Book & CD. Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. Having an increasingly significant impact on many applied industries, especially in modern biophysical and nanotechnological areas, molecular simulation provides a set of tools for predicting many functional properties of molecular systems. The chemical, pharmaceutical, materials and related industries -- all share the computer molecular simulation methods. The molecular simulation studies cover different fields of either biological processes -- protein folding and electron densities of DNA and proteins, or thin film formations and surface-cluster phenomena in nanoelectronics, synthetic copolymers and biopolymer design in biochemistry, so on. Practically all of the world's present supercomputers and many specially developed high performance computing clusters over the world are performing molecular simulations or are aimed on these needs. This book presents leading international research in this dynamic field.

In this book, original papers have been collected to demonstrate the efficient use of computer molecular dynamics simulation methods for the studying of nanoscale phenomena in the materials and life sciences. This book discusses modern molecular simulation methods for the study of molecular shape and properties in protein and polymer engineering, drugs and materials design, structure-function relationships, and related issues. This book contains the Proceedings of the MSSMBS-2014 and DSCMBS-2014 International Workshops which have been organised by the Joint Institute for Nuclear Research, the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and S.U. Umarov Physical-Technical Institute of the Academy of Sciences of the Republic of Tajikistan. The research topics discussed in the MSSMBS'14 & DSCMBS'14 International Workshops are as follows: computer molecular simulation methods and approaches; molecular dynamics and Monte-Carlo techniques; modelling of biological molecules; physical and biochemical systems; material fabrication and design; drug design in medicine; computational and computing physics, chemistry, biology and medicine; GPU accelerated molecular dynamics and related techniques.

This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

"This book provides comprehensive coverage of the latest innovations and advancements for pharmaceutical applications. Focusing on emerging drug development techniques and drug delivery for improved health outcomes"--Provided by publisher.

Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines

A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.

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.

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: - Transition path sampling and diffusive barrier crossing to simulaterare events - Dissipative particle dynamic as a course-grained simulation technique - Novel schemes to compute the long-ranged forces - Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations - Multiple-time step algorithms as an alternative for constraints - Defects in solids - The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules - Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.