Understanding Molecular Simulation: From Algorithms to Applications

by Daan Frenkel, Berend Smit

Overview

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.

Product Details

ISBN-13:	9780122673511
Publisher:	Elsevier Science
Publication date:	10/24/2001
Series:	Computational Science Series
Edition description:	REV
Pages:	664
Product dimensions:	6.00(w) x 9.00(h) x (d)

About the Author

Daan Frenkel is based at the FOM Institute for Atomic and Molecular Physics and at the Department of Chemistry, University of Amsterdam. His research has three central themes: prediction of phase behavior of complex liquids, modeling the (hydro) dynamics of colloids and microporous structures, and predicting the rate of activated processes. He was awarded the prestigious Spinoza Prize from the Dutch Research Council in 2000.

Berend Smit is Professor at the Department of Chemical Engineering of the Faculty of Science, University of Amsterdam. His research focuses on novel Monte Carlo simulations. Smit applies this technique to problems that are of technological importance, particularly those of interest in chemical engineering.

Table of Contents

1. Introduction

Part I Basics
2. Statistical Mechanics
3. Monte Carlo Simulations
4. Molecular Dynamics Simulations

Part II Ensembles
5. Monte Carlo Simulations in Various Ensembles
6. Molecular Dynamics in Various Ensembles

Part III Free Energies and Phase Equilibria
7. Free Energy Calculations
8. The Gibbs Ensemble
9. Other Methods to Study Coexistence
10. Free Energies of Solids
11. Free Energy of Chain Molecules

Part IV Advanced Techniques
12. Long-Range Interactions
13. Biased Monte Carlo Schemes
14. Accelerating Monte Carlo Sampling
15. Tackling Time-Scale Problems
16. Rare Events
17. Dissipative Particle Dynamics

What People are Saying About This

From the Publisher

Fully updated edition of this key text that supports those involved with studying, developing or applying molecular simulations

Editorial Reviews

A unified presentation of the computational tools that are currently used to study the equilibrium properties, and in particular, the phase behavior of molecular and supramolecular substances. This book explains the physics behind the "recipes" of molecular simulation for materials science. 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 in assumed--but the book is aimed at readers who are active in computer simulation or are planning to become so. Annotation c. Book News, Inc., Portland, OR (booknews.com)

Booknews

This work for nonexperts involved in computer simulation explains the physics behind the techniques of molecular simulation in materials science, allowing those using simulation to choose appropriate techniques and improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use is demonstrated in case studies. This edition presents new material on areas such as transition path sampling and diffusive barrier crossing to simulate rare events, dissipative particle dynamics as a course-grained simulation technique, and parallel tempering for glassy Hamiltonians. Frenkel is affiliated with the FOM Institute for Atomic and Molecular Physics and teaches chemical engineering at the University of Amsterdam, The Netherlands. Smit teaches chemical engineering at the University of Amsterdam. Annotation c. Book News, Inc., Portland, OR (booknews.com)

From the previous edition:
"... this book brilliantly lays down the scientific foundations of the simulational approach ..." —Prof. Kurt Binder in Physics World, 1997

"... a treasure. The book is a marvellous mix of just enough formalism with an informal and readable style, sufficient detail to understand methodological advances, appropriate mathematics ..." —Prof. Mark A. Ratner in Physics Today, 1997

From the Publisher