available for imaging macromolecular complexes. Our work computes and makes use of the geometric skeleton of the Michael Block density map to automate several model-building tasks, in- Bayer Technology Services GmbH cluding detecting secondary structure elements, identifying Technology Dev., Enabling Tech., Comp. Sys. Bio. their topology on the backbone, and flexibly fitting probe [email protected] structures into the map. The algorithms are distributed in our open-source tool, Gorgon.

MS62 Tao Ju Washington University in Saint Louis Leveraging Visualization and Probabilistic Think- Department of Computer Science & Engineering ing to Get Consensus on an Assay Level Target for [email protected] aCancerDrug

Quantitative thresholds can support effective clinical oncol- MS63 ogy program decisions. Such thresholds are often derived Accurate Electrostatics in 3D Classical Dft from preclinical and (sparse) clinical data. Here, nonlinear mixed-effect modeling allowed integration of variability and Abstract not available at time of publication. uncertainty in data, and enabled simulations identifying an biochemical assay level (threshold) predictive of clinical ef- Matthew G. Knepley ficacy. A kernel-based probabilistic model integrating these University of Chicago simulations captured the necessary phenomena. The model [email protected] allowed non-mathematical visualization enabling effective collaboration with the development team on the complex, multi-dimensional, probabilistic data. MS64 Surface Tension in Human Lungs: Modeling and Jeff Sachs, Jos Lommerse, Jeroen Elassaiss - Schaap Experiments Merck Research Laboratories Quantitative Pharmacology and Pharmacometrics Naturally produced surfactant, which lowers surface ten- jeff [email protected], [email protected], sion is required for normal human lung function. Prema- [email protected] ture babies born before surfactant production begins, are at risk for respiratory distress, and often require surfac- Yali Zhu tant replacement therapy. For 20 years mathematicians Merck Research Laboratories and scientists have sought to model the complicated flow Quantitative Pharm & PMx (current: Hurley Consulting) of fluid lining the passageways and alveoli of the lungs. [email protected] New experiments allow us to visualize a simplified system that includes a thin film of glycerol and a surface layer of surfactant. This talk will describe what we can learn from MS63 such experiments, how the results compare to a commonly accepted model, and how we might modify the experiments Chemical Insights, Matrix Approximations, and to better capture dynamics in the lungs. Boundary-Integral Equations Rachel Levy Abstract not available at time of publication. Harvey Mudd College [email protected] Jaydeep P. Bardhan Department of Electrical and Computer Engineering Karen Daniels Northeastern University North Carolina State University [email protected] [email protected]

Ellen Swanson MS63 Centre College Geometry of Surfaces in the Protein Images and [email protected] the Graph Algorithms Stephen Strickland Abstract not available at time of publication. North Carolina State University [email protected] Jing He Computer Science Dept. Peter Megson, Shreyas Kumar NMSU, Las Cruses, NM Harvey Mudd College LS14 Abstracts 113

[email protected], [email protected] Auburn University [email protected]

MS64 Fluid Dynamics of the Tracks of Tears MS65 Optimal Control in PDE/DE Model for an Anthrax In humans, tears are used to wash away irritants, lubricate Epizootic the eye, and express emotion. The chemical makeup of tears, as well as their mechanical properties, also varies. Anthrax is a fatal, infectious disease which occurs in many In addition to changes in chemical properties, the path animal species, particularly land mammals. It is a cause of that the tear exists the eye can change from the corner population decline in several national parks worldwide such of the eye to directly over the lid and eyelashes. In this as in bison at northern Canada in 1993. Due to the ability presentation, we use high-speed video to construct simple for anthrax spores to survive in soil for a long time even models of the dynamics of different tears. under harsh conditions, clearing anthrax spores from the environment is practically impossible. As infected animals Laura A. Miller die, their carcasses contribute bacteria in the surrounding University of North Carolina - Chapel Hill environment. Proper disposal of the carcasses and effec- Department of Mathematics tively controlling new infections are feasible ways to help [email protected] control the disease. In this talk, I will present some pre- liminary results of these measures of controlling the spread MS64 of the disease. Modeling and Simulation of Biofilm Flows Buddhi Pantha Biofilms are ubiquitous in nature. It consists of bacte- University of Tennessee, Knoxville ria, polysacharrides, water and nutrient. Bacteria are live [email protected] organisms while polysacharrides, also known as EPS, are biopolymers that cross-link into a resilient network encas- Suzanne M. Lenhart ing the bacteria. In this talk, we will report our efforts in University of Tennessee developing a hydrodynamic theory to study the viscoelas- Department of Mathematics ticity of the EPS and how they interact with the live bac- [email protected] teria and the host solvent matrix. Different bacterial phe- notypes and quorum sensing effect will be considered in the model. 3-D numerical simulation will be carried to MS65 benchmark the model with some available experiments. Habitat and Abundance Modeling of West Nile Virus Vector Qi Wang,JiaZhao University of South Carolina Mosquito-borne disease incidence is particularly influenced [email protected], [email protected] by climate through two main pathways. First, climate dic- tates the habitat available for breeding, immature devel- opment, and adult resting. Second, fluctuations in tem- MS64 perature and precipitation drive pathogen and mosquito Biofilm Pattern Formation Within Microfluidic development as well as changes in availability of breeding Chambers habitat. As a result of these associations researchers can predict where mosquitoes and mosquitoes-borne diseases Recently, many biological phenomena involving complex are likely to occur and, using dynamic simulation models, mechanical and biochemical interactions of multiple com- researchers can estimate mosquito abundance for specified ponents have been successfully modeled using a multiphase locations (i.e., climates). Such estimations facilitate our framework, including tumorigenesis, cell motility, and de- understanding of disease dynamics and spread. Using the velopmental processes. In this talk, I will present a two- mosquito-borne West Nile Virus disease as a case study, I dimensional multiphase model of the biofilm formation by will discuss how spatial and temporal models can be used Xylella fastidiosa, the causative agent of Pierce’s Disease. to understand emerging diseases and where they fall short Numerical simulations of this model demonstrate the regu- in our ability to predict new invasions. lar spatial patterning observed in microfluidic experiments representing an artificial plant xylem. Heidi Brown University of Arizona Mark E. Whidden [email protected] Florida State University [email protected] MS65 Nick Cogan, Matt Donahue Parameter Estimation and Model Discrepancy Department of Mathematics with Application to the Life Sciences Florida State University [email protected], [email protected] In this presentation we consider the problem of parame- ter estimation for systems governed by ordinary and de- Fernando Navarrete lay differential equations and discuss the impact of mod- Auburn University eling errors which are an important source of model dis- [email protected] crepancy. We present an approach based on assuming the model is defined as a dynamical system with uncertain dis- Leonardo de La Fuente turbances. This approach can be used to develop prior Department of Entomology and Plant Pathology knowledge about model discrepancy in order to improve 114 LS14 Abstracts

the models predictive usefulness. [email protected]

John A. Burns, Eugene Cliff Virginia Tech MS66 Interdisciplinary Center for Applied Mathematics Optimal Control Applied to Hospital-Acquired [email protected], ecliff@vt.edu and Community-Acquired Methicillin-Resistant Staphylococcus Aureus Strains in Hospitals

MS65 Optimal control are applied to a deterministic mathe- Basic Reproductive Ratios in Ecosystems and Dis- matical model to characterize the factors contributing to ease Models the replacement of hospital-acquired Methicillin-resistant Staphylococcus aureus (MRSA) with community-acquired In this talk, we will discuss the basic reproductive ratios in MRSA, and quantify the effectiveness of three interven- ecosystems and disease models. In general, for a periodic tions aimed at limiting the spread of CA-MRSA in health differential system with time delay, it is difficult to obtain care settings. Adjoint equations and the characterization explicit formula for the basic reproductive ratio in terms of the optimal control strategies are established, and var- of model parameters. We will provide a novel technique in ious numerical simulations are provided to illustrate the finding approximate formulas for basic reproductive ratios results. in various ecosystems and disease models. Wandi Ding Xiang-Sheng Wang Department of Mathematical Sciences Southeast Missouri State University Middle Tennessee State University Cape Girardeau, MO 63701, USA [email protected] [email protected] Glenn Webb Department of Mathematics MS66 Vanderbilt University Probability of Extinction in Stochastic Models of [email protected] Populations and Infectious Diseases: Importance of Time and Location MS66 Multitype branching process theory is used to estimate the Optimal Control of Continuous Systems with Im- probability of population or disease extinction in multi- pulse Controls patch, multi-group, and multi-stage models. The success of a species invasion or of a disease outbreak often depends Impulse control problems, in which a continuously evolving on the conditions of the environment at a specific time and state is modified by discrete control actions, have applica- location. Applications of the theory are discussed in terms tions in epidemiology, medicine, and ecology. In this paper of several zoonotic diseases. we present a simple method for solving impulse control problems for systems of differential equations. In particu- Linda J. Allen lar, we show how impulse control problems can be refor- Dept. of Mathematics and Statistics mulated and solved as discrete optimal control problems. Texas Tech University The method is illustrated with two examples. [email protected] Rachel Leander MS66 Middle TN State University [email protected] How Fish Ecology Affects the Effectiveness of Ma- rine Protected Areas S.M. Lenhart MPAs (Marine Protected Areas) are regions where fish- University of Tennessee, Knoxville ing is restricted or prohibited. As a fisheries management [email protected] tool, their purpose is to protect overharvested species and their habitats. Assume that the fish population consists Vladimir A. Protopopescu of a predator and a prey. One system of nonlinear ODEs Oak Ridge National Laboratory describes the predator-prey interaction in the MPA where [email protected] fishing is prohibited. A similar but different system de- scribes the interaction of predator and prey in the Fishing Grounds where fishing is allowed. Now assume that both MS67 predator and prey can move between MPA and Fishing Combined Parameter and State Estimation in En- Ground, in a way that mimics Fick’s albeit in an ODE semble Kalman Filters context. How does the resulting coupled model, consisting of 4 nonlinear ODEs behave? I will show that the coupling Ensemble Kalman filtering techniques have traditionally tends to stabilize the system. In the special case that the been developed to perform state estimation for nonlinear prey is immobilized, but the predator can move, I will out- dynamical systems with fixed parameters. However, in line a proof showing global stability based on the construc- many biological applications, there is often uncertainty in tion of a Lyapunov function, in conjunction with Lasalle’s the model parameter values. We propose a method for invariance principle. I will also discuss when diffusion is estimating the system parameters along with the states equalizing. in an ensemble Kalman filter framework. The effective- ness of the resulting algorithm is demonstrated in estimat- Patrick DeLeenheer ing the maximum reaction rates and affinity constants of Oregon State University Michaelis-Menten flux expressions in a model for skeletal LS14 Abstracts 115

muscle metabolism. johanne Gudmand-Hoeyer Roskilde University Daniela Calvetti [email protected] Case Western Reserve Univ Department of Mathematics [email protected] MS67 Uncertainty Quantification in ODE Modeling of Andrea N. Arnold Immune Response Case Western Reserve University Dept. of Mathematics, Applied Mathematics and Our team has utilized Bayesian inference for quantifying Statistics the uncertainty in parameter estimation for several models [email protected] of host immune response to bacterial and viral infection. Due to the scarcity of data we have supplemented the like- Erkki Somersalo lihood function with heuristic criteria designed to impose Case Western Reserve University restrictions on the qualitative behavior of modeled systems. [email protected] I will discuss our experience with the feasibility and utility of ensemble modeling, including the use of parallel temper- ing for speeding up convergence. MS67 David Swigon Model Calibration in Systems Biology: Making the Department of Mathematics Most of Limited Data University of Pittsburgh The field of Systems Biology was developed in response to [email protected] experimental advances that allow system-level observations of intracellular networks. While such high-throughput as- Ericka Mochan says provide valuable insight into cellular processes, they University of Pittsburgh typically fall short of providing sufficient data to calibrate [email protected] mechanistic models of intracellular dynamics. This talk will relate our experience with modelling in metabolism Jonathan Rubin and signal transduction, highlighting the tools we used to University of Pittsburgh gain insight from models that were calibrated against lim- Pittsburgh, PA ited data. [email protected]

Brian P. Ingalls Gilles Clermont Department of Applied Mathematics University of Pittsburgh University of Waterloo Critical Care Medicine [email protected] [email protected]

Rahul Rahul Department of Applied Mathematics, University of MS68 Waterloo A Multicell Model to Investigate How Vasculoge- Waterloo, Canada nesis Is Disrupted in Cerebral Cavernous Malfor- [email protected] mations

Abstract not available at time of publication. MS67 Patient Specific Modelling of the Endocrine HPA- Timothy Elston Axis and Its Relation to Depression: Ultradian and University of North Carolina, Chapel Hill Circadian Oscillations [email protected]

Correlation between depression and a recently defined index characterizing the hypothalamus-pituitary-adrenal MS68 (HPA) axis is established. A novel capturing circadian Diffusion in Soft Matter: Theory, Modeling, and as well as ultradian oscillations of hormone concentrations Simulations related to the HPA-axis is suggested. Three parameters related to depression are identified and estimated based on This lecture highlights anomalous diffusion of particles in data from 29 subjects using non-linear mixed effects mod- soft matter in general, and in lung airway fluids in par- elling and statistical hypothesis testing. These parameters ticular. We present particle path data from experiments, represent underlying physiological mechanisms of the HPA- discuss models that are consistent with the data, and pre- axis and may be used for diagnosing and understanding dictive simulations of models that have been fitted to the depression. data. Relevance to pulmonary medicine will be presented.

Johnny T. Ottesen Roskilde University M. Gregory Forest Department of Mathematics University of North Carolina at Chapel Hill [email protected] Dept of Math & Biomedical Engr. [email protected] Stine Timmerman Lundbeck John Mellnik [email protected] UNC Chapel Hill 116 LS14 Abstracts

Bioinformatics and Computational Biology Graduate [email protected], [email protected] Program [email protected] MS69 Paula Vasquez Ions in Channels: Natural Nanovalves University of South Carolina [email protected] Ions in channel proteins are the ultimate multiscale de- vice. They are natural nanovalves in which a handful of Scott McKinley atoms control many processes crucial to life by control- University of Florida ling macroscopic flows of ions. Statistical mechanics was [email protected] not designed with interacting systems in mind, let alone systems in which atoms control macroscopic flows and liv- David Hill ing machines. Variational mechanics (of dissipative flow- University of North Carolina at Chapel Hill ing systems like complex fluids) is needed to engineer the Cystic Fibrosis Center nanovalves of life, in my opinion. [email protected] Bob Eisenberg Department of Molecular Biophysics and Physiology MS68 Rush University Homeostatic Mechanisms in Biochemical Systems [email protected]

We will discuss the structure of homeostatic mechanisms in a variety of metabolic systems including folate metabolism, MS69 methylation reactions, and detoxification by glutathione in the liver. These mechanisms are designed to allow cells A Energy-Preserving Scheme for Pnp Equations to regulate crucial functions in the face of large fluctua- tions in inputs due to meals. From a mathematical point In this talk, we present a finite difference scheme that satis- of view, the question is how these mechanisms dampen fies the energy dissipation law of the Poisson-Nerst-Planck stochastic fluctuations as they propagate through the bio- equation exactly. We formulate the chemical potential dif- chemical network. ferently and show that the energy-preserving scheme comes out of the new formulation. Numerical results comparing MichaelC.Reed the energy-preserving scheme with the standard scheme Duke University will be shown. [email protected] Xiaofan Li Illinois Institute of Technology MS68 [email protected] Mathematical Understanding of Cancer Virother- apy MS69 Abstract not available at time of publication. Title Not Available at Time of Publication Jianjun Paul Tian Mathematics Department Abstract not available at time of publication. College of William and Mary [email protected] Tai-Chia Lin National Taiwan University, Taiwan, ROC [email protected] MS69 The Way Cells Talk: Modeling and Simulations of Ion Transport MS70 Neuromuscular Pumping in Jellyfish Bells Ion channels are fundamental components that conduct ionic exchanges through cellular membranes, thus they are critical in many biological process such as change of action A current question in jellyfish propulsion is how the un- potentials, signaling and interactions with extracellular mi- derlying neuromuscular organization of their bell allows for croenvironment. In this talk I will first briefly overview maneuvering. Using an immersed boundary framework, we the methodologies and models of ion channels, then focus will examine the neuromechanics of swimming by incorpo- a specific ionic transport, the proton transport through cel- rating neural and muscles models into a model of the elastic lular membranes. A multi scale and multi physic model is jellyfish bell. We then use this model to understand how proposed based on a total energy functional, from which variability in the electrophysiology allows for complicated the governing equations of proton dynamics and electro- swimming behavior, such as steering. We will compare the statics are derived. A set of highly accurate and efficient results of the simulations with experiment. numerical algorithms are developed to perform the simu- lations. A specific application of proton transport could Alexander Hoover be a better understanding of abnormal acidity in tumor University Of North Carolina at Chapel Hill microenvironment. [email protected]

Duan Chen, Duan Chen Laura A. Miller Department of Mathematics and Statistics University of North Carolina - Chapel Hill University of North Carolina at Charlotte Department of Mathematics LS14 Abstracts 117

[email protected] [email protected]

MS70 MS70 The Effects of In Phase and Out of Phase Pulsa- tions in Groups of Upside-down Jellyfish, Cassio- Experiments and Modeling Study of Low Reynolds pea sp Number Flows Generated by a Processing Nodal Cilia Upside-down jellyfish of the genus Cassiopea use bell con- tractions to generate feeding currents. These jellyfish typi- Theoretical study and experiments are developed to em- cally situate themselves on the bottom of the ocean floor in ulate dynamics biological interest such as primary cilia groups. Little is known about the costs and advantages of in developing embryos, where primary cilia are the main the different pulsation modes within a group and how these agent for the embryonic forms of nutrient circulation. Ex- trade-offs are related to the size of the individual jellyfish. periments are performed using high viscosity silicon oil In this study, the effects of synchronous and asynchronous with magnetically actuated precessing rod in a table-top pulsations are investigated using particle image velocime- setup. Stereoscopic Lagrangian tracking show quantified try. long-time agreement with an appropriately imaged slen- der body theory to enforce the no-slip condition at the Julia E. Samson floor. In contrast, breaking symmetry by a bent rod cre- University of North Carolina at Chapel Hill ates additional flow components which destroy quantitative [email protected] short time agreement with the theory while maintaining its qualitative features including the creation of large scale La- grangian tori. Arvind Santhanakrishnan Oklahoma State University [email protected] Longhua Zhao Case Western Reserve University Laura A. Miller [email protected] University of North Carolina - Chapel Hill Department of Mathematics Roberto Camassa [email protected] University of North Carolina [email protected]

MS70 James D. Martindale University of North Carolina at Chapel Hill The Metachronal Limb Stroke Pattern in Crus- [email protected] tacean Swimming

Crayfish and other long-tailed crustaceans swim by rhyth- Richard McLaughlin mically moving four or five pairs of limbs. Despite varia- UNC Chapel Hill tions in limb size and stroke frequency, movements of ipsi- [email protected] lateral limbs always maintain a tail-to-head metachronal rhythm with an approximate quarter-period inter-limb Leandra Vicci phase-difference. Relatively few studies have examined the Department of Computer Science fluid dynamics of metachronal limb stroke for the range of University of North Carolina Reynolds numbers under which crustaceans operate. Here, [email protected] we use a computational fluid dynamics model to address this issue. MS71 Calvin Zhang Courant Institute of Mathematical Sciences The Influence of Neurochemistry [email protected] Mathematical models in neuroscience often treat individual Robert D. Guy neurons as nodes in networks and biochemistry appears, if Mathematics Department at all, as some intermediate variables by which the neu- University of California Davis rons communicate with each other. In fact, many neurons [email protected] change brain function not by communicating in one-to- one fashion with other neurons, but instead by projecting Timothy Lewis changes in biochemistry over long distances. This biochem- Department of Mathematics ical network is of crucial importance for brain function and University of California, Davis it influences and is influenced by the more traditional elec- [email protected] trophysiological networks.

Boyce Griffith Janet Best New York University School of Medicine The Ohio State University griffi[email protected] Department of Mathematics [email protected] Charles S. Peskin Courant Institute of Mathematical Sciences Michael C. Reed, H Frederik Nijhout New York University Duke University 118 LS14 Abstracts

[email protected], [email protected] [email protected]

MS71 MS72 How Precise Can We Make a Biophysical Neural Large Reduction of Defibrillation Threshold Using Integrator? a Four-Electrode System

Recently, Boerlin et al 2013 derived a recurrent network of In this talk we propose a new shock protocol that is based leaky-integrate-and-fire neurons with instantaneous synap- on a four electrode system instead of the of standard pro- tic dynamics that can perform a variety of computations. cedure based with only two electrodes. The model is tested Although this framework is flexible in that the derived net- using one-dimensional ring with bidomain properties and work can perform any linear computation, it is important with the Beeler-Reuter model for the active properties of to ask whether the framework generalizes to more real- the membrane. Three different shock types are tested: istic synaptic and spike-generating dynamics. Here, we monophasic and two types of biphasic shock. The re- show that this framework can indeed be extended to in- sults are compared with those obtained with standard two clude slow, alpha function synaptic dynamics and Hodgkin- electrode protocol. Substantial reduction in defibrillation Huxley-like spike-generating currents. threshold is achieved with respect to the standard protocol. Michael Schwemmer The Ohio State University Jean Bragard [email protected] Depto de Fisica y Matematica Aplicada Universidad de Navarra, Pamplona, Spain [email protected] MS71 The Effects of Long-Range Coupling on Neural Ac- Ana Simic tivity in the Crayfish Swimmeret System University of Navarra, Spain [email protected] The crayfish swimmeret system exhibits a stable stroke pattern during forward swimming, where the limbs move in a back to front metachronal wave with a delay of ap- Jorge Elorza proximately 25%. A chain of nearest neighbor coupled os- University cillators indicates that the network topology of the cray- [email protected] fish neural circuit promotes the robust generation of this pattern (Zhang et al.). We extend this modeling work to consider the influence of the long-range connections that MS72 are present in this system. Unification of Electrical Restitution Dynamics and Ion Channel Dynamics in the Control of Cardiac Lucy Spardy Rhythm - An Eigenmode Approach Mathematical Biosciences Institute [email protected] The characterization of action potential dynamics in car- diac tissue has traditionally followed two parallel tracks: Brian Mulloney use of the dependence of action potential duration and University of California Davis wave propagation speed on the preceding diastolic inter- [email protected] val (called electrical restitution theory), and use of intri- cate ion channel models. In our work, we unify these two Tim Lewis approaches by applying eigenmode theory to the mapping University of California, Davis of perturbations of both sets of dynamical variables from [email protected] one action potential to the next. This link between the two approaches provides us with an important foundation on which we can discuss in a rigorous manner how drugs MS71 and electrical interventions impact the onset and control Interaction of Two Distinct Timescales in Compu- of fibrillation in the heart. tational a Model of in-Vitro Sigh Generation Niels Otani Augmented breaths, or sighs, increase air intake and a lack Rochester Institute of Technology of sighing is associated with sudden infant death syndrome. [email protected] Since sighs operate on significantly slower time scale than eupnoea, it is still debated if they are produced by the same network of neurons or by distinct sub-networks. We MS72 developed a mathematical model that proposes that sighs Local Termination of Cardiac Alternans Using and eupnoea are generated by the two neural sub-networks. Isostable Response Curve Techniques The model accounts for dynamics of sigh and eupnoea and reproduces several in-vitro experiments. Phase reduction methods have been tremendously useful for understanding the dynamics of nonlinear oscillators, Natalia Toporikova but have been difficult to extend to excitable systems with Washington and Lee University stable fixed points, such as those that commonly describe [email protected] individual cardiac cells. Here, we extend the notion of phase reduction to include excitable media, and use this re- Muriel Thoby-Brisson duction to formulate an energy-optimal control strategy for [email protected]) , collaborator INCIA terminating cardiac alternans in a high-dimensional model LS14 Abstracts 119

of cardiac cellular activity. netic Oscillators

Dan D. Wilson Understanding the effect of noise and the cell cycle on gene Mechanical Engineering networks is fundamental in developing accurate models. University of California, Santa Barbara Typically, comparing experimental data and simulations [email protected] only takes into account individual trajectories, but not the lineage and the corresponding variability and correlation. Jeff Moehlis Here we show that a model that includes extrinsic noise can Dept. of Mechanical Engineering capture the variability seen in a synthetic gene oscillator. University of California – Santa Barbara Furthermore, we show that it is sufficient to model extrinsic [email protected] noise as cell-to-cell variability at cell division. Alan Veliz-Cuba MS73 University of Houston Rice University Exact Protein Distributions for Stochastic Models [email protected] of Gene Expression

In this talk, I will discuss approaches developed by my MS74 group for obtaining analytical results for protein distribu- tions in stochastic models of gene expression. We invoke Optimal Control in Models of Management Involv- the partitioning property of Poisson processes to develop ing Trees and Forest Resources a mapping that significantly simplifies the analysis of such models. Using this mapping, we derive exact analytical re- Two applications of optimal control are presented in ex- sults for steady-state and time-dependent protein distribu- amples of managing populations related trees and forest tions for the basic 2-stage model of gene expression. Con- products. One example is a discrete model of gypsy moth sidering extensions of the basic model, we obtain exact pro- populations affecting tree defoliation. The other example tein steady-state distributions for models that include the is a system of ordinary differential equations modeling the effects of post-transcriptional and post-translational reg- harvesting (lethal and non-lethal) for forest products. ulation. Finally, I will introduce a model which includes Suzanne M. Lenhart the interplay between bursting and feedback regulation and University of Tennessee discuss insights gained from analyzing the corresponding Department of Mathematics steady-state protein distribution. [email protected] Rahul Kulkarni,NirajKumar University of Massachusetts Boston MS74 [email protected], [email protected] Modeling of Transgenic Or Sterile Mosquitoes in Hodjat Pendar Fighting Vertor-Borne Diseases Virginia Tech To prevent the transmission of malaria or other mosquito- [email protected] borne diseases, an effective weapon is to use genetically- altered (transgenic) mosquitoes or mosquitoes carrying Thierry Platini genetically-modified bacteria, that are resistant to the in- COventry University fection, to replace the wild mosquitoes, or to release ster- [email protected] ile mosquitoes to reduce the wild mosquito population. To study the impact of these mosquitoes mixing with wild mosquitoes on the diseases transmission and differ- MS73 ent strategies in releasing sterile mosquitoes, we formulate An Optimal Control Framework for Stochastic simple continuous- or discrete-time mathematical models Gene Regulatory Networks of interactive wild and transgenic or sterile mosquitoes. We present fundamental analysis of the model equations, Modeling stochasticity in gene regulation is an important and demonstrate the rich dynamical features of the models and complex problem in molecular systems biology due to by numerical examples. probabilistic nature of gene regulation. This talk will intro- duce a stochastic modeling framework for gene regulatory Jia Li networks which is an extension of the Boolean modeling Department of Mathematical Sciences approach. This framework incorporates propensity param- University of Alabama in Huntsville eters for activation and degradation and is able to capture [email protected] the cell-to-cell variability. In this setting, optimal control problems can be studied using methods from control theory for Markov decision processes for the purpose of develop- MS74 ing optimal intervention strategies. These control methods An Ecological Model for Producers and Scroungers will then be applied to the p53-mdm2 complex. in a Spatial Habitat

David Murrugarra We describe the dynamics of a producer-scrounger system School of Mathematics, Georgia Tech in a spatial habitat using a partial differential equation [email protected] model. Both species are assumed to increase logistically and to move randomly in their environment. Producers can obtain the resource directly from the environment, whereas MS73 scroungers must steal it from nearby producers. When Extrinsic Noise and Cell-Cycle Dependence of Ge- possible, parameter combinations which allow producers 120 LS14 Abstracts

and/or scroungers to persist either alone or together are of high-dimensional problems due to various limitations in distinguished from those in which they cannot. existing methods. Here we develop the very first graphical approach to analyze the identifiability of high-dimensional Chris Cosner systems that are governed by dynamic laws. We apply this University of Miami method to several real model structures, and show how Department of Mathematics model topology and experimental inputs and outputs af- [email protected] fect the identifiability. The proposed method provides a basis to systematically examine and refine the structures Andrew Nevai of a wide range of complex dynamic systems. Department of Mathematics University of Central Florida Hongyu Miao [email protected] University of Rochester hongyu [email protected]

MS74 The Role of Avian Stage-structure in the Trans- MS75 mission and Control of West Nile Virus Identifiability and Parameter Estimation in Sys- tems Biology and Drug Development The seasonal occurrence of West Nile Virus in humans has been associated with the end of the avian nesting season. Due to the high complexity of biological data it is diffi- Newly hatched nestlings are more vulnerable to mosquitoes cult to disentangle cellular processes relying only on intu- than older birds. While total avian population size in- itive interpretation of measurements. A Systems Biology creases throughout the season, nestling abundance declines approach, that combines quantitative experimental data at the end of the brooding season. This temporal variation with dynamic mathematical modeling promises to yield in host stage abundance may play an important role in deeper insights into these processes and makes a more ra- structuring WNV transmission. We develop and analyze a tional drug design possible. Nevertheless, with growing stage-structured differential equation model for WNV and complexity and increasing amount of quantitative exper- investigate the impact of vector preference for specific host imental data, building realistic and reliable mathematical life stages on the timing of WNV activity as well as impli- models can become a challenging task: unknown model pa- cations for public health interventions. rameters need to be estimated from the experimental data and uncertainties in model predictions has to be considered Suzanne Robertson realistically. I will present a case study (Raue et al., Bioin- Virginia Commonwealth University formatics 2014) using three current approaches for identi- [email protected] fiability analysis for an application from cell biology (Raia et al., Cancer Research 2011). The approaches are con- Kevin Caillouet ceptually different and are developed independently. The St. Tammany Parish Mosquito Abatement District results of the three approaches are in agreement but have [email protected] different strength and weaknesses. For the estimation of unknown model parameters, the performance of different optimization algorithms is compared systematically (Raue MS75 et al., PLOS ONE 2013). The results show that determin- Identifiability and Parameter Estimation in Mod- istic derivative-based optimization employing the sensitiv- eling Disease Dynamics ity equations in combination with a multi-start strategy based on Latin hypercube sampling outperforms the other Connecting differential equation models with data to yield methods by orders of magnitude in accuracy and speed. predictive results requires a variety of parameter estima- tion, identifiability, and uncertainty quantification tech- Andreas Raue niques. Identifiability analysis addresses the question of Physics Institute, University of Freiburg whether it is possible to uniquely recover the model pa- [email protected] rameters from a given set of data. In this talk, I will dis- cuss some recent work using and developing identifiability methods based on tools from computational differential al- MS75 gebra and systems theory, and present several clinical and Identifiability of Linear State Space Models public health applications to problems in human disease, including cholera and other infectious disease transmission Dynamical systems models described by linear systems of processes. ordinary differential equations are ubiquitous in applied Marisa Eisenberg mathematics and mathematical biology. Such a model is University of Michigan said to be identifiable if the parameters of the model can [email protected] be uniquely determined from given input and output data. I will discuss recent progress on developing precise combi- natorial methods to determine if a system is identifiable. MS75 Joint work with Nicolette Meshkat and Adam Mahdi. Identifiability of High-Dimensional Models Seth Sullivant The structure of a complex system ultimately deter- North Carolina State University mines whether key unknown parameters can be unambigu- [email protected] ously quantified from experimental observations. Although many identifiability techniques have been proposed to ex- amine model structures before parameter estimation, we MS76 have never gained the capability to explore the territory Modeling Cartilage Tissue Engineering in Cell- LS14 Abstracts 121

Seeded Scaffolds tains stable glomerular filtration rate within a physiologic range of perfusion pressure (80-180 mmHg). The contri- Chondrocytes or stem cells can be used to regenerate carti- bution of TGF to overall autoregulation is significant only lage extracellular matrix via tissue engineering approaches within a narrow band of perfusion pressure values (80-110 in which cells are seeded into porous scaffold materials. mmHg). In such systems, cell-mediated biosynthesis results in re- generation and accumulation of extracellular matrix con- Anita T. Layton stituents concurrent with scaffold degradation. Continuum Duke University models are presented for such systems and quantify the ef- Department of Mathematics fects of evolving porosity on functional outcomes. Both [email protected] tissue-scale mixture models and microscopic models with individual cells will be presented.

Mansoor A. Haider MS76 North Carolina State University Department of Mathematics Kinetic Monte Carlo Simulations of Multicellular m [email protected] Aggregate Self-Assembly in Biofabrication

We present a three-dimensional lattice model to study self- MS76 assembly and fusion of multicellular aggregate systems by Let There be Force: Modeling Cell-ECM Interac- using kinetic Monte Carlo (KMC) simulations. This model tions is developed to describe and predict the time evolution of postprinting morphological structure formation during tis- Extracellular matrix (ECM), a fibrous material that forms sue or organ maturation in a novel biofabrication process a network in a tissue, significantly affects many aspects (or technology) known as bioprinting. In this new tech- of cellular behavior, including cell movement and prolifer- nology, live multicellular aggregates as bio-ink are used to ation. Transgenic mouse tumor studies indicate that ex- make tissue or organ constructs via the layer-by-layer de- cess collagen, a major component of ECM, enhances tu- position technique in biocompatible hydrogels; the printed mor formation and invasiveness. Moreover, cell interac- bio-constructs embedded in the hydrogels are then placed tions with the collagen matrix result in aligned fibers that in bioreactors to undergo the self-assembly process to form facilitate cell invasion. However, the underlying mecha- the desired functional tissue or organ products. Here we nisms are unclear since the properties of ECM are com- implement our model with an efficient KMC algorithm to plex, with diverse topographies and mechanical properties simulate the making of a set of tissues/organs in several depending on various biophysical parameters. We have designer’s geometries like a ring, a sheet and a tube, which developed a three-dimensional elastic computational fiber can involve a large number of cells and various other sup- network model, and parameterized it with in vitro colla- port materials like agarose constructs etc. We also study gen tensile experiments. Using this model, we simulate the process of cell sorting/migration within the cellular ag- mechanical testing of fiber networks and examine the me- gregates formed by multiple types of cells with different chanical properties of fiber networks with varying density, adhesivities. alignment, and crosslinking. The computational model and simulation results can fill in the gap between microscopic single collagen fiber studies and macroscopic collagen gel Yi Sun studies. This model is the first step toward a fully biome- University of South Carolina chanical cell-matrix interaction model for changes in ma- [email protected] trix organization during cell migration and tumor invasion.

Yi Jiang MS77 Georgia State University [email protected] Pnp Equations with Steric Effects: A Model of Ion Flow Through Channels

MS76 Abstract not available at time of publication. Mathematical Modeling of Renal Hemodynamics

We have developed a mathematical model of the rat kid- Tzyy-Leng Horng ney’s blood flow control, and used that model to study Department of Applied Mathematics the individual contributions of two autoregulatory mecha- Feng Chia University nisms. The model represents an afferent arteriole, glomeru- [email protected] lar filtration, and a segment of a short-loop nephron. The afferent arteriole exhibits the an autoregulatory mecha- nism called the myogenic response, such that it responds MS77 to transmural pressure elevation with constriction, and to pressure reduction with dilation. Another autoregaula- Computer Simulation of Voltage Sensitive Calcium tory mechanism is the tubuloglomerular feedback (TGF): Ion Channels in a Dendritic Spine The tubule model predicts tubular fluid and Cl- transport. Macula densa Cl- concentration is sensed as the signal for TGF, which acts to constrict or dilate the afferent arteriole. Abstract not available at time of publication. In other words, TGF contributes to hemodynamics control by adjusting single nephron glomerular filtration rate ac- Pilhwa Lee cording to the chloride concentration sensed downstream. Department of Cell Biology With this configuration, the model afferent arteriole main- University of Connecticut Health Center 122 LS14 Abstracts

[email protected] [email protected]

MS77 MS78 Title Not Available at Time of Publication Clap and Fling Interaction of Bristled Wings in Tiny Insect Flight Abstract not available at time of publication. The flapping flight of the smallest insects that fly at Chun Liu Reynolds numbers (Re) on the order of 10 is often char- Penn. State University acterized by a ‘clap and fling’ of the wings. The effect [email protected] of a bristled wing characteristic of these insects is investi- gated using 2D numerical simulations based on a porous version of the immersed boundary method. A compari- MS77 son of the aerodynamic forces generated between solid and porous wings undergoing wing-wing interaction will be pre- A Model of Tissue Electrodiffusion and Osmosis sented. and Its Application to Cortical Spreading Depres- sion Arvind Santhanakrishnan Oklahoma State University We propose a PDE model of tissue-level electrodiffusive [email protected] and osmotic phenomena. An important feature of this model is that it satisfies an energy inequality. This model Alice Robinson will be applied to the study of cortical spreading depres- University of California, Irvine sion, a pathophysiological phenomenon in the brain that is [email protected] thought to underlie migraine aura and other pathologies.

Yoichiro Mori Tyson Hedrick University of Minnesota University of North Carolina, Chapel Hill [email protected] [email protected]

Laura A. Miller MS78 University of North Carolina - Chapel Hill Roles of Droplets and Bubbles in Pathogen Trans- Department of Mathematics mission Through Air [email protected]

Pathogen-bearing droplet creation from contaminated flu- MS78 ids results from the interplay between interfacial flow dy- namics and pathogens. Such interplay leads to various Microscale Gas Transport in Insect Respiratory modes of formation and ejection of contaminated droplets Systems into the air, thus shaping infectious disease transmission indoors. Particular mechanisms of fluid breakup leading Insects and some other terrestrial arthropods breathe us- to the creation of pathogen-bearing droplets from bursting ing a complex network of tracheal tubes. Air is drawn bubbles and violent expirations will be discussed. in through sets of openings called spiracles, and follows a branching path down to the tracheoles, which deliver Lydia Bourouiba oxygen directly to the cells for respiration. These tra- Department of Mathematics/Civil and Environmental cheal networks have recently been found to consist of essen- Eng 48-333 tially inelastic but locally (in time and space) collapsible #48-333, Massachusetts Institute of Technology tubes. Mathematical modeling and meshfree computations [email protected] are presented to describe this transport paradigm. Anne Staples Department of Engineering Science and Mechanics MS78 Virginia Tech Fluid Flow Through Many Bristled Wings [email protected]

The smallest flying insects are roughly 1mm in length and at this scale viscous effects are significant. Interestingly, MS79 these insects commonly possess wings with long bristles on Stochastic Switching: Mathematical Surprises and the fringes, and the physiological importance of the bristles Biological Insight remains a mystery. Depending on the Reynolds number and the local environment, bristled wings could act either Motivated by several biological questions, we consider as leaky sieves or solid paddles. We used the immersed ODEs with stochastically switching right-hand sides and boundary method to investigate the aerodynamic role of PDEs with stochastically switching boundary conditions. bristles in insect flight. In a variety of situations, we prove that the system exhibits surprising behavior. In this talk, we will highlight some of Shannon Jones the most interesting results and describe their implications University of North Carolina at Chapel Hill both for the mathematical study of stochastic hybrid sys- [email protected] tems and for the motivating biological problems.

Laura Miller Sean D. Lawley UNC-Chapel Hill Duke University LS14 Abstracts 123

[email protected] [email protected]

MS79 MS80 Multi-Motor Transport in Neurons: Moving Be- A Mathematical and Computational Structured- yond Tug-of-War Tree Model of the Pulmonary Circulation A multiscale mathematical and computational model of Transport in neurons is intrinsically bidirectional, with the pulmonary circulation is presented and used to analyse each movement modality carried out by molecular motors both arterial and venous pressure and flow. This work is a in either the kinesin (anterograde) or the dynein (retro- major advance over previous studies using structured trees grade) families. Because all motors are present at a given to model vascular beds, e.g. Olufsen et al. (2012), which time there must be competition and/or cooperation among only address the arterial circulation. For the first three gen- motors that simultaneously bind a single vesicle to nearby erations of vessels within the pulmonary circulation, the microtubules. It has been assumed for much of the last geometry is specified from patient-specific measurements decade that the competition must resolve itself though obtained using magnetic resonance imaging (MRI). Blood some kind of tug-of-war; but recent evidence shows con- flow and pressure in the larger arteries and veins are pre- clusively that this is not the case in vivo. In this talk, we dicted using a nonlinear, cross-sectional-area-averaged sys- will see a few biological mechanisms (and associated math- tem of equations for a Newtonian fluid in an elastic tube. ematical models) that may lead to resolving theory with The inflow to the main pulmonary artery is obtained from experimental observations. Joint work with Will Hancock MRI measurements, while pressure entering the left atrium (Penn State), John Fricks (Penn State), and Pete Kramer from the main pulmonary vein is kept constant at the nor- (RPI). mal mean value of 2 mmHg. Each terminal vessel in the network of ‘large’ arteries is connected to its correspond- Scott McKinley ing terminal vein via a network of vessels representing the University of Florida vascular bed of smaller arteries and veins. We develop scott.mckinley@ufl.edu and implement an algorithm to calculate the admittance of each vascular bed, using bifurcating structured trees and recursion. The structured-tree models take into account MS79 the geometry and material properties of the ‘smaller’ ar- Spontaneous Neural Activity Caused by Ion Chan- teries and veins of radii ¿ 50 microns. We study the ef- nel Fluctuations fects on flow and pressure associated with three classes of pulmonary hypertension expressed via stiffening of larger The membrane voltage of a neuron is modeled with a piece- and smaller vessels, and vascular rarefaction. The results wise deterministic stochastic process. The membrane volt- of simulating these pathological conditions are in agree- age changes deterministically while the population of open ment with clinical observations, showing that the model ion channels, which allow current to flow across the mem- has potential for assisting with diagnosis and treatment of brane, is constant. Ion channels open and close randomly, circulatory diseases within the lung. References: Olufsen, and the transition rates depend on voltage, making the M.S., Hill, N.A., Vaughan, G.D.A., Sainsbury, C. & John- process nonlinear. In the limit of infinite transition rates, son, M. (2012) Rarefaction and blood pressure in systemic the process becomes deterministic. The deterministic pro- and pulmonary arteries. J Fluid Mech 705:280-305 cess is the well known Morris-Lecar model. Under certain conditions, the deterministic process has one stable fixed Nicholas A. Hill point and is excitable. An excitable event, called an action Department of Mathematics potential, is a single large transient spike in voltage that University of Glasgow, UK eventually returns to the stable steady state. I will discuss [email protected] recent development of large deviation theory to study noise induced action potentials. M. Umar Qureshi International Islamic University, Pakistan Jay Newby & University of Glasgow, U.K. Mathematical Biosciences Institute [email protected] The Ohio State University [email protected] Gareth D.A. Vaughan School of Mathematics and Statistics University of Glasgow, MS79 [email protected] Measuring Edge Importance for Random Processes on Networks Christopher Sainsbury School of Medicine,University of Glasgow, U.K. Many neural systems can be represented as a Markov pro- [email protected] cess on a graph. We derived a new measure of the contribu- [email protected] tion of individual edges in the graph to the accuracy of an approximate process on the graph. We apply this measure Martin Johnson to the Hodgkin-Huxley system and extend it for a broad Scottish Pulmonary Vascular Unit class of random graph models. These results shed new light Western Infirmary, Glasgow, U.K. on the contributions of different ion channel transitions to [email protected] the variability of neural systems. Charles S. Peskin Deena Schmidt Courant Institute of Mathematical Sciences Case Western Reserve University New York University 124 LS14 Abstracts

[email protected] quired. In the absence of time delays, Langevin equations have proved to be a very important theoretical tool for the Mette S. Olufsen study of genetic networks. However, in models of gene net- Department of Mathematics works that include transcriptional delay, such theoretical North Carolina State University tools do not currently exist. In this talk, we present a proof [email protected] of the weak convergence of time-delayed birth death pro- cesses to a class of functional Langevin equations. We fur- ther prove that as the system size approaches infinity, both MS80 these descriptions converge to the mean field limit. Finally, Individualized Pulmonary Arterial Blood Flow we obtain quantitative estimates on the distance between Analysis the birth-death process and the approximating Langevin process. This lays a rigorous groundwork for studying the We propose an individualized pulmonary arterial blood dynamics of time-delayed birth-death processes by using flow analysis coupled to the lumped windkessel model of functional stochastic differential equations. heart circulation and mechanics. The pulmonary arterial vasculature is from image segmentation of a mouse simpli- Chinmaya Gupta,ManuelLopez fied as 1D centerline embedded in 3D with cross-sectional University of Houston radius. We reveal the changes in blood flow patterns and [email protected], [email protected] right ventricular adaptation from vascular remodeling and rarefaction, which are consequences of pulmonary hyper- Robert Azencott tension. Department of Mathematics University of Houston Pilhwa Lee, Shivendra Tewari, Daniel Beard [email protected] University of Michigan, Ann Arbor [email protected], [email protected], [email protected] Matthew Bennett Rice University [email protected] MS80 Analysis of Cardiovascular Dynamics in Pulmonary Kresimir Josic Hypertensive C57BL6/J Mice University of Houston Department of Mathematics Data on RV pressure and volume, and systemic arterial [email protected] pressure obtained before, during, and after inferior vena cava occlusion are analyzed using a mathematical model of William Ott realistic ventricular mechanics coupled with a simple model University of Houston of pulmonary and systemic vascular systems. Model analy- [email protected] sis suggests monotonic increase in PVR and PA elastance, consistent with prior experimental measurements. Model findings indicate a compensatory remodeling phase of RV MS81 precedes pathological remodeling that concludes with heart Impact of Stochastic Transcriptional Delay on failure in pulmonary hypertension. Gene Networks

Shivendra Tewari Abstract not available at time of publication. University of Michigan, Ann Arbor [email protected] Manuel Lopez University of Houston Naomi Chesler [email protected] University of Wisconsin, Madison [email protected] MS81 Daniel Beard Queueing Approaches to Multisite Enzyme Kinet- University of Michigan, Ann Arbor ics [email protected] Queueing theory was developed long ago to understand the stochastic dynamics of discrete elements processed by a fi- MS81 nite number of servers. Researchers have been developing a Rare Events for Genetic Networks: Studying Inter- new biological queueing theory to describe how processing actions Between Meta-Stability and Time-Delays bottlenecks can strongly influence the dynamics of cellular systems. We now present a biological queueing theory for The dynamics of gene networks are sometimes non-trivially enzymes that can bind multiple substrates simultaneously, influenced by events that happen on relatively short time as with the E. coli protease ClpXP. scales. To study the impact of such events on gene net- works it is not sufficient to study the steady state behav- William H. Mather ior. Instead, transient behaviors become very important. Virginia Tech Physics However, it is difficult to study relevant transient events [email protected] numerically because they are rare, and the majority of the simulation time is spent sampling events that are not of interest. Therefore, theoretical methods for reliably sam- MS81 pling relevant transient methods for gene networks are re- First-Passage Time Calculations for Gene Net- LS14 Abstracts 125

works: Implications for Phage Lambda Lysis Time we study the convergence and complexity of the method.

The inherent stochastic nature of biochemical processes Ibraheem Alolyan can drive differences in gene expression between otherwise King Saud University identical cells. While cell-to-cell variability in gene expres- [email protected] sion has received much attention, randomness in timing of events has been less studied. We investigate event timing at the single-cell level in a simple system, the lytic pathway PP1 of the bacterial virus phage lambda. In genetically identi- Staying in Shape: Patterns in Radial Symmetry cal single-cells, lysis occurs on average at 65 mins, with a Provide Protein Structural Stability and Function- standard deviation of 3.5 mins. Interestingly, mutations in ality the lysis protein, holin, alters both the lysis time mean and variance. Mathematically, lysis time is formulated as the Toroidal WD40 repeat proteins, such as the beta subunit of first-passage time for cellular holin levels to cross a critical heterotrimeric G-proteins, are important in cell signaling. threshold. Analytical expressions for the first-passage time Each repeating unit has about 40 amino acids, comprised of moments reveal how different model parameters modulate a trademark trpytophan and aspartate. With conventional lysis time moments, and these predictions are verified with comparative sequence analysis techniques, the strong sig- experiments. Finally, our analysis reveals regulatory mo- nal from these signature positions can mask the importance tifs that enhance the robustness of lysis timing to cellular of less conserved ones. We discuss how computational mu- noise. tagenesis can overcome these limitations, explaining both the fundamental features of WD40 stability and the advan- Abhyudai Singh tages of symmetry. University of Delaware [email protected] Loretta Au Department of Applied Mathematics & Statistics John Dennehy Stony Brook University CUNY [email protected] [email protected] PP1 Khem Ghusinga Modeling the Deformation of Proteins: from University of Delaware Coarse-Grained to Continuum [email protected] There has been much research in the area of mathemat- ically modeling of protein complexes using coarse-grained PP1 models or continuum models. We are proposing a new ap- Network Bursting in Inhibitory Neural Circuits proach that will combine the potential energy found in elas- tic network model or residual based coarse-grained models, We study the rhythmogenesis of oscillatory patterns emerg- and stress/strain components to produce a stiffness ma- ing in network motifs composed of inhibitory-coupled trix. This matrix will have the proteins anisotropic prop- parabolic bursters represented by the Plant model of erties encoded within it. The computed anisotropic elastic Aplysia-15 nerve cells. Such motifs are the building blocks moduli will be then used for simulating the deformation of of larger neural networks including central pattern genera- protein-complexes. tors controlling swim locomotion of sea slug Melibe leonine. George Borleske Deniz Alacam Graduate Student at Colorado State University Georgia State University [email protected] Mathematics Department [email protected] PP1 Andrey Shilnikov Demographics and Modeling of Multisite HPV In- Neuroscience Institute and Department of Mathematics fection and Transmission Georgia State University [email protected] The Human Papillomavirus (HPV) infects the epithe- lial layer at several anatomical sites in the human body (anogenital and oral/nasalpharyngeal), and certain HPV PP1 genotypes can lead to the development of cancer. We Test Criterion for Finding the Global Minimum of present a statistical analysis characterizing HPV trends a Function Using Exclusion Algorithm in the National Health and Nutrition Examination Survey (NHANES), with an emphasis on demographic differences The problem of finding the global minimum of a vector in multiple site concurrent and type-concordant infection. function is very common in science, economics and engi- Based on this data, we develop an ODE model of multisite neering. One of the most notable approaches to find the HPV infection and transmission. global minimum of a function is that based on interval analysis. In this area, the exclusion algorithms (EAs) are Andrew Brouwer a well-known tool for finding the global minimum of a func- University of Michigan tion over a compact domain. There are several choices for [email protected] the minimization condition In this paper, we introduce a new exclusion test and analyze the efficiency and compu- Rafael Meza tational complexity of exclusion algorithms based on this University of Michigan approach.We consider Lipschitz functions and give a new Department of Epidemiology minimization condition for the exclusion algorithm. Then [email protected] 126 LS14 Abstracts

Marisa Eisenberg sic mechanisms of release, escape, and post-inhibitory re- University of Michigan bound, reciprocally inhibitory Fitzhugh-Nagumo type net- [email protected] works can produce a range of phase-locked states such as anti-phase bursting, propagating waves, and peristaltic patterns with recurrently phase-varying lags. Phase-lag PP1 return maps identify phase states, with rhythm switching Binocular Rivalry Waves in Directionally Selective and attractor robustness revealed using external inhibition. Neural Fields Our qualification promotes the use of simplified modeling for CPG circuitries. Binocular rivalry is the phenomenon that occurs when an observer is presented with two different conflicting images Jarod Collens in the two eyes and the visual perception switches back Georgia State University and forth between the two images. We have analyzed this [email protected] by constructing traveling wave solutions to a system of integro-differential equations describing the network activ- Aaron Kelley ity of a population of directionally selective neurons. We GSU have shown that waves travel faster in the direction of stim- [email protected] ulus motion than against it. Sam R. Carroll Deniz Alacam University of Utah Georgia State University [email protected] Mathematics Department [email protected] Paul C. Bressloff University of Utah and University of Oxford, UK Tingli Xing Department of Mathematics Georgia State University bressloff@math.utah.edu USA [email protected]

PP1 Justus T. Schwabedal Modeling Interactions Between Two Major South- Division of Sleep Medicine, Brigham & Women’s Hospital eastern U.S. Sea Turtle Nest Predators and Their Harvard Medical School Effects on Nest Depredation Rates [email protected]

This project is investigating intraguild predation between Andrey Shilnikov two major sea turtle nest predators, North American rac- Neuroscience Institute and Department of Mathematics coons and Atlantic ghost crabs. In addition, ghost crab Georgia State University predation assists raccoons in finding nests, thereby facil- [email protected] itating secondary nest depredation (i.e., facilitative pre- dation). Our objectives are to characterize the dynamic interactions between intraguild predators and their effects PP1 on prey through the use of an ODE model and determine Modeling the Dynamics of Opioid Abuse the role that facilitative predation has in influencing nest densities. We extend previous models of the population-level dynam- ics of drug abuse to describe opioid abuse. In particular, Joshua Castro we derive a compartmental model that accounts for light University of Central Florida and heavy prescription opioid users, heroin users, and the [email protected] treatment-relapse cycle often observed in opioid addiction. We investigate the sensitivity of the models parameters to John Weishampel the heavy-prescription-opioid and heroin-using population. University of Central Florida Finally, we derive and analyze the stability of the models Department of Biology fixed points, estimate several model parameters, and make [email protected] predictions.

Andrew Nevai William Consagra Department of Mathematics Rochester Institute of Technology University of Central Florida School of Mathematical Sciences [email protected] [email protected]

Pedro Quintana-Ascencio University of Central Florida PP1 Department of Biology A Computational Model for a Porous Viscoelastic [email protected] Cytoskeleton with Applications to Cell Mechanics Cell movement is crucial to physiological processes such PP1 as wound healing, cancer metastasis, and embryonic de- Intrinsic Mechanisms for Pattern Generation in velopment. We present a computational framework to in- Three-Node Networks vestigate cell movement involving either pressure-driven or polymer-rich protrusions. Our framework incorporates a Bursting patterns can be qualified and modeled using low- porous viscoelastic cytoskeleton, a model of adhesion to the dimensional models. We show that, depending on intrin- substrate, and a cell environment with changing material LS14 Abstracts 127

properties. We quantify how cells mechanically sense their [email protected] surroundings and react to changing environments by alter- ing their shape and adhesion to the substrate to achieve Alicia Prieto Langarica optimal migration. Youngstown State University [email protected] Calina A. Copos University of California Davis Selenne Garcia-Torres [email protected] University of Southern California Department of Mathematics Robert D. Guy [email protected] Mathematics Department University of California Davis [email protected] PP1 How Robust Is the Zero-Lag Synchrony When Two PP1 Neurons Interact Via a Third Relay Neuron Predicting Severity and Periodicity of Mountain A remarkable zero time lag synchronization of two cerebral Pine Beetle Outbreaks cortical areas with long distant, which results significant conduction delays, have revealed experimentally and nu- We develop an age-structured forest demographic model merically. It has been proposed that the synchronization that incorporates temperature dependent bark beetle in- of two delay-coupled oscillators can be achieved by relaying festation. The model is parametrized using data from a the dynamics via a third mediating element. Using phase 1995-2005 outbreak in central Idaho. The stability of fixed oscillators, we have analytically investigated the dynam- points is analyzed as a function of (thermally controlled) ical relay problem for three oscillators.Our results show growth rates, and indicates the existence of periodic out- that the complete zero-lag synchrony can be achieved only breaks which increase with severity as growth rates in- in symmetric case, when the outer neurons are identical crease. We devise an analytical method to predict outbreak and the connections are symmetric. We have also shown severity and duration as well as expected time between out- that how phase lag of the outer neurons in the locked state breaks. depends on inhomogeneity in presence of small mismatch in the parameters of the neurons and the synapses. The Jacob P. Duncan, James Powell, Luis Gordillo results show very good agreement with numerical results Utah State University of the conductance based models. [email protected], [email protected], [email protected] Zahra Ghasemi Esfahani, Alireza Valizadeh Institute of Advanced Studies in Basic Science, Iran Joe Eason [email protected], [email protected] University of Utah [email protected] PP1 Investigating the Effect of Atropine on Barorecep- PP1 tor Heart Rate Regulation Temperature Effects on REM/Non-REM Sleep Dy- namics Atropine and metropolol (betablockers) act as competitive antagonists of the neurotransmitters acetylcholine and no- Experimental work and prior models suggest changes in radrenaline within the autonomic nervous system. This ambient temperature can affect sleep patterns in humans. study presents a non-linear baroreflex differential equa- We have designed a mathematical model describing nu- tions model, incorporating neurotransmitter concentra- merous features of the human sleep/wake cycle and as- tions. We investigate the impact of admission of atropine pects of REM/non-REM dynamics. The model simulates and metropolol on heart rate dynamics during head-up tilt. temperature changes detected by neurons in the POAH Global sensitivity analysis and optimization is used to val- that, in turn, affect the REM/non-REM cycles during idate and investigate the model using experimentally mea- sleep through a state-dependent homeostatic process. This sured blood pressure and heart rate data for different doses model will help to better understand temperature and sleep of medication. relationships and support experimental findings. Christian H. Haargaard Olsen Pamela B. Fuller PhD student Biomathematics Program Rensselaer Polytechnic Institute North Carolina State University [email protected] [email protected]

Janet Best Mette S. Olufsen The Ohio State University Department of Mathematics Department of Mathematics North Carolina State University [email protected] [email protected]

Gemma Huguet Johnny T. Ottesen Centre de Recerca Matematica Roskilde University [email protected] Department of Mathematics [email protected] Shelby Wilson Morehouse College Jesper Mehlsen 128 LS14 Abstracts

Frederiksberg Hospital stochastic in nature. We study the role of this stochastic- Denmark ity and how it relates to synchronization, especially in cases [email protected] when the time scale of the stochastic process is slow with regard the inherent time scale of the system. We find that Hien T. Tran such a system can favor synchrony, despite the network Department of Mathematics being disconnected for large time intervals. North Carolina State University [email protected] Russell Jeter, Igor Belykh Department of Mathematics and Statistics Georgia State University PP1 [email protected], [email protected] Accelerated Uzawa Iteration for the Stokes Equa- tions PP1 The finite-element discretization of the Stokes equations Two-Theta Neuron: Phase Models for Bursting leads to a saddle-point problem Networks      ABT u f = (1) We propose a reduction approach to study bursting out- B 0 p 0 comes of central pattern generators using coupled two- theta phase models. We examine several configurations A B where is symmetric positive-definite and is full-rank. of 3-cell CPGs with inhibitory, excitatory and electri- The system (1) is explored using the Uzawa iteration cal synapses, and compare our findings with correspond- T ing exemplary networks comprised of plausible Hodgkin- Auk+1 = f − B pk p p ωB . Huxley models. Occurrence, robustness and transforma- k+1 = k + uk+1 tions of CPG outcomes are studied using 2D return maps, Regarding this as a fixed-point iteration on u and p,we whose stable fixed points and invariant circles correspond augment it with Anderson acceleration to improve the con- to bursting patterns with fixed and varying phase lags. vergence. We show the results of a numerical study in which we compare the performance in several test cases of Aaron Kelley Uzawa iteration with and without acceleration as well as GSU several alternative solution approaches. [email protected]

Nguyenho Ho Mathematical Sciences Department PP1 Worcester Polytechnic Institute A Linear Analysis of a Straight Rod under Tension [email protected] Both With and Without Drag

SarahD.Olson,HomerF.Walker Starting with a straight rod under tension, we are studying Worcester Polytechnic Institute the perturbations in twist and bend using the Kirchhoff [email protected], [email protected] Rod Model. Additionally, we can include the effects of drag approximated by resisted force theory. Finally, this model can inform us about the response of internal forces PP1 compared to external ones. This work has applications to Determining An Optimal Mathematical Model for the study of worm locomotion, bacterial flagella, and DNA. Tumor Growth Cancer proves to be a major medical issue that is a lead- Victoria Kelley ing cause of death and much research is devoted to finding James Madison University effective treatments. Mathematical models play an impor- [email protected] tant role in this effort by providing a framework to optimize proposed treatments. In order to make accurate predic- tions, models need to correctly predict tumor growth. We PP1 test previously proposed models of tumor growth by fitting Conserved NPZ Models with Time Delay them to data to determine an optimal model. Nutrient-Phytoplankton-Zooplankton (NPZ) models are Hana Jaafari, Michael Ellis used to describe the bottom two trophic levels of an un- Texas Christian University derwater ecosystem. Time delays arise naturally in these [email protected], [email protected] models, such as the time it takes for juvenile plankton to reach maturity. Our focus is on models in which the total Hana Dobrovolny biomass in the system is conserved. We then explore how Department of Physics the quantity of biomass and the delay properties have on Ryerson University behaviour such as persistence and stability. [email protected] Matt Kloosterman University of Waterloo PP1 [email protected] Synchrony in Metapopulations with on-off Stochas- tic Dispersal Sue Ann Campbell University of Waterloo We consider ecological networks in which migration be- Dept of Applied Mathematics tween patches and other intrinsic system parameters are [email protected] LS14 Abstracts 129

Francis Poulin [email protected], [email protected] Department of Applied Mathematics University of Waterloo Adam Mahdi [email protected] North Carolina State University [email protected] PP1 Prediction of Biphasic Mitogenic Activity by Hgf, PP1 a Cancer-Associated Stroma-Derived Growth Fac- Periodic Accumulation of Genetic Variation in the tor, Using a Multi-Species Continuum Model. Genome of the Plant Sorghum bicolor A large number of growth factors and drugs are known An organism’s genome is a key determinant of its pheno- to act in a biphasic manner: at lower concentrations they cause increased division of target cells, whereas at higher type. Genetic variation produces much of the phenotypic concentrations the mitogenic effect is inhibited. Often, the variation on which evolutionary forces act, and we aim to molecular details of the mitogenic effect of the growth fac- identify signatures of factors influencing the accumulation tor are known, whereas the inhibitory effect is not. Hepa- of genetic variation. We show that periodic accumula- toctyte Growth Factor, HGF, has recently been recognized tion of genetic variation exists in the genome of the plant as a strong mitogen that is present in the microenviron- Sorghum bicolor and suggest that this periodicity is the re- ment of solid tumors. Recent evidence suggests that HGF sult of biological phenomena, such as chromatin structure acts in a biphasic manner on tumor growth. We build and selection. a multi-species model of HGF action on tumor cells us- Ryan F. McCormick, Sandra K. Truong, Sandra K. ing different hypotheses for high dose-HGF activation of Truong, John Mullet a growth inhibitor and show that the shape of the dose- Department of Biochemistry & Biophysics response curve is directly related to the mechanism of in- Texas A&M University hibitor activation. We thus hypothesize that the shape of a [email protected], [email protected], dose-response curve is informative of the molecular action [email protected], [email protected] of the growth factor on the growth inhibitor.

Anna Konstorum University of California, Irvine PP1 [email protected] Gene Regulatory Network Based on a Novel Evolv- able Partially Connected Artificial Neural Network

PP1 DNA microarray technology provides the expression lev- The Role of CD200-CD200R in Cancer Suppression els of thousands genes and make it possible to investigate and Promotion the complex biological processes. Finding relationships between genes and construct a Gene regulatory Network CD200-CD200R is an inhibitive signal that tumor cells (GRN) is subject of interest. To this aim, we proposed use it to silence macrophages in tumor microenvironment. a novel Partially connected Artificial Neural Network with It has been shown that CD200-CD200R has apparently Evolvable Topology (PANNET) in inferring the GRN from two contradictory experimental results in tumor growth: time series gene expression data. This approach can il- inhibition and promotion. We develop a mathematical lustrate the underlying biological behaviors without prior model to qualitative fits with experimental results and knowledge of the system explain why these two opposite experimental results can both take place depending on the ”affinity” of M1 and M2 Mina Moradi Kordmahalleh macrophages to form the complex CD200-CD200R with North Carolina A&T State Unviersity tumor. [email protected]

Kang-Ling Liao, Xue-Feng Bai, Avner Friedman Mohammad Gorji Sefidmazgi Ohio State University PhD Student [email protected], ., . North Carolina A&T State University [email protected] PP1 Abdollah Homaifar Patient-Specific Modeling of Average Cerebral North Carolina A&T State University Blood Flow During Orthostatic Stress [email protected] Cerebral autoregulation is a combination of local mecha- nisms responsible for maintaining a stable cerebral blood flow during changes in arterial blood pressure. This talk PP1 presents a simple patient-specific autoregulatory model Accumulation Behavior that predicts the average cerebral blood flow velocity amidst dramatic changes in arterial blood pressure during We introduce a Markov Chain variant to model the accu- the sit-to-stand procedure. The model will be validated mulation behavior of a population and provide a forecasted against experimental data and results will be compared confidence set of items to be accumulated in a future pe- to explore physiological differences between healthy young, riod which may differ in length from the derived period. In healthy elderly, and hypertensive elderly individuals. non-sequential accumulation it will be established that the eigenvalues of this model are always real. Gregory C. Mader, Mette S. Olufsen Department of Mathematics Thomas Morrisey North Carolina State University Infosys 130 LS14 Abstracts

[email protected] piecewise smoothness of coupling enables us to consider a sequence of fast subsystems in piecewise way. Our anal- ysis shows that slow dynamics as well as fast dynamics PP1 incorporate to determine where fast jumps actually go. Distribution of Correlated Spiking Events in Integrate-and-Fire Networks Choongseok Park Department of Mathematics Randomly connected populations of spiking neurons dis- North Carolina A&T State University play a rich variety of dynamics. We address the conceptual [email protected] issue of how to mathematically characterize the partially synchronous multiple firing events (MFEs) which manifest Jonathan Rubin in between homogeneous and total synchronous dynamics. University of Pittsburgh Using a geometric method for obtaining the distribution of Pittsburgh, PA magnitudes of these MFEs, we recast the cascading firing [email protected] event process as a first-passage time problem, establishing a link between the voltage distribution of excitatory and inhibitory neurons and the number of neurons firing in an PP1 MFE. Modeling the Effects of Craniosynostosis on In- tracranial Pressure Katherine Newhall Courant Institute of Mathematical Science Craniosynostosis is a condition where the plates in a new- New York University borns skull fuse prematurely. In some cases cognitive de- [email protected] velopment is impaired. Impairment is caused by increased intracranial pressure that arises in untreated craniosyn- Jiwei Zhang ostosis. Our research attempts to quantify the effect of New York University craniosynostosis by mathematically modeling the growing Courant Institute of Mathematical Science skull/brain system and investigating how the fusion of var- [email protected] ious plates affects pressures in this system. We use the finite element method to solve the model equations, and Adi Rangan conclude that in certain cases intracranial pressures rise Courant Institute of Mathematical Sciences above the critical value of 15 mmHg. [email protected] Jackson Penning, Madeline Anderson, Emily Van Heel, Douglas Zhou Magda Stolarska Shanghai Jiao Tong University University of St. Thomas [email protected] [email protected], [email protected], [email protected], [email protected]

PP1 PP1 Modeling Dynamics of Mosquito Populations and Assessing Abatement Strategies for West Nile Investigation of Dual Virus Infection of Human Virus Respiratory Tract We designed a mathematical model and compared it with Recent studies have revealed that about 40 percent of in- surveillance data for mosquitoes that are primary vectors of fluenza like illness are caused by simultaneous infections West Nile Virus (WNV). Based on the best fit of the model by more than one virus. The effect of multiple virus infec- to the data, we estimated key parameters such as the effec- tions on the severity of illness is not clear. We investigate a tiveness of insecticide treatments. We used these estimates mathematical model of dual virus infections to determine for modeling the spread of WNV to obtain more reliable conditions that make these infections more or less severe disease outbreak predictions and performed numerical sim- than single virus infections. ulations to test various mosquito abatement strategies. Lubna Pinky Kasia A. Pawelek, Patrick R. Niehaus, Cristian Salmeron Graduate student(Ph.D), University of South Carolina Beaufort Physics & Astronomy Department,TCU [email protected], [email protected], [email protected] [email protected] Hana Dovrobolny Elizabeth J. Hager, Gregg J. Hunt Assistant Professor Beaufort County Mosquito Control Physics and Astronomy Department,TCU [email protected], [email protected] [email protected]

PP1 PP1 Activity Patterns of Neuronal Network with Synchronization of Bursting Neurons: a Synergetic Voltage-Sensitive Piecewise Smooth Coupling Effect of Excitation and Inhibition We present an analysis of activity patterns in a neuronal We study synchronization of bursting neurons with excita- network of three mutually inhibitory cells with voltage- tory and inhibitory connections. Fast inhibition is known sensitive piecewise smooth coupling. While standard fast- to promote pairwise asynchrony in inhibitory bursting net- slow analysis fails to describe the dynamics during fast works. We show that the addition of such repulsive inhi- jumps due to the voltage-sensitive nature of coupling, bition to excitatory networks induces bursting synchrony, LS14 Abstracts 131

in contrast to one’s expectations. Through stability and Joel Tabak geometrical analysis, we reveal the mechanism underly- Dept of Biological Sciences ing this purely synergetic phenomenon and show that it Florida State University originates from the transition between bursting of different [email protected] types caused by excitatory-inhibitory synaptic coupling. Peter Duncan, Mike Shipston Reimbay Reimbayev, Igor Belykh Centre for Integrative Physiology Department of Mathematics and Statistics University of Edinburgh Georgia State University [email protected], [email protected] [email protected], [email protected] Richard Bertram PP1 Department of Mathematics Florida State University Determining Mechanism of Action and Efficacy of [email protected] Novel Influenza Antivirals

Influenza is a serious viral infection common in humans PP1 that can cause deadly pandemics. Drug treatment is a first Identifiability of Linear Dynamical Systems from a line of defense against pandemics and many compounds are Single Trajectory tested as influenza antivirals. We use mathematical models to identify experiments that can determine the mechanism In parameter estimation, before implementing numerical of action of an influenza antiviral. methods, it is important to determine whether the pa- rameter estimation problem will have a unique solution in Thalia Rodriguez the presence of unlimited and error free data. This is the Texas Christian University question of structural identifiability. For linear systems of [email protected] ODEs , I will present a straightforward criterion for iden- tifiability from one trajectory, solely based on geometric Hana Dobrovolny properties of the trajectory. Several illustrative examples Department of Physics will be discussed. Ryerson University [email protected] Shelby R. Stanhope University of Pittsburgh [email protected] PP1 Within-Host Models of Influenza Virus Infection: Jonathan Rubin TheRoleofMacrophages University of Pittsburgh Pittsburgh, PA Influenza strains can be categorized as either with low (LP) [email protected] or high pathogenicity (HP). We developed a mathematical model which includes the pathogenic role of the immune David Swigon system cells to study the within-host dynamics influenza Department of Mathematics infections caused by the HP viruses. By comparing mod- University of Pittsburgh eling predictions with both macrophage and viral kinetic [email protected] data, we examined their contribution to the overall patho- genesis of HP viruses and quantified the difference between seasonal and HP viruses. PP1 From Chaos to Periodicity: Revisiting the Logistic Cristian Salmeron, Kasia A. Pawelek Map with an Ecologically Realistic Spatial Struc- University of South Carolina Beaufort ture and Dispersal Mechanism [email protected], [email protected] We improve on traditional applications of the logistic map to spatially extended systems by explicitly introducing spa- PP1 tial length scale, dispersal shape, and absorbing boundary Bursting in the Pituitary Corticotroph: The Role conditions. In this way we greatly improve ability to ap- of Bk Ion Channels ply model outputs to real-world ecological systems. For a large range of parameters we find spatiotemporally chaotic Pituitary corticotrophs from male rats exhibit a variety of population distributions abruptly give way to periodicity. electrical activity patterns, including spiking and several As growth rate and dispersal distance increase, we witness forms of bursting. Stimulation with corticotrophin releas- an evolving metapopulation structure with three phases. ing hormone and arginine vasopressin convert the spiking to bursting. Surprisingly, the bursting occurs even though Laura Storch, James Pringle the SK type of calcium-activated potassium ion channels University of New Hampshire are not expressed. We use mathematical modeling to un- [email protected], [email protected] derstand how calcium- and voltage-dependent BK channels can produce the bursting produced by stimulated corti- cotrophs. PP1 Identifying Physiological Origins of Barorecep- Sevgi Sengul tor Firing Characteristics Through a Conductance Department of Mathematics Based Neural Model Florida State University [email protected] In this study we investigate aortic baroreceptors, stretch 132 LS14 Abstracts

sensitive neurons with endings embedded in the arterial Scale Oscillations walls. The firing rate of these neurons is a key physiologi- cal signal in cardiovascular regulation. We investigate the Our goal is to understand bursting dynamics in three time physiological basis of key characteristics of this firing pat- scale systems. Such systems arise in biological settings such tern through an ion channel based model of the membrane as the interaction of intrinsic calcium oscillations with a voltage. Comparisons of models with differing ensembles calcium-dependent, voltage-gated membrane potential os- of ion channels provide insight into the origins of certain cillation mechanism. With this motivation, we construct a firing characteristics. model having three time scales with two copies of Morris- Lecar equations. Using techniques from geometric singular Jacob Sturdy perturbation theory, we explain the mechanisms underly- North Carolina State University ing the dynamics and elucidate which characteristics truly [email protected] represent three time scale features.

Johnny T. Ottesen Yangyang Wang Roskilde University University of Pittsburgh Department of Mathematics [email protected] [email protected] Pingyu Nan, Vivien Kirk Mette S. Olufsen University of Auckland Department of Mathematics [email protected], [email protected] North Carolina State University [email protected] Jonathan Rubin University of Pittsburgh Pittsburgh, PA PP1 [email protected] Leaf Inclination Angle Regulates the Distribution of Light in the Sorghum Canopy PP1 Light interception is the first step in photosynthesis. Math- Coupling-Induced Synchronization of Mexican ematical modeling of the light environment of sorghum, an Jumping Beans agriculturally important crop, predicts that changes in the angle that a leaf emerges on a plant will confer changes in Mexican jumping beans jump to move from higher to lower its light interception. This led to the identification of loci temperatures for optimal survival. By characterizing their associated with the genetic regulation of leaf inclination jumping pattern containing two characteristic frequencies angle and continues to guide field experimentation toward of jumping and rest, and by inducing a physical nearest optimizing light interception in sorghum. neighbor coupling through the attachment of string, we seek to synchronize their motions experimentally. We com- Sandra K. Truong,SandraK.Truong,RyanF. pare this to computational results relating the behavior of McCormick, John Mullet the beans to an adaptation of Kuramoto model with fre- Department of Biochemistry & Biophysics quency modulated oscillators accounting for the atypical Texas A&M University jumping behavior. [email protected], [email protected], ryan- Andrea J. Welsh, Flavio Fenton, Ilija Uzelac [email protected], [email protected] Georgia Institute of Technology [email protected], fl[email protected], il- PP1 [email protected] Modeling the Effect of Antiarrhythmic Agents on the Action Potential of Human Ventricular Cells PP1 Phenotypic Modulation of Virulence Facilitates Sudden cardiac death from ventricular fibrillation is a ma- Pathogen Invasion of the Gut jor cause of death worldwide. Several different classes of antiarrhymia drugs are currently available each of which The interior lining of the human intestine is inhabited by alters a different membrane ion conductance. A human populations of commensal microbiota, which provide de- cardiac cell model is used to study the effect of the differ- fense against invasive bacteria. Surprisingly, Salmonella ent antiarrhythmia drugs on the physical characteristics of Typhimurium gains an environmental advantage over the cardiac action potentials. commensals by provoking the hosts inflammatory defenses. We develop and analyze a model of the competition be- Binaya Tuladhar tween the commensals and Salmonella, which incorporates Texas Christian University a simple model of the inflammatory response, to explore Fort Worth, TX possible mechanisms by which Salmonella exploits the im- [email protected] mune response to outcompete the commensals.

Hana Dobrovolny Glenn S. Young, Bard Ermentrout Department of Physics University of Pittsburgh Ryerson University Department of Mathematics [email protected] [email protected], [email protected]

Jonathan Rubin PP1 University of Pittsburgh Understanding and Distinguishing Three Time Pittsburgh, PA LS14 Abstracts 133

[email protected] 134 2014 SIAM Conference on the Life Sciences

LS14 Speaker and Organizer Index

Italicized names indicate session organizers. 2014 SIAM Conference on the Life Sciences 135

A Barranca, Victor, MS6, 11:00 Mon Carin, Larry, MS7, 10:00 Mon Abarbanel, Henry D., MS31, 9:30 Tue Barranca, Victor, MS14, 2:00 Mon Carr, Thomas W., CP2, 4:30 Mon Abbas, Kaja, MS24, 10:00 Tue Barreiro, Andrea K., MS20, 4:30 Mon Carroll, Sam R., PP1, 8:00 Tue Ackleh, Azmy S., MS1, 11:00 Mon Barreiro, Andrea K., MS20, 4:30 Mon Castro, Joshua, PP1, 8:00 Tue Agusto, Folashade, MS53, 3:30 Wed Bathe, Mark, MS26, 9:30 Tue Chaudhuri, Rishidev, MS58, 3:30 Wed Akudibillah, Gordon, MS54, 3:00 Wed Battista, Nicholas A., MS13, 2:30 Mon Chen, Duan, MS69, 9:30 Thu Alacam, Deniz, PP1, 8:00 Tue Beale, J. Thomas, MS42, 4:30 Tue Chen, Duan, MS69, 11:00 Thu Albasini Mourao, Marcio Duarte, CP12, Belair, Jacques, MS38, 2:00 Tue Chen, Duan, MS77, 2:15 Thu 5:30 Wed Belkhatir, Zehor, CP15, 5:30 Wed Chen, Zhan, MS63, 4:30 Wed Alford, John G., CP1, 2:00 Mon Bertram, Richard, MS23, 4:30 Mon Chen, Zi, MS3, 9:30 Mon Allard, Jun, MS19, 6:00 Mon Bertram, Richard, MS31, 9:30 Tue Chen, Zi, MS3, 11:00 Mon Allen, Linda J., MS66, 9:30 Thu Bertram, Richard, MS31, 10:30 Tue Cherry, Elizabeth M., MS51, 9:30 Wed Allen, Richard, CP7, 6:00 Tue Best, Janet, MS71, 9:30 Thu Cherry, Elizabeth M., MS51, 9:30 Wed Alolyan, Ibraheem, PP1, 8:00 Tue Best, Janet, MS71, 9:30 Thu Cherry, Elizabeth M., MS59, 2:00 Wed Aminzare, Zahra, CP7, 5:00 Tue Best, Janet, MS79, 2:15 Thu Cho, Carolyn, MS38, 3:30 Tue Amorim, Paulo V., CP13, 10:00 Thu Bickel, Scott T., CP8, 11:00 Wed Chung, Matthias, MS2, 9:30 Mon Amro, Rami M., CP4, 2:30 Tue Block, Michael, MS62, 6:00 Wed Chung, Matthias, MS2, 9:30 Mon Arciero, Julia, MS34, 2:00 Mon Boëte, Christophe, MS17, 5:30 Mon Chung, Matthias, MS10, 2:00 Mon Ardekani, Arezoo, MS27, 10:30 Tue Booth, Victoria, MS44, 4:30 Tue Chung, Matthias, MS33, 2:00 Tue Armiento, Aurora, MS16, 3:00 Mon Borleske, George, PP1, 8:00 Tue Cintron-Arias, Ariel, CP6, 5:00 Tue Arnold, Andrea N., MS67, 11:00 Thu Boros, Balázs, MS15, 3:30 Mon Ciupe, Stanca, MS2, 9:30 Mon Aston, Philip J., MS47, 9:30 Wed Bortz, David M., MS8, 9:30 Mon Ciupe, Stanca, MS10, 2:00 Mon Aston, Philip J., MS47, 9:30 Wed Bortz, David M., MS8, 10:00 Mon Collens, Jarod, PP1, 8:00 Tue Au, Loretta, MS45, 4:30 Tue Bortz, David M., MS16, 2:00 Mon Collins, James J., IP8, 1:00 Thu Au, Loretta, MS45, 4:30 Tue Bourgeron, Thibault, MS8, 11:00 Mon Conradi, Carsten, MS15, 3:00 Mon Au, Loretta, PP1, 8:00 Tue Bourouiba, Lydia, MS32, 2:30 Tue Consagra, William, PP1, 8:00 Tue Azer, Karim, MS43, 6:00 Tue Bourouiba, Lydia, MS78, 3:45 Thu Conway, Jessica M., MS2, 10:30 Mon Azer, Karim, MS62, 4:30 Wed Bragard, Jean, MS72, 10:00 Thu Copos, Calina A., PP1, 8:00 Tue Azer, Karim, MS62, 4:30 Wed Brauer, Fred, MS24, 9:30 Tue Craciun, Gheorghe, MS30, 11:00 Tue B Bressloff, Paul C., MS14, 2:00 Mon Craig, Morgan, MS38, 2:30 Tue Baker, Michelle, CP15, 4:30 Wed Brouwer, Andrew, PP1, 8:00 Tue Curto, Carina, MS49, 9:30 Wed Banaji, Murad, MS30, 9:30 Tue Brown, Heidi, MS65, 5:30 Wed Curtu, Rodica, MS50, 9:30 Tue Banerjee, Sandip, MS47, 10:00 Wed Browne, Cameron, MS10, 2:00 Mon Curtu, Rodica, MS50, 9:30 Wed Banks, H. T., MS62, 5:30 Wed Burns, John A., MS65, 5:00 Wed Curtu, Rodica, MS58, 2:00 Wed Banks, H. Thomas, MS8, 10:30 Mon C D Bannish, Brittany, MS29, 9:30 Tue Cai, Wei, MS69, 9:30 Thu Dahari, Harel, MS61, 4:30 Wed Bannish, Brittany, MS29, 11:00 Tue Cai, Wei, MS77, 2:15 Thu Dai, Shibin, MS48, 10:00 Wed Bardhan, Jaydeep P., MS63, 4:30 Wed Cai, Yongli, CP2, 5:00 Mon Darcy, Isabel, MS49, 10:00 Wed Bardhan, Jaydeep P., MS63, 4:30 Wed Canic, Suncica, MS57, 3:30 Wed Das, Jayajit, MS41, 6:00 Tue Barnett, William H., MS28, 10:30 Tue Cappelletti, Daniele, MS39, 3:00 Tue Daun-Gruhn, Silvia, MS28, 10:00 Tue Barranca, Victor, MS6, 9:30 Mon David, Tim, MS25, 11:00 Tue

continued on next page 136 2014 SIAM Conference on the Life Sciences

David, Timothy, PD3, 8:45 Wed Forest, M. Gregory, MS68, 9:30 Thu Gupta, Chinmaya, MS73, 9:30 Thu Debroy, Swati, MS53, 2:00 Wed Fricks, John, MS41, 5:00 Tue Gupta, Chinmaya, MS81, 2:15 Thu Debroy, Swati, MS61, 4:30 Wed Frieboes, Hermann, MS7, 10:30 Mon Gupta, Chinmaya, MS81, 2:15 Thu Debroy, Swati, MS61, 5:00 Wed Fry, Brendan C., MS25, 9:30 Tue Gutierrez, Juan B., MS46, 10:30 Wed DeLeenheer, Patrick, MS66, 11:00 Thu Fry, Brendan C., MS25, 9:30 Tue Guy, Robert D., MS27, 9:30 Tue Denham, Sue, MS50, 10:00 Tue Fry, Brendan C., MS34, 2:00 Tue Guy, Robert D., MS36, 2:00 Tue Diao, Yuanan, MS49, 9:30 Wed Fryer, Dashiell, CP8, 10:30 Wed Guy, Robert D., MS36, 2:30 Tue Diao, Yuanan, MS49, 10:30 Wed Fu, Henry, MS36, 3:00 Tue Diao, Yuanan, MS56, 2:00 Wed Fu, Yibin, MT2, 9:30 Wed H Haargaard Olsen, Christian H., PP1, 8:00 Fuller, Pamela B., MS20, 5:30 Mon Ding, Wandi, MS66, 9:30 Thu Tue Fuller, Pamela B., MS44, 4:30 Tue Ding, Wandi, MS66, 10:00 Thu Haider, Mansoor A., MS43, 4:30 Tue Fuller, Pamela B., PP1, 8:00 Tue Ding, Wandi, MS74, 2:15 Thu Haider, Mansoor A., MS76, 2:15 Thu Fung, Isaac Chun-Hai, MS24, 9:30 Tue Donnell, Pete, MS30, 10:00 Tue Hamlet, Christina, MS5, 9:30 Mon Fung, Isaac Chun-Hai, MS32, 2:00 Tue Dorratoltaj, Nargesalsadat, MS32, 2:00 Hamlet, Christina, MS13, 2:00 Mon Tue Hamlet, Christina, MS13, 3:00 Mon Dovzhenok, Andrey A., CP11, 4:30 Wed G Galvani, Alison, IP5, 8:15 Wed Harper, Marc, CP9, 2:30 Wed Doyle, Matthew G., MS11, 3:00 Mon Gao, Tony, MS36, 3:30 Tue Hasan, Md Mehedi M., CP5, 5:00 Tue Duke-Sylvester, Scott, MS17, 5:00 Mon Garcia-Torres, Selenne, MS44, 5:00 Tue Hastings, Alan M., IP7, 8:15 Thu Duncan, Jacob P., PP1, 8:00 Tue Gardiner, Bruce S., MS25, 10:00 Tue He, Jing, MS63, 5:00 Wed E Garlick, Martha J., CP13, 10:30 Thu Heberling, Tamra, CP14, 2:45 Thu Eisenberg, Bob, MS69, 9:30 Thu Geng, Weihua, MS42, 4:30 Tue Heffernan, Jane, MS10, 3:00 Mon Eisenberg, Marisa, MS75, 2:15 Thu Geng, Weihua, MS42, 6:00 Tue Hellevik, Leif, MT2, 9:30 Wed Elston, Timothy, PD3, 8:45 Wed, George, Uduak Z., MS57, 2:30 Wed Hendrix, Angelean O., MS38, 3:00 Tue Elston, Timothy, MS68, 10:00 Thu Ghasemi Esfahani, Zahra, PP1, 8:00 Hill, Nicholas A., MS43, 4:30 Tue Ernst, Claus, MS49, 11:00 Wed Tue Hill, Nicholas A., MT2, 9:30 Wed Everett, Rebecca A., CP1, 2:30 Mon Gnacadja, Gilles, MS22, 5:00 Mon Hill, Nicholas A., MS80, 2:45 Thu Goldman, Daniel, MS34, 2:30 Mon Ho, Nguyenho, PP1, 8:00 Tue F Golowasch, Jorge, MS37, 3:30 Tue Hoffman, Kathleen A., MS4, 10:00 Mon Fan, Guihong, MS65, 4:30 Wed Golubitsky, Martin, MS58, 2:30 Wed Hoffman, Matthew J., MS59, 3:30 Wed Fancourt, Craig, MS21, 5:30 Mon Gopalkrishnan, Manoj, MS39, 2:00 Tue Holmes, William, MS60, 3:00 Wed Faulwell, Cullen J., PP1, 8:00 Tue Gopinath, Arvind, MS27, 10:00 Tue Hoover, Alexander, MS70, 9:30 Thu Feliu, Elisenda, MT1, 8:00 Tue Gordillo, Luis, CP9, 3:00 Wed Hoover, Alexander, MS70, 9:30 Thu Feliu, Elisenda, MS15, 2:00 Mon Gou, Kun, MS3, 9:30 Mon Hoover, Alexander, MS78, 2:15 Thu Feliu, Elisenda, MS22, 4:30 Mon Gou, Kun, MS3, 9:30 Mon Horng, Tzyy-Leng, MS77, 3:15 Thu Feng, Peng, MS40, 4:30 Tue Grabe, Michael, MS48, 9:30 Wed Hu, Dan, MS14, 3:30 Mon Feng, Zhilan, MS17, 4:30 Mon Graham, Erica J., MS21, 6:00 Mon Huang, Jingfang, MS42, 5:00 Tue Feng, Zhilan, MS17, 4:30 Mon Graham, Erica J., MS29, 9:30 Tue Hubbard, Letitia, MS59, 3:00 Wed Fenton, Flavio, MS51, 10:30 Wed Graham, Erica J., MS29, 9:30 Tue Hughes, John, MS41, 4:30 Tue Fenton, Flavio, MS72, 9:30 Thu Graham, Jason, MS18, 5:00 Mon Huguet, Gemma, MS50, 9:30 Wed Fletcher, Patrick A., MS23, 5:30 Mon Green, David F., MS26, 10:00 Tue Huguet, Gemma, MS58, 2:00 Wed Fok, Pak-Wing, MS11, 2:00 Mon Gudmand-Høyer, Johanne, CP11, 5:30 Huguet, Gemma, MS58, 2:00 Wed Fok, Pak-Wing, MS11, 2:00 Mon Wed Forde, Jonathan, MS10, 2:30 Mon Gumel, Abba, MS1, 10:00 Mon continued on next page 2014 SIAM Conference on the Life Sciences 137

I Kovacic, Gregor, MS6, 10:00 Mon Liu, Chun, MS77, 2:15 Thu Ingalls, Brian P., MS67, 10:30 Thu Krogh-Madsen, Trine, MS51, 11:00 Wed Liu, Xinfeng, MS52, 9:30 Wed Iron, David, MS60, 2:30 Wed Krueger, Justin, MS33, 2:00 Tue Liu, Xinfeng, MS60, 2:00 Wed Kuegler, Philipp, CP5, 4:30 Tue Liu, Xinfeng, MS60, 3:30 Wed J Kulkarni, Rahul, MS73, 10:30 Thu Lopez, Manuel, MS81, 3:45 Thu Jaafari, Hana, PP1, 8:00 Tue Losert, Wolfgang, MS7, 11:00 Mon Jang, Sophia, MS40, 4:30 Tue L Lu, Benzhuo, MS26, 9:30 Tue Jang, Sophia, MS40, 5:00 Tue Lander, Arthur, IP4, 1:00 Tue Lu, Benzhuo, MS26, 10:30 Tue Jang, Sophia, MS46, 9:30 Wed Lanz, Aprillya, MS61, 5:30 Wed Lu, Benzhuo, MS35, 2:00 Tue Jensen, Oliver E., IP3, 8:15 Tue Lau, Kevin D., MS43, 5:00 Tue Lubkin, Sharon, MS57, 2:00 Wed Jensen, Oliver E., PD3, 8:45 Wed Lawley, Sean D., MS79, 3:15 Thu Luo, Xiaoyu, MT2, 9:30 Wed Jeter, Russell, PP1, 8:00 Tue Layton, Anita T., MS76, 2:45 Thu Luo, Xiaoyu, MT2, 9:30 Wed Jiang, Yi, MS76, 3:15 Thu Leander, Rachel, MS66, 9:30 Thu Ly, Cheng, MS20, 5:00 Mon Jilkine, Alexandra, MS60, 2:00 Wed Leander, Rachel, MS66, 10:30 Thu Johnson, Maya E., MS3, 10:00 Mon Leander, Rachel, MS74, 2:15 Thu M Johnston, Matthew, MS22, 6:00 Mon Lee, Christopher, CP9, 2:00 Wed Ma, Baoling, MS16, 2:30 Mon Jones, Shannon, MS78, 2:45 Thu Lee, Pilhwa, MS80, 2:15 Thu Ma, Junling, MS24, 11:00 Tue Joshi, Badal, MS22, 4:30 Mon Lee, Pilhwa, MS80, 2:15 Thu MacGregor, Duncan J., MS23, 4:30 Mon Joshi, Sunnie, MS3, 10:30 Mon Lee, Pilhwa, MS77, 3:45 Thu MacGregor, Duncan J., MS23, 5:00 Mon Josic, Kresimir, MS6, 9:30 Mon Lee, Sunmi, MS40, 5:30 Tue MacGregor, Duncan J., MS31, 9:30 Tue Josic, Krešimir, CP11, 5:00 Wed Leiderman, Karin, MS36, 2:00 Tue Maclaurin, James, CP4, 3:00 Tue Ju, Tao, MS63, 6:00 Wed Lejon, Annelies, CP1, 3:00 Mon Mader, Gregory C., PP1, 8:00 Tue Lenhart, Suzanne M., MS54, 2:00 Wed Mahdi, Adam, MS75, 2:15 Thu K Lenhart, Suzanne M., PD3, 8:45 Wed Malka, Roy, CP15, 5:00 Wed Kang, Yun, MS40, 4:30 Tue Lenhart, Suzanne M., MS74, 2:15 Thu Malutina, Elena, CP4, 3:30 Tue Kang, Yun, MS40, 6:00 Tue Leviyang, Sivan, MS2, 10:00 Mon Martcheva, Maia, MS1, 9:30 Mon Kang, Yun, MS46, 9:30 Wed Levy, Doron, MS46, 9:30 Wed Martcheva, Maia, MS1, 9:30 Mon Kappel, Franz, MS47, 10:30 Wed Levy, Rachel, MS64, 5:30 Wed Martcheva, Maia, MS9, 2:00 Mon Karabiyik, Tugba, CP13, 11:00 Thu Levy, Rachel, PD3, 8:45 Wed Mascagni, Michael, MS26, 11:00 Tue Keck, Dustin, MS16, 2:00 Mon Lewis, Owen, MS13, 2:00 Mon Mather, William H., MS81, 2:45 Thu Kelley, Aaron, PP1, 8:00 Tue Li, Bingtuan, MS18, 6:00 Mon Mazer, Norman, IP6, 1:00 Wed Kelley, Victoria, PP1, 8:00 Tue Li, Jia, MS74, 2:45 Thu McCormick, Ryan F., PP1, 8:00 Tue Kelly, Michael, MS54, 2:00 Wed Li, Jing, CP3, 10:30 Tue McKinley, Scott, MS79, 2:15 Thu Khan, Adnan, CP3, 9:30 Tue Li, Jun, MS38, 2:00 Tue Medlock, Jan, MS53, 2:00 Wed Kightley, Eric, MS16, 3:30 Mon Li, Michael, MS1, 10:30 Mon Meshkat, Nicolette, MT1, 2:00 Wed Kilpatrick, Zachary, MS58, 3:00 Wed Li, Sheng, MS24, 10:30 Tue Meshkat, Nicolette, MS15, 2:30 Mon Kim, Oleg, MS29, 10:00 Tue Li, Shuwang, MS48, 9:30 Wed Meshkat, Nicolette, MS75, 2:15 Thu Kloosterman, Matt, PP1, 8:00 Tue Li, Shuwang, MS55, 2:00 Wed Miao, Hongyu, MS75, 2:45 Thu Knepley, Matthew G., MS63, 5:30 Wed Li, Shuwang, MS55, 3:30 Wed Mikucki, Michael, MS55, 2:00 Wed Knutsdottir, Hildur, MS19, 5:00 Mon Li, Songting, MS14, 2:30 Mon Miller, Laura A., MS57, 2:00 Wed Kondic, Anna, MS21, 5:30 Mon Li, Xiaofan, MS69, 10:30 Thu Miller, Laura A., MS64, 4:30 Wed Konstorum, Anna, PP1, 8:00 Tue Liao, Kang-Ling, PP1, 8:00 Tue Miller, Laura A., MS64, 4:30 Wed Kostina, Ekaterina, MS33, 3:30 Tue Lin, Tai-Chia, MS69, 10:00 Thu Miller, Laura, MS70, 9:30 Thu continued on next page 138 2014 SIAM Conference on the Life Sciences

Miller, Laura, MS78, 2:15 Thu P S Mincheva, Maya, MS30, 9:30 Tue Pantea, Casian, MS30, 9:30 Tue Sachs, Jeff, MS62, 4:30 Wed Mincheva, Maya, MS39, 2:00 Tue Pantea, Casian, MS39, 2:00 Tue Sachs, Jeff, MS62, 5:00 Wed Mohammed-Awel, Jemal, MS46, 11:00 Park, Choongseok, PP1, 8:00 Tue Sachs, Jeff, PD3, 8:45 Wed Wed Pasour, Virginia B., MS13, 3:30 Mon Salac, David, MS55, 2:30 Wed Moradi Kordmahalleh, Mina, PP1, 8:00 Salmeron, Cristian, PP1, 8:00 Tue Tue Patel, Mainak, MS20, 6:00 Mon Samson, Julia E., MS70, 10:30 Thu Mori, Yoichiro, MS77, 2:45 Thu Patel, Swati, CP8, 10:00 Wed Santhanakrishnan, Arvind, MS78, 2:15 Morrisey, Thomas, PP1, 8:00 Tue Peercy, Bradford E., MS4, 9:30 Mon Thu Mubayi, Anuj, MS53, 2:00 Wed Peercy, Bradford E., MS4, 11:00 Mon Saucedo, Omar, MS53, 3:00 Wed Mubayi, Anuj, MS61, 4:30 Wed Penning, Jackson, PP1, 8:00 Tue Sauer, Timothy, MS31, 10:00 Tue Mueller, Stefan, MS30, 10:30 Tue Perminov, Valeriy D., CP3, 11:00 Tue Schmidt, Deena, MS79, 2:45 Thu Munoz, Laura, MS59, 2:00 Wed Phillips, Andrew, MS44, 6:00 Tue Schwabedal, Justus T., CP10, 4:30 Wed Murrugarra, David, MS73, 10:00 Thu Pinky, Lubna, PP1, 8:00 Tue Schwemmer, Michael, MS71, 10:30 Thu Murthy, Abhishek, MS59, 2:30 Wed Presse, Steve, MS41, 4:30 Tue Presse, Steve, MS41, 5:30 Tue Secomb, Timothy W., MS34, 3:00 Mon N Prieto Langarica, Alicia, MS44, 5:30 Selgrade, James F., MS21, 4:30 Mon Nagahara, Larry, MS7, 9:30 Mon Tue Selgrade, James F., MS21, 4:30 Mon Nekka, Fahima, MS38, 2:00 Tue Prosper, Olivia, MS53, 2:30 Wed Sengul, Sevgi, PP1, 8:00 Tue Nekka, Fahima, MS38, 2:00 Tue Sgouralis, Ioannis, MS25, 10:30 Tue Nevai, Andrew, MS9, 3:00 Mon R Shilnikov, Andrey, MS37, 2:30 Tue Ramirez, Samuel A., CP12, 4:30 Wed Nevai, Andrew, MS74, 3:15 Thu Shiu, Anne, MS15, 2:00 Mon Rangamani, Padmini, MS45, 5:30 Tue Newby, Jay, MS79, 3:45 Thu Shuai, Zhisheng, MS24, 9:30 Tue Rankin, James, MS50, 10:30 Tue Newhall, Katherine, MS20, 4:30 Mon Shuai, Zhisheng, MS32, 2:00 Tue Raue, Andreas, MS75, 3:15 Thu Newhall, Katherine, PP1, 8:00 Tue Shuai, Zhisheng, MS32, 3:30 Tue Rawdon, Eric, MS56, 2:30 Wed Newton, Paul, MS7, 9:30 Mon Siegel, David, MS39, 2:30 Tue Reed, Michael C., MS71, 9:30 Thu Nie, Qing, MS52, 9:30 Wed Simons, Julie, MS5, 9:30 Mon Reed, Michael C., MS68, 10:30 Thu Niehaus, Patrick R., PP1, 8:00 Tue Singh, Abhyudai, MS81, 3:15 Thu Reed, Michael C., MS79, 2:15 Thu Nirody, Jasmine, MS45, 6:00 Tue Skataric, Maja, CP7, 5:30 Tue Reimbayev, Reimbay, PP1, 8:00 Tue Novozhilov, Artem S., CP8, 9:30 Wed Snyder, Abigail, MS28, 9:30 Tue Reinitz, John, MS45, 5:00 Tue Numfor, Eric, MS54, 2:00 Wed Sobie, Eric, MS23, 6:00 Mon Rejniak, Katarzyna A., MS5, 10:00 Mon Numfor, Eric, MS54, 2:30 Wed Sontag, Eduardo, MS12, 2:00 Mon Remien, Christopher, MS47, 11:00 Wed Soofi, Wafa, MS37, 3:00 Tue Rendall, Alan, MS39, 3:30 Tue O Spardy, Lucy, MS28, 9:30 Tue O’Leary, Timothy, MS31, 11:00 Tue Reynolds, Angela M., CP6, 5:30 Tue Spardy, Lucy, MS37, 2:00 Tue Olson, Sarah D., MS5, 11:00 Mon Rinzel, John, IP1, 8:15 Mon Spardy, Lucy, MS71, 11:00 Thu Olufsen, Mette S., MS43, 4:30 Tue Robertson, Suzanne, MS74, 3:45 Thu Stamoulis, Catherine, CP10, 5:30 Wed Olufsen, Mette S., MS67, 9:30 Thu Robinson, Phyllis R., MS4, 9:30 Mon Stanhope, Shelby R., PP1, 8:00 Tue Opron, Kristopher, MS56, 2:00 Wed Rodriguez, Thalia, PP1, 8:00 Tue Staples, Anne, MS78, 3:15 Thu Oremland, Matthew, MS54, 3:30 Wed Rong, Libin, MS9, 2:30 Mon Starz-Gaiano, Michelle, MS4, 10:30 Osan, Remus, MS14, 3:00 Mon Rubin, Jonathan E., MS28, 9:30 Tue Mon Otani, Niels, MS72, 10:30 Thu Rubin, Jonathan E., MS37, 2:00 Tue Stepien, Tracy L., MS18, 4:30 Mon Ottesen, Johnny T., MS67, 9:30 Thu Ryan, Shawn, MS12, 3:00 Mon Stepien, Tracy L., MS18, 4:30 Mon Ottesen, Johnny T., MS67, 9:30 Thu

continued on next page 2014 SIAM Conference on the Life Sciences 139

Stoetzel, Claudia, MS21, 5:00 Mon U Wolgemuth, Charles, MS27, 11:00 Tue Stolarska, Magdalena, MS11, 2:30 Mon Udiani, Oyita, CP13, 9:30 Thu Wrobel, Jacek K., MS5, 9:30 Mon Storch, Laura, PP1, 8:00 Tue Wrobel, Jacek K., MS5, 10:30 Mon Strawbridge, Eva M., CP5, 5:30 Tue V Wrobel, Jacek K., MS13, 2:00 Mon Vaidya, Naveen K., CP6, 4:30 Tue Strychalski, Wanda, MS19, 4:30 Mon Wu, Hulin, MS2, 11:00 Mon Vandiver, Rebecca, MS11, 2:00 Mon Strychalski, Wanda, MS19, 5:30 Mon Vattikuti, Shashaank, MS50, 11:00 Tue Sturdy, Jacob, PP1, 8:00 Tue X Veliz-Cuba, Alan, CP7, 4:30 Tue Xia, Kelin, MS49, 9:30 Wed Sullivant, Seth, MS75, 3:45 Thu Veliz-Cuba, Alan, MS73, 9:30 Thu Xia, Kelin, MS56, 2:00 Wed Sun, Yi, MS68, 9:30 Thu Veliz-Cuba, Alan, MS73, 9:30 Thu Xie, Dexuan, MS35, 2:30 Tue Sun, Yi, MS76, 2:15 Thu Veliz-Cuba, Alan, MS81, 2:15 Thu Xue, Chuan, MS12, 2:00 Mon Sun, Yi, MS76, 3:45 Thu Veneroni, Marco, MS48, 11:00 Wed Xue, Chuan, MS12, 3:30 Mon Sutton, Karyn L., MS10, 3:30 Mon Vogl, Chris, MS55, 3:00 Wed Swanson, Kristin Rae, IP2, 1:00 Mon Y Voit, Eberhard O., MS33, 2:30 Tue Swigon, David, MS67, 10:00 Thu Yang, Li, CP10, 5:00 Wed Vologodskii, Alexander, MS56, 3:00 Yong, Kamuela E., MS18, 4:30 Mon Wed T Yong, Kamuela E., MS18, 5:30 Mon Takaidza, Isaac, CP3, 10:00 Tue W Yordanov, Pencho, MS22, 5:30 Mon Taylor, Bradford, CP14, 2:15 Thu Waldrop, Lindsay, MS57, 3:00 Wed Young, Glenn S., PP1, 8:00 Tue Teboh-Ewungkem, Miranda I., MS17, Walton, Jay R., MS11, 3:30 Mon Younger, John G., MS8, 9:30 Mon 4:30 Mon Wang, Jin, MS32, 3:00 Tue Younger, John G., MS8, 9:30 Mon Teboh-Ewungkem, Miranda I., MS17, 6:00 Mon Wang, Qi, MS64, 5:00 Wed Younger, John G., MS16, 2:00 Mon Teboh-Ewungkem, Miranda I., MS46, Wang, Qi, MS68, 9:30 Thu Yu, Jin, MS35, 3:00 Tue 10:00 Wed Wang, Qi, MS76, 2:15 Thu Yunlong, Huo, MS43, 5:30 Tue Tewari, Shivendra, MS80, 3:15 Thu Wang, Xiang-Sheng, MS65, 4:30 Wed Thomas, Peter J., MS28, 11:00 Tue Wang, Xiang-Sheng, MS65, 4:30 Wed Z Zapata-Allegro, Cheryl, MS29, 10:30 Thomases, Becca, MS27, 9:30 Tue Wang, Xueying, CP4, 2:00 Tue Tue Thomases, Becca, MS27, 9:30 Tue Wang, Yangyang, MS37, 2:00 Tue Zauhar, Randy, MS42, 5:30 Tue Thomases, Becca, MS36, 2:00 Tue Wang, Yangyang, PP1, 8:00 Tue Zhang, Calvin, MS70, 10:00 Thu Tian, Jianjun Paul, MS52, 10:00 Wed Waters, Ryan S., CP6, 6:00 Tue Zhang, Lei, MS52, 9:30 Wed Tian, Jianjun Paul, MS68, 11:00 Thu Watts, Margaret A., MS23, 4:30 Mon Zhang, Lei, MS52, 10:30 Wed Tien, Joseph, MS9, 3:30 Mon Wei, Guo-Wei, MS56, 3:30 Wed Zhang, Lei, MS60, 2:00 Wed Tolkacheva, Elena, MS51, 10:00 Wed Welsh, Andrea J., PP1, 8:00 Tue Zhang, Yongtao, MS52, 9:30 Wed Tomasetti, Cristian, CP1, 3:30 Mon Whidden, Mark E., MS64, 6:00 Wed Zhang, Yongtao, MS52, 11:00 Wed Toporikova, Natalia, MS71, 10:00 Thu Wilson, Dan D., MS72, 9:30 Thu Zhang, Yongtao, MS60, 2:00 Wed Tran, Hien T., MS47, 9:30 Wed Wilson, Shelby, MS44, 4:30 Tue Zhao, Kun, MS12, 2:30 Mon Transtrum, Mark K., MS33, 3:00 Tue Wiuf, Carsten, MT1, 9:30 Mon Zhao, Lihong, CP9, 3:30 Wed Treloar, Katrina, CP12, 5:00 Wed Wiuf, Carsten, MT1, 9:30 Mon Zhao, Longhua, MS70, 11:00 Thu Truong, Sandra K., PP1, 8:00 Tue Wiuf, Carsten, MS15, 2:00 Mon Zhao, Shan, MS26, 9:30 Tue Tuladhar, Binaya, PP1, 8:00 Tue Wiuf, Carsten, MS22, 4:30 Mon Zhao, Shan, MS35, 2:00 Tue Tuncer, Necibe, MS1, 9:30 Mon Wolfram, Marie-Therese, MS35, 2:00 Zhao, Shan, MS35, 3:30 Tue Tue Tuncer, Necibe, MS9, 2:00 Mon Zhao, Yanxiang, MS48, 10:30 Wed Wolgemuth, Charles, MS19, 4:30 Mon Tuncer, Necibe, MS9, 2:00 Mon Zhou, Douglas, MS6, 9:30 Mon 140 2014 SIAM Conference on the Life Sciences

Zhou, Douglas, MS6, 10:30 Mon Zhou, Douglas, MS14, 2:00 Mon Zhou, Yongcheng, MS48, 9:30 Wed Zhou, Yongcheng, MS55, 2:00 Wed 2014 SIAM Conference on the Life Sciences 141

LS14 Budget

Conference Budget SIAM Conference on Life Sciences August 4-7, 2014 Charlotte, North Carolina

Expected Paid Attendance 320

Revenue Registration Income $103,910 Total $103,910

Expenses Printing $2,800 Organizing Committee $3,600 Invited Speakers $9,800 Food and Beverage $22,000 AV Equipment and Telecommunication $15,900 Advertising $7,000 Conference Labor (including benefits) $34,514 Other (supplies, staff travel, freight, misc.) $8,000 Administrative $11,287 Accounting/Distribution & Shipping $5,542 Information Systems $9,910 Customer Service $3,670 Marketing $5,700 Office Space (Building) $3,112 Other SIAM Services $3,528 Total $146,363

Net Conference Expense ($42,453)

Support Provided by SIAM $42,453 $0

Estimated Support for Travel Awards not included above:

Early Career and Students 35 $23,250

Sheraton Charlotte

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