Chemical Theory And Multiscale Simulation In Biomolecules

Author : Guohui Li
Publisher : Elsevier
Page : 399 pages
File Size : 54,6 Mb
Release : 2024-03-28
Category : Science
ISBN : 9780323959186

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Chemical Theory and Multiscale Simulation in Biomolecules by Guohui Li Pdf

Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. Presents computational theory alongside case studies to help readers understand the use of simulation in practice Includes extensive examples of different types of simulation methods and approaches to result analysis Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems

Author : W.F. van Gunsteren,P.K. Weiner,A.J. Wilkinson
Publisher : Springer Science & Business Media
Page : 633 pages
File Size : 48,7 Mb
Release : 2013-11-27
Category : Technology & Engineering
ISBN : 9789401711203

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Computer Simulation of Biomolecular Systems by W.F. van Gunsteren,P.K. Weiner,A.J. Wilkinson Pdf

The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...

Author : Anonim
Publisher : Academic Press
Page : 331 pages
File Size : 44,7 Mb
Release : 2014-10-11
Category : Science
ISBN : 9780128007891

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Biomolecular Modelling and Simulations by Anonim Pdf

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in biomolecular modelling and simulations Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables

Author : Richard B. Ross,Sanat Mohanty
Publisher : John Wiley & Sons
Page : 300 pages
File Size : 44,9 Mb
Release : 2008-02-04
Category : Science
ISBN : 9780470191668

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Multiscale Simulation Methods for Nanomaterials by Richard B. Ross,Sanat Mohanty Pdf

This book stems from the American Chemical Society symposium, Large Scale Molecular Dynamics, Nanoscale, and Mesoscale Modeling and Simulation: Bridging the Gap, that delved into the latest methodologies and applications for largescale, multiscale, and mesoscale modeling and simulation. It presents real-world applications of simulated and synthesized materials, including organic-, inorganic-, bio-, and nanomaterials, and helps readers determine the best method for their simulation. It gets novices up to speed quickly and helps experienced practitioners discover novel approaches and alternatives.

Author : Achi Brandt,Jerzy Bernholc,Kurt Binder
Publisher : Unknown
Page : 384 pages
File Size : 46,5 Mb
Release : 2001
Category : Chemistry
ISBN : STANFORD:36105110367567

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Multiscale Computational Methods in Chemistry and Physics by Achi Brandt,Jerzy Bernholc,Kurt Binder Pdf

This book brings together interdisciplinary contributions ranging from applied mathematics, theoretical physics, quantum chemistry and molecular biology, all addressing various facets of the problem to connect the many different scales that one has to deal with in the computer simulation of many systems of interest in chemistry (e.g. polymeric materials, biological molecules, clusters, surface and interface structure). Particular emphasis is on the "multigrid technique" and its applications, ranging from electronic structure calculations to the statistical mechanics of polymers.

Author : Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro
Publisher : Frontiers Media SA
Page : 235 pages
File Size : 50,8 Mb
Release : 2020-10-27
Category : Science
ISBN : 9782889661091

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Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro Pdf

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

Author : Darrin M. York,Tai-Sung Lee
Publisher : Springer Science & Business Media
Page : 426 pages
File Size : 50,7 Mb
Release : 2009-05-30
Category : Science
ISBN : 9781402099564

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Multi-scale Quantum Models for Biocatalysis by Darrin M. York,Tai-Sung Lee Pdf

“Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

Author : Dennis R. Salahub,Dongqing Wei
Publisher : Royal Society of Chemistry
Page : 411 pages
File Size : 52,6 Mb
Release : 2021-09-24
Category : Science
ISBN : 9781839164675

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Multiscale Dynamics Simulations by Dennis R. Salahub,Dongqing Wei Pdf

Over the past decade, great strides have been taken in developing methodologies that can treat more and more complex nano- and nano-bio systems embedded in complex environments. Multiscale Dynamics Simulations covers methods including DFT/MM-MD, DFTB and semi-empirical QM/MM-MD, DFT/MMPOL as well as Machine-learning approaches to all of the above. Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options so that they can better chart their course in the nano/bio world.

Author : Michael King,David Gee
Publisher : John Wiley & Sons
Page : 398 pages
File Size : 53,6 Mb
Release : 2010-03-30
Category : Science
ISBN : 9780470579824

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Multiscale Modeling of Particle Interactions by Michael King,David Gee Pdf

Discover how the latest computational tools are building our understanding of particle interactions and leading to new applications With this book as their guide, readers will gain a new appreciation of the critical role that particle interactions play in advancing research and developing new applications in the biological sciences, chemical engineering, toxicology, medicine, and manufacturing technology The book explores particles ranging in size from cations to whole cells to tissues and processed materials. A focus on recreating complex, real-world dynamical systems helps readers gain a deeper understanding of cell and tissue mechanics, theoretical aspects of multiscale modeling, and the latest applications in biology and nanotechnology. Following an introductory chapter, Multiscale Modeling of Particle Interactions is divided into two parts: Part I, Applications in Nanotechnology, covers: Multiscale modeling of nanoscale aggregation phenomena: applications in semiconductor materials processing Multiscale modeling of rare events in self-assembled systems Continuum description of atomic sheets Coulombic dragging and mechanical propelling of molecules in nanofluidic systems Molecular dynamics modeling of nanodroplets and nanoparticles Modeling the interactions between compliant microcapsules and patterned surfaces Part II, Applications in Biology, covers: Coarse-grained and multiscale simulations of lipid bilayers Stochastic approach to biochemical kinetics In silico modeling of angiogenesis at multiple scales Large-scale simulation of blood flow in microvessels Molecular to multicellular deformation during adhesion of immune cells under flow Each article was contributed by one or more leading experts and pioneers in the field. All readers, from chemists and biologists to engineers and students, will gain new insights into how the latest tools in computational science can improve our understanding of particle interactions and support the development of novel applications across the broad spectrum of disciplines in biology and nanotechnology.

Author : Anonim
Publisher : Marco Giulini
Page : 174 pages
File Size : 52,6 Mb
Release : 2022-05-16
Category : Science
ISBN : 8210379456XXX

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The mapping problem in coarse-grained modelling of biomolecules by Anonim Pdf

Author : Ilia A. Solov’yov,Andrey V. Korol,Andrey V. Solov’yov
Publisher : Springer
Page : 451 pages
File Size : 43,7 Mb
Release : 2017-05-16
Category : Science
ISBN : 9783319560878

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Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer by Ilia A. Solov’yov,Andrey V. Korol,Andrey V. Solov’yov Pdf

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).

Author : Michael Springborg
Publisher : Royal Society of Chemistry
Page : 228 pages
File Size : 40,5 Mb
Release : 2012-11-08
Category : Science
ISBN : 9781849734790

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Chemical Modelling by Michael Springborg Pdf

Chemical Modelling: Applications and Theory comprises critical literature reviews of all aspects of molecular modelling. Molecular modelling in this context refers to modelliing the structure, properties and reactions of atoms, molecules and materials. Each chapter provides a selective review of recent literature, incorporating sufficient historical perspective for the non-specialist to gain an understanding. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves with major developments in the area.

Author : Oren M. Becker,Martin Karplus
Publisher : Springer Science & Business Media
Page : 225 pages
File Size : 55,7 Mb
Release : 2006-06-26
Category : Science
ISBN : 9781402035876

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Guide to Biomolecular Simulations by Oren M. Becker,Martin Karplus Pdf

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. The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.

Author : William Graham Hoover,Carol Griswold Hoover
Publisher : World Scientific Publishing Company
Page : 324 pages
File Size : 42,7 Mb
Release : 2015-02-02
Category : Science
ISBN : 9789814656849

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Simulation and Control of Chaotic Nonequilibrium Systems by William Graham Hoover,Carol Griswold Hoover Pdf

This book aims to provide a lively working knowledge of the thermodynamic control of microscopic simulations, while summarizing the historical development of the subject, along with some personal reminiscences. Many computational examples are described so that they are well-suited to learning by doing. The contents enhance the current understanding of the reversibility paradox and are accessible to advanced undergraduates and researchers in physics, computation, and irreversible thermodynamics.

Author : Tanmoy Chakraborty,Ramon Carbo-Dorca
Publisher : CRC Press
Page : 635 pages
File Size : 49,5 Mb
Release : 2018-06-19
Category : Science
ISBN : 9781351170949

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Theoretical and Quantum Chemistry at the Dawn of the 21st Century by Tanmoy Chakraborty,Ramon Carbo-Dorca Pdf

This volume, edited by a well-known specialist in the field of theoretical chemistry, gathers together a selection of papers on theoretical chemistry within the themes of mathematical, computational, and quantum chemistry. The authors present a rich assembly of some of the most important current research in the field of quantum chemistry in modern times. In Quantum Chemistry at the Dawn of the 21st Century, the editors aim to replicate the tradition of the fruitful Girona Workshops and Seminars, held at the University of Girona, Italy, annually for many years, which offered important scientific gatherings focusing on quantum chemistry. This volume, like the workshops, showcases a large variety of quantum chemical contributions from different points of view from some of the leading scientists in the field today. This unique volume does not pretend to provide a complete overview of quantum chemistry, but it does provide a broad set of contributions by some of the leading scientists on the field, under the expert editorship of two leaders in the field.