Download or read book New Algorithms for Macromolecular Simulation written by Benedict Leimkuhler and published by Springer Science & Business Media. This book was released on 2006-03-22 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

Download or read book Computational Methods for Macromolecules Challenges and Applications written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: This special volume collects invited articles by participants of the Third International Workshop on Methods for Macromolecular Modeling, Courant Institute of Mathematical Sciences, Oct. 12-14, 2000. Leading developers of methods for biomolecular simulations review advances in Monte Carlo and molecular dynamics methods, free energy computational methods, fast electrostatics (particle-mesh Ewald and fast multipole methods), mathematics, and molecular neurobiology, nucleic acid simulations, enzyme reactions, and other essential applications in biomolecular simulations. A Perspectives article by the editors assesses the directions and impact of macromolecular modeling research, including genomics and proteomics. These reviews and original papers by applied mathematicians, theoretical chemists, biomedical researchers, and physicists are of interest to interdisciplinary research students, developers and users of biomolecular methods in academia and industry.

Download or read book Computational Molecular Dynamics Challenges Methods Ideas written by Peter Deuflhard and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2023-07-13 with total page 868 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text. Since the second edition's publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed. - Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results - Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields - Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning

Download or read book A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems written by and published by . This book was released on 1994 with total page 22 pages. Available in PDF, EPUB and Kindle. Book excerpt: Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter-processor communication scales as N, the number of atoms, independent of P, the number of processors. Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this paper a new parallel method called force-decomposition for simulating macromolecular or small-molecule systems is presented. Its memory and communication costs scale as N/(square root)P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load-balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor.

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 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 Scientific Computing with MATLAB and Octave written by Alfio Quarteroni and published by Springer Science & Business Media. This book was released on 2010-05-30 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Preface to the First Edition This textbook is an introduction to Scienti?c Computing. We will illustrate several numerical methods for the computer solution of c- tain classes of mathematical problems that cannot be faced by paper and pencil. We will show how to compute the zeros or the integrals of continuous functions, solve linear systems, approximate functions by polynomials and construct accurate approximations for the solution of di?erential equations. With this aim, in Chapter 1 we will illustrate the rules of the game thatcomputersadoptwhenstoringandoperatingwith realandcomplex numbers, vectors and matrices. In order to make our presentation concrete and appealing we will 1 adopt the programming environment MATLAB as a faithful c- panion. We will gradually discover its principal commands, statements and constructs. We will show how to execute all the algorithms that we introduce throughout the book. This will enable us to furnish an - mediate quantitative assessment of their theoretical properties such as stability, accuracy and complexity. We will solve several problems that will be raisedthrough exercises and examples, often stemming from s- ci?c applications.

Download or read book Elements of Scientific Computing written by Aslak Tveito and published by Springer Science & Business Media. This book was released on 2010-09-27 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Science used to be experiments and theory, now it is experiments, theory and computations. The computational approach to understanding nature and technology is currently flowering in many fields such as physics, geophysics, astrophysics, chemistry, biology, and most engineering disciplines. This book is a gentle introduction to such computational methods where the techniques are explained through examples. It is our goal to teach principles and ideas that carry over from field to field. You will learn basic methods and how to implement them. In order to gain the most from this text, you will need prior knowledge of calculus, basic linear algebra and elementary programming.

Download or read book Isogeometric Analysis and Applications 2018 written by Harald van Brummelen and published by Springer Nature. This book was released on 2021-01-13 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: This proceedings volume gathers a selection of outstanding research papers presented at the third Conference on Isogeometric Analysis and Applications, held in Delft, The Netherlands, in April 2018. This conference series, previously held in Linz, Austria, in 2012 and Annweiler am Trifels, Germany, in 2014, has created an international forum for interaction between scientists and practitioners working in this rapidly developing field. Isogeometric analysis is a groundbreaking computational approach that aims to bridge the gap between numerical analysis and computational geometry modeling by integrating the finite element method and related numerical simulation techniques into the computer-aided design workflow, and vice versa. The methodology has matured over the last decade both in terms of our theoretical understanding, its mathematical foundation and the robustness and efficiency of its practical implementations. This development has enabled scientists and practitioners to tackle challenging new applications at the frontiers of research in science and engineering and attracted early adopters for this his novel computer-aided design and engineering technology in industry. The IGAA 2018 conference brought together experts on isogeometric analysis theory and application, share their insights into challenging industrial applications and to discuss the latest developments as well as the directions of future research and development that are required to make isogeometric analysis an established mainstream technology.

Download or read book Programming for Computations Python written by Svein Linge and published by Springer. This book was released on 2016-07-25 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents computer programming as a key method for solving mathematical problems. There are two versions of the book, one for MATLAB and one for Python. The book was inspired by the Springer book TCSE 6: A Primer on Scientific Programming with Python (by Langtangen), but the style is more accessible and concise, in keeping with the needs of engineering students. The book outlines the shortest possible path from no previous experience with programming to a set of skills that allows the students to write simple programs for solving common mathematical problems with numerical methods in engineering and science courses. The emphasis is on generic algorithms, clean design of programs, use of functions, and automatic tests for verification.

Download or read book Isogeometric Analysis and Applications 2014 written by Bert Jüttler and published by Springer. This book was released on 2015-12-21 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: Isogeometric Analysis is a groundbreaking computational approach that promises the possibility of integrating the finite element method into conventional spline-based CAD design tools. It thus bridges the gap between numerical analysis and geometry, and moreover it allows to tackle new cutting edge applications at the frontiers of research in science and engineering. This proceedings volume contains a selection of outstanding research papers presented at the second International Workshop on Isogeometric Analysis and Applications, held at Annweiler, Germany, in April 2014.

Download or read book Computing Characterizations of Drugs for Ion Channels and Receptors Using Markov Models written by Aslak Tveito and published by Springer. This book was released on 2016-04-19 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: Flow of ions through voltage gated channels can be represented theoretically using stochastic differential equations where the gating mechanism is represented by a Markov model. The flow through a channel can be manipulated using various drugs, and the effect of a given drug can be reflected by changing the Markov model. These lecture notes provide an accessible introduction to the mathematical methods needed to deal with these models. They emphasize the use of numerical methods and provide sufficient details for the reader to implement the models and thereby study the effect of various drugs. Examples in the text include stochastic calcium release from internal storage systems in cells, as well as stochastic models of the transmembrane potential. Well known Markov models are studied and a systematic approach to including the effect of mutations is presented. Lastly, the book shows how to derive the optimal properties of a theoretical model of a drug for a given mutation defined in terms of a Markov model.

Download or read book Programming for Computations MATLAB Octave written by Svein Linge and published by Springer. This book was released on 2016-08-01 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents computer programming as a key method for solving mathematical problems. There are two versions of the book, one for MATLAB and one for Python. The book was inspired by the Springer book TCSE 6: A Primer on Scientific Programming with Python (by Langtangen), but the style is more accessible and concise, in keeping with the needs of engineering students. The book outlines the shortest possible path from no previous experience with programming to a set of skills that allows the students to write simple programs for solving common mathematical problems with numerical methods in engineering and science courses. The emphasis is on generic algorithms, clean design of programs, use of functions, and automatic tests for verification.

Download or read book Meshfree Methods for Partial Differential Equations VII written by Michael Griebel and published by Springer. This book was released on 2014-12-02 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meshfree methods, particle methods, and generalized finite element methods have witnessed substantial development since the mid 1990s. The growing interest in these methods is due in part to the fact that they are extremely flexible numerical tools and can be interpreted in a number of ways. For instance, meshfree methods can be viewed as a natural extension of classical finite element and finite difference methods to scattered node configurations with no fixed connectivity. Furthermore, meshfree methods offer a number of advantageous features which are especially attractive when dealing with multiscale phenomena: a priori knowledge about particular local behavior of the solution can easily be introduced in the meshfree approximation space, and coarse-scale approximations can be seamlessly refined with fine-scale information. This volume collects selected papers presented at the Seventh International Workshop on Meshfree Methods, held in Bonn, Germany in September 2013. They address various aspects of this highly dynamic research field and cover topics from applied mathematics, physics and engineering.

Download or read book Domain Decomposition Methods in Science and Engineering XXII written by Thomas Dickopf and published by Springer. This book was released on 2016-03-11 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: These are the proceedings of the 22nd International Conference on Domain Decomposition Methods, which was held in Lugano, Switzerland. With 172 participants from over 24 countries, this conference continued a long-standing tradition of internationally oriented meetings on Domain Decomposition Methods. The book features a well-balanced mix of established and new topics, such as the manifold theory of Schwarz Methods, Isogeometric Analysis, Discontinuous Galerkin Methods, exploitation of modern HPC architectures and industrial applications. As the conference program reflects, the growing capabilities in terms of theory and available hardware allow increasingly complex non-linear and multi-physics simulations, confirming the tremendous potential and flexibility of the domain decomposition concept.

Download or read book Meshfree Methods for Partial Differential Equations VIII written by Michael Griebel and published by Springer. This book was released on 2017-04-05 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: There have been substantial developments in meshfree methods, particle methods, and generalized finite element methods since the mid 1990s. The growing interest in these methods is in part due to the fact that they offer extremely flexible numerical tools and can be interpreted in a number of ways. For instance, meshfree methods can be viewed as a natural extension of classical finite element and finite difference methods to scattered node configurations with no fixed connectivity. Furthermore, meshfree methods have a number of advantageous features that are especially attractive when dealing with multiscale phenomena: A-priori knowledge about the solution’s particular local behavior can easily be introduced into the meshfree approximation space, and coarse scale approximations can be seamlessly refined by adding fine scale information. However, the implementation of meshfree methods and their parallelization also requires special attention, for instance with respect to numerical integration.