understanding molecular simulation from algorithms to applications computational science

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Understanding Molecular Simulation

Author : Daan Frenkel
ISBN : 0080519989
Genre : Science
File Size : 21. 32 MB
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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.

Industrial Applications Of Molecular Simulations

Author : Marc Meunier
ISBN : 9781439861028
Genre : Science
File Size : 80. 24 MB
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The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations demonstrates the capability of molecular modeling to tackle problems of industrial relevance. This book presents a wide range of various modeling techniques, including methods based on quantum or classical mechanics, molecular dynamics, Monte Carlo simulations, etc. It also explores a wide range of materials, from soft materials such as polymeric blends widely used in the chemical industry to hard or inorganic materials such as glasses and alumina. Features Demonstrates how modeling can solve everyday problems for scientists in industry Provides a broad overview of theoretical approaches Presents a wide range of applications in areas such as materials research, catalysis, pharmaceutical development and electronics Emphasizes the relationship between theory and experiments

Molecular Modeling And Simulation An Interdisciplinary Guide

Author : Tamar Schlick
ISBN : 1441963510
Genre : Mathematics
File Size : 85. 35 MB
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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

Computational Materials Science

Author : Wofram Hergert
ISBN : 3540210512
Genre : Science
File Size : 84. 51 MB
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Computational Physics is now a discipline in its own right, comparable with theoretical and experimental physics. Computational Materials Science concentrates on the calculation of materials properties starting from microscopic theories. It has become a powerful tool in industrial research for designing new materials, modifying materials properties and optimizing chemical processes. This book focusses on the application of computational methods in new fields of research, such as nanotechnology, spintronics and photonics, which will provide the foundation for important technological advances in the future. Methods such as electronic structure calculations, molecular dynamics simulations and beyond are presented, the discussion extending from the basics to the latest applications.

Emerging Trends In Applications And Infrastructures For Computational Biology Bioinformatics And Systems Biology

Author : Hamid R Arabnia
ISBN : 9780128042595
Genre : Computers
File Size : 32. 90 MB
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Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications covers the latest trends in the field with special emphasis on their applications. The first part covers the major areas of computational biology, development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques for the study of biological and behavioral systems. The second part covers bioinformatics, an interdisciplinary field concerned with methods for storing, retrieving, organizing, and analyzing biological data. The book also explores the software tools used to generate useful biological knowledge. The third part, on systems biology, explores how to obtain, integrate, and analyze complex datasets from multiple experimental sources using interdisciplinary tools and techniques, with the final section focusing on big data and the collection of datasets so large and complex that it becomes difficult to process using conventional database management systems or traditional data processing applications. Explores all the latest advances in this fast-developing field from an applied perspective Provides the only coherent and comprehensive treatment of the subject available Covers the algorithm development, software design, and database applications that have been developed to foster research

Computational Science And Its Applications Iccsa 2004

Author : Antonio Laganà
ISBN : 9783540247098
Genre : Computers
File Size : 44. 15 MB
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The natural mission of Computational Science is to tackle all sorts of human problems and to work out intelligent automata aimed at alleviating the b- den of working out suitable tools for solving complex problems. For this reason ComputationalScience,thoughoriginatingfromtheneedtosolvethemostch- lenging problems in science and engineering (computational science is the key player in the ?ght to gain fundamental advances in astronomy, biology, che- stry, environmental science, physics and several other scienti?c and engineering disciplines) is increasingly turning its attention to all ?elds of human activity. In all activities, in fact, intensive computation, information handling, kn- ledge synthesis, the use of ad-hoc devices, etc. increasingly need to be exploited and coordinated regardless of the location of both the users and the (various and heterogeneous) computing platforms. As a result the key to understanding the explosive growth of this discipline lies in two adjectives that more and more appropriately refer to Computational Science and its applications: interoperable and ubiquitous. Numerous examples of ubiquitous and interoperable tools and applicationsaregiveninthepresentfourLNCSvolumescontainingthecontri- tions delivered at the 2004 International Conference on Computational Science and its Applications (ICCSA 2004) held in Assisi, Italy, May 14–17, 2004.

Computational Science Iccs 2006

Author : Vassil Alexandrov
ISBN : 9783540343813
Genre : Computers
File Size : 56. 30 MB
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Annotation The four-volume set LNCS 3991-3994 constitutes the refereed proceedings of the 6th International Conference on Computational Science, ICCS 2006, held in Reading, UK, in May 2006. The main conference and its 32 topical workshops attracted over 1400 submissions. The 98 revised full papers and 29 revised poster papers of the main track presented together with 500 accepted workshop papers were carefully reviewed and selected for inclusion in the four volumes. The papers span the whole range of computational science, with focus on the following major themes: tackling grand challenges problems; modelling and simulations of complex systems; scalable algorithms and tools and environments for computational science. Of particular interest were the following major recent developments in novel methods and modelling of complex systems for diverse areas of science, scalable scientific algorithms, advanced software tools, computational grids, advanced numerical methods, and novel application areas where the above novel models, algorithms and tools can be efficiently applied such as physical systems, computational and systems biology, environmental systems, finance, and others.

Molecular Simulation Studies In Material And Biological Sciences

Author : Kholmirzo Kholmurodov
ISBN : 159454607X
Genre : Science
File Size : 84. 68 MB
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Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. The chemical, pharmaceutical, materials and related industries - all share the computer molecular simulation methods. This book presents leading international research in this dynamic field.

Mathematical Tools For Physicists

Author : Michael Grinfeld
ISBN : 9783527684274
Genre : Science
File Size : 77. 97 MB
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The new edition is significantly updated and expanded. This unique collection of review articles, ranging from fundamental concepts up to latest applications, contains individual contributions written by renowned experts in the relevant fields. Much attention is paid to ensuring fast access to the information, with each carefully reviewed article featuring cross-referencing, references to the most relevant publications in the field, and suggestions for further reading, both introductory as well as more specialized. While the chapters on group theory, integral transforms, Monte Carlo methods, numerical analysis, perturbation theory, and special functions are thoroughly rewritten, completely new content includes sections on commutative algebra, computational algebraic topology, differential geometry, dynamical systems, functional analysis, graph and network theory, PDEs of mathematical physics, probability theory, stochastic differential equations, and variational methods.

Statistical Methods For Stochastic Differential Equations

Author : Mathieu Kessler
ISBN : 9781439849767
Genre : Mathematics
File Size : 49. 86 MB
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The seventh volume in the SemStat series, Statistical Methods for Stochastic Differential Equations presents current research trends and recent developments in statistical methods for stochastic differential equations. Written to be accessible to both new students and seasoned researchers, each self-contained chapter starts with introductions to the topic at hand and builds gradually towards discussing recent research. The book covers Wiener-driven equations as well as stochastic differential equations with jumps, including continuous-time ARMA processes and COGARCH processes. It presents a spectrum of estimation methods, including nonparametric estimation as well as parametric estimation based on likelihood methods, estimating functions, and simulation techniques. Two chapters are devoted to high-frequency data. Multivariate models are also considered, including partially observed systems, asynchronous sampling, tests for simultaneous jumps, and multiscale diffusions. Statistical Methods for Stochastic Differential Equations is useful to the theoretical statistician and the probabilist who works in or intends to work in the field, as well as to the applied statistician or financial econometrician who needs the methods to analyze biological or financial time series.

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