Printed Edition of the Special Issue Published in Entropy

The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Molecular dynamics is an important technique with applications in many areas, including drug design, protein engineering, macromolecular structure determination, and molecular recognition. This book concentrates on these exciting applications while briefly summarizing the essential mathematical background. Using standard molecular dynamics and related algorithms, results are presented on protein, carbohydrate, and nucleotide modeling and dynamics. Chapters covering relatively new applications, such as simulated annealing protocol and the free energy perturbation method, are also included. Molecular biologists, biochemists, and researchers in structural molecular biology, chemistry, crystallography, and computer modelling will find this book a useful reference resource.

This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field.

This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

A unique selection of papers on the most recent progress in the modelling of biological molecules containing metal ions. New approaches and techniques in this field are allowing researchers to discuss structures, electronic properties and reaction mechanisms of metalloproteins on the basis of computational studies. The book discusses different approaches in the development of new force fields and their application to the computation of the structures, electronic properties and dynamics of bioinorganic compounds as well as quantum mechanical and integrated QM/MM methods for understanding the function of metalloenzymes and the calculation of electrostatic interactions.

Written by leading experts from around the world, Monte Carlo and Molecular Dynamics Simulations in Polymer Science comprehensively reviews the latest simulation techniques for macromolecular materials. Focusing in particular on numerous new techniques, the book offers authoritative introductions to solutions of neutral polymers and polyelectrolytes; dynamics of polymer melts, rubbers and gels, and glassy materials; thermodynamics of polymer mixing and mesophase formation, and polymers confined at interfaces and grafted to walls. Throughout, contributors offer practical advice on how to overcome the unique challenges posed by the large size and slow relaxation of polymer coils. Students and researchers in polymer chemistry, polymer physics, chemical engineering, and materials and computational science will all benefit from the cogent, step-by-step introductions contained in this important new book.

This book highlights the latest experimental and theoretical developments in the field of femtochemistry, with papers describing the physics and chemistry of ultrafast processes in small molecules, complex molecular systems, clusters, biological systems, solids, matrices, liquids and at surfaces and interfaces. The recent developments in frequency-domain studies of femtodynamics are also presented. In addition, the latest achievements in femtosecond control of chemical reactions are presented, together with the newest techniques in real-time probing of reactions such as ultrafast x-ray or electron diffraction. The papers are rich in references giving a clearcut state-of-the-art of the topics being discussed. The book should be a valuable tool to all persons in the field and to young scientists.Contributors include: A H Zewail, J Jortner, V S Letokhov, J Manz, R S Berry, C Wittig, K B Eisenthal, A W Castleman Jr., J T Hynes, W H Gadzuk, R Kosloff, S Mukamel, K R Wilson; G Fleming, D Wiersma, K Yoshihara, V Sundström, A Apkarian, N Scherer, A Myers, R Schinke, J R Huber, R B Gerber, G Gerber and P M Champion.