Download or read book Many Body Effects and Electrostatics in Biomolecules written by Qiang Cui and published by CRC Press. This book was released on 2016-03-30 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Multiscale Modeling From Macromolecules to Cell Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational Approaches for Studying Enzyme Mechanism written by and published by Academic Press. This book was released on 2016-08-04 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Fragmentation Toward Accurate Calculations on Complex Molecular Systems written by Mark S. Gordon and published by John Wiley & Sons. This book was released on 2017-10-23 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Coherent Multidimensional Spectroscopy written by Minhaeng Cho and published by Springer. This book was released on 2019-08-06 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Electrostatics of Soft and Disordered Matter written by David S. Dean and published by CRC Press. This book was released on 2014-05-02 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Applied Theoretical Organic Chemistry written by Tantillo Dean J and published by World Scientific. This book was released on 2018-03-07 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Amber 2021 written by David A. Case and published by University of California, San Francisco. This book was released on 2021-06-13 with total page 959 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Amber 2022 written by David A. Case and published by University of California, San Francisco. This book was released on 2022-04-28 with total page 998 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Amber 2023 written by David A. Case and published by University of California, San Francisco. This book was released on 2023-04-30 with total page 1016 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] 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: AmberTools23, 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.

Download or read book Coarse Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.

Download or read book Electrical Interactions in Molecular Biophysics written by Raymond Gabler and published by Elsevier. This book was released on 2012-12-02 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational Approaches in Physics written by Maria Fyta and published by Morgan & Claypool Publishers. This book was released on 2016-11-01 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches in Physics reviews computational schemes which are used in the simulations of physical systems. These range from very accurate ab initio techniques up to coarse-grained and mesoscopic schemes. The choice of the method is based on the desired accuracy and computational efficiency. A bottom-up approach is used to present the various simulation methods used in Physics, starting from the lower level and the most accurate methods, up to particle-based ones. The book outlines the basic theory underlying each technique and its complexity, addresses the computational implications and issues in the implementation, as well as present representative examples. A link to the most common computational codes, commercial or open source is listed in each chapter. The strengths and deficiencies of the variety of techniques discussed in this book are presented in detail and visualization tools commonly used to make the simulation data more comprehensive are also discussed. In the end, specific techniques are used as bridges across different disciplines. To this end, examples of different systems tackled with the same methods are presented. The appendices include elements of physical theory which are prerequisites in understanding the simulation methods.

Download or read book Electrostatics of Atoms and Molecules written by Shridhar R. Gadre and published by Universities Press. This book was released on 2000 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces the subject of molecular electrostatics to postgraduate students, teachers and young researchers in chemistry, physics and biology. It discusses rigorous as well as applied aspects of the molecular electrostatic potential (MESP) and provides an essence of relevant mathematical arguments, without going into detailed derivations. A number of color illustrations highlight the salient features of MESP.

Download or read book Electrostatic Effects in Soft Matter and Biophysics written by Christian Holm and published by Springer. This book was released on 2001-11-30 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soft Condensed Matter commonly deals with materials that are mechanically soft and, more importantly, particularly prone to thermal fluctuation effects. Charged soft matter systems are especially interesting: they can be manufactured artificially as polyelectrolytes to serve as superabsorbers in dypers, as flocculation and retention agents, as thickeners and gelling agents, and as oil-recovery process aids. They are also abundant in living organisms, mostly performing important structural (e.g. membranes) and functional (e.g. DNA) tasks. The book describes the many areas in soft matter and biophysics where electrostatic interactions play an important role. It offers in-depth coverage of recent theoretical approaches, advances in computer simulation, and novel experimental techniques. Readership: Advanced undergraduate level in physics, physical chemistry, and theoretical biochemistry.

Download or read book Advances in Quantum Chemistry written by and published by Elsevier. This book was released on 2023-09-28 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Quantum Chemistry, Volume 88 presents the latest ongoing research at the forefront of Electronic structure theory. Chapters in the updated release include Spin-constrained Hartree-Fock and the generator coordinate method for the 2-site Hubbard model, Analytical evaluation of Hylleraas-CI Coulomb and Hybrid two-center Integrals over Slater orbitals, Hartree-Fock-Roothaan Theory of Molecular Compton Profiles Via Position Space Method, Analysis of Research Trend on the Molecular Integrals Over Slater Type Orbitals, An efficient approximation for accelerating convergence of numerical power series, Results for the 1D-Schroedinger equation, The aims and objectives of algebraic molecular orbital theory, and much more. Includes new theoretical methods Provides state-of-the art electron correlation, methods and effects Covers the challenge of excited electronic states

Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations