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

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

Author: Valentina Tozzini

Publisher: Frontiers Media SA

Published: 2020-10-27

Total Pages: 235

ISBN-13: 2889661091

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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.


Coarse-Grained Modeling of Biomolecules

Coarse-Grained Modeling of Biomolecules

Author: Garegin A. Papoian

Publisher: CRC Press

Published: 2017-10-30

Total Pages: 430

ISBN-13: 1466576170

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"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.


Protein Self-Assembly

Protein Self-Assembly

Author: Jennifer J. McManus

Publisher: Humana

Published: 2020-08-08

Total Pages: 266

ISBN-13: 9781493996803

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This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.


Structure and Function of Intrinsically Disordered Proteins

Structure and Function of Intrinsically Disordered Proteins

Author: Peter Tompa

Publisher: CRC Press

Published: 2009-11-18

Total Pages: 362

ISBN-13: 1420078933

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The existence and functioning of intrinsically disordered proteins (IDPs) challenge the classical structure-function paradigm that equates function with a well-defined 3D structure. Uncovering the disordered complement of proteomes and understanding their functioning can extend the structure-function paradigm to herald new breakthroughs in drug dev


Solvation Thermodynamics

Solvation Thermodynamics

Author: Arieh Y. Ben-Naim

Publisher: Springer Science & Business Media

Published: 2013-03-09

Total Pages: 253

ISBN-13: 1475765509

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This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther modynamics alone. However, solvation is inherently a molecular pro cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 based on analysis at the molecular level. During the past ten years, I have introduced several new quantities which, in my opinion, should replace the conventional measures of solvation thermodynamics. To avoid confusing the new quantities with those referred to conventionally in the literature as standard quantities of solvation, I called these "nonconventional," "generalized," and "local" standard quantities and attempted to point out the advantages of these new quantities over the conventional ones.


Hydrogen Bond Networks

Hydrogen Bond Networks

Author: Marie-Claire Bellisent-Funel

Publisher: Springer

Published: 2014-03-14

Total Pages: 558

ISBN-13: 9789401583336

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The almost universal presence of water in our everyday lives and the very `common' nature of its presence and properties possibly deflects attention from the fact that it has a number of very unusual characteristics which, furthermore, are found to be extremely sensitive to physical parameters, chemical environment and other influences. Hydrogen-bonding effects, too, are not restricted to water, so it is necessary to investigate other systems as well, in order to understand the characteristics in a wider context. Hydrogen Bond Networks reflects the diversity and relevance of water in subjects ranging from the fundamentals of condensed matter physics, through aspects of chemical reactivity to structure and function in biological systems.


An Introduction to Tissue-Biomaterial Interactions

An Introduction to Tissue-Biomaterial Interactions

Author: Kay C. Dee

Publisher: John Wiley & Sons

Published: 2003-04-14

Total Pages: 250

ISBN-13: 0471461121

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An Introduction to Tissue-Biomaterial Interactions acquaints an undergraduate audience with the fundamental biological processes that influence these sophisticated, cutting-edge procedures. Chapters one through three provide more detail about the molecular-level events that happen at the tissue-implant interface, while chapters four through ten explore selected material, biological, and physiological consequences of these events. The importance of the body’s wound-healing response is emphasized throughout. Specific topics covered include:Structure and properties of biomaterials Proteins Protein-surface interactions Blood-biomaterial interactions Inflammation and infection The immune system Biomaterial responses to implantation Biomaterial surface engineering Intimal hyperplasia and osseointegration as examples of tissue-biomaterial interactions The text also provides extensive coverage of the three pertinent interfaces between the body and the biomaterial, between the body and the living cells, and between the cells and the biomaterial that are critical in the development of tissue-engineered products that incorporate living cells within a biomaterial matrix. Ideal for a one-semester, biomedical engineering course, An Introduction to Tissue-Biomaterial Interactions provides a solid framework for understanding today’s and tomorrow’s implantable biomedical devices.


Protein Structure, Stability, and Folding

Protein Structure, Stability, and Folding

Author: Kenneth P. Murphy

Publisher: Springer Science & Business Media

Published: 2008-02-04

Total Pages: 258

ISBN-13: 1592591930

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In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.


Computational Structural Biology

Computational Structural Biology

Author: Torsten Schwede

Publisher: World Scientific

Published: 2008

Total Pages: 790

ISBN-13: 9812778780

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This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.