Computational Electrostatics for Biological Applications PDF Download

Author: Walter Rocchia
Publisher: Springer
ISBN: 3319122118
Category : Science
Languages : en
Pages : 306

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Book Description
This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biological Applications international meeting, which brought together researchers in computational disciplines to discuss and explore diverse methods to improve electrostatic calculations. Fostering an interdisciplinary approach to the description of complex physical and biological problems, this book encompasses contributions originating in the fields of geometry processing, shape modeling, applied mathematics, and computational biology and chemistry. The main topics covered are theoretical and numerical aspects of the solution of the Poisson-Boltzmann equation, surveys and comparison among geometric approaches to the modelling of molecular surfaces and related discretization and computational issues. It also includes a number of contributions addressing applications in biology, biophysics and nanotechnology. The book is primarily intended as a reference for researchers in the computational molecular biology and chemistry fields. As such, it also aims at becoming a key source of information for a wide range of scientists who need to know how modeling and computing at the molecular level may influence the design and interpretation of their experiments.

Author: Qiang Cui
Publisher: CRC Press
ISBN: 9814613932
Category : Science
Languages : en
Pages : 596

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Book Description
As computational hardware continues to develop at a rapid pace, quantitative computations are playing an increasingly essential role in the study of biomolecular systems. One of the most important challenges that the field faces is to develop the next generation of computational models that strike the proper balance of computational efficiency and accuracy, so that the problems of increasing complexity can be tackled in a systematic and physically robust manner. In particular, properly treating intermolecular interactions is fundamentally important for the reliability of all computational models. In this book, contributions by leading experts in the area of biomolecular simulations discuss cutting-edge ideas regarding effective strategies to describe many-body effects and electrostatics at quantum, classical, and coarse-grained levels. The goal of the book is to not only provide an up-to-date snapshot of the current simulation field but also stimulate exchange of ideas across different sub-fields of modern computational (bio)chemistry. The text will be a useful reference for the biomolecular simulation community and help attract talented young students into this exciting frontier of research.

Author: Wei Cai
Publisher: Cambridge University Press
ISBN: 1107021057
Category : Mathematics
Languages : en
Pages : 463

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Book Description
The first book of its kind to cover a wide range of computational methods for electromagnetic phenomena, from atomistic to continuum scales, this integrated and balanced treatment of mathematical formulations, algorithms and the underlying physics enables us to engage in innovative and advanced interdisciplinary computational research.

Author: J.S. Murray
Publisher: Elsevier
ISBN: 9780080536859
Category : Science
Languages : en
Pages : 664

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Book Description
Over the past 25 years, the molecular electrostatic potential has become firmly established as an effective guide to molecular interactions. With the recent advances in computational technology, it is currently being applied to a variety of important chemical and biological systems. Its range of applicability has expanded from primarily a focus on sites for electrophilic and nucleophilic attack to now include solvent effects, studies of zeolite, molecular cluster and crystal behavior, and the correlation and prediction of a wide range of macroscopic properties. Moreover, the increasing prominence of density functional theory has raised the molecular electrostatic potential to a new stature on a more fundamental conceptual level. It is rigorously defined in terms of the electron density, and has very interesting topological characteristics since it explicitly reflects opposing contributions from the nuclei and the electrons. This volume opens with a survey chapter by one of the original pioneers of the use of the electrostatic potential in studies of chemical reactivity, Jacopo Tomasi. Though the flow of the succeeding chapters is not stringently defined, the overall trend is that the emphasis changes gradually from methodology to applications. Chapters discussing more theoretical topics are placed near the end. Readers will find the wide variety of topics provided by an international group of authors both convincing and useful.

Author: A.H-D. Cheng
Publisher: WIT Press
ISBN: 1784660272
Category : Mathematics
Languages : en
Pages : 361

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Book Description
Containing the latest in a long line of conferences covering the most recent advances in Boundary Elements and Mesh Reduction Methods (BEM/MRM), this book contains an important chapter in the history of this important method used in science and engineering. The BEM/MRM conference has long been recognised as THE international forum on the technique. The proceedings of the conference therefore constitute a record of the development of the method, running from the initial successful development of boundary integral techniques into the BEM, a method that eliminates the need for an internal mesh, to the recent and most sophisticated Mesh Reduction and even Meshless Methods. Since the boundary elements, mesh reduction, and meshless methods are used in many engineering and scientific fields, the book will be of great interest to all engineers and scientists working within the areas of numerical analysis, boundary elements and meshless methods. Topics covered include: Advanced formulations; Advanced meshless and mesh reduction methods; Structural mechanics applications; Solid mechanics; Heat and mass transfer, Electrical engineering and electromagnetics; Computational methods; Fluid flow modelling; Damage mechanics and fracture; Dynamics and Vibrations Engineering applications.

Author: Kenny B. Lipkowitz
Publisher: John Wiley & Sons
ISBN: 0470126094
Category : Science
Languages : en
Pages : 482

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Book Description
Führende Experten auf dem Gebiet der Computer-Chemie präsentieren in dem fünften Band der erfolgreichen Reihe 'Reviews in Computational Chemistry' die neuesten Entwicklungen. Um den interessierten Chemiker auf dem aktuellen Stand zu halten, ist der Reihe im Anhang eine Liste mit der Software zum Thema beigefügt

Author: Om Silakari
Publisher: Academic Press
ISBN: 0128205474
Category : Medical
Languages : en
Pages : 398

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Book Description
Concepts and Experimental Protocols of Modelling and Informatics in Drug Design discusses each experimental protocol utilized in the field of bioinformatics, focusing especially on computer modeling for drug development. It helps the user in understanding the field of computer-aided molecular modeling (CAMM) by presenting solved exercises and examples. The book discusses topics such as fundamentals of molecular modeling, QSAR model generation, protein databases and how to use them to select and analyze protein structure, and pharmacophore modeling for drug targets. Additionally, it discusses data retrieval system, molecular surfaces, and freeware and online servers. The book is a valuable source for graduate students and researchers on bioinformatics, molecular modeling, biotechnology and several members of biomedical field who need to understand more about computer-aided molecular modeling. Presents exercises with solutions to aid readers in validating their own protocol Brings a thorough interpretation of results of each exercise to help readers compare them to their own study Explains each parameter utilized in the algorithms to help readers understand and manipulate various features of molecules and target protein to design their study

Author: John J. Correia
Publisher: Academic Press
ISBN: 9780080554945
Category : Science
Languages : en
Pages : 1014

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Book Description
Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vitro and their applications to cellular biology. Biophysical Tools for Biologists covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval. Describes techniques in the context of important biological problems Delineates critical steps and potential pitfalls for each method Includes full-color plates to illustrate techniques

Author:
Publisher: World Scientific
ISBN: 9811223246
Category : Science
Languages : en
Pages : 1495

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Book Description
This four-volume handbook gives a state-of-the-art overview of porous materials, from synthesis and characterization and simulation all the way to manufacturing and industrial applications. The editors, coming from academia and industry, are known for their didactic skills as well as their technical expertise. Coordinating the efforts of 37 expert authors in 14 chapters, they construct the story of porous carbons, ceramics, zeolites and polymers from varied viewpoints: surface and colloidal science, materials science, chemical engineering, and energy engineering. Volumes 1 and 2 cover the fundamentals of preparation, characterisation, and simulation of porous materials. Working from the fundamentals all the way to the practicalities of industrial production processes, the subjects include hierarchical materials, in situ and operando characterisation using NMR, X-Ray scattering and tomography, state-of-the-art molecular simulations of adsorption and diffusion in crystalline nanoporous materials, as well as the emerging areas of bio-artificing and drug delivery. Volume 3 focuses on porous materials in industrial separation applications, including adsorption separation, membrane separation, and osmotic distillation. Finally, and highly relevant to tomorrow's energy challenges, Volume 4 explains the energy engineering aspects of applying porous materials in supercapacitors, fuel cells, batteries, electrolysers and sub-surface energy applications.The text contains many high-quality colourful illustrations and examples, as well as thousands of up-to-date references to peer-reviewed articles, reports and websites for further reading. This comprehensive and well-written handbook is a must-have reference for universities, research groups and companies working with porous materials.Related Link(s)

Author: Adam Liwo
Publisher: Springer Science & Business Media
ISBN: 3642285546
Category : Technology & Engineering
Languages : en
Pages : 810

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Book Description
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.