Understanding Molecular Simulation

Author: Daan Frenkel
Publisher: Elsevier
ISBN: 9780080519982
Format: PDF, Mobi
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Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: · Transition path sampling and diffusive barrier crossing to simulaterare events · Dissipative particle dynamic as a course-grained simulation technique · Novel schemes to compute the long-ranged forces · Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations · Multiple-time step algorithms as an alternative for constraints · Defects in solids · The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules · Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Statistical Mechanics Theory and Molecular Simulation

Author: Mark Tuckerman
Publisher: OUP Oxford
ISBN: 9780191523465
Format: PDF, ePub, Docs
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Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.

Molecular Modelling for Beginners

Author: Alan Hinchliffe
Publisher: John Wiley & Sons
ISBN: 1119964814
Format: PDF, Kindle
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A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry. Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages and many realistic examples with solutions Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian .gjf files and sample outputs. Revised with changes in emphasis and presentation to appeal to the modern student.

Essentials of Computational Chemistry

Author: Christopher J. Cramer
Publisher: John Wiley & Sons
ISBN: 1118712277
Format: PDF, Mobi
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Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.

Industrial Applications of Molecular Simulations

Author: Marc Meunier
Publisher: CRC Press
ISBN: 1439861021
Format: PDF, Mobi
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The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations demonstrates the capability of molecular modeling to tackle problems of industrial relevance. This book presents a wide range of various modeling techniques, including methods based on quantum or classical mechanics, molecular dynamics, Monte Carlo simulations, etc. It also explores a wide range of materials, from soft materials such as polymeric blends widely used in the chemical industry to hard or inorganic materials such as glasses and alumina. Features Demonstrates how modeling can solve everyday problems for scientists in industry Provides a broad overview of theoretical approaches Presents a wide range of applications in areas such as materials research, catalysis, pharmaceutical development and electronics Emphasizes the relationship between theory and experiments

Metastable Liquids

Author: Pablo G. Debenedetti
Publisher: Princeton University Press
ISBN: 9780691085951
Format: PDF
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Metastable Liquids provides a comprehensive treatment of the properties of liquids under conditions where the stable state is a vapor, a solid, or a liquid mixture of different composition. It examines the fundamental principles that govern the equilibrium properties, stability, relaxation mechanisms, and relaxation rates of metastable liquids. Building on the interplay of kinetics and thermodynamics that determines the thermophysical properties and structural relaxation of metastable liquids, it offers an in-depth treatment of thermodynamic stability theory, the statistical mechanics of metastability, nucleation, spinodal decomposition, supercooled liquids, and the glass transition. Both traditional topics--such as stability theory--and modern developments--including modern theories of nucleation and the properties of supercooled and glassy water--are treated in detail. An introductory chapter illustrates, with numerous examples, the importance and ubiquity of metastable liquids. Examples include the ascent of sap in plants, the strategies adopted by many living organisms to survive prolonged exposure to sub-freezing conditions, the behavior of proteins at low temperatures, metastability in mineral inclusions, ozone depletion, the preservation and storage of labile biochemicals, and the prevention of natural gas clathrate hydrate formation. All mathematical symbols are defined in the text and key equations are clearly explained. More complex mathematical explanations are available in the appendixes.

Molecular Modeling and Simulation

Author: Tamar Schlick
Publisher: Springer Science & Business Media
ISBN: 0387224645
Format: PDF
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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Scientific Computing with MATLAB and Octave

Author: Alfio Quarteroni
Publisher: Springer Science & Business Media
ISBN: 3642453678
Format: PDF, Mobi
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This textbook is an introduction to Scientific Computing, in which several numerical methods for the computer-based solution of certain classes of mathematical problems are illustrated. The authors show how to compute the zeros, the extrema, and the integrals of continuous functions, solve linear systems, approximate functions using polynomials and construct accurate approximations for the solution of ordinary and partial differential equations. To make the format concrete and appealing, the programming environments Matlab and Octave are adopted as faithful companions. The book contains the solutions to several problems posed in exercises and examples, often originating from important applications. At the end of each chapter, a specific section is devoted to subjects which were not addressed in the book and contains bibliographical references for a more comprehensive treatment of the material. From the review: ".... This carefully written textbook, the third English edition, contains substantial new developments on the numerical solution of differential equations. It is typeset in a two-color design and is written in a style suited for readers who have mathematics, natural sciences, computer sciences or economics as a background and who are interested in a well-organized introduction to the subject." Roberto Plato (Siegen), Zentralblatt MATH 1205.65002.

Petascale Computing

Author: David A. Bader
Publisher: CRC Press
ISBN: 9781584889106
Format: PDF, Mobi
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Although the highly anticipated petascale computers of the near future will perform at an order of magnitude faster than today’s quickest supercomputer, the scaling up of algorithms and applications for this class of computers remains a tough challenge. From scalable algorithm design for massive concurrency toperformance analyses and scientific visualization, Petascale Computing: Algorithms and Applications captures the state of the art in high-performance computing algorithms and applications. Featuring contributions from the world’s leading experts in computational science, this edited collection explores the use of petascale computers for solving the most difficult scientific and engineering problems of the current century. Covering a wide range of important topics, the book illustrates how petascale computing can be applied to space and Earth science missions, biological systems, weather prediction, climate science, disasters, black holes, and gamma ray bursts. It details the simulation of multiphysics, cosmological evolution, molecular dynamics, and biomolecules. The book also discusses computational aspects that include the Uintah framework, Enzo code, multithreaded algorithms, petaflops, performance analysis tools, multilevel finite element solvers, finite element code development, Charm++, and the Cactus framework. Supplying petascale tools, programming methodologies, and an eight-page color insert, this volume addresses the challenging problems of developing application codes that can take advantage of the architectural features of the new petascale systems in advance of their first deployment.