Download or read book Introduction to Practice of Molecular Simulation written by Akira Satoh and published by Elsevier. This book was released on 2010-12-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-06-29 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.

Download or read book Introduction to Practice of Molecular Simulation written by Akira Satoh and published by Elsevier. This book was released on 2010-12-17 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 661 pages. Available in PDF, EPUB and Kindle. 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.

Download or read book The Art of Molecular Dynamics Simulation written by D. C. Rapaport and published by Cambridge University Press. This book was released on 2004-04 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Download or read book Computer Meets Theoretical Physics written by Giovanni Battimelli and published by Springer Nature. This book was released on 2020-06-17 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a vivid account of the early history of molecular simulation, a new frontier for our understanding of matter that was opened when the demands of theoretical physicists were met by the availability of the modern computers. Since their inception, electronic computers have enormously increased their performance, thus making possible the unprecedented technological revolution that characterizes our present times. This obvious technological advancement has brought with it a silent scientific revolution in the practice of theoretical physics. In particular, in the physics of matter it has opened up a direct route from the microscopic physical laws to observable phenomena. One can now study the time evolution of systems composed of millions of molecules, and simulate the behaviour of macroscopic materials and actually predict their properties. Molecular simulation has provided a new theoretical and conceptual tool that physicists could only dream of when the foundations of statistical mechanics were laid. Molecular simulation has undergone impressive development, both in the size of the scientific community involved and in the range and scope of its applications. It has become the ubiquitous workhorse for investigating the nature of complex condensed matter systems in physics, chemistry, materials and the life sciences. Yet these developments remain largely unknown outside the inner circles of practitioners, and they have so far never been described for a wider public. The main objective of this book is therefore to offer a reasonably comprehensive reconstruction of the early history of molecular simulation addressed to an audience of both scientists and interested non-scientists, describing the scientific and personal trajectories of the main protagonists and discussing the deep conceptual innovations that their work produced.

Download or read book Molecular Quantum Dynamics written by Fabien Gatti and published by Springer Science & Business Media. This book was released on 2014-04-09 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Download or read book Molecular Dynamics Simulation of Nanostructured Materials written by Snehanshu Pal and published by CRC Press. This book was released on 2020-04-28 with total page 334 pages. Available in PDF, EPUB and Kindle. 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.

Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer Science & Business Media. This book was released on 2007-08-16 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Molecular Simulations and Biomembranes written by Mark S P Sansom and published by Royal Society of Chemistry. This book was released on 2010-08-01 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.

Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. 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

Download or read book Reviews in Computational Chemistry Volume 28 written by Abby L. Parrill and published by John Wiley & Sons. This book was released on 2015-04-27 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protein Folding Pathways Assessing Structural Predictions of Protein-Protein Recognition Kinetic Monte Carlo Simulation of Electrochemical Systems Reactivity and Dynamics at Liquid Interfaces

Download or read book Biomolecular and Bioanalytical Techniques written by Vasudevan Ramesh and published by John Wiley & Sons. This book was released on 2019-06-10 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book An Introduction to Molecular Dynamics written by Mark S. Kemp and published by Nova Science Publishers. This book was released on 2019 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: "In the opening chapter of An Introduction to Molecular Dynamics, 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"--

Download or read book Molecular Dynamics Simulation written by J. M. Haile and published by Wiley-Interscience. This book was released on 1997-03-14 with total page 0 pages. Available in PDF, EPUB and Kindle. 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

Download or read book Adsorption and Diffusion written by Hellmut G. Karge and published by Springer Science & Business Media. This book was released on 2008-06-17 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Molecular Sieves - Science and Technology" covers, in a comprehensive manner, the science and technology of zeolites and all related microporous and mesoporous materials. The contributions are grouped together topically in such a way that each volume deals with a specific sub-field. Volume 7 treats fundamentals and analyses of adsorption and diffusion in zeolites including single-file diffusion. Various methods of measuring adsorption and diffusion are described and discussed.