Molecular Dynamics Simulations in Statistical Physics: Theory and Applications PDF Download
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Author: Hiqmet Kamberaj
Publisher: Springer Nature
ISBN: 3030357023
Category : Science
Languages : en
Pages : 470
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Book Description
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.
Author: Hiqmet Kamberaj
Publisher: Springer Nature
ISBN: 3030357023
Category : Science
Languages : en
Pages : 470
Get Book Here
Book Description
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.
Author: Mark Tuckerman
Publisher: OUP Oxford
ISBN: 0191523461
Category : Science
Languages : en
Pages : 719
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Book Description
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.
Author: Daan Frenkel
Publisher: Elsevier
ISBN: 0080519989
Category : Science
Languages : en
Pages : 661
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Book Description
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.
Author: David P. Landau
Publisher: Cambridge University Press
ISBN: 9780521653664
Category : Mathematics
Languages : en
Pages : 402
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Book Description
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.
Author: Valeriy A. Ryabov
Publisher:
ISBN: 9780750313414
Category : Molecular dynamics
Languages : en
Pages : 0
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Book Description
"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.
Author: David P. Landau
Publisher: Cambridge University Press
ISBN: 9780521842389
Category : Computers
Languages : en
Pages : 456
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Book Description
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.
Author: Hiqmet Kamberaj
Publisher:
ISBN: 9783030357030
Category : Statistical physics
Languages : en
Pages : 470
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Book Description
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. .
Author: R.K. Pathria
Publisher: Elsevier
ISBN: 1483186881
Category : Science
Languages : en
Pages : 542
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Book Description
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.
Author: J. M. Haile
Publisher: Wiley-Interscience
ISBN: 9780471184393
Category : Technology & Engineering
Languages : en
Pages : 0
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Book Description
"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
Author: Harvey Gould
Publisher: Princeton University Press
ISBN: 0691230846
Category : Science
Languages : en
Pages : 527
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Book Description
A completely revised edition that combines a comprehensive coverage of statistical and thermal physics with enhanced computational tools, accessibility, and active learning activities to meet the needs of today's students and educators This revised and expanded edition of Statistical and Thermal Physics introduces students to the essential ideas and techniques used in many areas of contemporary physics. Ready-to-run programs help make the many abstract concepts concrete. The text requires only a background in introductory mechanics and some basic ideas of quantum theory, discussing material typically found in undergraduate texts as well as topics such as fluids, critical phenomena, and computational techniques, which serve as a natural bridge to graduate study. Completely revised to be more accessible to students Encourages active reading with guided problems tied to the text Updated open source programs available in Java, Python, and JavaScript Integrates Monte Carlo and molecular dynamics simulations and other numerical techniques Self-contained introductions to thermodynamics and probability, including Bayes' theorem A fuller discussion of magnetism and the Ising model than other undergraduate texts Treats ideal classical and quantum gases within a uniform framework Features a new chapter on transport coefficients and linear response theory Draws on findings from contemporary research Solutions manual (available only to instructors)
