Computational Models of Plant Development and Form
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Biophysics, Structural and Computational Biology (BSCB) Faculty Administers the Ph.D
UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY Graduate Studies in BIOPHYSICS, STRUCTURAL AND COMPUTATIONAL BIOLOGY Student Handbook August 2019 David Mathews, Program Director Joseph Wedekind, Education Committee Chair Melissa Vera, Graduate Studies Coordinator PREFACE The Biophysics, Structural and Computational Biology (BSCB) Faculty administers the Ph.D. degree program in Biophysics for the Department of Biochemistry and Biophysics. This handbook is intended to outline the major features and policies of the program. The general features of the graduate experience at the University of Rochester are summarized in the Graduate Bulletin, which is updated every two years. Students and advisors will need to consult both sources, though it is our intent to provide the salient features here. Policy, of course, continues to evolve in response to the changing needs of the graduate programs and the students in them. Thus, it is wise to verify any crucial decisions with the Graduate Studies Coordinator. i TABLE OF CONTENTS Page I. DEFINITIONS 1 II. BIOPHYSICS CURRICULUM 2 A. Courses 2 1. Core Curriculum 2. Elective Courses 3 B. Suggested Progress Toward the Ph.D. in Biophysics 4 C. Other Educational Opportunities 4 1. Departmental Seminars 4 2. BSCB Program Retreat 5 3. Bioinformatics Cluster 5 D. Exemptions from Course Requirements 5 E. Minimum Course Performance 5 F. M.D./Ph.D. Students 6 III. ADDITIONAL DETAILS OF PROCEDURES AND REQUIREMENTS 7 A. Faculty Advisors for Entering Students 7 B. Student Laboratory Rotations 7 C. Radiation Certificate 8 D. Student Research Seminar 8 E. First Year Preliminary Examination and Evaluation 9 F. Teaching Assistantship 12 G. -
A Sample Workload for Bioinformatics and Computational Biology for Optimizing Next-Generation High-Performance Computer Systems
BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation high-performance computer systems David A. Bader∗ Vipin Sachdeva Department of Electrical and Computer Engineering University of New Mexico, Albuquerque, NM 87131 Virat Agarwal Gaurav Goel Abhishek N. Singh Indian Institute of Technology, New Delhi May 1, 2005 Abstract BioSPLASH is a suite of representative applications that we have assembled from the com- putational biology community, where the codes are carefully selected to span a breadth of algorithms and performance characteristics. The main results of this paper are the assembly of a scalable bioinformatics workload with impact to the DARPA High Produc- tivity Computing Systems Program to develop revolutionarily-new economically- viable high-performance computing systems,andanalyses of the performance of these codes for computationally demanding instances using the cycle-accurate IBM MAMBO simulator and real performance monitoring on an Apple G5 system. Hence, our work is novel in that it is one of the first efforts to incorporate life science application per- formance for optimizing high-end computer system architectures. 1 Algorithms in Computational Biology In the 50 years since the discovery of the structure of DNA, and with new techniques for sequencing the entire genome of organisms, biology is rapidly moving towards a data-intensive, computational science. Biologists are in search of biomolecular sequence data, for its comparison with other genomes, and because its structure determines function and leads to the understanding of bio- chemical pathways, disease prevention and cure, and the mechanisms of life itself. Computational biology has been aided by recent advances in both technology and algorithms; for instance, the ability to sequence short contiguous strings of DNA and from these reconstruct the whole genome (e.g., see [34, 2, 33]) and the proliferation of high-speed micro array, gene, and protein chips (e.g., see [27]) for the study of gene expression and function determination. -
Biology (BA) Biology (BA)
Biology (BA) Biology (BA) This program is offered by the College of Arts & Sciences/ • CHEM 1110 General Chemistry II (3 hours) Biological Sciences Department and is only available at the St. and CHEM 1111 General Chemistry II: Lab (1 hour) Louis home campus. • CHEM 2100 Organic Chemistry I (3 hours) and CHEM 2101 Organic Chemistry I: Lab (1 hour) Program Description • MATH 1430 College Algebra (3 hours) • MATH 2200 Statistics (3 hours) The bachelor of arts degree is designed for students who seek or STAT 3100 Inferential Statistics (3 hours) a broad education in biology. This degree is suitable preparation or PSYC 2750 Introduction to Measurement and Statistics (3 for a diverse range of careers including health science, science hours) education and ecology-related fields. • PHYS 1710 College Physics I (3 hours) Students can earn the BA in biology alone, or with one of four and PHYS 1711 College Physics I: Lab (1 hour) emphases: biodiversity, computational biology, education or • PHYS 1720 College Physics II (3 hours) health science. and PHYS 1721 College Physics II: Lab (1 hour) Learning Outcomes BA in Biology (66 hours) Students who complete any of the bachelor of arts in biology will The general degree offers the greatest flexibility, allowing students be able to: to select 12 hours of electives from any of our 2000+ level BIOL, CHEM or PHYS courses in addition to the 54 credits of core • Describe biological, chemical and physical principles as they coursework in biology listed above. (Up to 3 credit hours of BIOL relate to the natural world in writings and presentations to a 4700/CHEM 4700/PHYS 4700 can be used toward these 12 credit diverse audience. -
6 Phyllotaxis in Higher Plants Didier Reinhardt and Cris Kuhlemeier
6 Phyllotaxis in higher plants Didier Reinhardt and Cris Kuhlemeier 6.1 Introduction In plants, the arrangement of leaves and flowers around the stem is highly regular, resulting in opposite, alternate or spiral arrangements.The pattern of the lateral organs is called phyllotaxis, the Greek word for ‘leaf arrangement’. The most widespread phyllotactic arrangements are spiral and distichous (alternate) if one organ is formed per node, or decussate (opposite) if two organs are formed per node. In flowers, the organs are frequently arranged in whorls of 3-5 organs per node. Interestingly, phyllotaxis can change during the course of develop- ment of a plant. Usually, such changes involve the transition from decussate to spiral phyllotaxis, where they are often associated with the transition from the vegetative to reproductive phase. Since the first descriptions of phyllotaxis, the apparent regularity, especially of spiral phyllotaxis, has attracted the attention of scientists in various dis- ciplines. Philosophers and natural scientists were among the first to consider phyllotaxis and to propose models for its regulation. Goethe (1 830), for instance, postulated the existence of a general ‘spiral tendency in plant vegetation’. Mathematicians have described the regularity of phyllotaxis (Jean, 1994), and developed computer models that can recreate phyllotactic patterns (Meinhardt, 1994; Green, 1996). It was recognized early that phyllotactic patterns are laid down in the shoot apical meristem, the site of organ formation. Since scientists started to pos- tulate mechanisms for the regulation of phyllotaxis, two main concepts have dominated the field. The first principle holds that the geometry of the apex, and biophysical forces in the meristem determine phyllotaxis (van Iterson, 1907; Schiiepp, 1938; Snow and Snow, 1962; Green, 1992, 1996). -
Multidimensional Generalization of Phyllotaxis
CYBERNETICS AND PHYSICS, VOL. 8, NO. 3, 2019, 153–160 MULTIDIMENSIONAL GENERALIZATION OF PHYLLOTAXIS Andrei Lodkin Dept. of Mathematics & Mechanics St. Petersburg State University Russia [email protected] Article history: Received 28.10.2019, Accepted 28.11.2019 Abstract around a stem, seeds on a pine cone or a sunflower head, The regular spiral arrangement of various parts of bi- florets, petals, scales, and other units usually shows a ological objects (leaves, florets, etc.), known as phyl- regular character, see the pictures below. lotaxis, could not find an explanation during several cen- turies. Some quantitative parameters of the phyllotaxis (the divergence angle being the principal one) show that the organization in question is, in a sense, the same in a large family of living objects, and the values of the divergence angle that are close to the golden number prevail. This was a mystery, and explanations of this phenomenon long remained “lyrical”. Later, similar pat- terns were discovered in inorganic objects. After a se- ries of computer models, it was only in the XXI cen- tury that the rigorous explanation of the appearance of the golden number in a simple mathematical model has been given. The resulting pattern is related to stable fixed points of some operator and depends on a real parame- ter. The variation of this parameter leads to an inter- esting bifurcation diagram where the limiting object is the SL(2; Z)-orbit of the golden number on the segment [0,1]. We present a survey of the problem and introduce a multidimensional analog of phyllotaxis patterns. -
A Method of Constructing Phyllotaxically Arranged Modular Models by Partitioning the Interior of a Cylinder Or a Cone
A method of constructing phyllotaxically arranged modular models by partitioning the interior of a cylinder or a cone Cezary St¸epie´n Institute of Computer Science, Warsaw University of Technology, Poland [email protected] Abstract. The paper describes a method of partitioning a cylinder space into three-dimensional sub- spaces, congruent to each other, as well as partitioning a cone space into subspaces similar to each other. The way of partitioning is of such a nature that the intersection of any two subspaces is the empty set. Subspaces are arranged with regard to phyllotaxis. Phyllotaxis lets us distinguish privileged directions and observe parastichies trending these directions. The subspaces are created by sweeping a changing cross-section along a given path, which enables us to obtain not only simple shapes but also complicated ones. Having created these subspaces, we can put modules inside them, which do not need to be obligatorily congruent or similar. The method ensures that any module does not intersect another one. An example of plant model is given, consisting of modules phyllotaxically arranged inside a cylinder or a cone. Key words: computer graphics; modeling; modular model; phyllotaxis; cylinder partitioning; cone partitioning; genetic helix; parastichy. 1. Introduction Phyllotaxis is the manner of how leaves are arranged on a plant stem. The regularity of leaves arrangement, known for a long time, still absorbs the attention of researchers in the fields of botany, mathematics and computer graphics. Various methods have been used to describe phyllotaxis. A historical review of problems referring to phyllotaxis is given in [7]. Its connections with number sequences, e.g. -
Computational and Systems Biology
COMPUTATIONAL AND SYSTEMS BIOLOGY COMPUTATIONAL AND SYSTEMS BIOLOGY quantitative imaging; regulatory genomics and proteomics; single cell manipulations and measurement; stem cell and developmental systems biology; and synthetic biology and biological design. The eld of computational and systems biology represents a synthesis of ideas and approaches from the life sciences, physical The CSB PhD program is an Institute-wide program that has been sciences, computer science, and engineering. Recent advances jointly developed by the Departments of Biology, Biological in biology, including the human genome project and massively Engineering, and Electrical Engineering and Computer Science. parallel approaches to probing biological samples, have created new The program integrates biology, engineering, and computation to opportunities to understand biological problems from a systems address complex problems in biological systems, and CSB PhD perspective. Systems modeling and design are well established students have the opportunity to work with CSBi faculty from across in engineering disciplines but are newer in biology. Advances in the Institute. The curriculum has a strong emphasis on foundational computational and systems biology require multidisciplinary teams material to encourage students to become creators of future tools with skill in applying principles and tools from engineering and and technologies, rather than merely practitioners of current computer science to solve problems in biology and medicine. To approaches. Applicants must have an undergraduate degree in provide education in this emerging eld, the Computational and biology (or a related eld), bioinformatics, chemistry, computer Systems Biology (CSB) program integrates MIT's world-renowned science, mathematics, statistics, physics, or an engineering disciplines in biology, engineering, mathematics, and computer discipline, with dual-emphasis degrees encouraged. -
Phyllotaxis: a Remarkable Example of Developmental Canalization in Plants Christophe Godin, Christophe Golé, Stéphane Douady
Phyllotaxis: a remarkable example of developmental canalization in plants Christophe Godin, Christophe Golé, Stéphane Douady To cite this version: Christophe Godin, Christophe Golé, Stéphane Douady. Phyllotaxis: a remarkable example of devel- opmental canalization in plants. 2019. hal-02370969 HAL Id: hal-02370969 https://hal.archives-ouvertes.fr/hal-02370969 Preprint submitted on 19 Nov 2019 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. Phyllotaxis: a remarkable example of developmental canalization in plants Christophe Godin, Christophe Gol´e,St´ephaneDouady September 2019 Abstract Why living forms develop in a relatively robust manner, despite various sources of internal or external variability, is a fundamental question in developmental biology. Part of the answer relies on the notion of developmental constraints: at any stage of ontogenenesis, morphogenetic processes are constrained to operate within the context of the current organism being built, which is thought to bias or to limit phenotype variability. One universal aspect of this context is the shape of the organism itself that progressively channels the development of the organism toward its final shape. Here, we illustrate this notion with plants, where conspicuous patterns are formed by the lateral organs produced by apical meristems. -
Phyllotaxis: a Model
Phyllotaxis: a Model F. W. Cummings* University of California Riverside (emeritus) Abstract A model is proposed to account for the positioning of leaf outgrowths from a plant stem. The specified interaction of two signaling pathways provides tripartite patterning. The known phyllotactic patterns are given by intersections of two ‘lines’ which are at the borders of two determined regions. The Fibonacci spirals, the decussate, distichous and whorl patterns are reproduced by the same simple model of three parameters. *present address: 136 Calumet Ave., San Anselmo, Ca. 94960; [email protected] 1 1. Introduction Phyllotaxis is the regular arrangement of leaves or flowers around a plant stem, or on a structure such as a pine cone or sunflower head. There have been many models of phyllotaxis advanced, too numerous to review here, but a recent review does an admirable job (Kuhlemeier, 2009). The lateral organs are positioned in distinct patterns around the cylindrical stem, and this alone is often referred to phyllotaxis. Also, often the patterns described by the intersections of two spirals describing the positions of florets such as (e.g.) on a sunflower head, are included as phyllotactic patterns. The focus at present will be on the patterns of lateral outgrowths on a stem. The patterns of intersecting spirals on more flattened geometries will be seen as transformations of the patterns on a stem. The most common patterns on a stem are the spiral, distichous, decussate and whorled. The spirals must include especially the common and well known Fibonacci patterns. Transition between patterns, for instance from decussate to spiral, is common as the plant grows. -
Spiral Phyllotaxis: the Natural Way to Construct a 3D Radial Trajectory in MRI
Magnetic Resonance in Medicine 66:1049–1056 (2011) Spiral Phyllotaxis: The Natural Way to Construct a 3D Radial Trajectory in MRI Davide Piccini,1* Arne Littmann,2 Sonia Nielles-Vallespin,2 and Michael O. Zenge2 While radial 3D acquisition has been discussed in cardiac MRI methods feature properties that are particularly well suited for its excellent results with radial undersampling, the self- for cardiac MRI applications. navigating properties of the trajectory need yet to be exploited. In the field of cardiac MRI, it has to be considered that Hence, the radial trajectory has to be interleaved such that the anatomy of the heart is very complex. Furthermore, the first readout of every interleave starts at the top of the sphere, which represents the shell covering all readouts. If this in many cases, the location and orientation of the heart is done sub-optimally, the image quality might be degraded by differ individually within the thorax. Up to now, only eddy current effects, and advanced density compensation is experienced operators are able to perform a comprehen- needed. In this work, an innovative 3D radial trajectory based on sive cardiac MR examination. As a consequence, the option a natural spiral phyllotaxis pattern is introduced, which features to acquire a 3D volume that covers the whole heart with optimized interleaving properties: (1) overall uniform readout high and isotropic resolution is a much desirable goal (11). distribution is preserved, which facilitates simple density com- In this configuration, some of the preparatory steps of a pensation, and (2) if the number of interleaves is a Fibonacci cardiac examination are obsolete since the complexity of number, the interleaves self-arrange such that eddy current effects are significantly reduced. -
Dynamical System Approach to Phyllotaxis
Downloaded from orbit.dtu.dk on: Dec 17, 2017 Dynamical system approach to phyllotaxis D'ovidio, Francesco; Mosekilde, Erik Published in: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics Link to article, DOI: 10.1103/PhysRevE.61.354 Publication date: 2000 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): D'ovidio, F., & Mosekilde, E. (2000). Dynamical system approach to phyllotaxis. Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 61(1), 354-365. DOI: 10.1103/PhysRevE.61.354 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. PHYSICAL REVIEW E VOLUME 61, NUMBER 1 JANUARY 2000 Dynamical system approach to phyllotaxis F. d’Ovidio1,2,* and E. Mosekilde1,† 1Center for Chaos and Turbulence Studies, Building 309, Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark 2International Computer Science Institute, 1947 Center Street, Berkeley, California 94704-1198 ͑Received 13 August 1999͒ This paper presents a bifurcation study of a model widely used to discuss phyllotactic patterns, i.e., leaf arrangements. -
Fibonacci Numbers and the Golden Ratio in Biology, Physics, Astrophysics, Chemistry and Technology: a Non-Exhaustive Review
Fibonacci Numbers and the Golden Ratio in Biology, Physics, Astrophysics, Chemistry and Technology: A Non-Exhaustive Review Vladimir Pletser Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, China; [email protected] Abstract Fibonacci numbers and the golden ratio can be found in nearly all domains of Science, appearing when self-organization processes are at play and/or expressing minimum energy configurations. Several non-exhaustive examples are given in biology (natural and artificial phyllotaxis, genetic code and DNA), physics (hydrogen bonds, chaos, superconductivity), astrophysics (pulsating stars, black holes), chemistry (quasicrystals, protein AB models), and technology (tribology, resistors, quantum computing, quantum phase transitions, photonics). Keywords Fibonacci numbers; Golden ratio; Phyllotaxis; DNA; Hydrogen bonds; Chaos; Superconductivity; Pulsating stars; Black holes; Quasicrystals; Protein AB models; Tribology; Resistors; Quantum computing; Quantum phase transitions; Photonics 1. Introduction Fibonacci numbers with 1 and 1 and the golden ratio φlim → √ 1.618 … can be found in nearly all domains of Science appearing when self-organization processes are at play and/or expressing minimum energy configurations. Several, but by far non- exhaustive, examples are given in biology, physics, astrophysics, chemistry and technology. 2. Biology 2.1 Natural and artificial phyllotaxis Several authors (see e.g. Onderdonk, 1970; Mitchison, 1977, and references therein) described the phyllotaxis arrangement of leaves on plant stems in such a way that the overall vertical configuration of leaves is optimized to receive rain water, sunshine and air, according to a golden angle function of Fibonacci numbers. However, this view is not uniformly accepted (see Coxeter, 1961). N. Rivier and his collaborators (2016) modelized natural phyllotaxis by the tiling by Voronoi cells of spiral lattices formed by points placed regularly on a generative spiral.