الصفحة 1
الصفحة 1
Numerical Simulation in Molecular Dynamics : Numerics, Algorithms, Parallelization, Applications
Particle models play an important role in many applications in physics, chemistry and biology. They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the necessary numerical methods and techniques (linked-cell method, SPME-method, tree codes, multipole technique) and the theoretical background and foundations. It illustrates the aspects modelling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. Furthermore, detailed explanations are given to the different steps of numerical simulation, and code examples are provided.
Neutron Spin Echo in Polymer Systems
Neutron spin echo spectroscopy (NSE) provides the unique opportunity to unravel the molecular dynamics of polymer chains in space and time, covering most of the relevant length and time scales. This article reviews in a comprehensive form recent advances in the application of NSE to problems in polymer physics and describes in terms of examples expected future trends. The review commences with a description of NSE covering both the generic longitudinal field set-up as well as the resonance technique. Then, NSE results for homopolymers chains are presented, covering all length scales from the very local secondary J3-relaxation to large scale reptation. This overview is the core of the review. Thereafter the dynamics of more complex systems is addressed. Starting from polymer blends, diblock copolymers, gels, micelles, stars and dendrirners, rubbery electrolytes and biological macromolecules are discussed. Wherever possible the review relates the NSE findings to the results of other techniques, in particular emphasizing computer simulations.
Nanostructured Soft Matter : Experiment, Theory, Simulation and Perspectives
This book provides an interdisciplinary overview of a new and broad class of materials under the unifying name Nanostructured Soft Matter. It covers materials ranging from short amphiphilic molecules to block copolymers, proteins, colloids and their composites, microemulsions and bio-inspired systems.
Multiscale Modeling and Simulation of Composite Materials and Structures
Multiscale Modeling and Simulation of Composite Materials and Structures presents the state of the art in multiscale modeling and simulation techniques for composite materials and structures. The text focuses on the structural and functional properties of engineering composites and the sustainable high performance of components and structures. With contributions from leading experts in the field, Multiscale Modeling and Simulation of Composite Materials and Structures proves to be an invaluable resource for researchers, graduate students and engineers in the field of Composite Materials.
Molecular Materials with Specific Interactions - Modeling and Design
One of the first requirements to initiate the molecular modeling of molecular materials is an accurate and realistic description of the electronic structure, intermolecular interactions and chemical reactions at microscopic and macroscopic scale. Therefore the first four chapters contain an extensive introduction into the latest theories of intermolecular interactions, functional density techniques, microscopic and mezoscopic modeling techniques as well as first-principle molecular dynamics.In the following chapters, techniques bridging microscopic and mezoscopic modeling scales are presented. The authors then illustrate various successful applications of molecular design of new materials, drugs, biocatalysts, etc. before presenting challenging topics in molecular materials design.
Molecular interactions : Concepts and methods
A modern, comprehensive text and reference describing intermolecular forces, this book begins with coverage of the concepts and methods for simpler systems, then moves on to more advanced subjects for complex systems – emphasizing concepts and methods used in calculations with realistic models and compared with empirical data.
Modern Aspects of Electrochemistry ; Vol. 39
This volume of Modern Aspects covers a wide spread of topics presented in an authoritative, informative and instructive manner by some internationally renowned specialists. Professors Politzer and Dr. Murray provide a comprehensive description of the various theoretical treatments of solute-solvent interactions, including ion-solvent interactions. Both continuum and discrete molecular models for the solvent molecules are discussed, including Monte Carlo and molecular dynamics simulations. The advantages and drawbacks of the resulting models and computational approaches are discussed and the impressive progress made in predicting the properties of molecular and ionic solutions is surveyed.
Modeling in membranes and membrane-based processes
This book explores almost every major aspect of modeling and the techniques applied in membrane separation studies and applications. This includes first principle-based models, thermodynamics models, computational fluid dynamics simulations, molecular dynamics simulations, and artificial intelligence-based modeling for membrane separation processes. These models have been discussed in light of various applications ranging from desalination to gas separation.
High-dimensional chaotic and attractor systems : A comprehensive introduction
If we try to describe real world in mathematical terms, we will see that real life is very often a high–dimensional chaos. Sometimes, by ‘pushing hard’, we manage to make order out of it; yet sometimes, we need simply to accept our life as it is. To be able to still live successfully, we need tounderstand, predict, and ultimately control this high–dimensional chaotic dynamics of life. This is the main theme of the present book.
Guide to Biomolecular Simulations
Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures.
Frontiers of Computational Science ; Proceedings of the International Symposium on Frontiers of Computational Science 2005
With the dramatic increase in speed and capacity of modern computers, computational approaches are becoming of crucial importance in various fields of science and engineering. Computational science is the interdisciplinary science, which promotes systematic development of methodologies and framework of computational approaches, basic studies of algorithms and soft-computation technologies and vast areas of applications. This volume is the proceedings of International Symposium on Frontiers of Computational Science 2005, containing papers from 7 plenary and keynote lecturers, 17 invited lecturers and 33 contributed papers. This book discusses the high-level use of computers in a wide variety of areas such as fluid mechanics, material and genome sciences.
Free Energy Calculations : Theory and Applications in Chemistry and Biology
This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles.
Diffusion in Condensed Matter : Methods, Materials, Models
Diffusion as the process of particle transport due to stochastic movement is a phenomenon of crucial relevance for a large variety of processes and materials. This comprehensive, handbook-style survey of diffusion in condensed matter gives detailed insight into diffusion as the process of particle transport due to stochastic movement. Leading experts in the field describe in 23 chapters the different aspects of diffusion, covering microscopic and macroscopic experimental techniques and exemplary results for various classes of solids, liquids and interfaces as well as several theoretical concepts and models. Students and scientists in physics, chemistry, materials science, and biology will benefit from this detailed compilation.
Computer simulations in condensed matter : From materials to chemical biology ; Vol.1
This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. It will enable the graduate student and both the specialist and nonspecialist researcher to get acquainted with the tools necessary to carry out numerical simulations at an advanced level. Volume 2 published as LNP 704 (ISBN 3-540-35283-X) is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology.
Computer simulation studies in condensed-matter physics XVIII ; Proceedings of the Eighteenth Workshop, Athens, GA, USA, March 7-11, 2005
This volume represents a "status report" emanating from presentations made during the 18th Annual Workshop on Computer Simulations Studies in Condensed Matter Physics at the Center for Simulational Physics at the University of Georgia in March 2005. It provides a broad overview of the most recent advances in the field, spanning the range from statistical physics to soft condensed matter and biological systems. Results on nanostructures and materials are included as are several descriptions of advances in quantum simulations and quantum computing as well as.methodological advances.
Computer simulation studies in condensed-matter physics XVI ; Proceedings of the Seventeenth Workshop, Athens, GA, USA, February 16-20, 2004
This status report features the most recent developments in the field, spanning a wide range of topical areas in the computer simulation of condensed matter/materials physics. Both established and new topics are included, ranging from the statistical mechanics of classical magnetic spin models to electronic structure calculations, quantum simulations, and simulations of soft condensed matter. The book presents new physical results as well as novel methods of simulation and data analysis. Highlights of this volume include various aspects of non-equilibrium statistical mechanics, studies of properties of real materials using both classical model simulations and electronic structure calculations, and the use of computer simulations in teaching.
Computational studies of RNA and DNA
Computational Studies of RNA and DNA includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.The systems and problems studied include: Accurate calculations of base pairing energies / Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid / Calculating DNA elasticity
Computational Multiscale Modeling of Fluids and Solids : Theory and Applications
The book includes the micro-scale, the meso-scale and the macro-scale. The chapters follow this classification. The book will explain in detail many tricks of the trade of some of the most important methods and techniques that are used to simulate materials on the perspective levels of spatial and temporal resolution. Case studies are occasionally included to further illustrate some methods or theoretical considerations. Example applications for all techniques are provided, some of which are from the author’s own contributions to some of the research areas. Methods are explained, if possible, on the basis of the original publications but also references to standard text books established in the various fields are mentioned.
Computational Granular Dynamics : Models and Algorithms
Computer simulations not only belong to the most important methods for the theoretical investigation of granular materials, but also provide the tools that have enabled much of the expanding research by physicists and engineers. The present book is intended to serve as an introduction to the application of numerical methods to systems of granular particles. Accordingly, emphasis is placed on a general understanding of the subject rather than on the presentation of the latest advances in numerical algorithms. Although a basic knowledge of C++ is needed for the understanding of the numerical methods and algorithms in the book, it avoids usage of elegant but complicated algorithms to remain accessible for those who prefer to use a different programming language. While the book focuses more on models than on the physics of granular material, many applications to real systems are presented.
Machine learning and its application to reacting flows: ml and combustion
These two fields, ML and turbulent combustion, have large body of work and knowledge on their own, and this book brings them together and explain the complexities and challenges involved in applying ML techniques to simulate and study reacting flows. This is important as to the world’s total primary energy supply (TPES), since more than 90% of this supply is through combustion technologies and the non-negligible effects of combustion on environment. Although alternative technologies based on renewable energies are coming up, their shares for the TPES is are less than 5% currently and one needs a complete paradigm shift to replace combustion sources. The book covers the current state of the art in these two topics and outlines the challenges involved, merits and drawbacks of using ML for turbulent combustion simulations including avenues which can be explored to overcome the challenges.
