New Algorithms for Macromolecular Simulation
New Algorithms for Macromolecular Simulation

Author: Benedict Leimkuhler

Publisher: Springer Science & Business Media

Published: 2006-03-22

Total Pages: 364

ISBN-13: 3540316183

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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.

Computational Molecular Dynamics: Challenges, Methods, Ideas
Computational Molecular Dynamics: Challenges, Methods, Ideas

Author: Peter Deuflhard

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 500

ISBN-13: 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.

Scientific Computing with MATLAB and Octave
Scientific Computing with MATLAB and Octave

Author: Alfio Quarteroni

Publisher: Springer Science & Business Media

Published: 2010-05-30

Total Pages: 379

ISBN-13: 3642124305

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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.

Elements of Scientific Computing
Elements of Scientific Computing

Author: Aslak Tveito

Publisher: Springer Science & Business Media

Published: 2010-09-27

Total Pages: 470

ISBN-13: 3642112986

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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.

Isogeometric Analysis and Applications 2018
Isogeometric Analysis and Applications 2018

Author: Harald van Brummelen

Publisher: Springer Nature

Published: 2021-01-13

Total Pages: 279

ISBN-13: 3030498360

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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.

Programming for Computations - Python
Programming for Computations - Python

Author: Svein Linge

Publisher: Springer

Published: 2016-07-25

Total Pages: 244

ISBN-13: 3319324284

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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.

Isogeometric Analysis and Applications 2014
Isogeometric Analysis and Applications 2014

Author: Bert Jüttler

Publisher: Springer

Published: 2015-12-21

Total Pages: 301

ISBN-13: 3319233157

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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.

Computing Characterizations of Drugs for Ion Channels and Receptors Using Markov Models
Computing Characterizations of Drugs for Ion Channels and Receptors Using Markov Models

Author: Aslak Tveito

Publisher: Springer

Published: 2016-04-19

Total Pages: 279

ISBN-13: 331930030X

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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.

Programming for Computations - MATLAB/Octave
Programming for Computations - MATLAB/Octave

Author: Svein Linge

Publisher: Springer

Published: 2016-08-01

Total Pages: 228

ISBN-13: 3319324527

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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.

Meshfree Methods for Partial Differential Equations VII
Meshfree Methods for Partial Differential Equations VII

Author: Michael Griebel

Publisher: Springer

Published: 2014-12-02

Total Pages: 323

ISBN-13: 3319068989

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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.