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Molecular Dynamics Simulations In Statistical Physics
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Book Synopsis Molecular Dynamics Simulations in Statistical Physics: Theory and Applications by : Hiqmet Kamberaj
Download or read book Molecular Dynamics Simulations in Statistical Physics: Theory and Applications written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2020-03-20 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field.
Book Synopsis Statistical Mechanics: Theory and Molecular Simulation by : Mark Tuckerman
Download or read book Statistical Mechanics: Theory and Molecular Simulation written by Mark Tuckerman and published by OUP Oxford. This book was released on 2010-02-11 with total page 719 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Understanding Molecular Simulation by : Daan Frenkel
Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Dynamics Simulations in Statistical Physics by : Hiqmet Kamberaj
Download or read book Molecular Dynamics Simulations in Statistical Physics written by Hiqmet Kamberaj and published by . This book was released on 2020 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field. .
Book Synopsis A Guide to Monte Carlo Simulations in Statistical Physics by : David P. Landau
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David P. Landau and published by Cambridge University Press. This book was released on 2000-08-17 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics and statistical mechanics, as well as in related fields, such as polymer science and lattice gauge theory. The authors give a succinct overview of simple sampling methods and develop the importance sampling method. In addition they introduce quantum Monte Carlo methods, aspects of simulations of growth phenomena and other systems far from equilibrium, and the Monte Carlo Renormalization Group approach to critical phenomena. The book includes many applications, examples, and current references, and exercises to help the reader.
Book Synopsis A Guide to Monte Carlo Simulations in Statistical Physics by : David P. Landau
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David P. Landau and published by Cambridge University Press. This book was released on 2009-09-10 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dealing with all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics and statistical mechanics, this book provides an introduction to computer simulations in physics. This edition now contains material describing powerful new algorithms that have appeared since the previous edition was published, and highlights recent technical advances and key applications that these algorithms now make possible. Updates also include several new sections and a chapter on the use of Monte Carlo simulations of biological molecules. Throughout the book there are many applications, examples, recipes, case studies, and exercises to help the reader understand the material. It is ideal for graduate students and researchers, both in academia and industry, who want to learn techniques that have become a third tool of physical science, complementing experiment and analytical theory.
Book Synopsis Simulation of Liquids and Solids by : Giovanni Ciccotti
Download or read book Simulation of Liquids and Solids written by Giovanni Ciccotti and published by North Holland. This book was released on 1987 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis A Guide to Monte Carlo Simulations in Statistical Physics by : David P. Landau
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David P. Landau and published by Cambridge University Press. This book was released on 2005-09 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This updated edition deals with the Monte Carlo simulation of complex physical systems encountered in condensed-matter physics, statistical mechanics, and related fields. It contains many applications, examples, and exercises to help the reader. It is an excellent guide for graduate students and researchers who use computer simulations in their research.
Book Synopsis Principles of Statistical Physics and Numerical Modelling by : Valeriy A. Ryabov
Download or read book Principles of Statistical Physics and Numerical Modelling written by Valeriy A. Ryabov and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This unique text provides an introduction to classical statistical mechanics, using molecular dynamic simulations to teach and explore the subject. Illustrated by numerous figures and animations the book will be useful for students and professionals wishing to receive a contemporary understanding of statistical physics and use the methods in their research." -- Prové de l'editor.
Book Synopsis Monte Carlo and Molecular Dynamics Simulations in Polymer Science by : Kurt Binder
Download or read book Monte Carlo and Molecular Dynamics Simulations in Polymer Science written by Kurt Binder and published by Oxford University Press. This book was released on 1995-08-03 with total page 602 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by leading experts from around the world, Monte Carlo and Molecular Dynamics Simulations in Polymer Science comprehensively reviews the latest simulation techniques for macromolecular materials. Focusing in particular on numerous new techniques, the book offers authoritative introductions to solutions of neutral polymers and polyelectrolytes; dynamics of polymer melts, rubbers and gels, and glassy materials; thermodynamics of polymer mixing and mesophase formation, and polymers confined at interfaces and grafted to walls. Throughout, contributors offer practical advice on how to overcome the unique challenges posed by the large size and slow relaxation of polymer coils. Students and researchers in polymer chemistry, polymer physics, chemical engineering, and materials and computational science will all benefit from the cogent, step-by-step introductions contained in this important new book.
Book Synopsis Computer Meets Theoretical Physics by : Giovanni Battimelli
Download or read book Computer Meets Theoretical Physics written by Giovanni Battimelli and published by Springer Nature. This book was released on 2020-06-17 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a vivid account of the early history of molecular simulation, a new frontier for our understanding of matter that was opened when the demands of theoretical physicists were met by the availability of the modern computers. Since their inception, electronic computers have enormously increased their performance, thus making possible the unprecedented technological revolution that characterizes our present times. This obvious technological advancement has brought with it a silent scientific revolution in the practice of theoretical physics. In particular, in the physics of matter it has opened up a direct route from the microscopic physical laws to observable phenomena. One can now study the time evolution of systems composed of millions of molecules, and simulate the behaviour of macroscopic materials and actually predict their properties. Molecular simulation has provided a new theoretical and conceptual tool that physicists could only dream of when the foundations of statistical mechanics were laid. Molecular simulation has undergone impressive development, both in the size of the scientific community involved and in the range and scope of its applications. It has become the ubiquitous workhorse for investigating the nature of complex condensed matter systems in physics, chemistry, materials and the life sciences. Yet these developments remain largely unknown outside the inner circles of practitioners, and they have so far never been described for a wider public. The main objective of this book is therefore to offer a reasonably comprehensive reconstruction of the early history of molecular simulation addressed to an audience of both scientists and interested non-scientists, describing the scientific and personal trajectories of the main protagonists and discussing the deep conceptual innovations that their work produced.
Book Synopsis Understanding Molecular Simulation by : Daan Frenkel
Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2023-07-13 with total page 868 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text. Since the second edition’s publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed. Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning
Book Synopsis Molecular Simulations by : Saman Alavi
Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-06-29 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.
Book Synopsis Statistical Mechanics by : R.K. Pathria
Download or read book Statistical Mechanics written by R.K. Pathria and published by Elsevier. This book was released on 2017-02-21 with total page 542 pages. Available in PDF, EPUB and Kindle. Book excerpt: Statistical Mechanics discusses the fundamental concepts involved in understanding the physical properties of matter in bulk on the basis of the dynamical behavior of its microscopic constituents. The book emphasizes the equilibrium states of physical systems. The text first details the statistical basis of thermodynamics, and then proceeds to discussing the elements of ensemble theory. The next two chapters cover the canonical and grand canonical ensemble. Chapter 5 deals with the formulation of quantum statistics, while Chapter 6 talks about the theory of simple gases. Chapters 7 and 8 examine the ideal Bose and Fermi systems. In the next three chapters, the book covers the statistical mechanics of interacting systems, which includes the method of cluster expansions, pseudopotentials, and quantized fields. Chapter 12 discusses the theory of phase transitions, while Chapter 13 discusses fluctuations. The book will be of great use to researchers and practitioners from wide array of disciplines, such as physics, chemistry, and engineering.
Book Synopsis An Introduction to Applied Statistical Thermodynamics by : Stanley I. Sandler
Download or read book An Introduction to Applied Statistical Thermodynamics written by Stanley I. Sandler and published by John Wiley & Sons. This book was released on 2010-11-16 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the goals of An Introduction to Applied Statistical Thermodynamics is to introduce readers to the fundamental ideas and engineering uses of statistical thermodynamics, and the equilibrium part of the statistical mechanics. This text emphasises on nano and bio technologies, molecular level descriptions and understandings offered by statistical mechanics. It provides an introduction to the simplest forms of Monte Carlo and molecular dynamics simulation (albeit only for simple spherical molecules) and user-friendly MATLAB programs for doing such simulations, and also some other calculations. The purpose of this text is to provide a readable introduction to statistical thermodynamics, show its utility and the way the results obtained lead to useful generalisations for practical application. The text also illustrates the difficulties that arise in the statistical thermodynamics of dense fluids as seen in the discussion of liquids.
Book Synopsis Molecular Dynamics Simulation by : J. M. Haile
Download or read book Molecular Dynamics Simulation written by J. M. Haile and published by Wiley-Interscience. This book was released on 1997-03-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes
Book Synopsis Bridging the Time Scales by : Peter Nielaba
Download or read book Bridging the Time Scales written by Peter Nielaba and published by Springer Science & Business Media. This book was released on 2007-10-13 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: The behaviour of many complex materials extends over time- and lengthscales well beyond those that can normally be described using standard molecular dynamics or Monte Carlo simulation techniques. As progress is coming more through refined simulation methods than from increased computer power, this volume is intended as both an introduction and a review of all relevant modern methods that will shape molecular simulation in the forthcoming decade. Written as a set of tutorial reviews, the book will be of use to specialists and nonspecialists alike.
