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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.
This work 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. It also covers important topics such as free-energy calculations, linear-response theory and critical phenomena.
Graduate level textbook presenting some of the most fundamental processes that underlie physical, chemical and biological phenomena in complex condensed phase systems. Includes in-depth descriptions of relevant methodologies, and provides ample introductory material for readers of different backgrounds.
This book deals with a central topic at the interface of chemistry and physics - the understanding of how the transformation of matter takes place at the atomic level. Building on the laws of physics, the book focuses on the theoretical framework for predicting the outcome of chemical reactions. The style is highly systematic with attention to basic concepts and clarity of presentation. Molecular reaction dynamics is about the detailed atomic-level description of chemical reactions. Based on quantum mechanics and statistical mechanics or, as an approximation, classical mechanics, the dynamics of uni- and bi-molecular elementary reactions are described. The book features a detailed presentation of transition-state theory which plays an important role in practice, and a comprehensive discussion of basic theories of reaction dynamics in condensed phases. Examples and end-of-chapter problems are included in order to illustrate the theory and its connection to chemical problems.
This is a 2002 introduction to statistical mechanics, intended for advanced undergraduate or beginning graduate students.
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.

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