Coarse Grained Modeling Of Biomolecules

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Coarse-Grained Modeling of Biomolecules

Author : Garegin A. Papoian
Publisher : CRC Press
Page : 430 pages
File Size : 42,7 Mb
Release : 2017-10-30
Category : Science
ISBN : 9781466576179

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Coarse-Grained Modeling of Biomolecules by Garegin A. Papoian Pdf

"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.

Coarse-Grained Modeling of Biomolecules

Author : Garegin A. Papoian
Publisher : CRC Press
Page : 436 pages
File Size : 47,5 Mb
Release : 2017-10-30
Category : Science
ISBN : 9781315356709

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Coarse-Grained Modeling of Biomolecules by Garegin A. Papoian Pdf

"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.

Coarse-Graining of Condensed Phase and Biomolecular Systems

Author : Gregory A. Voth
Publisher : CRC Press
Page : 492 pages
File Size : 44,6 Mb
Release : 2008-09-22
Category : Science
ISBN : 9781420059564

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Coarse-Graining of Condensed Phase and Biomolecular Systems by Gregory A. Voth Pdf

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Author : Adam Liwo
Publisher : Springer
Page : 851 pages
File Size : 42,9 Mb
Release : 2018-12-19
Category : Technology & Engineering
ISBN : 9783319958439

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo Pdf

This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 381 pages
File Size : 41,5 Mb
Release : 2012
Category : Biomolecules
ISBN : 9781849734615

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Innovations in Biomolecular Modeling and Simulations by Tamar Schlick Pdf

This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.

Hybrid Biomolecular Modeling

Author : Slavica Jonic,Osamu Miyashita,Isabelle Callebaut
Publisher : Frontiers Media SA
Page : 128 pages
File Size : 48,5 Mb
Release : 2019-01-24
Category : Electronic
ISBN : 9782889456994

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Hybrid Biomolecular Modeling by Slavica Jonic,Osamu Miyashita,Isabelle Callebaut Pdf

Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.

Practical Aspects of Computational Chemistry V

Author : Jerzy Leszczynski,Manoj K. Shukla
Publisher : Springer Nature
Page : 292 pages
File Size : 50,7 Mb
Release : 2021-10-21
Category : Science
ISBN : 9783030832445

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Practical Aspects of Computational Chemistry V by Jerzy Leszczynski,Manoj K. Shukla Pdf

This book presents contributions on a wide range of computational research applied to fields ranging from molecular systems to bulk structures. This volume highlights current trends in modern computational chemistry and discusses the development of theoretical methodologies, state-of-the-art computational algorithms and their practical applications. This volume is part of a continuous effort by the editors to document recent advances by prominent researchers in the area of computational chemistry. Most of the chapters are contributed by invited speakers and participants to International annual conference “Current Trends in Computational Chemistry”, organized by Jerzy Leszczynski, one of the editors of the current volume. This conference series has become an exciting platform for eminent theoretical and computational chemists to discuss their recent findings and is regularly honored by the presence of Nobel laureates. Topics covered in the book include reactive force-field methodologies, coarse-grained modeling, DNA damage radiosensitizers, modeling and simulation of surfaces and interfaces, non-covalent interactions, and many others. The book is intended for theoretical and computational chemists, physical chemists, material scientists and those who are eager to apply computational chemistry methods to problems of chemical and physical importance. It is a valuable resource for undergraduate, graduate and PhD students as well as for established researchers.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 380 pages
File Size : 51,6 Mb
Release : 2012-05-24
Category : Science
ISBN : 9781849735049

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Innovations in Biomolecular Modeling and Simulations by Tamar Schlick Pdf

The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Biomolecular and Bioanalytical Techniques

Author : Vasudevan Ramesh
Publisher : John Wiley & Sons
Page : 576 pages
File Size : 50,7 Mb
Release : 2019-06-10
Category : Science
ISBN : 9781119483960

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Biomolecular and Bioanalytical Techniques by Vasudevan Ramesh Pdf

An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.

Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics

Author : Xiakun Chu,Yong Wang,Pengfei Tian,Wenfei Li,Davide Mercadante
Publisher : Frontiers Media SA
Page : 164 pages
File Size : 54,6 Mb
Release : 2022-01-07
Category : Science
ISBN : 9782889719921

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Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics by Xiakun Chu,Yong Wang,Pengfei Tian,Wenfei Li,Davide Mercadante Pdf

Modeling of Biomolecules and Protein Based Materials

Author : Mark Branchk
Publisher : Unknown
Page : 290 pages
File Size : 45,9 Mb
Release : 2013-04
Category : Biomolecules
ISBN : 1781543100

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Modeling of Biomolecules and Protein Based Materials by Mark Branchk Pdf

Over the past 40 years the field of molecular simulations has evolved from picoseconds studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In this book, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques.

Modeling Solvent Environments

Author : Michael Feig
Publisher : John Wiley & Sons
Page : 334 pages
File Size : 50,6 Mb
Release : 2009-12-09
Category : Science
ISBN : 9783527629268

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Modeling Solvent Environments by Michael Feig Pdf

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.

Functional Properties of Advanced Engineering Materials and Biomolecules

Author : Felipe A. La Porta,Carlton A. Taft
Publisher : Springer Nature
Page : 778 pages
File Size : 43,8 Mb
Release : 2021-05-17
Category : Technology & Engineering
ISBN : 9783030622268

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Functional Properties of Advanced Engineering Materials and Biomolecules by Felipe A. La Porta,Carlton A. Taft Pdf

This book shows how a small toolbox of experimental techniques, physical chemistry concepts as well as quantum/classical mechanics and statistical methods can be used to understand, explain and even predict extraordinary applications of these advanced engineering materials and biomolecules. It highlights how improving the material foresight by design, including the fundamental understanding of their physical and chemical properties, can provide new technological levels in the future.

Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

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 : 45,6 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.