Modeling Solvent Environments

Modeling Solvent Environments
Author: Michael Feig
Publisher: John Wiley & Sons
Total Pages: 334
Release: 2009-12-09
Genre: Science
ISBN: 3527629262

A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.

Protein Modelling

Protein Modelling
Author: Andrew Gamble
Publisher: Springer
Total Pages: 332
Release: 2014-11-13
Genre: Science
ISBN: 3319099760

In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.

Annual Reports in Computational Chemistry

Annual Reports in Computational Chemistry
Author: Ralph A. Wheeler
Publisher: Elsevier
Total Pages: 271
Release: 2008-10-30
Genre: Science
ISBN: 0080932789

Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry.* Broad coverage of computational chemistry and up-to-date information * Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings * Each chapter reviews the most recent literature on a specific topic of interest to computational chemists

Variational Methods in Molecular Modeling

Variational Methods in Molecular Modeling
Author: Jianzhong Wu
Publisher: Springer
Total Pages: 331
Release: 2016-12-17
Genre: Science
ISBN: 9811025029

This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical understanding rather than on rigorous mathematical derivations, the content is accessible to graduate students and researchers in the broad areas of materials science and engineering, chemistry, chemical and biomolecular engineering, applied mathematics, condensed-matter physics, without specific training in theoretical physics or calculus of variations.

Molecular Modeling and Dynamics of Bioinorganic Systems

Molecular Modeling and Dynamics of Bioinorganic Systems
Author: Lucia Banci
Publisher: Springer Science & Business Media
Total Pages: 471
Release: 2012-12-06
Genre: Science
ISBN: 9401151717

A unique selection of papers on the most recent progress in the modelling of biological molecules containing metal ions. New approaches and techniques in this field are allowing researchers to discuss structures, electronic properties and reaction mechanisms of metalloproteins on the basis of computational studies. The book discusses different approaches in the development of new force fields and their application to the computation of the structures, electronic properties and dynamics of bioinorganic compounds as well as quantum mechanical and integrated QM/MM methods for understanding the function of metalloenzymes and the calculation of electrostatic interactions.

Chemical Theory and Multiscale Simulation in Biomolecules

Chemical Theory and Multiscale Simulation in Biomolecules
Author: Guohui Li
Publisher: Elsevier
Total Pages: 399
Release: 2024-03-29
Genre: Science
ISBN: 0323959180

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

Molecular Modeling of Geochemical Reactions

Molecular Modeling of Geochemical Reactions
Author: James D. Kubicki
Publisher: John Wiley & Sons
Total Pages: 440
Release: 2016-07-22
Genre: Science
ISBN: 1118845161

Molecular processes in nature affect human health, the availability of resources and the Earth’s climate. Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible. Molecular Modeling of Geochemical Reactions: An Introduction applies computational chemistry to geochemical problems. Chapters focus on geochemical applications in aqueous, petroleum, organic, environmental, bio- and isotope geochemistry, covering the fundamental theory, practical guidance on applying techniques, and extensive literature reviews in numerous geochemical sub-disciplines. Topics covered include: • Theory and Methods of Computational Chemistry • Force Field Application and Development • Computational Spectroscopy • Thermodynamics • Structure Determination • Geochemical Kinetics This book will be of interest to graduate students and researchers looking to understand geochemical processes on a molecular level. Novice practitioners of molecular modelling, experienced computational chemists, and experimentalists seeking to understand this field will all find information and knowledge of use in their research.

Process Modeling, Simulation, and Environmental Applications in Chemical Engineering

Process Modeling, Simulation, and Environmental Applications in Chemical Engineering
Author: Bharat A. Bhanvase
Publisher: CRC Press
Total Pages: 344
Release: 2016-10-14
Genre: Science
ISBN: 1315342227

In this valuable volume, new and original research on various topics on chemical engineering and technology is presented on modeling and simulation, material synthesis, wastewater treatment, analytical techniques, and microreactors. The research presented here can be applied to technology in food, paper and pulp, polymers, petrochemicals, surface coatings, oil technology aspects, among other uses. The book is divided into five sections: modeling and simulation environmental applications materials and applications processes and applications analytical methods Topics include: modeling and simulation of chemical processes process integration and intensification separation processes advances in unit operations and processes chemical reaction engineering fuel and energy advanced materials CFD and transport processes wastewater treatment The valuable research presented here will be of interest to researchers, scientists, industry practitioners, as well as upper-level students.

Solvents and Solvent Effects in Organic Chemistry

Solvents and Solvent Effects in Organic Chemistry
Author: Christian Reichardt
Publisher: John Wiley & Sons
Total Pages: 722
Release: 2011-08-04
Genre: Science
ISBN: 3527642137

Now in its 4th edition, this book remains the ultimate reference for all questions regarding solvents and solvent effects in organic chemistry. Retaining its proven concept, there is no other book which covers the subject in so much depth, the handbook is completely updated and contains 15% more content, including new chapters on "Solvents and Green chemistry", "Classification of Solvents by their Environmental Impact", and "Ionic Liquids". An essential part of every organic chemist's library.

Physics-Based and Data-Driven Mulitiscale Modeling of the Structural Formation in Macromolecular Systems (Band 25)

Physics-Based and Data-Driven Mulitiscale Modeling of the Structural Formation in Macromolecular Systems (Band 25)
Author: Philipp Nicolas Depta
Publisher: Cuvillier Verlag
Total Pages: 297
Release: 2024-02-27
Genre:
ISBN: 3736969724

In order to improve knowledge on macromolecular structural formation and self-assembly, this work proposes a physics-based and data-driven multiscale modeling framework capable of describing structural formation on micro-meter and milli-second scales near molecular-level precision. The framework abstracts macromolecules as anisotropic unit objects and models the interactions and environment using data-driven approaches. The models are parameterized in a bottom-up fashion and validated top-down by comparison with literature and collaborator data for self-assembly of three model system: alginate gelation, hepatitis B virus capsids, and the pyruvate dehydrogenase complex.