Shoals Wreck Is Cornell Archaeologists' Delight by ROBERT W

Total Page:16

File Type:pdf, Size:1020Kb

Shoals Wreck Is Cornell Archaeologists' Delight by ROBERT W Cornell Chronicle Volume 14, Number 29 Thursday, April 28, 1983 el A popular spot as the pressure grows late in the term is the comic book stand at the Campus Store, Where one may make a brief escape to the lands of Thor, Conan and X-Men. Shoals Wreck Is Cornell Archaeologists' Delight By ROBERT W. SMITH can have experience with a vessel in this On a bright August day in 1982. near Duck context." he said. Island in waters off the coast of Maine, five What's more important is that this dis- neophyte underwater archaeologists began covery represents the first step in a five or the unglamourous task of marking the area six-year program of careful analysis of the >n which they'd be diving. But then... land and underwater archaeology of Ap- "The first bucket of equipment thrown , pledore. °ver the side of our boat landed on the "The area was settled early," Farrell substantial remains of a wooden vessel." said. "It was attractive to early peoples according to the group's instructor, Robert because of the fresh water supply. We may T. Farrell. professor of English. Medieval find continuity of habitation since well Studies and Archaeology. before Christ'" But what about the story, the history of For a week. Farrell directed the five the underwater "mystery" ship? divers as they took pictures, made sketches Details indicated that the wooden ship of and drawings and drew maps of their find a peg construction was from the 19th cen- nd the area. Farrell. himself a veteran tury, Farrell said. The students began Underwater archaeologist, was kept out of interviewing captains and crews of various the water by a case of bronchitis for all but tn vessels at the Isles of Shoals, as well as e last two days. talking to old residents, to learn the ship's But that didn't diminish his pleasure at name and type. watching his five students "investigating, faking scientific decisions, without touch- it was incredible to see the kids going n mad tracing down bits and pieces of in- ' g or bringing up and exposing to air " the formation well into the night," Farrell discovery made during the week-long recalled. course offered bv Shoals Marine Labora- Their tentative conclusion is that they tory. found a sailing ship, the Samuel J. Goucher, The laboratory is a seasonal teaching and Prot. Kobert T. Farrell (left) and an underwater archaeology student a five-masted coal transport launched in research field station operated by Cornell investigate the entire area in which they are diving in order to record their 1904 and sunk Nov. 12,1911. No Spanish ^nd the University of New Hampshire on findings in detail. man-of-war. No pirate ship filled with jJPpledore Island in the southern Gulf of booty. Also, no coal. V'aine, 10 miles to seaward of Portsmouth, course is repeated. "We'll be measuring, of the ship: information without excava- "I have my doubts about it being a coaler sampling, analyzing and dating by den- tion." because we've found no coal... and we Farrell and some 10 students will be drochronology the timbers in the ship, " he "It's important and unusual that students should," Farrell said. "It just may be e at work again this August when the explained. "We want minimal disturbance working to learn underwater archaeology something else." 2 Thursday, April 28, 1983 People Extension's Carol Anderson Wins Kellogg Fellowship Carol L. Anderson, associate director of Anderson, who is also assistant dean of Outstanding Extension Educator for Iowa lion since its beginning in 1930. to support the Cooperative Extension Service, is one the New York State College of Human State in 1979, as well as its Outstanding projects that are focused on the application of 47 outstanding young American pro- Ecology and an associate professor of Young Alunnus in 1977. of existing knowledge to the problems of fessionals chosen for Class IV of the W.K. human development and family studies, Foundation Chairman of the Board Rus- people. The foundation's three fields of Kellogg Foundation National Fellowship held extension and home economics staff sell G. Mawby said the foundation has interest are agriculture, education and Program. positions before joining the Cornell staff. made grants totaling more than $643 mil- health. The Fellowship Program, initiated in Active in community affairs, she has 1980, is aimed at helping the nation expand served on local citizen action committees its vital pool of capable leaders. The pro- Anderson, 39, earned her doctor's degree Scheraga Receives Danish gram is structured to increase individuals' in home economics and adult education skills and insights into areas outside their from Iowa State and her master's degree in chosen disciplines so they can deal more child development and children/family Prize for Biochemistry Work creatively and effectively with society's from Wisconsin, where she also received Harold A. Scheraga, the Todd Professor given every three years to recognize out- complex problems. the bachelor's degree in home economics of Chemistry, will receive the 1983 Kaj standing contributions in the areas of Each Kellogg National Fellow receives a education. Author of extension publications Linderstrom-Lang Prize of the Carlsberg biochemistry or physiology. The Carlsberg three-year grant of up to $35,000 to pursue a on home economics, she was a delegate to Foundation of Denmark in ceremonies May Foundation and Laboratory are supported professionally broadening self-designed the national assembly of the American 10 in Copenhagen. by profits of the Carlsberg and Tuborg plan of study. Participation in Foundation- Home Economics Association in 1976,1977 An internationally recognized researcher breweries. designed seminars that focus on issues and 1978. in the physical chemistry of proteins, Scheraga's experimental and theoretical facing leaders in domestic and interna- Anderson was the first woman ever to Scheraga will be cited for his "outstanding work is directed toward two fundamental tional settings is also required. Travel receive a University of Wisconsin Ex- experimental and theoretical studies of the problems: How do polypeptide chains fold experiences and consultations add to the tension fellowship. She was also named folding of proteins and the factors de- into the native, biologically active struc- program's scope. termining the shapes of biological macro- tures of proteins? and how do these folded molecules." proteins express their biological function? The prize which includes a gold medal One of the systems investigated in his Five Young Scientists Here Receive and an award of 30,000 Danish kroner research program is the thrombin-induced (about $5,000), is named for the late direc- conversion of fibrinogen to fibrin, an im- NATO Postdoctoral Fellowships tor of the Carlsberg Laboratory and is portant step in the blood-clotting process. Five young scientists here are among 50 Fellowships in 1983. in the U.S. to be awarded North Atlantic The fellowship program was initiated by Treaty Organization (NATO) Postdoctoral NATO in 1959 to advance science and Feigenbaum Wins Atomic Energy Award Fellowships in Science. technology and to promote closer col- Mitchell J. Feigenbaum, professor of Feigenbaum was a Fellow at the Institute The awards, announced Tuesday, April laboration among NATO members and physics in the Laboratory of Atomic and for Advanced Studies in 1978 and in 1981 was 12, by the National Science Foundation and associated countries. Each NATO country Solid State Physics, is among five Ameri- named a Fellow in the Thoretical Division the Department of State, allow full-time administers the program for its own na- can scientists to receive the 1982 Ernest of Los Alamos National laboratory, a posi- postgraduate study abroad at institutions tionals. At the request of the Department of Orlando Lawrence Memorial Award for tion he still holds. He was appointed pro- and laboratories in NATO countries or in State, the National Science Foundation outstanding contributions in the field of fessor of physics at Cornell in 1982. countries that cooperate with NATO. administers the NATO-funded program for atomic energy. Feigenbaum's discoveries are leading to Receiving postdoctoral fellowships at U.S. nationals. The award, which includes a gold medal, major progress in the studies of the onset o> Cornell are Douglas C. Knipple, who will NATO Fellows will receive a stipend of a citation and $5,000, is given by the U.S. turbulence and are having an impact on the study molecular biology at the Max Planck $1,500 a month for up to 12 months. In Department of Energy to U.S. citizens who understanding of a wide variety of physical Institut fur Virusforschung, West Germa- addition, dependency allowances and lim- are early in their careers and who have phenomena. As a result of his work, physi- ny; Kenneth G. Ross, entomology, Institut ited allowances for round-trip travel are made recent meritorious contributions to cists are better able to predict such meas- fur Biologie III, Tubingen, West Germany; provided. the development, use or control of atomic urable properties as the velocity and tem- Jan Svejnar, economics, University of Lou- The awardees were selected by the Na- energy. perature fluctuations in real fluids and to vain, Belgium; Jonathan D. Walton, tional Science Foundation from 350 appli- understand these universal predictions. phytopathology, University of Rome, Italy, cants on the basis of their proposed plans of In the past, the prize has been awarded to and Nancy G. Wolf, ecology, McGill Uni- study after initial review and evaluation by distinguished physicists in both high energy Norman T. Uphoff, member of the facul- versity, Canada. panels of scientists who are expert in their and condensed matter physics, including ty of the Department of Government at specialized fields.
Recommended publications
  • Downloading Our Newsletter
    Department of Chemistry Biochemistry& NEWSLETTER In This Issue Page Chair’s Message................2 Jorge Torres Discovers Key Role for a Motor Awards...........................2-5 Protein in Cancer Cell Proliferation Seaborg Symposium........6-7 Happenings....................7-10 Biochemistry Professor high-throughput genetic Distinguished Lectures....11-14 Jorge Torres discovered that screen that knocked the Research.......................15-17 suppressing STARD9, a proteins out one by one to In Memoriam................17-19 newly identified protein see how that affected involved in regulating cell spindle function. Calendar.........................19 division, could be a novel “The idea was to find strategy for fighting certain something that arrested the Spring 2012 cancers, as it stops malignant cells while they were Volume 31 - Number 2 cells from dividing and trying to divide and causes them to die quickly. injured them in such a way that cell death occurred quickly,” The study was published in Torres said. “We were looking for a way to attack the cancer the December 9, 2011 issue cells as they were dividing.” of Cell. From the screens, Torres and his team selected the most During the five-year promising protein. This was STARD9, a kinesin-like protein Jorge Torres study, designed to seek — a sort of molecular motor — that functions to form a targets for anti-cancer stable mitotic spindle. therapies, Torres and co-workers found that depleting “When STARD9 is depleted in the cancer cells, the STARD9 also helped the commonly used chemotherapy chromosomes attempt to align for transmission into the drug Taxol work more effectively against cancers such as daughter cells but fail,” he said.
    [Show full text]
  • DNA Ejection from Bacteriophage: Towards a General Behavior for Osmotic Suppression Experiments Martin Castelnovo, Alex Evilevitch
    DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments Martin Castelnovo, Alex Evilevitch To cite this version: Martin Castelnovo, Alex Evilevitch. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments. European Physical Journal E: Soft matter and biological physics, EDP Sciences: EPJ, 2007, 24, pp.9-18. 10.1140/epje/i2007-10205-5. hal-00196724 HAL Id: hal-00196724 https://hal.archives-ouvertes.fr/hal-00196724 Submitted on 13 Dec 2007 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. DNA ejection from bacteriophage: towards a general behavior for osmotic suppression experiments M. Castelnovo∗ and A. Evilevitch† (Dated: December 18, 2007) We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and λ) using the osmotic ejection suppression technique. Our datas are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed. I. INTRODUCTION Viruses have developped various specific strategies over the evolution in order to infect higher organisms.
    [Show full text]
  • Two-Stage Dynamics of in Vivo Bacteriophage Genome Ejection
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE PHYSICAL REVIEW X 8, 021029 (2018) provided by Caltech Authors Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection † ‡ Yi-Ju Chen,1,* David Wu,2, William Gelbart,3 Charles M. Knobler,3 Rob Phillips,2,4, and Willem K. Kegel5,§ 1Department of Physics, California Institute of Technology, Pasadena, California 91125, USA 2Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California 91125, USA 3Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA 4Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA 5Van ’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands (Received 1 July 2017; revised manuscript received 27 January 2018; published 1 May 2018) Biopolymer translocation is a key step in viral infection processes. The transfer of information-encoding genomes allows viruses to reprogram the cell fate of their hosts. Constituting 96% of all known bacterial viruses [A. Fokine and M. G. Rossmann, Molecular architecture of tailed double-stranded DNA phages, Bacteriophage 4, e28281 (2014)], the tailed bacteriophages deliver their DNA into host cells via an “ejection” process, leaving their protein shells outside of the bacteria; a similar scenario occurs for mammalian viruses like herpes, where the DNA genome is ejected into the nucleus of host cells, while the viral capsid remains bound outside to a nuclear-pore complex. In light of previous experimental measurements of in vivo bacteriophage λ ejection, we analyze here the physical processes that give rise to the observed dynamics.
    [Show full text]
  • Biosoft Frontiers: Physics of Soft And
    BioSoft Frontiers: Physics of Soft and Biological Matter Research Workshop of the Israel Science Foundation September 18-21, 2016 Weizmann Institute and Tel Aviv University Sponsors Israel Science Foundation Weizmann Institute of Science Tel Aviv University Chorafas Institute for Scientific Exchange, Weizmann Institute Clore Center for Biological Physics, Weizmann Institute Schmidt Minerva Center, Weizmann Institute Department of Materials and Interfaces, Weizmann Institute Faculty of Exact Sciences, Tel Aviv University School of Physics & Astronomy, Tel Aviv University School of Chemistry, Tel Aviv University Sackler Institute of Solid State Physics, Tel Aviv University Sackler Institute of Chemical Physics, Tel Aviv University 1 Scientific Program 18/9/16 Weizmann Institute (Lopatie Center) 12:00-13:45 Arrival and Lunch 13:45-14:00 Opening 14:00-15:25 Session 1. Chair: Jacques Prost (Institut Curie, Paris) 14:00-14:30 Fred MacKintosh (VU University, Amsterdam) Phase transitions and non-equilibrium behavior in living systems 14:30-14:50 Ayelet Lesman (Tel Aviv University) The influence of contractile forces on biological processes 14:50-15:05 Xingpeng Xu (Weizmann Institute) Nonlinear elastic responses of biopolymer gels under compression 15:05-15:35 Tsvi Tlusty (IAS, Princeton) Proteins as learning amorphous matter: dimension and spectrum of the genotype-to-phenotype map 15:35-16:20 Coffee 16:20-17:25 Session 2. Chair: Nihat Berker (Sabanci University, Istanbul) 16:20-16:50 Christoph Schmidt (Universitaet Goettingen) Active soft matter builds life 16:50-17:05 Kinjal Dasbiswas (University of Chicago) Mechanobiological induction of long-range contractility by diffusing biomolecules and size scaling in cell assemblies 17:05-17:25 Yoram Burak (Hebrew University) Encoding of an animal's trajectory by grid cells in the entorhinal cortex 18:00 Dinner (Lopatie Center) 2 19/9/16 Weizmann Institute (Lopatie Center) 09:00-09:30 Arrival and coffee 09:30-10:35 Session 3.
    [Show full text]
  • How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi
    How a Virus Circumvents Energy Barriers to Form Symmetric Shells Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, Roya Zandi To cite this version: Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset, et al.. How a Virus Circumvents Energy Barriers to Form Symmetric Shells. ACS Nano, American Chemical Society, 2020, 14 (3), pp.3170-3180. 10.1021/acsnano.9b08354. hal-03035711 HAL Id: hal-03035711 https://hal.archives-ouvertes.fr/hal-03035711 Submitted on 4 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. How a virus circumvents energy barriers to form symmetric shells Sanaz Panahandeh,y Siyu Li,y Laurent Marichal,z Rafael Leite Rubim,z Guillaume Tresset,z and Roya Zandi∗,y yDepartment of Physics and Astronomy, University of California, Riverside, California 92521, USA zLaboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France E-mail: [email protected] Abstract Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially binds to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly or- dered structure in the host cell.
    [Show full text]
  • From the President's Desk
    APRIL 2005 From the President’s desk: The sequence of the human genome underscores the necessity for genetic analysis to define gene function and validates the importance of genomic and genetic approaches in model organisms for gene discovery. The GSA promotes genetic research in model organisms and its application to human genetics via our journal Genetics, supporting public education and congressional lobbying through the Joint Steering Committee for Public Policy (www.jscpp.org) and in its sponsorship of scientific meetings. The GSA support of scientific meetings includes providing the crucial infrastructure, organization, administration, and financial foundation, as well as recognition for students and postdocs through the awards we sponsor. The society’s sponsorship of model organisms meetings in C. elegans, Drosophila, Fungi, Yeast and Zebrafish has enabled those research communities to hold conferences that are particularly accessible to students and postdocs who are our future. The support of the GSA has been key in enabling these very successful meetings while permitting each of the model organism communities the independence to organize the meeting according to their needs. In recognition of the importance of genomics in our field, this year the GSA will support a new meeting of biocurators and database developers with the goal of bringing together developers of these bioinformatics tools for a variety of organisms. Your membership in the GSA entitles you to a reduced registration fee for all of these meetings. The GSA will organize its own meeting “Genetic Analysis: Model Organisms to Human Biology,” Jan. 5-7, 2006 in San Diego to draw together the entire constituency of our society and to promote interactions with our colleagues directly studying human disease.
    [Show full text]
  • Assembly and Disassembly of Viral Capsids
    Journal of Theoretical Medicine, Vol. 6, No. 2, June 2005, 69–72 Assembly and disassembly of viral capsids ROYA ZANDI†*, DAVID REGUERA†, ROBIJN BRUINSMA‡, WILLIAM GELBART† and JOSEPH RUDNICK‡{ †Department of Chemistry, University of California, Los Angeles, LA 90095, USA ‡Department of Physics, University of California, Los Angeles, LA 90095, USA We address here a theoretical basis for the icosahedral symmetry that is observed so commonly for viral capsids, i.e., the single-protein-thick rigid shells that protect the viral genome. In particular, we outline the phenomenological hamiltonian approach developed recently (see Zandi, R., Reguera, D., Bruinsma, R., Gelbart, W.M. and Rudnick, J. (2004), Original of icosahedral symmetry in viruses, Proc. Natl. Acad. Sci., 101, 15556–15560) to account for the overwhelming prevalence of the Caspar-Klug “T- number” structures that are found for “spherical” viruses. We feature the role of “conformational switching energies” defining the competing multimeric states of the protein subunits. The results of Monte Carlo simulation of this model are argued to shed light as well on the mechanical properties and genome release mechanism for these viruses. Keywords: Viral self-assembly; Icosahedral symmetry; Structural transitions; T-number 1. Introduction believed to describe the generic structure of protein shells.§ However, with current computational capabilities The cowpea rotic mottle virus (CCMV) is a classical it is neither possible to verify this claim through all-atom T ¼ 3 RNA virus with a shell composed of 180 identical molecular dynamics simulations nor can we design subunits, [2] see also A. Zlotnick, this volume. Figure 1(a) artificial protein shells by all-atom simulations.
    [Show full text]
  • Assembly from Atoms to Life October 3 to 5, 2016
    Self-assembly from atoms to life October 3 to 5, 2016. Tuxtla Gutiérrez, Chiapas, México. Organizers: Prof. Charles M. Knobler / University of California Los Angeles (USA) Prof. Alexander J. Levine / University of California Los Angeles (USA) Prof. Jaime Ruiz García / Universidad Autónoma de San Luis Potosí (México) Dr. Elías Castellano Alcantara / Mesoamerican Centre for Theoretical Physics (MCTP) Sponsor: UCLA Center for Biological Physics, UCLA College of Letters and Sciences, UCLA ICAM branch, ICAM, 12 ICAM (http://icam-i2cam.org/), ICTP, MCTP, UNACH and CONACYT. The three-day October 2016 workshop in Mexico will honor of Professor William Gelbart’s 70th birthday. The "Self-assembly from atoms to life" workshop will bring together both young and senior scientists from around the world and it covers research areas that match UCLA physical chemistry professor Gelbart's broad range of interests that he has pursued over a 45- year career in research. It will take place October 3-5, 2016, at the Mesoamerican Centre for Theoretical Physics in Tuxtla Gutiérrez, Chiapas, Mexico. To facilitate travel to and from the event, the Marriott Tuxtla Gutiérrez Hotel has reserved a block a rooms at the special conference rate for October 2 through October 6. The workshop organizers are Profs. Alex Levine and Chuck Knobler from the UCLA Department of Chemistry and Biochemistry and Prof. Jaime Ruiz-Garcia, of the Physics Institute of the University of San Luis Potosi, in Mexico. One archetypal example of emergent phenomena in nature is found in the self-assembly of complex spatio-temporal structures, either in the relaxation of many-body systems toward their thermal equilibrium or in non-equilibrium steady states characterized by continuous energy throughput.
    [Show full text]
  • Arxiv:1907.00469V1 [Cond-Mat.Soft] 30 Jun 2019
    Spontaneous Domain Formation in Spherically-Confined Elastic Filaments Tine Curk,1, 2, ∗ James Daniel Farrell,1, ∗ Jure Dobnikar,1, 3, 4, y and Rudolf Podgornik5, 1, z 1Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. 2Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia 3Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China. 4Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom. 5School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China. (Dated: July 2, 2019) Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity{driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously-ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers. Introduction. Spatial organization of constrained elas- liquid-crystalline order of compacted DNA was found to tic filaments underlies a range of packing problems from play a crucial role promoting the formation of knots [19]. macroscopic wires in spherical cavities [1, 2] to genomes The slow dynamics of stiff chains in confinement in bacteriophages [3, 4]. A theoretical interpretation implies that the configurations observed in the non- of single molecule experiments on DNA packaging in equilibrium simulations crucially depend on the applied viruses [5] suggests single-domain spool-like structures protocol, e.g., on how the external force is applied in with axial symmetry as a prevailing morphology.
    [Show full text]
  • UCLA UCLA Electronic Theses and Dissertations
    UCLA UCLA Electronic Theses and Dissertations Title Three-dimensional Semiflexible Network with Transient Cross-links: A Finite Element Kinetic Monte Carlo Approach Permalink https://escholarship.org/uc/item/0322c42m Author Shen, Lu Publication Date 2018 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Three-dimensional Semiflexible Network with Transient Cross-links: A Finite Element Kinetic Monte Carlo Approach A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry by Lu Shen 2018 c Copyright by Lu Shen 2018 ABSTRACT OF THE DISSERTATION Three-dimensional Semiflexible Network with Transient Cross-links: A Finite Element Kinetic Monte Carlo Approach by Lu Shen Doctor of Philosophy in Chemistry University of California, Los Angeles, 2018 Professor Alexander Jacob Levine, Chair Semiflexible biopolymer networks cross-linked by noncovalent bonds allow the networks topology to evolve over time and in response to applied stress. We developed a finite el- ement kinetic Monte Carlo simulation approach, which allows cross-links to reorganize in a three-dimensional network, to explore the dynamics of semiflexible networks with transient cross-links. We will first discuss this simulation strategy, and then apply this tool to explore the following aspects of semiflexible networks: The natural bundle formation and the dy- namics of bundle growth, especially in density and energy. The stress relaxation of networks with constrained filaments under affine strain field, and we find the linear shear elasticity of these networks mainly arises from the deformation change of the high-energy cross-links orientating in certain directions, and both the number and the elastic energy growth of these cross-links scales linearly with strain.
    [Show full text]
  • Physics of RNA and Viral Assembly
    Eur. Phys. J. E 19, 303{310 (2006) THE EUROPEAN DOI 10.1140/epje/i2005-10071-1 PHYSICAL JOURNAL E Physics of RNA and viral assembly R.F. Bruinsmaa Department of Physics and Astronomy, The University of California at Los Angeles, Los Angeles 90049, CA, USA Received 11 August 2005 / Published online: 23 March 2006 { °c EDP Sciences / Societ`a Italiana di Fisica / Springer-Verlag 2006 Abstract. The overview discusses the application of physical arguments to structure and function of single- stranded viral RNA genomes. PACS. 87.15.Nn Properties of solutions; aggregation and crystallization of macromolecules { 61.50.Ah Theory of crystal structure, crystal symmetry; calculations and modeling { 81.16.Dn Self-assembly The other contributions to this Focus Point discuss how physical descriptions of DNA and RNA can illumi- nate our understanding of cell functioning. Here, the fo- cus will be on dysfunctional nucleic acids, speci¯cally the genomes of infectious viruses. A virus is a shadowy citizen of a borderland between living and dead matter; a par- asite that reproduces only in the environment of a host cell, in fact by the mobilization of the macromolecular machinery of the host. A virus also does not carry out any metabolic activity, which means that, unlike living cells, it e®ectively is in a state of thermal equilibrium with its environment; one reason why physics |and statistical Fig. 1. Image reconstruction of the MS2 virus, viewed along physics in particular| can be a useful tool. Another rea- a 5-fold icosahedral symmetry axis. From reference [2]. son is apparent from an image reconstruction of a virus.
    [Show full text]
  • Foundations of Nanoscience
    Foundations of Nanoscience Snowbird Cliff Lodge~Snowbird, Utah April 21- 23, 2004. Self-Assembled Architectures and Devices Sponsor: Defense Advanced Research Projects Agency (DARPA) Foundations of Nanoscience Snowbird, Utah April 21- 23, 2004 Sponsor: Defense Advanced Research Projects Agency (DARPA) Self-Assembled Architectures and Devices © 2004 by ScienceTechnica, Inc. The papers in this volume were presented at the Conference “Foundations of Nanoscience: Self-Assembled Architectures and Devices” held in Snowbird, Utah, April 21-23, 2004. THANKS: The conference was sponsored by the Defense Advance Research Projects Agency (DARPA). We express our gratitude to Sri Kumar, Program Manager in DARPA / IPTO, for his generous support of this enterprise. Also thanks to Mitra Basu, of the National Science Foundation(NSF) and to K. Birgitta Whaley, Department of Chemistry, University of California, Berkeley, CA, for their aid arranging indirect travel support for some of the invitees via a co-located NSF Workshop on Self-Assembled Architectures. Special thanks also to the Department of Computer Science at Duke University, and in particular to Richard Braun, Courtney Packard, Diane Robinson, Jewel Wheeler for their hours of work on this project. CONFERENCE OVERVIEW: The construction of molecular scale structures at the scale of the 1 - 100 nanometer range is one of the key challenges facing science and technology in the twenty-first century. This challenge is at the core of an emerging discipline of Nanoscience, which is at a critical stage of development. There have been some notable successes in the construction of individual molecular components (e.g., carbon nanotubes, and various molecular electronic devices), and the individual manipulation of molecules by probing devices.
    [Show full text]