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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: Daan Frenkel
Publisher: Elsevier
ISBN: 0080519989
Category : Science
Languages : en
Pages : 661
Get Book Here
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: Daan Frenkel
Publisher:
ISBN: 9780122673702
Category : Forces intermoléculaires - Simulation par ordinateur
Languages : en
Pages : 443
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Book Description
This book 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. Since a wide variety of computational tools exists, 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. Examples are included that highlight current applications, and the codes of the case studies are available on the World Wide Web. No prior knowledge of computer simulation is assumed.
Author: Daan Frenkel
Publisher: Academic Press
ISBN: 9780122673511
Category : Science
Languages : en
Pages : 664
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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: Martin J. Field
Publisher: Cambridge University Press
ISBN: 1139465813
Category : Science
Languages : en
Pages : 294
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Book Description
Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.
Author: Snehanshu Pal
Publisher: CRC Press
ISBN: 0429672454
Category : Mathematics
Languages : en
Pages : 334
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Book Description
Molecular dynamics simulation is a significant technique to gain insight into the mechanical behavior of nanostructured (NS) materials and associated underlying deformation mechanisms at the atomic scale. The purpose of this book is to detect and correlate critically current achievements and properly assess the state of the art in the mechanical behavior study of NS material in the perspective of the atomic scale simulation of the deformation process. More precisely, the book aims to provide representative examples of mechanical behavior studies carried out using molecular dynamics simulations, which provide contributory research findings toward progress in the field of NS material technology.
Author: Daan Frenkel
Publisher: Elsevier
ISBN: 0323913180
Category : Science
Languages : en
Pages : 868
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Book Description
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
Author: Saman Alavi
Publisher: John Wiley & Sons
ISBN: 3527341056
Category : Technology & Engineering
Languages : en
Pages : 342
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Book Description
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.
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: Kun Zhou
Publisher: Academic Press
ISBN: 0128166169
Category : Technology & Engineering
Languages : en
Pages : 375
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Book Description
Molecular Dynamic Simulation: Fundamentals and Applications explains the basic principles of MD simulation and explores its recent developments and roles in advanced modeling approaches. The implementation of MD simulation and its application to various aspects of materials science and engineering including mechanical, thermal, mass transportation, and physical/chemical reaction problems are illustrated. Innovative modeling techniques that apply MD to explore the mechanics of typical nanomaterials and nanostructures and to characterize crystalline, amorphous, and liquid systems are also presented. The rich research experience of the authors in MD simulation will ensure that the readers are provided with both an in-depth understanding of MD simulation and clear technical guidance. - Provides a comprehensive overview of the underlying theories of molecular dynamics (MD) simulation - Presents application-based examples pertaining to a broad range of mechanical, thermal, and mass transport problems - Explores innovative modeling techniques for simulating typical nanomaterials and nanostructures and for characterizing crystalline, amorphous, and liquid systems
Author: Iain D. Boyd
Publisher: Cambridge University Press
ISBN: 1107073448
Category : Science
Languages : en
Pages : 383
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Book Description
7.1 Introduction -- 7.2 Rotational Energy Exchange Models -- 7.2.1 Constant Collision Number -- 7.2.2 The Parker Model -- 7.2.3 Variable Probability Exchange Model of Boyd -- 7.2.4 Nonequilibrium Direction Dependent Model -- 7.2.5 Model Results -- 7.3 Vibrational Energy Exchange Models -- 7.3.1 Constant Collision Number -- 7.3.2 The Millikan-White Model -- 7.3.3 Quantized Treatment for Vibration -- 7.3.4 Model Results -- 7.4 Dissociation Chemical Reactions -- 7.4.1 Total Collision Energy Model -- 7.4.2 Redistribution of Energy Following a Dissociation Reaction -- 7.4.3 Vibrationally Favored Dissociation Model -- 7.5 General Chemical Reactions -- 7.5.1 Reaction Rates and Equilibrium Constant -- 7.5.2 Backward Reaction Rates in DSMC -- 7.5.3 Three-Body Recombination Reactions -- 7.5.4 Post-Reaction Energy Redistribution and General Implementation -- 7.5.5 DSMC Solutions for Reacting Flows -- 7.6 Summary -- Appendix A: Generating Particle Properties -- Appendix B: Collisional Quantities -- Appendix C: Determining Post-Collision Velocities -- Appendix D: Macroscopic Properties -- Appendix E: Common Integrals -- References -- Index
