The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation
Author: D. C. Rapaport,Rapaport, Dennis C. Rapaport
Publsiher: Cambridge University Press
Total Pages: 568
Release: 2004-04
ISBN: 9780521825689
Category: Science
Language: EN, FR, DE, ES & NL

The Art of Molecular Dynamics Simulation Book Excerpt:

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

Molecular Dynamics Simulation

Molecular Dynamics Simulation
Author: Kun Zhou,Bo Liu
Publsiher: Academic Press
Total Pages: 374
Release: 2022-02-10
ISBN: 0128166169
Category: Technology & Engineering
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation Book Excerpt:

Molecular Dynamic Simulation: Fundamentals and Applications 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

Supercomputing for Molecular Dynamics Simulations

Supercomputing for Molecular Dynamics Simulations
Author: Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
Publsiher: Springer
Total Pages: 76
Release: 2015-04-09
ISBN: 9783319171470
Category: Computers
Language: EN, FR, DE, ES & NL

Supercomputing for Molecular Dynamics Simulations Book Excerpt:

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
Author: Snehanshu Pal,Bankim Chandra Ray
Publsiher: CRC Press
Total Pages: 314
Release: 2020-05-12
ISBN: 9780367029821
Category: Materials
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation of Nanostructured Materials Book Excerpt:

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 Dynamics Simulation

Molecular Dynamics Simulation
Author: Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Publsiher: MDPI
Total Pages: 627
Release: 2018-10-08
ISBN: 3906980650
Category: Electronic book
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation Book Excerpt:

Printed Edition of the Special Issue Published in Entropy

Molecular Dynamics Simulation

Molecular Dynamics Simulation
Author: J. M. Haile
Publsiher: Wiley-Interscience
Total Pages: 489
Release: 1992-06-05
ISBN: 9780471819660
Category: Technology & Engineering
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation Book Excerpt:

"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 of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
Author: Snehanshu Pal,Bankim Chandra Ray
Publsiher: CRC Press
Total Pages: 305
Release: 2020-05-15
ISBN: 0429670966
Category: Mathematics
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation of Nanostructured Materials Book Excerpt:

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 Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio  Lammps and Gromacs
Author: Sumit Sharma
Publsiher: Elsevier
Total Pages: 365
Release: 2019-08-09
ISBN: 0128169559
Category: Technology & Engineering
Language: EN, FR, DE, ES & NL

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

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

Computer Simulations Of Molecules And Condensed Matter From Electronic Structures To Molecular Dynamics

Computer Simulations Of Molecules And Condensed Matter  From Electronic Structures To Molecular Dynamics
Author: Wang Enge,Li Xin-zheng
Publsiher: World Scientific
Total Pages: 280
Release: 2018-01-17
ISBN: 9813230460
Category: Science
Language: EN, FR, DE, ES & NL

Computer Simulations Of Molecules And Condensed Matter From Electronic Structures To Molecular Dynamics Book Excerpt:

This book provides a relatively complete introduction to the methods used in computational condensed matter. A wide range of electronic structure theories are introduced, including traditional quantum chemistry methods, density functional theory, many-body perturbation theory, and more. Molecular dynamics simulations are also discussed, with extensions to enhanced sampling and free-energy calculation techniques including umbrella sampling, meta-dynamics, integrated tempering sampling, etc. As a further extension beyond the standard Born-Oppenheimer molecular dynamics, some simulation techniques for the description of quantum nuclear effects are also covered, based on Feynman's path-integral representation of quantum mechanics. The book aims to help beginning graduate students to set up a framework of the concepts they should know before tackling the physical/chemical problems they will face in their research. Contents: Introduction to Computer Simulations of Molecules and Condensed MatterQuantum Chemistry Methods and Density-Functional TheoryPseudopotentials, Full Potential, and Basis SetsMany-Body Green's Function Theory and the GW ApproximationMolecular DynamicsExtension of Molecular Dynamics, Enhanced Sampling and the Free-Energy CalculationsQuantum Nuclear EffectsAppendices: Useful Mathematical RelationsExpansion of a Non-Local FunctionThe Brillouin-Zone IntegrationThe Frequency IntegrationReferencesAcknowledgements Readership: Researchers in computational condensed matter physics. Keywords: Electronic Structures;First-Principle;Molecular Dynamics;Path-IntegralReview: Key Features: Elaboration on a framework of concepts based on the authors' research experiencesIllustrations of methods ranging from electronic structures to molecular dynamicsDetailed explanation of the path-integral method

Supercomputing for Molecular Dynamics Simulations

Supercomputing for Molecular Dynamics Simulations
Author: Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
Publsiher: Springer
Total Pages: 76
Release: 2015-03-30
ISBN: 3319171488
Category: Computers
Language: EN, FR, DE, ES & NL

Supercomputing for Molecular Dynamics Simulations Book Excerpt:

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 Simulations of Disordered Materials

Molecular Dynamics Simulations of Disordered Materials
Author: Carlo Massobrio,Jincheng Du,Marco Bernasconi,Philip S. Salmon
Publsiher: Springer
Total Pages: 529
Release: 2015-04-22
ISBN: 3319156756
Category: Technology & Engineering
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulations of Disordered Materials Book Excerpt:

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.

Molecular Dynamics Simulations in Statistical Physics Theory and Applications

Molecular Dynamics Simulations in Statistical Physics  Theory and Applications
Author: Hiqmet Kamberaj
Publsiher: Springer Nature
Total Pages: 463
Release: 2020-03-20
ISBN: 3030357023
Category: Science
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulations in Statistical Physics Theory and Applications Book Excerpt:

This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field.

Molecular Simulation of Fluids

Molecular Simulation of Fluids
Author: Richard Sadus
Publsiher: Elsevier
Total Pages: 644
Release: 2002-05-17
ISBN: 9780444510822
Category: Computers
Language: EN, FR, DE, ES & NL

Molecular Simulation of Fluids Book Excerpt:

The aim of this book is to examine some of the important aspects of recent progress in the use of molecular simulation for investigating fluids. It encompasses both Monte Carlo and molecular dynamic techniques providing details of theory, algorithms and implementation.

Monte Carlo and Molecular Dynamics Simulations in Polymer Science

Monte Carlo and Molecular Dynamics Simulations in Polymer Science
Author: Kurt Binder
Publsiher: Oxford University Press
Total Pages: 608
Release: 1995-08-03
ISBN: 9780195357462
Category: Science
Language: EN, FR, DE, ES & NL

Monte Carlo and Molecular Dynamics Simulations in Polymer Science Book Excerpt:

Written by leading experts from around the world, Monte Carlo and Molecular Dynamics Simulations in Polymer Science comprehensively reviews the latest simulation techniques for macromolecular materials. Focusing in particular on numerous new techniques, the book offers authoritative introductions to solutions of neutral polymers and polyelectrolytes; dynamics of polymer melts, rubbers and gels, and glassy materials; thermodynamics of polymer mixing and mesophase formation, and polymers confined at interfaces and grafted to walls. Throughout, contributors offer practical advice on how to overcome the unique challenges posed by the large size and slow relaxation of polymer coils. Students and researchers in polymer chemistry, polymer physics, chemical engineering, and materials and computational science will all benefit from the cogent, step-by-step introductions contained in this important new book.

Understanding Molecular Simulation

Understanding Molecular Simulation
Author: Daan Frenkel,Berend Smit
Publsiher: Elsevier
Total Pages: 664
Release: 2001-10-19
ISBN: 9780080519982
Category: Science
Language: EN, FR, DE, ES & NL

Understanding Molecular Simulation Book Excerpt:

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.

An Introduction to Molecular Dynamics

An Introduction to Molecular Dynamics
Author: Mark S. Kemp
Publsiher: Unknown
Total Pages: 169
Release: 2019-08-08
ISBN: 9781536160543
Category: Molecular dynamics
Language: EN, FR, DE, ES & NL

An Introduction to Molecular Dynamics Book Excerpt:

In the opening chapter the method of statistical geometry, based on the construction of a Voronoi polyhedral, is applied to the pattern recognition of atomic environments and to the investigation of the local order in molecular dynamics-simulated materials. Next, the authors discuss the methodology of bimolecular simulations and their advancements, as well as their applications in the field of nanoparticle-biomolecular interactions. The theory of molecular dynamics simulation and some of the recent molecular dynamics methods such as steered molecular dynamics, umbrella sampling, and coarse-grained simulation are also discussed. The use of auxiliary programs in the cases of modified cyclodextrins is discussed. Additionally, results from molecular dynamics studies on cases of inclusion compounds of molecules of different sizes and shapes encapsulated in the same host cyclodextrin have been examined and compared. In closing, the authors discuss the methodology of molecular dynamics simulation with a non-constant force field. In the context of molecular simulations, the term "force field" refers to a set of equations and parameters for the calculation of forces acting on the particles of the system and its potential energy.

Statistical Mechanics Theory and Molecular Simulation

Statistical Mechanics  Theory and Molecular Simulation
Author: Mark Tuckerman
Publsiher: Oxford University Press
Total Pages: 719
Release: 2010-02-11
ISBN: 0198525265
Category: Computers
Language: EN, FR, DE, ES & NL

Statistical Mechanics Theory and Molecular Simulation Book Excerpt:

By uniting basic concepts in equilibrium and time-dependent statistical mechanics with modern computational techniques, the book provides a comprehensive view of how theory proceeds from concepts to model construction to practical algorithms.

Molecular Dynamics Simulations of Deoxyribonucleic Acids and Repair Enzyme T4 Endonuclease V

Molecular Dynamics Simulations of Deoxyribonucleic Acids and Repair Enzyme T4 Endonuclease V
Author: Miroslav Pinak
Publsiher: Unknown
Total Pages: 48
Release: 1999
ISBN: 1928374650XXX
Category: DNA repair
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulations of Deoxyribonucleic Acids and Repair Enzyme T4 Endonuclease V Book Excerpt:

The Molecular Dynamics of Liquid Crystals

The Molecular Dynamics of Liquid Crystals
Author: G.R. Luckhurst,C.A. Veracini
Publsiher: Springer Science & Business Media
Total Pages: 634
Release: 1994-04-30
ISBN: 9780792328094
Category: Science
Language: EN, FR, DE, ES & NL

The Molecular Dynamics of Liquid Crystals Book Excerpt:

This book is based on a NATO Advanced Study Institute held to enhance our understanding, at both an experimental and a theoretical level, of the molecular dynamics in liquid crystals. The lecturers at the Institute, each leaders in their respective fields, have contributed chapters to the book with the aim of producing, for the first time, a coherent, pedagogical account of this interdisciplinary subject. The range of materials considered is wide, including lyotropic and thermotropic liquid crystals, biological membranes and polymeric systems. The formalism needed to characterise the rotational, translational and conformational dynamics is developed. Then the use of experimental techniques to investigate the dynamics is described; these techniques include NMR and ESR spectroscopy, neutron scattering, dielectric relaxation, infrared spectroscopy and fluorescence depolarisation. Some of these experiments are influenced by the collective orientations or director modes which are also considered. The results of these experiments are presented and the theory necessary to understand them is described, with particular attention being paid to the influence of the long range liquid--crystalline order on the dynamics.

Carbon Nanotubes as Nanodelivery Systems

Carbon Nanotubes as Nanodelivery Systems
Author: Melvin Choon Giap Lim,ZhaoWei Zhong
Publsiher: Springer Science & Business Media
Total Pages: 60
Release: 2013-05-18
ISBN: 9814451398
Category: Technology & Engineering
Language: EN, FR, DE, ES & NL

Carbon Nanotubes as Nanodelivery Systems Book Excerpt:

This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.