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Computational Molecular Dynamics: Challenges, Methods, Ideas

Computational Molecular Dynamics: Challenges, Methods, Ideas
Author: Peter Deuflhard
Publisher: Springer Science & Business Media
Total Pages: 500
Release: 2012-12-06
Genre: Mathematics
ISBN: 3642583601
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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.

Computational Methods for Macromolecules: Challenges and Applications

Computational Methods for Macromolecules: Challenges and Applications
Author: Tamar Schlick
Publisher: Springer Science & Business Media
Total Pages: 504
Release: 2012-12-06
Genre: Mathematics
ISBN: 3642560806
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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.

Challenges in Scientific Computing - CISC 2002

Challenges in Scientific Computing - CISC 2002
Author: Eberhard Baensch
Publisher: Springer Science & Business Media
Total Pages: 300
Release: 2012-12-06
Genre: Mathematics
ISBN: 3642190146
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The conference Challenges In Scientific Computing (CISC 2002) took place from October, 2 to 5, 2002. The hosting institution was the Weierstrass Insti tute for Applied Analysis and Stochastics (WIAS) in Berlin, Germany. The main purpose of this meeting was to draw together researchers working in the fields of numerical analysis and scientific computing with a common interest in the numerical treatment and the computational solution of systems of nonlinear partial differential equations arising from applications of physical and engineering problems. The main focus of the conference was on the problem class of non linear transport/diffusion/reaction systems, chief amongst these being: the Navier-Stokes equations, semiconductor-device equations and porous media flow problems. The emphasis was on unsolved problems, challenging open questions from applications and assessing the various numerical methods used to handle them, rather than concentrate on accurate results from "solved" problems. Thanks to the participants it was an interesting meeting. The presentations stimulated exchanging ideas and lively discussions. This proceedings comprises 13 papers form the conference, ranging from numerical methods for flow problems, multigrid methods, semiconductor and microwave simulation, solution methods, finite element analysis to software aspects. This interesting conference would not have been possible without the help of the staff of the WIAS. I thank all participants, and all our supporters, especially those not onstage, for making the conference a success.

Computational Chemistry

Computational Chemistry
Author: Philippe G. Ciarlet
Publisher: Gulf Professional Publishing
Total Pages: 928
Release: 1990
Genre: Mathematics
ISBN: 9780444512482
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Aiming to provide the reader with a general overview of the mathematical and numerical techniques used for the simulation of matter at the microscopic scale, this book lays the emphasis on the numerics, but modelling aspects are also addressed. The contributors come from different scientific communities: physics, theoretical chemistry, mathematical analysis, stochastic analysis, numerical analysis, and the text should be suitable for graduate students in mathematics, sciences and engineering and technology.

Topics in Computational Wave Propagation

Topics in Computational Wave Propagation
Author: Mark Ainsworth
Publisher: Springer Science & Business Media
Total Pages: 408
Release: 2012-12-06
Genre: Mathematics
ISBN: 3642554830
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These ten detailed and authoritative survey articles on numerical methods for direct and inverse wave propagation problems are written by leading experts. Researchers and practitioners in computational wave propagation, from postgraduate level onwards, will find the breadth and depth of coverage of recent developments a valuable resource. The articles describe a wide range of topics on the application and analysis of methods for time and frequency domain PDE and boundary integral formulations of wave propagation problems. Electromagnetic, seismic and acoustic equations are considered. Recent developments in methods and analysis ranging from finite differences to hp-adaptive finite elements, including high-accuracy and fast methods are described with extensive references.

Advanced Topics in Computational Partial Differential Equations

Advanced Topics in Computational Partial Differential Equations
Author: Hans Petter Langtangen
Publisher: Springer Science & Business Media
Total Pages: 676
Release: 2012-09-22
Genre: Mathematics
ISBN: 3642182372
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A gentle introduction to advanced topics such as parallel computing, multigrid methods, and special methods for systems of PDEs. The goal of all chapters is to ‘compute’ solutions to problems, hence algorithmic and software issues play a central role. All software examples use the Diffpack programming environment - some experience with Diffpack is required. There are also some chapters covering complete applications, i.e., the way from a model, expressed as systems of PDEs, through to discretization methods, algorithms, software design, verification, and computational examples. Suitable for readers with a background in basic finite element and finite difference methods for partial differential equations.

Molecular Dynamics

Molecular Dynamics
Author: Ben Leimkuhler
Publisher: Springer
Total Pages: 0
Release: 2016-10-09
Genre: Mathematics
ISBN: 9783319353241
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This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.

A Primer on Scientific Programming with Python

A Primer on Scientific Programming with Python
Author: Hans Petter Langtangen
Publisher: Springer
Total Pages: 942
Release: 2016-07-28
Genre: Computers
ISBN: 3662498871
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The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language. The exposition is example and problem-oriented, where the applications are taken from mathematics, numerical calculus, statistics, physics, biology and finance. The book teaches "Matlab-style" and procedural programming as well as object-oriented programming. High school mathematics is a required background and it is advantageous to study classical and numerical one-variable calculus in parallel with reading this book. Besides learning how to program computers, the reader will also learn how to solve mathematical problems, arising in various branches of science and engineering, with the aid of numerical methods and programming. By blending programming, mathematics and scientific applications, the book lays a solid foundation for practicing computational science. From the reviews: Langtangen ... does an excellent job of introducing programming as a set of skills in problem solving. He guides the reader into thinking properly about producing program logic and data structures for modeling real-world problems using objects and functions and embracing the object-oriented paradigm. ... Summing Up: Highly recommended. F. H. Wild III, Choice, Vol. 47 (8), April 2010 Those of us who have learned scientific programming in Python ‘on the streets’ could be a little jealous of students who have the opportunity to take a course out of Langtangen’s Primer.” John D. Cook, The Mathematical Association of America, September 2011 This book goes through Python in particular, and programming in general, via tasks that scientists will likely perform. It contains valuable information for students new to scientific computing and would be the perfect bridge between an introduction to programming and an advanced course on numerical methods or computational science. Alex Small, IEEE, CiSE Vol. 14 (2), March /April 2012 “This fourth edition is a wonderful, inclusive textbook that covers pretty much everything one needs to know to go from zero to fairly sophisticated scientific programming in Python...” Joan Horvath, Computing Reviews, March 2015

Spectral and High Order Methods for Partial Differential Equations ICOSAHOM 2018

Spectral and High Order Methods for Partial Differential Equations ICOSAHOM 2018
Author: Spencer J. Sherwin
Publisher: Springer Nature
Total Pages: 658
Release: 2020-08-11
Genre: Mathematics
ISBN: 3030396479
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This open access book features a selection of high-quality papers from the presentations at the International Conference on Spectral and High-Order Methods 2018, offering an overview of the depth and breadth of the activities within this important research area. The carefully reviewed papers provide a snapshot of the state of the art, while the extensive bibliography helps initiate new research directions.

Meshfree Methods for Partial Differential Equations VI

Meshfree Methods for Partial Differential Equations VI
Author: Michael Griebel
Publisher: Springer Science & Business Media
Total Pages: 243
Release: 2012-12-16
Genre: Computers
ISBN: 3642329799
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Meshfree methods are a modern alternative to classical mesh-based discretization techniques such as finite differences or finite element methods. Especially in a time-dependent setting or in the treatment of problems with strongly singular solutions their independence of a mesh makes these methods highly attractive. This volume collects selected papers presented at the Sixth International Workshop on Meshfree Methods held in Bonn, Germany in October 2011. They address various aspects of this very active research field and cover topics from applied mathematics, physics and engineering. ​