Understanding Molecular Simulation

From Algorithms to Applications
Author: Daan Frenkel,Berend Smit
Publisher: Elsevier
ISBN: 9780080519982
Category: Science
Page: 664
View: 2640
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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.

Computational Biochemistry and Biophysics


Author: Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe
Publisher: CRC Press
ISBN: 9780203903827
Category: Science
Page: 512
View: 7756
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Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.

Statistical Mechanics: Theory and Molecular Simulation


Author: Mark Tuckerman
Publisher: OUP Oxford
ISBN: 9780191523465
Category: Science
Page: 720
View: 2399
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Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.

Molecular Modelling for Beginners


Author: Alan Hinchliffe
Publisher: John Wiley & Sons
ISBN: 1119964814
Category: Science
Page: 428
View: 4047
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A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry. Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages and many realistic examples with solutions Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian .gjf files and sample outputs. Revised with changes in emphasis and presentation to appeal to the modern student.

Essentials of Computational Chemistry

Theories and Models
Author: Christopher J. Cramer
Publisher: John Wiley & Sons
ISBN: 1118712277
Category: Science
Page: 624
View: 1451
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Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.

Introduction to Computational Chemistry


Author: Frank Jensen
Publisher: John Wiley & Sons
ISBN: 1118825950
Category: Science
Page: 664
View: 5187
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Introduction to Computational Chemistry 3rd Edition provides a comprehensive account of the fundamental principles underlying different computational methods. Fully revised and updated throughout to reflect important method developments and improvements since publication of the previous edition, this timely update includes the following significant revisions and new topics: * Polarizable force fields * Tight-binding DFT * More extensive DFT functionals, excited states and time dependent molecular properties * Accelerated Molecular Dynamics methods * Tensor decomposition methods * Cluster analysis * Reduced scaling and reduced prefactor methods Additional information is available at: www.wiley.com/go/jensen/computationalchemistry3

Molecular Electronic-Structure Theory


Author: Trygve Helgaker,Poul Jorgensen,Jeppe Olsen
Publisher: John Wiley & Sons
ISBN: 1119019559
Category: Science
Page: 944
View: 1416
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Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluation * Hartree-Fock theory * Configuration-interaction and multi-configurational self-consistent theory * Coupled-cluster theory for ground and excited states * Perturbation theory for single- and multi-configurational states * Linear-scaling techniques and the fast multipole method * Explicity correlated wave functions * Basis-set convergence and extrapolation * Calibration and benchmarking of computational methods, with applications to moelcular equilibrium structure, atomization energies and reaction enthalpies. Molecular Electronic-Structure Theory makes extensive use of numerical examples, designed to illustrate the strengths and weaknesses of each method treated. In addition, statements about the usefulness and deficiencies of the various methods are supported by actual examples, not just model calculations. Problems and exercises are provided at the end of each chapter, complete with hints and solutions. This book is a must for researchers in the field of quantum chemistry as well as for nonspecialists who wish to acquire a thorough understanding of ab initio molecular electronic-structure theory and its applications to problems in chemistry and physics. It is also highly recommended for the teaching of graduates and advanced undergraduates.

Molecular Modeling and Simulation

An Interdisciplinary Guide
Author: Tamar Schlick
Publisher: Springer Science & Business Media
ISBN: 0387224645
Category: Science
Page: 635
View: 5889
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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

Molecular Modelling: Principles And Applications, 2/E


Author: Leach
Publisher: Pearson Education India
ISBN: 9788131728604
Category:
Page: 768
View: 3431
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Chemical Dynamics in Condensed Phases

Relaxation, Transfer and Reactions in Condensed Molecular Systems
Author: Abraham Nitzan
Publisher: Oxford University Press
ISBN: 0198529791
Category: Science
Page: 719
View: 5456
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Graduate level textbook presenting some of the most fundamental processes that underlie physical, chemical and biological phenomena in complex condensed phase systems. Includes in-depth descriptions of relevant methodologies, and provides ample introductory material for readers of different backgrounds.

Molecular Theory of Capillarity


Author: J. S. Rowlinson,B. Widom
Publisher: Courier Corporation
ISBN: 0486317099
Category: Science
Page: 352
View: 3338
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History of surface phenomena offers critical and detailed examination and assessment of modern theories, focusing on statistical mechanics and application of results in mean-field approximation to model systems. 1989 edition.

The Theory of Polymer Dynamics


Author: Masao Doi,Sam F. Edwards
Publisher: Oxford University Press
ISBN: 9780198520337
Category: Foreign Language Study
Page: 391
View: 475
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'This book is destined to join the classics of polymer science...an essential purchase for any serious student of polymer dynamics.' British Polymer Journal

Ab Initio Molecular Dynamics

Basic Theory and Advanced Methods
Author: Dominik Marx,Jürg Hutter
Publisher: Cambridge University Press
ISBN: 9781139477192
Category: Science
Page: N.A
View: 9868
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Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.

Colloidal Dispersions


Author: W. B. Russel,D. A. Saville,W. R. Schowalter
Publisher: Cambridge University Press
ISBN: 9780521426008
Category: Mathematics
Page: 525
View: 499
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Imparts a sound, quantitative understanding of colloidal science, based on fundamental theory and experiments with well-characterised model systems.

Algorithms in Structural Molecular Biology


Author: Bruce R. Donald
Publisher: MIT Press
ISBN: 0262297841
Category: Science
Page: 464
View: 6187
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Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules.Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility.The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes


Author: Samuel Safran
Publisher: CRC Press
ISBN: 0429976763
Category: Science
Page: 288
View: 9732
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Understanding the structural and thermodynamic properties of surfaces, interfaces, and membranes is important for both fundamental and practical reasons. Important applications include coatings, dispersants, encapsulating agents, and biological materials. Soft materials, important in the development of new materials and the basis of many biological systems, cannot be designed using trial and error methods due to the multiplicity of components and parameters. While these systems can sometimes be analyzed in terms of microscopic mixtures, it is often conceptually simpler to regard them as dispersions and to focus on the properties of the internal interfaces found in these systems. The basic physics centers on the properties of quasi-two-dimensional systems embedded in the three-dimensional world, thus exhibiting phenomena that do not exist in bulk materials. This approach is the basis behind the theoretical presentation of Statistical Thermodynamics of Surfaces, Interfaces, and Membranes. The approach adapted allows one to treat the rich diversity of phenomena investigated in the field of soft matter physics (including both colloid/interface science as well as the materials and macromolecular aspects of biological physics) such as interfacial tension, the roughening transition, wetting, interactions between surfaces, membrane elasticity, and self-assembly. Presented as a set of lecture notes, this book is aimed at physicists, physical chemists, biological physicists, chemical engineers, and materials scientists who are interested in the statistical mechanics that underlie the macroscopic, thermodynamic properties of surfaces, interfaces, and membranes. This paperback edition contains all the material published in the original hard-cover edition as well as additional clarifications and explanations.

Introduction to Practice of Molecular Simulation

Molecular Dynamics, Monte Carlo, Brownian Dynamics, Lattice Boltzmann and Dissipative Particle Dynamics
Author: Akira Satoh
Publisher: Elsevier
ISBN: 0123851491
Category: Science
Page: 330
View: 4359
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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

Petascale Computing

Algorithms and Applications
Author: David A. Bader
Publisher: CRC Press
ISBN: 9781584889106
Category: Computers
Page: 616
View: 7486
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Although the highly anticipated petascale computers of the near future will perform at an order of magnitude faster than today’s quickest supercomputer, the scaling up of algorithms and applications for this class of computers remains a tough challenge. From scalable algorithm design for massive concurrency toperformance analyses and scientific visualization, Petascale Computing: Algorithms and Applications captures the state of the art in high-performance computing algorithms and applications. Featuring contributions from the world’s leading experts in computational science, this edited collection explores the use of petascale computers for solving the most difficult scientific and engineering problems of the current century. Covering a wide range of important topics, the book illustrates how petascale computing can be applied to space and Earth science missions, biological systems, weather prediction, climate science, disasters, black holes, and gamma ray bursts. It details the simulation of multiphysics, cosmological evolution, molecular dynamics, and biomolecules. The book also discusses computational aspects that include the Uintah framework, Enzo code, multithreaded algorithms, petaflops, performance analysis tools, multilevel finite element solvers, finite element code development, Charm++, and the Cactus framework. Supplying petascale tools, programming methodologies, and an eight-page color insert, this volume addresses the challenging problems of developing application codes that can take advantage of the architectural features of the new petascale systems in advance of their first deployment.

Molecular Dynamics Simulation

Elementary Methods
Author: J. M. Haile
Publisher: University of Texas Press
ISBN: 9780471184393
Category: Mathematics
Page: 489
View: 9921
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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

Computational Geometry

Algorithms and Applications
Author: Mark de Berg
Publisher: Springer Science & Business Media
ISBN: 3540779736
Category: Computers
Page: 386
View: 3066
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This introduction to computational geometry focuses on algorithms. Motivation is provided from the application areas as all techniques are related to particular applications in robotics, graphics, CAD/CAM, and geographic information systems. Modern insights in computational geometry are used to provide solutions that are both efficient and easy to understand and implement.