Protein Folding And Self Avoiding Walks Polyhedral Studies And Solutions

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Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions

Author : Agnes Dittel
Publisher : Logos Verlag Berlin GmbH
ISBN 13 : 3832520236
Total Pages : 362 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions by : Agnes Dittel

Download or read book Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions written by Agnes Dittel and published by Logos Verlag Berlin GmbH. This book was released on 2008 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Author : Michael Jünger
Publisher : Springer Science & Business Media
ISBN 13 : 3642381898
Total Pages : 510 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Facets of Combinatorial Optimization by : Michael Jünger

Download or read book Facets of Combinatorial Optimization written by Michael Jünger and published by Springer Science & Business Media. This book was released on 2013-07-03 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Planning Algorithms

Author : Steven M. LaValle
Publisher : Cambridge University Press
ISBN 13 : 9780521862059
Total Pages : 844 pages
Book Rating : 4.8/5 (62 download)

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Book Synopsis Planning Algorithms by : Steven M. LaValle

Download or read book Planning Algorithms written by Steven M. LaValle and published by Cambridge University Press. This book was released on 2006-05-29 with total page 844 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Ant Colony Optimization

Author : Marco Dorigo
Publisher : MIT Press
ISBN 13 : 9780262042192
Total Pages : 324 pages
Book Rating : 4.0/5 (421 download)

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Book Synopsis Ant Colony Optimization by : Marco Dorigo

Download or read book Ant Colony Optimization written by Marco Dorigo and published by MIT Press. This book was released on 2004-06-04 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein Structure

Author : Harold A. Scheraga
Publisher : Academic Press
ISBN 13 : 1483258971
Total Pages : 320 pages
Book Rating : 4.4/5 (832 download)

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Book Synopsis Protein Structure by : Harold A. Scheraga

Download or read book Protein Structure written by Harold A. Scheraga and published by Academic Press. This book was released on 2014-07-01 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein-Nanoparticle Interactions

Author : Masoud Rahman
Publisher : Springer Science & Business Media
ISBN 13 : 3642375553
Total Pages : 95 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Protein-Nanoparticle Interactions by : Masoud Rahman

Download or read book Protein-Nanoparticle Interactions written by Masoud Rahman and published by Springer Science & Business Media. This book was released on 2013-06-24 with total page 95 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, the fabrication of nanomaterials and exploration of their properties have attracted the attention of various scientific disciplines such as biology, physics, chemistry, and engineering. Although nanoparticulate systems are of significant interest in various scientific and technological areas, there is little known about the safety of these nanoscale objects. It has now been established that the surfaces of nanoparticles are immediately covered by biomolecules (e.g. proteins, ions, and enzymes) upon their entrance into a biological medium. This interaction with the biological medium modulates the surface of the nanoparticles, conferring a “biological identity” to their surfaces (referred to as a “corona”), which determines the subsequent cellular/tissue responses. The new interface between the nanoparticles and the biological medium/proteins, called “bio-nano interface,” has been very rarely studied in detail to date, though the interest in this topic is rapidly growing. In this book, the importance of the physiochemical characteristics of nanoparticles for the properties of the protein corona is discussed in detail, followed by comprehensive descriptions of the methods for assessing the protein-nanoparticle interactions. The advantages and limitations of available corona evaluation methods (e.g. spectroscopy methods, mass spectrometry, nuclear magnetic resonance, electron microscopy, X-ray crystallography, and differential centrifugal sedimentation) are examined in detail, followed by a discussion of the possibilities for enhancing the current methods and a call for new techniques. Moreover, the advantages and disadvantages of protein-nanoparticle interaction phenomena are explored and discussed, with a focus on the biological impacts.

Protein Self-Assembly

Author : Jennifer J. McManus
Publisher : Humana
ISBN 13 : 9781493996803
Total Pages : 266 pages
Book Rating : 4.9/5 (968 download)

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Book Synopsis Protein Self-Assembly by : Jennifer J. McManus

Download or read book Protein Self-Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

The Protein Folding Problem

Author : Donald B Wetlaufer
Publisher : Routledge
ISBN 13 : 9780367310851
Total Pages : 0 pages
Book Rating : 4.3/5 (18 download)

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Book Synopsis The Protein Folding Problem by : Donald B Wetlaufer

Download or read book The Protein Folding Problem written by Donald B Wetlaufer and published by Routledge. This book was released on 2024-10-31 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces the central problem of folding mechanisms as well as a number of other closely related issues. This book is neither a textbook nor a treatise. Rather, it is an attempt by several investigators to convey the excitement and challenges of those aspects of the folding problem in which they are actively engaged.

Mathematical Snapshots

Author : H. Steinhaus
Publisher : Courier Corporation
ISBN 13 : 0486166481
Total Pages : 340 pages
Book Rating : 4.4/5 (861 download)

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Book Synopsis Mathematical Snapshots by : H. Steinhaus

Download or read book Mathematical Snapshots written by H. Steinhaus and published by Courier Corporation. This book was released on 2012-07-12 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Science Citation Index

Author :
Publisher :
ISBN 13 :
Total Pages : 2560 pages
Book Rating : 4.0/5 ( download)

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Book Synopsis Science Citation Index by :

Download or read book Science Citation Index written by and published by . This book was released on 1993 with total page 2560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1964- have guides and journal lists.

Fibrous Proteins: Coiled-Coils, Collagen and Elastomers

Author : David A.D. Parry
Publisher : Gulf Professional Publishing
ISBN 13 : 9780120342709
Total Pages : 588 pages
Book Rating : 4.3/5 (427 download)

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Book Synopsis Fibrous Proteins: Coiled-Coils, Collagen and Elastomers by : David A.D. Parry

Download or read book Fibrous Proteins: Coiled-Coils, Collagen and Elastomers written by David A.D. Parry and published by Gulf Professional Publishing. This book was released on 2005-05-06 with total page 588 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Materials Nanoarchitectonics

Author : Katsuhiko Ariga
Publisher : Elsevier
ISBN 13 : 0323994733
Total Pages : 648 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Materials Nanoarchitectonics by : Katsuhiko Ariga

Download or read book Materials Nanoarchitectonics written by Katsuhiko Ariga and published by Elsevier. This book was released on 2023-12-07 with total page 648 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Mathematics and Computation

Author : Avi Wigderson
Publisher : Princeton University Press
ISBN 13 : 0691189137
Total Pages : 434 pages
Book Rating : 4.6/5 (911 download)

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Book Synopsis Mathematics and Computation by : Avi Wigderson

Download or read book Mathematics and Computation written by Avi Wigderson and published by Princeton University Press. This book was released on 2019-10-29 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: From the winner of the Turing Award and the Abel Prize, an introduction to computational complexity theory, its connections and interactions with mathematics, and its central role in the natural and social sciences, technology, and philosophy Mathematics and Computation provides a broad, conceptual overview of computational complexity theory—the mathematical study of efficient computation. With important practical applications to computer science and industry, computational complexity theory has evolved into a highly interdisciplinary field, with strong links to most mathematical areas and to a growing number of scientific endeavors. Avi Wigderson takes a sweeping survey of complexity theory, emphasizing the field’s insights and challenges. He explains the ideas and motivations leading to key models, notions, and results. In particular, he looks at algorithms and complexity, computations and proofs, randomness and interaction, quantum and arithmetic computation, and cryptography and learning, all as parts of a cohesive whole with numerous cross-influences. Wigderson illustrates the immense breadth of the field, its beauty and richness, and its diverse and growing interactions with other areas of mathematics. He ends with a comprehensive look at the theory of computation, its methodology and aspirations, and the unique and fundamental ways in which it has shaped and will further shape science, technology, and society. For further reading, an extensive bibliography is provided for all topics covered. Mathematics and Computation is useful for undergraduate and graduate students in mathematics, computer science, and related fields, as well as researchers and teachers in these fields. Many parts require little background, and serve as an invitation to newcomers seeking an introduction to the theory of computation. Comprehensive coverage of computational complexity theory, and beyond High-level, intuitive exposition, which brings conceptual clarity to this central and dynamic scientific discipline Historical accounts of the evolution and motivations of central concepts and models A broad view of the theory of computation's influence on science, technology, and society Extensive bibliography

Computational Topology

Author : Herbert Edelsbrunner
Publisher : American Mathematical Society
ISBN 13 : 1470467690
Total Pages : 241 pages
Book Rating : 4.4/5 (74 download)

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Book Synopsis Computational Topology by : Herbert Edelsbrunner

Download or read book Computational Topology written by Herbert Edelsbrunner and published by American Mathematical Society. This book was released on 2022-01-31 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combining concepts from topology and algorithms, this book delivers what its title promises: an introduction to the field of computational topology. Starting with motivating problems in both mathematics and computer science and building up from classic topics in geometric and algebraic topology, the third part of the text advances to persistent homology. This point of view is critically important in turning a mostly theoretical field of mathematics into one that is relevant to a multitude of disciplines in the sciences and engineering. The main approach is the discovery of topology through algorithms. The book is ideal for teaching a graduate or advanced undergraduate course in computational topology, as it develops all the background of both the mathematical and algorithmic aspects of the subject from first principles. Thus the text could serve equally well in a course taught in a mathematics department or computer science department.

Biological Physics

Author : Philip Nelson
Publisher : Macmillan Higher Education
ISBN 13 : 1319038948
Total Pages : 661 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Biological Physics by : Philip Nelson

Download or read book Biological Physics written by Philip Nelson and published by Macmillan Higher Education. This book was released on 2013-12-16 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological Physics focuses on new results in molecular motors, self-assembly, and single-molecule manipulation that have revolutionized the field in recent years, and integrates these topics with classical results. The text also provides foundational material for the emerging field of nanotechnology.

A Fuller Explanation

Author : Amy C. Edmondson
Publisher : Springer Science & Business Media
ISBN 13 : 1468474855
Total Pages : 320 pages
Book Rating : 4.4/5 (684 download)

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Book Synopsis A Fuller Explanation by : Amy C. Edmondson

Download or read book A Fuller Explanation written by Amy C. Edmondson and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: In a broad sense Design Science is the grammar of a language of images rather than of words. Modern communication techniques enable us to transmit and reconstitute images without the need of knowing a specific verbal sequential language such as the Morse code or Hungarian. International traffic signs use international image symbols which are not specific to any particular verbal language. An image language differs from a verbal one in that the latter uses a linear string of symbols, whereas the former is multidimensional. Architectural renderings commonly show projections onto three mutually perpendicular planes, or consist of cross sections at differ ent altitudes representing a stack of floor plans. Such renderings make it difficult to imagine buildings containing ramps and other features which disguise the separation between floors; consequently, they limit the creativity of the architect. Analogously, we tend to analyze natural structures as if nature had used similar stacked renderings, rather than, for instance, a system of packed spheres, with the result that we fail to perceive the system of organization determining the form of such structures.

Shaping Space

Author : Marjorie Senechal
Publisher : Springer Science & Business Media
ISBN 13 : 038792714X
Total Pages : 334 pages
Book Rating : 4.3/5 (879 download)

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Book Synopsis Shaping Space by : Marjorie Senechal

Download or read book Shaping Space written by Marjorie Senechal and published by Springer Science & Business Media. This book was released on 2013-03-22 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition is based off of the very popular Shaping Space: A Polyhedral Approach, first published twenty years ago. The book is expanded and updated to include new developments, including the revolutions in visualization and model-making that the computer has wrought. Shaping Space is an exuberant, richly-illustrated, interdisciplinary guide to three-dimensional forms, focusing on the suprisingly diverse world of polyhedra. Geometry comes alive in Shaping Space, as a remarkable range of geometric ideas is explored and its centrality in our cultre is persuasively demonstrated. The book is addressed to designers, artists, architects, engineers, chemists, computer scientists, mathematicians, bioscientists, crystallographers, earth scientists, and teachers at all levels—in short, to all scholars and educators interested in, and working with, two- and three-dimensinal structures and patterns.