Computational Molecular Dynamics Challenges Methods Ideas

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.

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.

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.

This book reports recent mathematical developments in the Programme "Analysis, Modeling and Simulation of Multiscale Problems", which started as a German research initiative in 2006. Multiscale problems occur in many fields of science, such as microstructures in materials, sharp-interface models, many-particle systems and motions on different spatial and temporal scales in quantum mechanics or in molecular dynamics. The book presents current mathematical foundations of modeling, and proposes efficient numerical treatment.

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.

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.

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.

This book provides state-of-the-art and interdisciplinary topics on solving matrix eigenvalue problems, particularly by using recent petascale and upcoming post-petascale supercomputers. It gathers selected topics presented at the International Workshops on Eigenvalue Problems: Algorithms; Software and Applications, in Petascale Computing (EPASA2014 and EPASA2015), which brought together leading researchers working on the numerical solution of matrix eigenvalue problems to discuss and exchange ideas – and in so doing helped to create a community for researchers in eigenvalue problems. The topics presented in the book, including novel numerical algorithms, high-performance implementation techniques, software developments and sample applications, will contribute to various fields that involve solving large-scale eigenvalue problems.