Many Body Effects And Electrostatics In Biomolecules
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Many Body Effects And Electrostatics In Biomolecules
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Author : Qiang Cui
language : en
Publisher: CRC Press
Release Date : 2016-03-30
Many Body Effects And Electrostatics In Biomolecules written by Qiang Cui and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-03-30 with Science categories.
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.
Multiscale Modeling From Macromolecules To Cell Opportunities And Challenges Of Biomolecular Simulations
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Author : Valentina Tozzini
language : en
Publisher: Frontiers Media SA
Release Date : 2020-10-27
Multiscale Modeling From Macromolecules To Cell Opportunities And Challenges Of Biomolecular Simulations written by Valentina Tozzini and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-10-27 with Science categories.
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.
Electrostatics Of Soft And Disordered Matter
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Author : David S. Dean
language : en
Publisher: CRC Press
Release Date : 2014-05-02
Electrostatics Of Soft And Disordered Matter written by David S. Dean and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-05-02 with Science categories.
Recently, there has been a surge of activity to elucidate the behavior of highly charged soft matter and Coulomb fluids in general. Such systems are ubiquitous, especially in biological matter where the length scale and the strength of the interaction between highly charged biomolecules are governed by strong electrostatic effects. Several interesting limits have been discovered in the parameter space of highly charged many-particle Coulomb matter where analytical progress is possible and completely novel and unexpected results have been obtained. One of the challenges in highly charged matter is to correctly describe systems with finite coupling strength in the transition regime between weak and strong couplings. After studying the fluctuations of both, several theories have been developed that describe this experimentally highly relevant regime. At the same time, computer simulation algorithms and computing power have advanced to the level where all-ion simulations, including many-body and polarization effects, are possible; the new theories thus can be subjected to numerical confirmation. Another important question is the effect of the structural disorder on electrostatic interactions. It has recently been demonstrated, both theoretically and experimentally, that charge disorder can impose long-range interaction between charged or even uncharged surfaces. These interactions might become very significant in biological processes. Filling a void in the literature, this volume cross-pollinates different theoretical and simulation approaches with new experiments and ties together the low temperature, high coupling constant, and disorder parameters in a unified description of the electrostatic interactions, which largely determine the stability and conformations of most important biological macromolecules. With striking graphical illustrations, the book presents a unified view of the current advances in the field of Coulomb (bio)colloidal systems, building on previous literature that summarized the field over 20 years ago. Leading scientists in the field offer a detailed introduction to different modern methods in statistical physics of Coulomb systems. They detail various approaches to elucidate the behavior of strongly charged soft matter. They also provide experimental and theoretical descriptions of disorder effects in Coulomb systems, which have not been discussed in any other book.
Computational Approaches For Studying Enzyme Mechanism
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Author :
language : en
Publisher: Academic Press
Release Date : 2016-08-04
Computational Approaches For Studying Enzyme Mechanism written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-04 with Medical categories.
Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. Focuses on computational approaches for studying enzyme mechanism Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers
Fragmentation Toward Accurate Calculations On Complex Molecular Systems
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Author : Mark S. Gordon
language : en
Publisher: John Wiley & Sons
Release Date : 2017-10-23
Fragmentation Toward Accurate Calculations On Complex Molecular Systems written by Mark S. Gordon and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-23 with Science categories.
Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.
Coherent Multidimensional Spectroscopy
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Author : Minhaeng Cho
language : en
Publisher: Springer
Release Date : 2019-08-06
Coherent Multidimensional Spectroscopy written by Minhaeng Cho and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-08-06 with Science categories.
This book will fulfill the needs of time-domain spectroscopists who wish to deepen their understanding of both the theoretical and experimental features of this cutting-edge spectroscopy technique. Coherent Multidimensional Spectroscopy (CMDS) is a state-of-the-art technique with applications in a variety of subjects like chemistry, molecular physics, biochemistry, biophysics, and material science. Due to dramatic advancements of ultrafast laser technologies, diverse multidimensional spectroscopic methods utilizing combinations of THz, IR, visible, UV, and X-ray radiation sources have been developed and used to study real time dynamics of small molecules in solutions, proteins and nucleic acids in condensed phases and membranes, single and multiple excitons in functional materials like semiconductors, quantum dots, and solar cells, photo-excited states in light-harvesting complexes, ions in battery electrolytes, electronic and conformational changes in charge or proton transfer systems, and excess electrons and protons in water and biological systems.
Applied Theoretical Organic Chemistry
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Author : Tantillo Dean J
language : en
Publisher: World Scientific
Release Date : 2018-03-07
Applied Theoretical Organic Chemistry written by Tantillo Dean J and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-03-07 with Science categories.
This book provides state-of-the-art information on how studies in applied theoretical organic chemistry are conducted. It highlights the many approaches and tools available to those interested in using computational chemistry to predict and rationalize structures and reactivity of organic molecules. Chapters not only describe theoretical techniques in detail, but also describe recent applications and offer practical advice. Authored by many of the world leaders in the field of applied theoretical chemistry, this book is perfect for both practitioners of computational chemistry and synthetic and mechanistic organic chemists curious about applying computational techniques to their research. Contents: Modeling Organic Reactions — General Approaches, Caveats, and Concerns (Stephanie R Hare, Brandi M Hudson and Dean J Tantillo)Overview of Computational Methods for Organic Chemists (Edyta M Greer and Kitae Kwon)Brief History of Applied Theoretical Organic Chemistry (Steven M Bachrach)Solvation (Carlos Silva Lopez and Olalla Nieto Faza)Conformational Searching for Complex, Flexible Molecules (Alexander C Brueckner, O Maduka Ogba, Kevin M Snyder, H Camille Richardson and Paul Ha-Yeon Cheong)NMR Prediction (Kelvin E Jackson and Robert S Paton)Energy Decomposition Analysis and Related Methods (Israel Fernández)Systems with Extensive Delocalization (L Zoppi and K K Baldridge)Modern Treatments of Aromaticity (Judy I-Chia Wu)Weak Intermolecular Interactions (Rajat Maji and Steven E Wheeler)Predicting Reaction Pathways from Reactants (Romain Ramozzi, W M C Sameera and Keiji Morokuma)Unusual Potential Energy Surfaces and Nonstatistical Dynamic Effects (Charles Doubleday)The Distortion/Interaction Model for Analysis of Activation Energies of Organic Reactions (K N Houk, Fang Liu, Yun-Fang Yang and Xin Hong)Spreadsheet-Based Computational Predictions of Isotope Effects (O Maduka Ogba, John D Thoburn and Daniel J O'Leary)Stereoelectronic Effects: Analysis by Computational and Theoretical Methods (Gabriel dos Passos Gomes and Igor Alabugin)pKa Prediction (Yijie Niu and Jeehiun K Lee)Issues Particular to Organometallic Reactions (Gang Lu, Huiling Shao, Humair Omer and Peng Liu)Computationally Modeling Nonadiabatic Dynamics and Surface Crossings in Organic Photoreactions (Arthur Winter)Challenges in Predicting Stereoselectivity (Elizabeth H Krenske) Readership: Practitioners of computational chemistry and synthetic and mechanistic organic chemists curious about applying computational techniques to their research. Keywords: Organic Chemistry;Theoretical Chemistry;Stereoselectivity;NMR Prediction;pKa Prediction;Organic PhotoreactionsReview: Key Features: A particular strength is the mix of theoretical background, informative examples and practical advice providedChapters are authored by many of world leaders in the field of applied theoretical chemistry
Amber 2021
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Author : David A. Case
language : en
Publisher: University of California, San Francisco
Release Date : 2021-06-13
Amber 2021 written by David A. Case and has been published by University of California, San Francisco this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-13 with Computers categories.
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Electrical Interactions In Molecular Biophysics
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Author : Raymond Gabler
language : en
Publisher: Elsevier
Release Date : 2012-12-02
Electrical Interactions In Molecular Biophysics written by Raymond Gabler and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-02 with Science categories.
Electrical Interactions in Molecular Biophysics: An Introduction deals with electrical interactions between biomolecules and therefore encompasses two disciplines, molecular biology and physics. The emphasis is on the electrical nature of biochemical or molecular biological reactions. The principles of electrostatics are used to explain some of the basic units of structure on a molecular level. Comprised of nine chapters, this book opens with an overview of the concepts and structures of biochemistry, with particular reference to different structural biochemical groups and how they are used as building blocks in forming molecules. The following chapters discuss the basics of elementary electrostatics; dielectric constants and dipoles; the dipole moments of biomolecules; van der Waals forces; and Debye-Huckel theory. Water and water structure are also considered from a physical standpoint. The final chapter is devoted to experimental techniques that rely upon the electrical properties of biomolecules and explains what types of information can be obtained from each experimental form. This monograph will be of interest to students and practitioners in biochemistry, molecular biology, biophysics, or microbiology.
Amber 2022
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Author : David A. Case
language : en
Publisher: University of California, San Francisco
Release Date : 2022-04-28
Amber 2022 written by David A. Case and has been published by University of California, San Francisco this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-28 with Computers categories.
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools22, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.