Protein Folding And Self Avoiding Walks Polyhedral Studies And Solutions
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Protein Folding And Self Avoiding Walks Polyhedral Studies And Solutions
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Author : Agnes Dittel
language : en
Publisher: Logos Verlag Berlin GmbH
Release Date : 2008
Protein Folding And Self Avoiding Walks Polyhedral Studies And Solutions written by Agnes Dittel and has been published by Logos Verlag Berlin GmbH this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with categories.
The protein folding problem refers to the correlation of a protein's amino acid sequence and its native three-dimensional structure which is essential for functionality. It still constitutes one of the major challenges in computational biology. One commonly studied model for the protein folding problem is the HP lattice model in which proteins are considered in a fairly abstract representation. However, the HP model proteins exhibit significant parallels to proteins occurring in nature. The solution of the HP lattice mode as a combinatorial optimization problem has been proven to be NP-complete, and there have already been developed various different approaches for efficient algorithms. We study an integer programming formulation of the problem. Starting with an analysis of this model, where we concentrate on symmetry issues, we show how the model can be consolidated by exploiting symmetry properties of the underlying lattice. The main focus lies in the development of specific components of a branch-and-cut framework for the computation of solutions for the HP model by means of integer programming methods. In order to understand the structure of the model, we perform a series of polyhedral studies from which we derive two main classes of cutting planes. Furthermore, we exploit the knowledge of folding principles which are also valid for HP model proteins for the development of related branching strategies. For the solution of a special class of instances, we present an implementation of a genetic algorithm for the generation of primal feasible start solutions. Finally, we document the performance of the methods developed for each of the four topics (model consolidation, primal method, branching strategy and cutting planes) within the branch-and-cut procedure. We present computational results for different types of lattices, where we both consider known benchmark instances from literature and random instances.
Facets Of Combinatorial Optimization
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Author : Michael Jünger
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-07-03
Facets Of Combinatorial Optimization written by Michael Jünger and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-07-03 with Mathematics categories.
Martin Grötschel is one of the most influential mathematicians of our time. He has received numerous honors and holds a number of key positions in the international mathematical community. He celebrated his 65th birthday on September 10, 2013. Martin Grötschel’s doctoral descendant tree 1983–2012, i.e., the first 30 years, features 39 children, 74 grandchildren, 24 great-grandchildren and 2 great-great-grandchildren, a total of 139 doctoral descendants. This book starts with a personal tribute to Martin Grötschel by the editors (Part I), a contribution by his very special “predecessor” Manfred Padberg on “Facets and Rank of Integer Polyhedra” (Part II), and the doctoral descendant tree 1983–2012 (Part III). The core of this book (Part IV) contains 16 contributions, each of which is coauthored by at least one doctoral descendant. The sequence of the articles starts with contributions to the theory of mathematical optimization, including polyhedral combinatorics, extended formulations, mixed-integer convex optimization, super classes of perfect graphs, efficient algorithms for subtree-telecenters, junctions in acyclic graphs and preemptive restricted strip covering, as well as efficient approximation of non-preemptive restricted strip covering. Combinations of new theoretical insights with algorithms and experiments deal with network design problems, combinatorial optimization problems with submodular objective functions and more general mixed-integer nonlinear optimization problems. Applications include VLSI layout design, systems biology, wireless network design, mean-risk optimization and gas network optimization. Computational studies include a semidefinite branch and cut approach for the max k-cut problem, mixed-integer nonlinear optimal control, and mixed-integer linear optimization for scheduling and routing of fly-in safari planes. The two closing articles are devoted to computational advances in general mixed integer linear optimization, the first by scientists working in industry, the second by scientists working in academia. These articles reflect the “scientific facets” of Martin Grötschel who has set standards in theory, computation and applications.
Deutsche Nationalbibliographie Und Bibliographie Der Im Ausland Erschienenen Deutschsprachigen Ver Ffentlichungen
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Author :
language : de
Publisher:
Release Date : 2008
Deutsche Nationalbibliographie Und Bibliographie Der Im Ausland Erschienenen Deutschsprachigen Ver Ffentlichungen written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Dissertations, Academic categories.
Geometric Folding Algorithms
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Author : Erik D. Demaine
language : en
Publisher: Cambridge University Press
Release Date : 2007-07-16
Geometric Folding Algorithms written by Erik D. Demaine and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-07-16 with Computers categories.
Did you know that any straight-line drawing on paper can be folded so that the complete drawing can be cut out with one straight scissors cut? That there is a planar linkage that can trace out any algebraic curve, or even 'sign your name'? Or that a 'Latin cross' unfolding of a cube can be refolded to 23 different convex polyhedra? Over the past decade, there has been a surge of interest in such problems, with applications ranging from robotics to protein folding. With an emphasis on algorithmic or computational aspects, this treatment gives hundreds of results and over 60 unsolved 'open problems' to inspire further research. The authors cover one-dimensional (1D) objects (linkages), 2D objects (paper), and 3D objects (polyhedra). Aimed at advanced undergraduate and graduate students in mathematics or computer science, this lavishly illustrated book will fascinate a broad audience, from school students to researchers.
Protein Self Assembly
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Author : Jennifer J. McManus
language : en
Publisher: Humana
Release Date : 2020-08-08
Protein Self Assembly written by Jennifer J. McManus and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-08 with Science categories.
This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Planning Algorithms
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Author : Steven Michael LaValle
language : en
Publisher:
Release Date : 2006
Planning Algorithms written by Steven Michael LaValle and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Algorithms categories.
Written for computer scientists and engineers with interests in artificial intelligence, robotics, or control theory, this is the only book on this topic that integrates literature from several fields into a coherent source for teaching and reference in applications including robotics, computational biology, computer graphics, manufacturing, aerospace applications, and medicine.
Ant Colony Optimization
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Author : Marco Dorigo
language : en
Publisher: MIT Press
Release Date : 2004-06-04
Ant Colony Optimization written by Marco Dorigo and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-06-04 with Computers categories.
An overview of the rapidly growing field of ant colony optimization that describes theoretical findings, the major algorithms, and current applications. The complex social behaviors of ants have been much studied by science, and computer scientists are now finding that these behavior patterns can provide models for solving difficult combinatorial optimization problems. The attempt to develop algorithms inspired by one aspect of ant behavior, the ability to find what computer scientists would call shortest paths, has become the field of ant colony optimization (ACO), the most successful and widely recognized algorithmic technique based on ant behavior. This book presents an overview of this rapidly growing field, from its theoretical inception to practical applications, including descriptions of many available ACO algorithms and their uses. The book first describes the translation of observed ant behavior into working optimization algorithms. The ant colony metaheuristic is then introduced and viewed in the general context of combinatorial optimization. This is followed by a detailed description and guide to all major ACO algorithms and a report on current theoretical findings. The book surveys ACO applications now in use, including routing, assignment, scheduling, subset, machine learning, and bioinformatics problems. AntNet, an ACO algorithm designed for the network routing problem, is described in detail. The authors conclude by summarizing the progress in the field and outlining future research directions. Each chapter ends with bibliographic material, bullet points setting out important ideas covered in the chapter, and exercises. Ant Colony Optimization will be of interest to academic and industry researchers, graduate students, and practitioners who wish to learn how to implement ACO algorithms.
Mathematical Snapshots
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Author : H. Steinhaus
language : en
Publisher: Courier Corporation
Release Date : 2012-07-12
Mathematical Snapshots written by H. Steinhaus and has been published by Courier Corporation this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-07-12 with Mathematics categories.
Numerous photographs and diagrams explain mathematical phenomena in series of thought-provoking expositions. From simple puzzles to more advanced problems, topics include psychology of lottery players, new and larger prime numbers, and more. 391 illustrations.
Protein Structure
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Author : Harold A. Scheraga
language : en
Publisher: Academic Press
Release Date : 2014-07-01
Protein Structure written by Harold A. Scheraga and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-01 with Technology & Engineering categories.
Protein Structure deals with the chemistry and physics of biologically important molecules—the proteins—particularly the determination of the structure of various proteins, their thermodynamics, their kinetics, and the mechanisms of different reactions of individual proteins. The book approaches the study of protein structure in two ways: firstly, by determining the general features of protein structure, the overall size, and shape of the molecule; and secondly, by investigating the molecule internally along with the various aspects of the internal configuration of protein molecules. It describes in detail experimental methods for determining protein structure in solution, such as the hydrodynamic method, the thermodynamic optical method, and the electrochemical method. The book then explains the results of experiments carried out on insulin, lysozyme, and ribonuclease. The text notes that the experiments, carried out on native and denatured proteins as well as on derivatives prepared by chemical modification (e.g., by methylation, iodination, acetylation, etc.), can lead to greater understanding of secondary and tertiary structures of proteins of known sequence. The book is suitable for biochemists, micro-biologists, cellular researchers, or investigators involved in protein structure and other biological sciences related to muscle physiologists, geneticists, enzymologists, or immunologists.
Fibrous Proteins Coiled Coils Collagen And Elastomers
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Author : David A.D. Parry
language : en
Publisher: Gulf Professional Publishing
Release Date : 2005-05-06
Fibrous Proteins Coiled Coils Collagen And Elastomers written by David A.D. Parry and has been published by Gulf Professional Publishing this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-05-06 with Science categories.
Fibrous Protein: Coiled-Coils, Collagen and Elastomers is the first of a three-part series on Fibrous Proteins. The books are based on a very successful workshop in Alpbach, Austria on the general topic of Fibrous Proteins that gave rise to the award winning issue of Journal of Structural Biology. Part II will contain an extensive discussion of Molecular Motors and Muscle, Part III on Amyloids, Prions and Beta Proteins. Advances in Protein Chemistry is available online on ScienceDirect - full-text online of volumes 53 onwards. Reveals new structural and functional aspects of fibrous proteins Based on Fibrous Protein workshop in Alpbach, Austria that gave rise to 2003 Nobel Prize winners in Chemistry