Molecular Simulations

Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 46,8 Mb
Release : 2020-06-29
Category : Technology & Engineering
ISBN : 9783527341054

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Molecular Simulations by Saman Alavi Pdf

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 : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 45,5 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

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 : Marc Meunier
Publisher : CRC Press
Page : 425 pages
File Size : 44,9 Mb
Release : 2011-11-28
Category : Science
ISBN : 9781439861011

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Industrial Applications of Molecular Simulations by Marc Meunier Pdf

The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations demonstrates the capability of molecular modeling to tackle problems of industrial relevance. This book presents a wide range of various modeling techniques, including methods based on quantum or classical mechanics, molecular dynamics, Monte Carlo simulations, etc. It also explores a wide range of materials, from soft materials such as polymeric blends widely used in the chemical industry to hard or inorganic materials such as glasses and alumina. Features Demonstrates how modeling can solve everyday problems for scientists in industry Provides a broad overview of theoretical approaches Presents a wide range of applications in areas such as materials research, catalysis, pharmaceutical development and electronics Emphasizes the relationship between theory and experiments

Author : Martin J. Field
Publisher : Cambridge University Press
Page : 294 pages
File Size : 43,8 Mb
Release : 2007-07-19
Category : Science
ISBN : 9781139465816

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A Practical Introduction to the Simulation of Molecular Systems by Martin J. Field Pdf

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 : D. C. Rapaport
Publisher : Cambridge University Press
Page : 568 pages
File Size : 49,9 Mb
Release : 2004-04
Category : Science
ISBN : 0521825687

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The Art of Molecular Dynamics Simulation by D. C. Rapaport Pdf

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

Author : Tamar Schlick
Publisher : Springer Science & Business Media
Page : 669 pages
File Size : 49,9 Mb
Release : 2013-04-18
Category : Science
ISBN : 9780387224640

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Molecular Modeling and Simulation by Tamar Schlick Pdf

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

Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Publisher : MDPI
Page : 627 pages
File Size : 45,6 Mb
Release : 2018-10-08
Category : Electronic book
ISBN : 9783906980652

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Molecular Dynamics Simulation by Giovanni Ciccotti,Mauro Ferrario,Christof Schuette Pdf

Printed Edition of the Special Issue Published in Entropy

Author : Akira Satoh
Publisher : Elsevier
Page : 333 pages
File Size : 52,8 Mb
Release : 2010-12-17
Category : Technology & Engineering
ISBN : 9780123851499

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Introduction to Practice of Molecular Simulation by Akira Satoh Pdf

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

Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Page : 476 pages
File Size : 48,6 Mb
Release : 2007-08-16
Category : Science
ISBN : 9783540680956

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Numerical Simulation in Molecular Dynamics by Michael Griebel,Stephan Knapek,Gerhard Zumbusch Pdf

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.

Author : Dongshuai Hou
Publisher : Springer Nature
Page : 197 pages
File Size : 40,6 Mb
Release : 2019-09-26
Category : Technology & Engineering
ISBN : 9789811387111

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Molecular Simulation on Cement-Based Materials by Dongshuai Hou Pdf

This book presents a number of studies on the molecular dynamics of cement-based materials. It introduces a practical molecular model of cement-hydrate, delineates the relationship between molecular structure and nanoscale properties, reveals the transport mechanism of cement-hydrate, and provides useful methods for material design. Based on the molecular model presented here, the book subsequently sheds light on nanotechnology applications in the design of construction and building materials. As such, it offers a valuable asset for researchers, scientists, and engineers in the field of construction and building materials.

Author : Steffen Köhler
Publisher : Nova Science Publishers
Page : 208 pages
File Size : 47,5 Mb
Release : 2021-05-18
Category : Science
ISBN : 1536197343

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Advances in Molecular Dynamics Simulations Research by Steffen Köhler Pdf

"This work presents three chapters, each of which detail a recent advancement in the field of molecular dynamics simulations research. Chapter One describes the molecular dynamics method to simulate the transport processes in nanofluids and the molecular dynamics simulation of transport processes in confined conditions and in nanochannels in particular. Chapter Two provides a comprehensive review on the investigations into the nanoscopic deformation mechanisms of silicon carbide (SiC) and potassium dihydrogen phosphate (KDP) crystals using molecular dynamics simulations under various mechanical loading conditions. Chapter Three reports the effects of pressures applied during rapid solidification of local structures formed in the glassy NiTi alloy based on molecular dynamics simulation results"--

Author : Dominik Marx,Jürg Hutter
Publisher : Cambridge University Press
Page : 128 pages
File Size : 49,6 Mb
Release : 2009-04-30
Category : Science
ISBN : 1139477196

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Ab Initio Molecular Dynamics by Dominik Marx,Jürg Hutter Pdf

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.

Author : Mark S P Sansom,Philip C. Biggin
Publisher : Royal Society of Chemistry
Page : 330 pages
File Size : 49,7 Mb
Release : 2010-08-01
Category : Science
ISBN : 9781849732154

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Molecular Simulations and Biomembranes by Mark S P Sansom,Philip C. Biggin Pdf

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.

Author : Yinglong Miao,Weiliang Zhu,Chia-en A. Chang,J. Andrew McCammon
Publisher : Frontiers Media SA
Page : 179 pages
File Size : 55,5 Mb
Release : 2023-02-24
Category : Science
ISBN : 9782832515129

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Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning by Yinglong Miao,Weiliang Zhu,Chia-en A. Chang,J. Andrew McCammon Pdf

Author : Marc Meunier
Publisher : CRC Press
Page : 421 pages
File Size : 40,9 Mb
Release : 2016-04-19
Category : Science
ISBN : 9781439861028

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Industrial Applications of Molecular Simulations by Marc Meunier Pdf

The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations demonstrates the capability of molecular modeling to tackle problems of industrial relevance. This book presents a wide range of various modeling techniques, including methods based on quantum or classical mechanics, molecular dynamics, Monte Carlo simulations, etc. It also explores a wide range of materials, from soft materials such as polymeric blends widely used in the chemical industry to hard or inorganic materials such as glasses and alumina. Features Demonstrates how modeling can solve everyday problems for scientists in industry Provides a broad overview of theoretical approaches Presents a wide range of applications in areas such as materials research, catalysis, pharmaceutical development and electronics Emphasizes the relationship between theory and experiments