Download and read online Statistical Mechanics Theory and Molecular Simulation in PDF and EPUB 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.
Download and read online Molecular Dynamics in PDF and EPUB This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.
Download and read online High resolution Simulations of Strongly Coupled Coulomb Systems with a Parallel Tree Code in PDF and EPUB
Download and read online Chemical Dynamics in Condensed Phases in PDF and EPUB 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.
Download and read online Computer Simulation of Liquids in PDF and EPUB This book describes how to use computers to simulate the properties of liquids. It provides an introduction and practical guide to the molecular dynamics and Monte Carlo methods. 'The book is comprehensive, thorough and readable' Chemistry in Britain
Download and read online Theories of Molecular Reaction Dynamics in PDF and EPUB 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.
Download and read online Understanding Molecular Simulation in PDF and EPUB 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.
Download and read online Nonequilibrium Statistical Mechanics in PDF and EPUB This is a presentation of the main ideas and methods of modern nonequilibrium statistical mechanics. It is the perfect introduction for anyone in chemistry or physics who needs an update or background in this time-dependent field. Topics covered include fluctuation-dissipation theorem; linear response theory; time correlation functions, and projection operators. Theoretical models are illustrated by real-world examples and numerous applications such as chemical reaction rates and spectral line shapes are covered. The mathematical treatments are detailed and easily understandable and the appendices include useful mathematical methods like the Laplace transforms, Gaussian random variables and phenomenological transport equations.
Download and read online Statistical Mechanics Algorithms and Computations in PDF and EPUB This book discusses the computational approach in modern statistical physics, adopting simple language and an attractive format with many illustrations, tables and printed algorithms. The style will appeal to students, teachers and researchers in the physical sciences. The focus is on orientation, with implementation details kept to a minimum.
Download and read online Statistical Physics of Biomolecules in PDF and EPUB From the hydrophobic effect to protein-ligand binding, statistical physics is relevant in almost all areas of molecular biophysics and biochemistry, making it essential for modern students of molecular behavior. But traditional presentations of this material are often difficult to penetrate. Statistical Physics of Biomolecules: An Introduction brings "down to earth" some of the most intimidating but important theories of molecular biophysics. With an accessible writing style, the book unifies statistical, dynamic, and thermodynamic descriptions of molecular behavior using probability ideas as a common basis. Numerous examples illustrate how the twin perspectives of dynamics and equilibrium deepen our understanding of essential ideas such as entropy, free energy, and the meaning of rate constants. The author builds on the general principles with specific discussions of water, binding phenomena, and protein conformational changes/folding. The same probabilistic framework used in the introductory chapters is also applied to non-equilibrium phenomena and to computations in later chapters. The book emphasizes basic concepts rather than cataloguing a broad range of phenomena. Focuses on what students need to know now Students build a foundational understanding by initially focusing on probability theory, low-dimensional models, and the simplest molecular systems. The basics are then directly developed for biophysical phenomena, such as water behavior, protein binding, and conformational changes. The book’s accessible development of equilibrium and dynamical statistical physics makes this a valuable text for students with limited physics and chemistry backgrounds.
Download and read online Nonequilibrium Statistical Physics in PDF and EPUB This book presents a united approach to the statistical physics of systems near equilibrium: it brings out the profound unity of the laws which govern them and gathers together results usually fragmented in the literature. It will be useful both as a textbook about irreversible phenomena and as a reference book for researchers.
Download and read online The Art of Molecular Dynamics Simulation in PDF and EPUB The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.
Download and read online Statistical Mechanics of Nonequilibrium Liquids in PDF and EPUB Statistical Mechanics of Nonequilibrium Liquids deals with theoretical rheology. The book discusses nonlinear response of systems and outlines the statistical mechanical theory. In discussing the framework of nonequilibrium statistical mechanics, the book explains the derivation of a nonequilibrium analogue of the Gibbsian basis for equilibrium statistical mechanics. The book reviews the linear irreversible thermodynamics, the Liouville equation, and the Irving-Kirkwood procedure. The text then explains the Green-Kubo relations used in linear transport coefficients, the linear response theory, the isothermal linear response theory, as well as the equivalence of thermostatted linear responses. The book also describes how thermostatted linear mechanical response of many-body systems can be related to equilibrium fluctuations. The text explains the procedure for calculating the linear Navier-Stokes transport coefficients through computer simulation algorithms. The book also discusses the van Kampen objection to linear response theory, the steady-state fluctuations, and the thermodynamics of steady states. The text will prove valuable for researchers in molecular chemistry, scientists, and academicians involved in advanced physics.
Download and read online Soft Matter Physics in PDF and EPUB Soft matter (polymers, colloids, surfactants, liquid crystals) are an important class of materials for modern and future technologies. They are complex materials that behave neither like a fluid nor a solid. This book describes the characteristics of such materials and how we can understand such characteristics in the language of physics.
Download and read online The Theory of Intermolecular Forces in PDF and EPUB The theory of intermolecular forces has advanced very greatly in recent years. It has become possible to carry out accurate calculations of intermolecular forces for molecules of useful size, and to apply the results to important practical applications such as understanding protein structure and function, and predicting the structures of molecular crystals. The Theory of Intermolecular Forces sets out the mathematical techniques that are needed to describe and calculate intermolecular interactions and to handle the more elaborate mathematical models. It describes the methods that are used to calculate them, including recent developments in the use of density functional theory and symmetry-adapted perturbation theory. The use of higher-rank multipole moments to describe electrostatic interactions is explained in both Cartesian and spherical tensor formalism, and methods that avoid the multipole expansion are also discussed. Modern ab initio perturbation theory methods for the calculation of intermolecular interactions are discussed in detail, and methods for calculating properties of molecular clusters and condensed matter for comparison with experiment are surveyed.