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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 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.

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 Simulation

Molecular Dynamics Simulation Book
Author : Kun Zhou,Bo Liu
Publisher : Academic Press
Release : 2022-02-10
ISBN : 0128166169
Language : En, Es, Fr & De

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Book Description :

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 Book
Author : Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
Publisher : Springer
Release : 2015-04-09
ISBN : 9783319171470
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

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 Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials Book
Author : Snehanshu Pal,Bankim Chandra Ray
Publisher : CRC Press
Release : 2020-05-15
ISBN : 0429670966
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.

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.

                    Book
Author : Anonim
Publisher : Unknown
Release : 1953
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

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.

Molecular Dynamics Simulations in Statistical Physics Theory and Applications

Molecular Dynamics Simulations in Statistical Physics  Theory and Applications Book
Author : Hiqmet Kamberaj
Publisher : Springer Nature
Release : 2020-03-20
ISBN : 3030357023
Language : En, Es, Fr & De

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Book Description :

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.

Monte Carlo and Molecular Dynamics Simulations in Polymer Science

Monte Carlo and Molecular Dynamics Simulations in Polymer Science Book
Author : Kurt Binder
Publisher : Oxford University Press
Release : 1995-08-03
ISBN : 9780195357462
Language : En, Es, Fr & De

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Book Description :

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.

Efficient Molecular Dynamics Simulation on Reconfigurable Models with MultiGrid Method

Efficient Molecular Dynamics Simulation on Reconfigurable Models with MultiGrid Method Book
Author : Eunjung Cho
Publisher : Unknown
Release : 2008
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N^2) for an N particle system. In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N^2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O(N) or O(logN) time complexity for the Direct method on N linear R-Mesh and NxN R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an XxYxZ R-Mesh. r is N/M and M = XxYxZ is the number of finest grid points.

Key Issues of Classical Molecular Dynamics Simulation

Key Issues of Classical Molecular Dynamics Simulation Book
Author : Jun Wang
Publisher : LAP Lambert Academic Publishing
Release : 2010-09
ISBN : 9783843351454
Language : En, Es, Fr & De

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Book Description :

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. In this book, we mainly discussed key issues of MD simulations and investigated the melting point, surface tension (liquid-vapor and liquid-solid) of model fluids including Lennard-Jones model, Stockmayer model and a couple of water models (TIP4P/Ew, TIP5P/Ew) by means of MD simulation. In addition, some new structures of water confined in carbon nanotube were discovered and transport behaviors of water and ions through nano-channels were also revealed

Molecular Dynamics

Molecular Dynamics Book
Author : Lichang Wang
Publisher : IntechOpen
Release : 2012-04-05
ISBN : 9789535104438
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

Molecular Dynamics Book
Author : Perla Balbuena,Jorge M. Seminario
Publisher : Elsevier
Release : 1999-04-22
ISBN : 9780080536842
Language : En, Es, Fr & De

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Book Description :

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 Simulation

Molecular Dynamics Simulation Book
Author : Anonim
Publisher : Unknown
Release : 2022-06-29
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Molecular Dynamics Simulation book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Molecular Dynamics Simulation of Metallic Clusters and Heteroclusters

Molecular Dynamics Simulation of Metallic Clusters and Heteroclusters Book
Author : Ming-Wen Sung
Publisher : Unknown
Release : 1994
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Molecular Dynamics Simulation of Metallic Clusters and Heteroclusters book written by Ming-Wen Sung, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.