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Author: Agnes Dittel Publisher: Logos Verlag Berlin GmbH ISBN: 3832520236 Category : Languages : en Pages : 362
Book Description
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.
Author: Agnes Dittel Publisher: Logos Verlag Berlin GmbH ISBN: 3832520236 Category : Languages : en Pages : 362
Book Description
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.
Author: Michael Jünger Publisher: Springer Science & Business Media ISBN: 3642381898 Category : Mathematics Languages : en Pages : 510
Book Description
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.
Author: Erik D. Demaine Publisher: Cambridge University Press ISBN: 1107394090 Category : Computers Languages : en Pages : 388
Book Description
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.
Author: Jennifer J. McManus Publisher: Humana ISBN: 9781493996803 Category : Science Languages : en Pages : 266
Book Description
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.
Author: Marco Dorigo Publisher: MIT Press ISBN: 9780262042192 Category : Computers Languages : en Pages : 324
Book Description
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.
Author: Steven M. LaValle Publisher: Cambridge University Press ISBN: 9780521862059 Category : Computers Languages : en Pages : 844
Book Description
Planning algorithms are impacting technical disciplines and industries around the world, including robotics, computer-aided design, manufacturing, computer graphics, aerospace applications, drug design, and protein folding. Written for computer scientists and engineers with interests in artificial intelligence, robotics, or control theory, this is the only book on this topic that tightly integrates a vast body of literature from several fields into a coherent source for teaching and reference in a wide variety of applications. Difficult mathematical material is explained through hundreds of examples and illustrations.
Author: H. Steinhaus Publisher: Courier Corporation ISBN: 0486166481 Category : Mathematics Languages : en Pages : 340
Book Description
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.
Author: Katsuhiko Ariga Publisher: Elsevier ISBN: 0323994733 Category : Technology & Engineering Languages : en Pages : 648
Book Description
Materials Nanoarchitectonics: From Integrated Molecular Systems to Advanced Devices provides the latest information on the design and molecular manipulation of self-organized hierarchically structured systems using tailor-made nanoscale materials as structural and functional units. The book is organized into three main sections that focus on molecular design of building blocks and hybrid materials, formation of nanostructures, and applications and devices. Bringing together emerging materials, synthetic aspects, nanostructure strategies, and applications, the book aims to support further progress, by offering different perspectives and a strong interdisciplinary approach to this rapidly growing area of innovation. This is an extremely valuable resource for researchers, advanced students, and scientists in industry, with an interest in nanoarchitectonics, nanostructures, and nanomaterials, or across the areas of nanotechnology, chemistry, surface science, polymer science, electrical engineering, physics, chemical engineering, and materials science. Offers a nanoarchitectonic perspective on emerging fields, such as metal-organic frameworks, porous polymer materials, or biomimetic nanostructures Discusses different approaches to utilizing "soft chemistry" as a source for hierarchically organized materials Offers an interdisciplinary approach to the design and construction of integrated chemical nano systems Discusses novel approaches towards the creation of complex multiscale architectures
Author: David A.D. Parry Publisher: Gulf Professional Publishing ISBN: 9780120342709 Category : Science Languages : en Pages : 588
Book Description
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
Author: Agnes Dittel
Author: Agnes Dittel
Author: Michael Jünger
Author: Erik D. Demaine
Author: Jennifer J. McManus
Author: Marco Dorigo
Author: Steven M. LaValle
Author: H. Steinhaus
Author: 
Author: Katsuhiko Ariga
Author: David A.D. Parry