Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions

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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

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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.

Geometric Folding Algorithms

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Publisher : Cambridge University Press
ISBN 13 : 1107394090
Total Pages : 388 pages
Book Rating : 4.1/5 (73 download)

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Book Synopsis Geometric Folding Algorithms by : Erik D. Demaine

Download or read book Geometric Folding Algorithms written by Erik D. Demaine and published by Cambridge University Press. This book was released on 2007-07-16 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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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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.

Ant Colony Optimization

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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.

Planning Algorithms

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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.

Mathematical Snapshots

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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

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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.

Protein Structure

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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.

Materials Nanoarchitectonics

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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 2023-12-15 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

Computational Topology

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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.

Fibrous Proteins: Coiled-Coils, Collagen and Elastomers

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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

Mathematics and Computation

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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: 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

The Cognitive-Theoretic Model of the Universe: A New Kind of Reality Theory

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Publisher : Mega Foundation Press
ISBN 13 : 0971916225
Total Pages : 94 pages
Book Rating : 4.9/5 (719 download)

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Book Synopsis The Cognitive-Theoretic Model of the Universe: A New Kind of Reality Theory by : Christopher Michael Langan

Download or read book The Cognitive-Theoretic Model of the Universe: A New Kind of Reality Theory written by Christopher Michael Langan and published by Mega Foundation Press. This book was released on 2002-06-01 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt: Paperback version of the 2002 paper published in the journal Progress in Information, Complexity, and Design (PCID). ABSTRACT Inasmuch as science is observational or perceptual in nature, the goal of providing a scientific model and mechanism for the evolution of complex systems ultimately requires a supporting theory of reality of which perception itself is the model (or theory-to-universe mapping). Where information is the abstract currency of perception, such a theory must incorporate the theory of information while extending the information concept to incorporate reflexive self-processing in order to achieve an intrinsic (self-contained) description of reality. This extension is associated with a limiting formulation of model theory identifying mental and physical reality, resulting in a reflexively self-generating, self-modeling theory of reality identical to its universe on the syntactic level. By the nature of its derivation, this theory, the Cognitive Theoretic Model of the Universe or CTMU, can be regarded as a supertautological reality-theoretic extension of logic. Uniting the theory of reality with an advanced form of computational language theory, the CTMU describes reality as a Self Configuring Self-Processing Language or SCSPL, a reflexive intrinsic language characterized not only by self-reference and recursive self-definition, but full self-configuration and self-execution (reflexive read-write functionality). SCSPL reality embodies a dual-aspect monism consisting of infocognition, self-transducing information residing in self-recognizing SCSPL elements called syntactic operators. The CTMU identifies itself with the structure of these operators and thus with the distributive syntax of its self-modeling SCSPL universe, including the reflexive grammar by which the universe refines itself from unbound telesis or UBT, a primordial realm of infocognitive potential free of informational constraint. Under the guidance of a limiting (intrinsic) form of anthropic principle called the Telic Principle, SCSPL evolves by telic recursion, jointly configuring syntax and state while maximizing a generalized self-selection parameter and adjusting on the fly to freely-changing internal conditions. SCSPL relates space, time and object by means of conspansive duality and conspansion, an SCSPL-grammatical process featuring an alternation between dual phases of existence associated with design and actualization and related to the familiar wave-particle duality of quantum mechanics. By distributing the design phase of reality over the actualization phase, conspansive spacetime also provides a distributed mechanism for Intelligent Design, adjoining to the restrictive principle of natural selection a basic means of generating information and complexity. Addressing physical evolution on not only the biological but cosmic level, the CTMU addresses the most evident deficiencies and paradoxes associated with conventional discrete and continuum models of reality, including temporal directionality and accelerating cosmic expansion, while preserving virtually all of the major benefits of current scientific and mathematical paradigms.

Biological Physics

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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

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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.

Introduction to Soft Matter

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Publisher : John Wiley & Sons
ISBN 13 : 1118681428
Total Pages : 304 pages
Book Rating : 4.1/5 (186 download)

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Book Synopsis Introduction to Soft Matter by : Ian W. Hamley

Download or read book Introduction to Soft Matter written by Ian W. Hamley and published by John Wiley & Sons. This book was released on 2013-03-18 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to this exciting and relativelynew subject with chapters covering natural and synthetic polymers,colloids, surfactants and liquid crystals highlighting the many andvaried applications of these materials. Written by an expert in thefield, this book will be an essential reference for people workingin both industry and academia and will aid in understanding of thisincreasingly popular topic. Contains a new chapter on biological soft matter Newly edited and updated chapters including updated coverageof recent aspects of polymer science. Contain problems at the end of each chapter to facilitateunderstanding