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Author: Sidney Yip
Publisher: Springer Science & Business Media
ISBN: 1402032862
Category : Science
Languages : en
Pages : 2903
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Book Description
The first reference of its kind in the rapidly emerging field of computational approachs to materials research, this is a compendium of perspective-providing and topical articles written to inform students and non-specialists of the current status and capabilities of modelling and simulation. From the standpoint of methodology, the development follows a multiscale approach with emphasis on electronic-structure, atomistic, and mesoscale methods, as well as mathematical analysis and rate processes. Basic models are treated across traditional disciplines, not only in the discussion of methods but also in chapters on crystal defects, microstructure, fluids, polymers and soft matter. Written by authors who are actively participating in the current development, this collection of 150 articles has the breadth and depth to be a major contributor toward defining the field of computational materials. In addition, there are 40 commentaries by highly respected researchers, presenting various views that should interest the future generations of the community. Subject Editors: Martin Bazant, MIT; Bruce Boghosian, Tufts University; Richard Catlow, Royal Institution; Long-Qing Chen, Pennsylvania State University; William Curtin, Brown University; Tomas Diaz de la Rubia, Lawrence Livermore National Laboratory; Nicolas Hadjiconstantinou, MIT; Mark F. Horstemeyer, Mississippi State University; Efthimios Kaxiras, Harvard University; L. Mahadevan, Harvard University; Dimitrios Maroudas, University of Massachusetts; Nicola Marzari, MIT; Horia Metiu, University of California Santa Barbara; Gregory C. Rutledge, MIT; David J. Srolovitz, Princeton University; Bernhardt L. Trout, MIT; Dieter Wolf, Argonne National Laboratory.
Author: Sidney Yip
Publisher: Springer Science & Business Media
ISBN: 1402032862
Category : Science
Languages : en
Pages : 2903
Get Book Here
Book Description
The first reference of its kind in the rapidly emerging field of computational approachs to materials research, this is a compendium of perspective-providing and topical articles written to inform students and non-specialists of the current status and capabilities of modelling and simulation. From the standpoint of methodology, the development follows a multiscale approach with emphasis on electronic-structure, atomistic, and mesoscale methods, as well as mathematical analysis and rate processes. Basic models are treated across traditional disciplines, not only in the discussion of methods but also in chapters on crystal defects, microstructure, fluids, polymers and soft matter. Written by authors who are actively participating in the current development, this collection of 150 articles has the breadth and depth to be a major contributor toward defining the field of computational materials. In addition, there are 40 commentaries by highly respected researchers, presenting various views that should interest the future generations of the community. Subject Editors: Martin Bazant, MIT; Bruce Boghosian, Tufts University; Richard Catlow, Royal Institution; Long-Qing Chen, Pennsylvania State University; William Curtin, Brown University; Tomas Diaz de la Rubia, Lawrence Livermore National Laboratory; Nicolas Hadjiconstantinou, MIT; Mark F. Horstemeyer, Mississippi State University; Efthimios Kaxiras, Harvard University; L. Mahadevan, Harvard University; Dimitrios Maroudas, University of Massachusetts; Nicola Marzari, MIT; Horia Metiu, University of California Santa Barbara; Gregory C. Rutledge, MIT; David J. Srolovitz, Princeton University; Bernhardt L. Trout, MIT; Dieter Wolf, Argonne National Laboratory.
Author: Grisell Díaz Leines
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
"The biological functions of proteins are ultimately governed by the dynamical properties of their large conformational transitions rooted on multidimensional free energy landscapes. Straightforward molecular dynamics simulation provides a mechanistically detailed picture of conformational transitions, but is hampered by the long timescales of these processes, which are rare events compared to the molecular timescales. In order to overcome these difficulties, we present in this thesis a new method, path-metadynamics, for the study of rare events. Path-metadynamics aims to explore high dimensional free energy landscapes and determine local likely transition pathways. The formalism works within the framework of a history-dependent bias potential applied to a flexible path-variable. Control of the sampling of the orthogonal modes recovers the average path and the minimum free energy path as limiting cases. Simultaneously the bias potential estimates the free energy profile along the path. The method has trivial scaling with the number of order parameters and this makes it suitable for the study of complex transitions. We have applied path-metadynamics to investigate the partial unfolding of a relevant photoreceptor, the photoactive yellow protein, and the formation/dissociation mechanism of a coiled coil, the leucine zipper domain. Our results demonstrate that path-metadynamics enables the calculation of rate constants, the localization of transition states, and the mapping of the free energy along a transition path described on a high-dimensional space. The likely transition paths obtained provide unique molecular insight about the protein conformational changes investigated. This approach opens a new way for studying complex rare events transitions."--Samenvatting auteur.
Author: Abby L. Parrill
Publisher: John Wiley & Sons
ISBN: 1118407776
Category : Science
Languages : en
Pages : 570
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Book Description
The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protein Folding Pathways Assessing Structural Predictions of Protein-Protein Recognition Kinetic Monte Carlo Simulation of Electrochemical Systems Reactivity and Dynamics at Liquid Interfaces
Author: Wolfgang E. Nagel
Publisher: Springer Nature
ISBN: 3031179374
Category : Computers
Languages : en
Pages : 516
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Book Description
This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2021. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to computer science with a special emphasis on industrially relevant applications. Presenting findings of one of Europe’s leading systems, this volume covers a wide variety of applications that deliver a high level of sustained performance. The book covers the main methods in high-performance computing. Its outstanding results in achieving the best performance for production codes are of particular interest for both scientists and engineers. The book comes with a wealth of color illustrations and tables of results.
Author: Mauro Ferrario
Publisher: Springer
ISBN: 3540352732
Category : Science
Languages : en
Pages : 716
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Book Description
This comprehensive collection of lectures by 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. Volume 2 is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems.
Author: Adriano D. Andricopulo
Publisher: Frontiers Media SA
ISBN: 2889766314
Category : Science
Languages : en
Pages : 325
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Book Description
Author: J. Chris Slootweg
Publisher: Springer Nature
ISBN: 3030588882
Category : Science
Languages : en
Pages : 404
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Book Description
This volume highlights the latest research in frustrated Lewis pair (FLP) chemistry and its applications. The contributions present the recent developments of the use of FLPs in asymmetric catalysis, polymer synthesis, homogeneous and heterogeneous catalysis, as well as demonstrating their use as a pedagogical tool. The book will be of interest to researchers in academia and industry alike.
Author:
Publisher: Academic Press
ISBN: 0128118776
Category : Science
Languages : en
Pages : 277
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Book Description
Structural and Mechanistic Enzymology, Volume 109, the latest release in the Advances in Protein Chemistry and Structural Biology series, is an essential resource for protein chemists. Chapters in this new volume include Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights from Molecular Dynamics Studies, Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design, Computational Biochemistry-Enzyme Mechanisms Explored, and A Paradigm for C-H Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase. This series presents new information on protocols and analysis of proteins, with each volume guest edited by leading experts in a broad range of protein-related topics. This volume presents state-of-the-art contributions, providing insights into the relationship between enzyme structure, catalysis, and function. Provides cutting-edge developments in protein chemistry and structural biology Features new information about protocols and analysis of proteins Contains chapters written by authorities in their respective fields Targeted to a wide audience of researchers, specialists and students
Author: Ke-li Han
Publisher: Springer Science & Business Media
ISBN: 3319029703
Category : Medical
Languages : en
Pages : 488
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Book Description
This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Author: Javier Luque
Publisher: Royal Society of Chemistry
ISBN: 1849733538
Category : Medical
Languages : en
Pages : 443
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Book Description
This title covers a wide range of topics relevant to the development of drugs. It provides a comprehensive description of the major methodological strategies available for rational drug discovery.
