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Large Scale Molecular Simulation
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Book Synopsis Bridging the Time Scales by : Peter Nielaba
Download or read book Bridging the Time Scales written by Peter Nielaba and published by Springer Science & Business Media. This book was released on 2007-10-13 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: The behaviour of many complex materials extends over time- and lengthscales well beyond those that can normally be described using standard molecular dynamics or Monte Carlo simulation techniques. As progress is coming more through refined simulation methods than from increased computer power, this volume is intended as both an introduction and a review of all relevant modern methods that will shape molecular simulation in the forthcoming decade. Written as a set of tutorial reviews, the book will be of use to specialists and nonspecialists alike.
Book Synopsis Structure and Function of Membrane Proteins by : Ingeborg Schmidt-Krey
Download or read book Structure and Function of Membrane Proteins written by Ingeborg Schmidt-Krey and published by Humana. This book was released on 2021-04-21 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines detailed experimental and computational approaches for the analysis of many aspects vital to the understanding of membrane protein structure and function. Readers will receive guidance on the selection and use of methods for over-expression and purification, tools to characterize membrane proteins within different phospholipid bilayers, direction on functional studies, and approaches to determine the structures of membrane proteins. Detailed experimental steps for specific membrane proteins with critical notes allow the protocols to be modified to different systems. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of practical information and implementation advice that leads to excellent, reproducible results. Authoritative and up-to-date, Structure and Function Studies of Membrane Proteins serves as an ideal guide for biologists, biochemists, and biophysicists striving to further understand these essential proteins and their many biological roles.
Book Synopsis A Practical Introduction to the Simulation of Molecular Systems by : Martin J. Field
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by Cambridge University Press. This book was released on 2007-07-19 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.
Book Synopsis Molecular Simulations by : Saman Alavi
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.
Book Synopsis Large-Scale Molecular Systems by : Werner Gans
Download or read book Large-Scale Molecular Systems written by Werner Gans and published by Springer Science & Business Media. This book was released on 2013-03-08 with total page 588 pages. Available in PDF, EPUB and Kindle. Book excerpt: This NATO Advanced Study Institute centered on large-scale molecular systems: Quantum mechanics, although providing a general framework for the description of matter, is not easily applicable to many concrete systems of interest; classical statistical methods, on the other hand, allow only a partial picture of the behaviour of large systems. The aim of the ASI was to present both aspects of the subject matter and to foster interaction between the scientists working in these important areas of theoretical physics and theoretical chemistry. The quantum-mechanical part was mostly based on the operator-algebraic formulation of quantum mechanics and comprised quantum statistics of infinite systems with special em phasis on macroscopic observables, equilibrium conditions, irreversibility on the one hand, symmetry breaking for molecules in the radiation field and macroscopic quantum phenomena in the theory of superconductivity (BCS-theory) on the other hand. In addition, phase-space methods for many-body systems were also presented. Statistical physics was the main topic in the other lectures of the School; much emphasis was put on the statistical features of macros copic ("large") systems, the lectures dealt with mass and energy transport im polymers, in gels and in microemulsions, with aggregation and growth phenomena, with relaxation in complex, correlated systems, with conduction and optical properties of polymers, and with the means of describing disordered systems, above all fractals and related hierarchical models.
Book Synopsis Clay-water Interface and Its Rheological Implications by : Necip Güven
Download or read book Clay-water Interface and Its Rheological Implications written by Necip Güven and published by . This book was released on 1992 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis High Performance Computing - HiPC 2007 by : Srinivas Aluru
Download or read book High Performance Computing - HiPC 2007 written by Srinivas Aluru and published by Springer. This book was released on 2008-01-22 with total page 687 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Quantum Dynamics by : Fabien Gatti
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.
Book Synopsis Understanding Molecular Simulation by : Daan Frenkel
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.
Book Synopsis Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics by : Xiakun Chu
Download or read book Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics written by Xiakun Chu and published by Frontiers Media SA. This book was released on 2022-01-07 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick
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
Book Synopsis Atomistic Modeling of Materials Failure by : Markus J. Buehler
Download or read book Atomistic Modeling of Materials Failure written by Markus J. Buehler and published by Springer Science & Business Media. This book was released on 2008-08-07 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an introduction to molecular and atomistic modeling techniques applied to fracture and deformation of solids, focusing on a variety of brittle, ductile, geometrically confined and biological materials. The overview includes computational methods and techniques operating at the atomic scale, and describes how these techniques can be used to model cracks and other deformation mechanisms. The book aims to make new molecular modeling techniques available to a wider community.
Book Synopsis Molecular Dynamics Simulation by : J. M. Haile
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
Book Synopsis An Introduction to Molecular Dynamics by : Mark S. Kemp
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"--
Book Synopsis Special Purpose Computers by : Berni J. Alder
Download or read book Special Purpose Computers written by Berni J. Alder and published by Academic Press. This book was released on 2014-05-10 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: Special Purpose Computers describes special-purpose computers and compares them to general-purpose computers in terms of speed and cost. Examples of computers that were designed for the efficient solution of long established algorithms are given, including Navier-Stokes hydrodynamic solvers, classical molecular dynamic machines, and Ising model computers. Comprised of seven chapters, this volume begins by documenting the progress of the CalTech Concurrent Computation Program and its evolution from computational high-energy physics to a supercomputer initiative, with emphasis on the lessons learned including computer architecture issues and the trade-offs between in-house and commercial development. The reader is then introduced to the QCD Machine, a special-purpose parallel supercomputer that was designed and built to solve the lattice quantum chromodynamics problem. Subsequent chapters focus on the Geometry-Defining Processors and their application to the solution of partial differential equations; the Navier-Stokes computer; parallel processing using the Loosely Coupled Array of Processors (LCAP) system; and the Delft Ising system processor. The design and implementation of the Delft molecular-dynamics processor are also described. This book will be of interest to computer engineers and designers.
Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
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.
