Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
Author: Akira Satoh
Publisher: Elsevier
Total Pages: 0
Release: 2010-12-17
Genre: Science
ISBN: 9780323165198

This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use.

Molecular Simulations

Molecular Simulations
Author: Saman Alavi
Publisher: John Wiley & Sons
Total Pages: 342
Release: 2020-06-29
Genre: Technology & Engineering
ISBN: 3527341056

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.

Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
Author: Akira Satoh
Publisher: Elsevier
Total Pages: 333
Release: 2010-12-17
Genre: Technology & Engineering
ISBN: 0123851491

This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use. - Provides tools to develop skills in developing simulations programs - Includes sample simulation programs for the reader to use - Appendix explains Fortran and C languages in simple terms to allow the non-expert to use them

Understanding Molecular Simulation

Understanding Molecular Simulation
Author: Daan Frenkel
Publisher: Elsevier
Total Pages: 661
Release: 2001-10-19
Genre: Science
ISBN: 0080519989

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.

The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation
Author: D. C. Rapaport
Publisher: Cambridge University Press
Total Pages: 568
Release: 2004-04
Genre: Science
ISBN: 9780521825689

First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Modeling and Simulation

Molecular Modeling and Simulation
Author: Tamar Schlick
Publisher: Springer Science & Business Media
Total Pages: 669
Release: 2013-04-18
Genre: Science
ISBN: 0387224645

Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
Author: Snehanshu Pal
Publisher: CRC Press
Total Pages: 334
Release: 2020-04-28
Genre: Mathematics
ISBN: 0429672454

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.

Molecular Simulations and Biomembranes

Molecular Simulations and Biomembranes
Author: Mark S P Sansom
Publisher: Royal Society of Chemistry
Total Pages: 331
Release: 2010-08-01
Genre: Science
ISBN: 1849732159

The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.

Molecular Quantum Dynamics

Molecular Quantum Dynamics
Author: Fabien Gatti
Publisher: Springer Science & Business Media
Total Pages: 281
Release: 2014-04-09
Genre: Science
ISBN: 3642452906

This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics
Author: Michael Griebel
Publisher: Springer Science & Business Media
Total Pages: 472
Release: 2007-08-16
Genre: Science
ISBN: 3540680950

This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.