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Molecular Dynamics Simulation

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The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation Book
Author : D. C. Rapaport,Rapaport, Dennis C. Rapaport
Publisher : Cambridge University Press
Release : 2004-04
ISBN : 9780521825689
Language : En, Es, Fr & De

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Book Description :

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

Molecular Dynamics Simulation

Molecular Dynamics Simulation Book
Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Publisher : MDPI
Release : 2018-10-08
ISBN : 3906980650
Language : En, Es, Fr & De

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Book Description :

Printed Edition of the Special Issue Published in Entropy

Molecular Dynamics

Molecular Dynamics Book
Author : Lichang Wang
Publisher : BoD – Books on Demand
Release : 2012-04-05
ISBN : 9535104438
Language : En, Es, Fr & De

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Book Description :

Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This first book begins with a general description of underlying theories of molecular dynamics simulations and provides extensive coverage of molecular dynamics simulations in nanotechnology and energy. Coverage of this book includes: Recent advances of molecular dynamics theory Formation and evolution of nanoparticles of up to 106 atoms Diffusion and dissociation of gas and liquid molecules on silicon, metal, or metal organic frameworks Conductivity of ionic species in solid oxides Ion solvation in liquid mixtures Nuclear structures

Molecular Dynamics Simulation

Molecular Dynamics Simulation Book
Author : J. M. Haile
Publisher : University of Texas Press
Release : 1997-03-14
ISBN : 9780471184393
Language : En, Es, Fr & De

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Book Description :

"Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes

Molecular Dynamics Simulation

Molecular Dynamics Simulation Book
Author : J. M. Haile
Publisher : Wiley-Interscience
Release : 1997-03-14
ISBN : 9780471184393
Language : En, Es, Fr & De

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Book Description :

"Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes

Molecular Dynamics Simulations of Disordered Materials

Molecular Dynamics Simulations of Disordered Materials Book
Author : Carlo Massobrio,Jincheng Du,Marco Bernasconi,Philip S. Salmon
Publisher : Springer
Release : 2015-04-22
ISBN : 3319156756
Language : En, Es, Fr & De

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Book Description :

This book is a unique reference work in the area of atomic-scale simulation of glasses. For the first time, a highly selected panel of about 20 researchers provides, in a single book, their views, methodologies and applications on the use of molecular dynamics as a tool to describe glassy materials. The book covers a wide range of systems covering "traditional" network glasses, such as chalcogenides and oxides, as well as glasses for applications in the area of phase change materials. The novelty of this work is the interplay between molecular dynamics methods (both at the classical and first-principles level) and the structure of materials for which, quite often, direct experimental structural information is rather scarce or absent. The book features specific examples of how quite subtle features of the structure of glasses can be unraveled by relying on the predictive power of molecular dynamics, used in connection with a realistic description of forces.

Engineering Molecular Dynamics Simulation in Chemical Engineering

Engineering Molecular Dynamics Simulation in Chemical Engineering Book
Author : N.A
Publisher :
Release : 2015
ISBN :
Language : En, Es, Fr & De

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Book Description :

Abstract: Chemical engineering systems usually involve multiple spatio-temporal scales, grouped into different levels, from the molecular scale of reactants to the industrial scale of reactors. Molecular dynamics (MD) simulation is one of the most fundamental methods for the study of such systems, but it is too costly and hence formidable for simulating large-scale behavior directly. However, there are two great potentials in extending this method. First, the logic and algorithms of traditional MD simulations can be generalized from the material level to higher levels since the elements of each level are all discrete in nature, and can be well defined, allowing an MD-style simulation based on different elements. Second, MD simulations can be accelerated by realizing the structural consistency among the problem, model, software and hardware (the so-called EMMS paradigm). These two potentials give possibilities to engineer the method of MD simulation to deal with the whole spectrum of chemical engineering phenomena. In this review, we summarize our discrete simulation studies to explore such potentials, from the establishment of a general software and hardware framework, to the typical applications at different levels, including the reactions in coal pyrolysis, the dynamics in virion, the atomic behavior in silicon at millimeter scale, and finally continuum flow. The possibility of engineering MD simulation into a virtual experiment platform is discussed finally. Highlights: Traditional MD is generalized to accommodate discrete elements at different scales. Consistency among system, model, software and hardware to achieve high efficiency. Possibility of engineering MD into a virtual experiment platform is discussed.

Molecular Dynamics Simulation

Molecular Dynamics Simulation Book
Author : Kun Zhou,Bo Liu
Publisher : Academic Press
Release : 2020-11-01
ISBN : 0128166169
Language : En, Es, Fr & De

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Book Description :

Molecular Dynamic Simulation for Engineering and Materials explains the fundamentals of MD simulation and explores recent developments in advanced modeling approaches based on the MD method. The improvements in efficiency and accuracy delivered by this new research are explained to help readers apply them to a wide range of tasks. Details of the implementation of MD simulation are illustrated by presenting the applications of MD simulation in various aspects of materials study including mechanical, thermal, mass transportation, and absorption/desorption problems. Innovative methods of using MD to explore the mechanics of nano/micromaterials, and for the characterization of crystalline, amorphous and liquid materials are also presented. The rich research experience of the authors in molecular dynamic simulation will ensure that readers are provided with both an in-depth understanding of this method and clear technical guidance. Examines applications of MD to simulation of mechanics of nano/micromaterials, and characterization of crystalline, amorphous and liquid materials Provides a thorough overview of the theory behind molecular dynamics simulation Applies Molecular dynamic simulation to a broad range of mechanical, thermal, and mass transport problems

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio  Lammps and Gromacs Book
Author : Sumit Sharma
Publisher : Elsevier
Release : 2019-08-09
ISBN : 0128169559
Language : En, Es, Fr & De

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Book Description :

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems

Supercomputing for Molecular Dynamics Simulations

Supercomputing for Molecular Dynamics Simulations Book
Author : Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
Publisher : Springer
Release : 2015-03-30
ISBN : 3319171488
Language : En, Es, Fr & De

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Book Description :

This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials Book
Author : Snehanshu Pal,Bankim Chandra Ray
Publisher : CRC Press
Release : 2020-04-28
ISBN : 0429672454
Language : En, Es, Fr & De

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Book Description :

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.

Understanding Molecular Simulation

Understanding Molecular Simulation Book
Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Release : 2001-10-19
ISBN : 9780080519982
Language : En, Es, Fr & De

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Book Description :

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.

Molecular Simulation Studies in Material and Biological Sciences

Molecular Simulation Studies in Material and Biological Sciences Book
Author : Kholmirzo Kholmurodov
Publisher : Nova Publishers
Release : 2007
ISBN : 9781594546075
Language : En, Es, Fr & De

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Book Description :

Book & CD. Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. Having an increasingly significant impact on many applied industries, especially in modern biophysical and nanotechnological areas, molecular simulation provides a set of tools for predicting many functional properties of molecular systems. The chemical, pharmaceutical, materials and related industries -- all share the computer molecular simulation methods. The molecular simulation studies cover different fields of either biological processes -- protein folding and electron densities of DNA and proteins, or thin film formations and surface-cluster phenomena in nanoelectronics, synthetic copolymers and biopolymer design in biochemistry, so on. Practically all of the world's present supercomputers and many specially developed high performance computing clusters over the world are performing molecular simulations or are aimed on these needs. This book presents leading international research in this dynamic field.

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics Book
Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Release : 2007-08-16
ISBN : 3540680950
Language : En, Es, Fr & De

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Book Description :

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.

Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation Book
Author : Akira Satoh
Publisher : Elsevier
Release : 2010-12-17
ISBN : 0123851491
Language : En, Es, Fr & De

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Book Description :

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

Ab Initio Molecular Dynamics

Ab Initio Molecular Dynamics Book
Author : Dominik Marx,Jürg Hutter
Publisher : Cambridge University Press
Release : 2009-04-30
ISBN : 9781139477192
Language : En, Es, Fr & De

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Book Description :

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.