molecular dynamics simulation

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Molecular Dynamics Simulation
Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
Publisher : MDPI
Release Date : 2018-10-08
ISBN 10 : 3906980650
Pages : 636 pages
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Printed Edition of the Special Issue Published in Entropy

The Art of Molecular Dynamics Simulation
Author : D. C. Rapaport,Rapaport, Dennis C. Rapaport
Publisher : Cambridge University Press
Release Date : 2004-04
ISBN 10 : 9780521825689
Pages : 549 pages
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First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Dynamics Simulation
Author : J. M. Haile
Publisher : Wiley-Interscience
Release Date : 1997-03-14
ISBN 10 : 9780471184393
Pages : 512 pages
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"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
Author : Kun Zhou,Bo Liu
Publisher : Academic Press
Release Date : 2020-09
ISBN 10 : 9780128164198
Pages : 400 pages
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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.

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs
Author : Sumit Sharma
Publisher : Elsevier
Release Date : 2019-08-09
ISBN 10 : 0128169559
Pages : 365 pages
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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

Engineering Molecular Dynamics Simulation in Chemical Engineering
Author : N.A
Publisher : N.A
Release Date : 2015
ISBN 10 :
Pages : 329 pages
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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 Simulations of Disordered Materials
Author : Carlo Massobrio,Jincheng Du,Marco Bernasconi,Philip S. Salmon
Publisher : Springer
Release Date : 2015-04-22
ISBN 10 : 3319156756
Pages : 529 pages
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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 Simulation of Nanostructured Materials
Author : Snehanshu Pal,Bankim Chandra Ray
Publisher : CRC Press
Release Date : 2020-04-28
ISBN 10 : 0429672454
Pages : 314 pages
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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.

Numerical Simulation in Molecular Dynamics
Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Release Date : 2007-08-16
ISBN 10 : 3540680950
Pages : 476 pages
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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
Author : Perla Balbuena,Jorge M. Seminario
Publisher : Elsevier
Release Date : 1999-04-22
ISBN 10 : 9780080536842
Pages : 945 pages
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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
Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Release Date : 2001-10-19
ISBN 10 : 9780080519982
Pages : 664 pages
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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 Simulations to Study Drug Delivery Systems
Author : Juan M.R. Albano
Publisher : N.A
Release Date : 2018
ISBN 10 :
Pages : 329 pages
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Molecular dynamics simulation is a very powerful tool to understand biomolecular processes. In this chapter, we go over different applications of this methodology to drug delivery systems (DDS) carried out in the group. DDS-a formulation or a device that enables the introduction of a therapeutic substance in the body and improves its efficacy and safety by controlling the rate, time, and place of release of drugs-are an important component of drug development and therapeutics. Biocompatible nanoparticles are materials in the nanoscale that emerged as important players, improving efficacy of approved drugs, for example. The molecular understanding of the encapsulation process could be very helpful to guide the nanocarrier for a specific system. Here we discuss different applications of drug delivery carriers, such as liposomes, polymeric micelles, and polymersomes using atomistic and coarse grain (CG) molecular dynamics simulations.

Introduction to Practice of Molecular Simulation
Author : Akira Satoh
Publisher : Elsevier
Release Date : 2010-12-17
ISBN 10 : 0123851491
Pages : 330 pages
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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

Molecular Dynamics Simulation of a Model for (one-dimensional) Structural Phase Transitions
Author : N.A
Publisher : N.A
Release Date : 1975
ISBN 10 :
Pages : 329 pages
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Computer Simulations of Surfaces and Interfaces
Author : Burkhard Dünweg,David P. Landau,Andrey I. Milchev
Publisher : Springer Science & Business Media
Release Date : 2003-12-31
ISBN 10 : 9781402014642
Pages : 451 pages
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Proceedings of the NATO Advanced Study Institute, Albena, Bulgaria, from 9 to 20 September 2002

Molecular Dynamics Simulation of Horse-heart Cytochrome C in Water-methanol Solvent Systems
Author : Devaki Nandan Gautam
Publisher : N.A
Release Date : 2014
ISBN 10 :
Pages : 143 pages
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Molecular Dynamics simulations have been carried out to investigate the dynamics of horse heart Cytochrome C and associated crystallographic water molecules in different water-methanol systems. The 100 ns simulation predicts that hh-CytC undergoes different dynamical transitions with some common conformations in different solvents. With increase of methanol concentration in solvents, hh-CytC has increased flexibility, fluctuating its hydrophobic solvent accessible surface area (SASA), and number of persistent internal hydrogen bonds with long hydrogen-bond-lifetime. The protein became more liquid-like in mixed solvents compared to pure solvents; flexibility increases in the absence of the crystallographic water. Similarly, the number of hydrogen bonds between solvent molecules and hh-CytC decreased with increasing of methanol concentration. Water-protein and methanol-protein hydrogen bond lifetimes were computed 11.5 and 16.6 picoseconds, respectively, in pure solvents. However, in mixtures, solvent-protein hydrogen bond lifetime was higher in twenty percent methanol than in fourty percent in water. The surface crystallographic water molecules diffused easily in bulk solvents within 1 nanosecond and protein surface is stabilized by hydrogen bonds with a solvation layer. The two crystallographic water molecules which are buried internally in hh-CytC have 5 to more than 100 nanoseconds residence time in the conserved sites with 100's of picoseconds of hydrogen bond lifetime depending on the solvent compositions. The residence time might depend on the mechanism of conformational transition of protein in simulation. Solvent water molecules exchange these buried water molecules but exchange is less frequent than that in hydration layer. Even though methanol has succeeded to reside into these conserved sites in pure methanol solvent but its distance with hydrogen bonding partners more than 5 A with labile hydrogen bonding state.

Molecular Dynamics Simulation of Wetted Contacts: Fundamental Phenomena and Fluid Properties
Author : Martin Lautenschläger
Publisher : N.A
Release Date : 2019
ISBN 10 :
Pages : 329 pages
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Molecular Dynamics Simulations in Statistical Physics: Theory and Applications
Author : Hiqmet Kamberaj
Publisher : Springer Nature
Release Date : 2020-03-20
ISBN 10 : 3030357023
Pages : 463 pages
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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 Simulation of Fracture and Energy Dissipation in Polymer/Clay Nanocomposites
Author : Lei Chen
Publisher : N.A
Release Date : 2008
ISBN 10 :
Pages : 329 pages
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Biomolecular and Bioanalytical Techniques
Author : Vasudevan Ramesh
Publisher : Wiley
Release Date : 2019-05-13
ISBN 10 : 1119483964
Pages : 576 pages
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An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.