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Molecular Dynamics Simulation

Molecular Dynamics Simulation
  • Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
  • Publisher :Unknown
  • Release Date :2018-10-08
  • Total pages :636
  • ISBN : 9783906980652
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Summary : Printed Edition of the Special Issue Published in Entropy

Molecular Dynamics Simulation

Molecular Dynamics Simulation
  • Author : Kun Zhou,Bo Liu
  • Publisher :Unknown
  • Release Date :2020-09
  • Total pages :400
  • ISBN : 0128164190
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Summary : 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.

The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation
  • Author : D. C. Rapaport,Rapaport, Dennis C. Rapaport
  • Publisher :Unknown
  • Release Date :2004-04
  • Total pages :549
  • ISBN : 0521825687
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Summary : First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Dynamics Simulation

Molecular Dynamics Simulation
  • Author : J. M. Haile
  • Publisher :Unknown
  • Release Date :1997-03-14
  • Total pages :512
  • ISBN : 047118439X
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Summary : "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
  • Publisher :Unknown
  • Release Date :2020-04-28
  • Total pages :314
  • ISBN : 9780429672453
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Summary : 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.

Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
  • Author : Akira Satoh
  • Publisher :Unknown
  • Release Date :2010-12-17
  • Total pages :330
  • ISBN : 9780123851499
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Summary : 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

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics
  • Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
  • Publisher :Unknown
  • Release Date :2007-08-16
  • Total pages :476
  • ISBN : 9783540680956
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Summary : 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.

Molecular Dynamics

Molecular Dynamics
  • Author : Perla Balbuena,Jorge M. Seminario
  • Publisher :Unknown
  • Release Date :1999-04-22
  • Total pages :945
  • ISBN : 0080536840
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Summary : The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.

Understanding Molecular Simulation

Understanding Molecular Simulation
  • Author : Daan Frenkel,Berend Smit
  • Publisher :Unknown
  • Release Date :2001-10-19
  • Total pages :664
  • ISBN : 0080519989
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Summary : 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 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
  • Publisher :Unknown
  • Release Date :2019-08-09
  • Total pages :365
  • ISBN : 9780128169551
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Summary : 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

Molecular Simulations

Molecular Simulations
  • Author : Saman Alavi
  • Publisher :Unknown
  • Release Date :2020-06-03
  • Total pages :344
  • ISBN : 9783527341054
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Summary : Addressing the need of chemistry, biology and engineering students to understand and perform their own molecular simulations, the author introduces the fundamentals of molecular modeling for a broad, practice-oriented audience and presents versatile practical applications. The book presents a thorough overview of the underlying concepts.

High Performance Computing - HiPC 2007

High Performance Computing - HiPC 2007
  • Author : Srinivas Aluru,Manish Parashar,Ramamurthy Badrinath,Viktor K. Prasanna
  • Publisher :Unknown
  • Release Date :2008-01-22
  • Total pages :663
  • ISBN : 9783540772200
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Summary : This book constitutes the refereed proceedings of the 14th International Conference on High-Performance Computing, HiPC 2007, held in Goa, India, in December 2007. The 53 revised full papers presented together with the abstracts of five keynote talks were carefully reviewed and selected from 253 submissions. The papers are organized in topical sections on a broad range of applications including I/O and FPGAs, and microarchitecture and multiprocessor architecture.

Industrial Applications of Molecular Simulations

Industrial Applications of Molecular Simulations
  • Author : Marc Meunier
  • Publisher :Unknown
  • Release Date :2016-04-19
  • Total pages :421
  • ISBN : 9781439861028
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Summary : 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

Molecular Dynamics of Nanostructures and Nanoionics

Molecular Dynamics of Nanostructures and Nanoionics
  • Author : Junko Habasaki
  • Publisher :Unknown
  • Release Date :2020-12-01
  • Total pages :318
  • ISBN : 9781000066807
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Summary : Nanostructured materials with multiple components and complex structures are the current focus of research and are expected to develop further for material designs in many applications in electrochemical, colloidal, medical, pharmaceutical, and several other fields. This book discusses complex nanostructured systems exemplified by nanoporous silicates, spontaneously formed gels from silica-nanocolloidal solutions, and related systems, and examines them using molecular dynamics simulations. Nanoporous materials, nanocolloidal systems, and gels are useful in many applications and can be used in electric devices and storage, and for gas, ion, and drug delivery. The book gives an overview of the history, current status, and frontiers of the field. It also discusses the fundamental aspects related to the common behaviors of some of these systems and common analytical methods to treat them.

Computer Simulations of Surfaces and Interfaces

Computer Simulations of Surfaces and Interfaces
  • Author : Burkhard Dünweg,David P. Landau,Andrey I. Milchev
  • Publisher :Unknown
  • Release Date :2003-12-31
  • Total pages :451
  • ISBN : 1402014643
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Summary : Proceedings of the NATO Advanced Study Institute, Albena, Bulgaria, from 9 to 20 September 2002

Supercomputing for Molecular Dynamics Simulations

Supercomputing for Molecular Dynamics Simulations
  • Author : Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
  • Publisher :Unknown
  • Release Date :2015-04-09
  • Total pages :76
  • ISBN : 331917147X
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Summary : 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
  • Publisher :Unknown
  • Release Date :2015-04-22
  • Total pages :529
  • ISBN : 9783319156750
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Summary : 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
  • Publisher :Unknown
  • Release Date :2020-03-20
  • Total pages :463
  • ISBN : 9783030357023
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Summary : 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 Dynamics

Molecular Dynamics
  • Author : Perla B. Balbuena,J. M. Seminario
  • Publisher :Unknown
  • Release Date :1999
  • Total pages :946
  • ISBN : 0444829105
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Summary : The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.

Molecular Dynamics Simulations

Molecular Dynamics Simulations
  • Author : Fumiko Yonezawa
  • Publisher :Unknown
  • Release Date :2011-12-27
  • Total pages :257
  • ISBN : 3642847153
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Summary : This volume contains papers presented at the Thirteenth Taniguchi Symposium on the Theory of Condensed Matter, which was held at Kashikojima (in Ise Shima National Park), Japan, from 6th to 9th November, 1990. The topic of the symposium was Molecular Dynamics Simulations. The general objective of this series of the Taniguchi Symposia is to encour age developing fields of great promise in condensed matter physics. Our theme, molecular dynamics (MD) simulations, certainly fulfills this requirement, be cause the field is developing at a remarkable pace and its future is considered almost boundless. It was in the 1950s that the original idea of the MD methods was first pro posed and applied to the study of physical systems composed of many particles. In fact, the invention of the MD techniques occurred soon after the construction of the first computers. For almost 35 years since then, MD methods, together with Monte Carlo methods, have played major parts in the drama of computer simulations. The triumph of MD simulations is not confined to numerical aspects of detailed analyses of physical systems. MD simulations have verified some un expected facts and introduced some new concepts, all of which had never been predicted previously from analytical theories. The occurrence of the Alder tran sition in a system of repulsive particles and the behavior of the long-time tails of the velocity autocorrelation function for a liquid are just two examples of the results achieved by means of MD studies.

Protein Simulations

Protein Simulations
  • Author : Valerie Daggett
  • Publisher :Unknown
  • Release Date :2003-11-26
  • Total pages :459
  • ISBN : 9780080493787
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Summary : Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields * Ligand Binding * Protein Membrane Simulation * Enzyme Dynamics * Protein Folding and unfolding simulations