Download or read book Explicit solvent effects on protein physics written by Giovanni Salvi and published by Sudwestdeutscher Verlag Fur Hochschulschriften AG. This book was released on 2009 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding stands as one of the major interdisciplinary challenges of the last fifteen years, involving biology, chemistry, medicine and physics. In this book solvent effects, and the related hydrophobic effect, on proteins are investigated. Using a simple lattice model of proteins, in which the solvent is semi-explicitly taken into account, thermodynamical quantities can be investigated and the crucial role the solvent plays in protein folding can be demonstrated. Of particular relevance is our observation that a simple model, in which the potential energy is described in terms of the interactions between amino-acids only, does not correctly reproduce solvent effects. Approaches like this, in which solvent effects are treated implicitly, are commonly employed in many of more sophisticated models for protein folding dynamics. Our results are then of great importance as they suggest the treatment of the solvent in these models may need to be re-examined.
Download or read book Theory and Simulation of Explicit Solvent Effects on Protein Folding in Vitro and in Vivo written by Jeremy L. England and published by . This book was released on 2009 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Self Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Continuum Solvation Models in Chemical Physics written by Benedetta Mennucci and published by John Wiley & Sons. This book was released on 2008-02-28 with total page 636 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the theory and applications of continuum solvation models. The main focus is on the quantum-mechanical version of these models, but classical approaches and combined or hybrid techniques are also discussed. Devoted to solvation models in which reviews of the theory, the computational implementation Solvation continuum models are treated using the different points of view from experts belonging to different research fields Can be read at two levels: one, more introductive, and the other, more detailed (and more technical), on specific physical and numerical aspects involved in each issue and/or application Possible limitations or incompleteness of models is pointed out with, if possible, indications of future developments Four-colour representation of the computational modeling throughout.
Download or read book Solvent Effects on Chemical Phenomena written by Edward Amis and published by Elsevier. This book was released on 2012-12-02 with total page 487 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solvent Effects on Chemical Phenomena, Volume I discusses the developments in the understanding of solvent effects on chemical phenomena in solution. This five-chapter volume begins with a discussion on the general concepts of various solvation types, including positive and negative, inner and outer sphere, and mixed component. The subsequent chapter deals with the determination of the actual solvation number for single ions. A short list of the total effective hydration numbers of electrolytes determined from temperature dependence of proton shifts is also provided in this chapter. Another chapter presents a number of examples of the unusual properties of certain mixed aqueous systems. The solvent effects on reaction rates and mechanisms are highlighted in the concluding chapter. This chapter also covers various types of solvents, such as protic and dipolar aprotic. The enthalpy and entropy of activation in salvation and the Finkelstein reactions are also discussed. Research chemists and scientists, teachers, and students with courses in solution chemistry will greatly benefit from this volume.
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
Download or read book Protein Actions Principles and Modeling written by Ivet Bahar and published by Garland Science. This book was released on 2017-02-14 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Download or read book Physics of Molecular and Cellular Processes written by Krastan B. Blagoev and published by Springer Nature. This book was released on 2022-09-08 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a graduate-level introduction to quantitative concepts and methods in the science of living systems. It relies on a systems approach for understanding the physical principles operating in biology. Physical phenomena are treated at the appropriate spatio-temporal scale and phenomenological equations are used in order to reflect the system of interest. Biological details enter to the degree necessary for understanding specific processes, but in many cases the approach is not reductionist. This is in line with the approach taken by physics to many other complex systems. The book bridges the gap between graduate students’ general physics courses and research papers published in professional journals. It gives students the foundations needed for independent research in biological physics and for working in collaborations aimed at quantitative biology and biomedical research. Also included are modern mathematical and theoretical physics methods, giving the student a broad knowledge of tools that can shed light on the sophisticated mechanisms brought forth by evolution in biological systems. The content covers many aspects that have been the focus of active research over the past twenty years, reflecting the authors' experience as leading researchers and teachers in this field.
Download or read book Fluctuation Theory of Solutions written by Paul E. Smith and published by CRC Press. This book was released on 2016-04-19 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are essentially two theories of solutions that can be considered exact: the McMillan-Mayer theory and Fluctuation Solution Theory (FST). The first is mostly limited to solutes at low concentrations, while FST has no such issue. It is an exact theory that can be applied to any stable solution regardless of the number of components and their co
Download or read book New Algorithms for Macromolecular Simulation written by Benedict Leimkuhler and published by Springer Science & Business Media. This book was released on 2006-03-22 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Download or read book Advances in Chemical Physics Volume 150 written by Stuart A. Rice and published by John Wiley & Sons. This book was released on 2012-03-27 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Advances in Chemical Physics series the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series presents contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics. This volume explores: Multidimensional Incoherent Time-Resolved Spectroscopy and Complex Kinetics (Mark A. Berg) Complex Multiconfigurational Self-Consistent Field-Based Methods to Investigate Electron-Atom/Molecule Scattering Resonances (Kousik Samanta and Danny L. Yeager) Determination of Molecular Orientational Correlations in Disordered Systems from Diffraction Data (Szilvia Pothoczki, László Temleitner, and László Pusztai) Recent Advances in Studying Mechanical Properties of DNA (Reza Vafabakhsh, Kyung Suk Lee, and Taekjip Ha) Viscoelastic Subdiffusion: Generalized Langevin Equation Approach (Igor Goychuk) Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics (Xiongwu Wu, Ana Damjanovic, and Bernard R. Brooks)
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David Landau and published by Cambridge University Press. This book was released on 2021-07-29 with total page 583 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dealing with all aspects of Monte Carlo simulation of complex physical systems encountered in condensed matter physics and statistical mechanics, this book provides an introduction to computer simulations in physics. The 5th edition contains extensive new material describing numerous powerful algorithms and methods that represent recent developments in the field. New topics such as active matter and machine learning are also introduced. Throughout, there are many applications, examples, recipes, case studies, and exercises to help the reader fully comprehend the material. This book is ideal for graduate students and researchers, both in academia and industry, who want to learn techniques that have become a third tool of physical science, complementing experiment and analytical theory.
Download or read book Protein Structure Prediction written by Mohammed Zaki and published by Springer Science & Business Media. This book was released on 2007-09-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.
Download or read book Computational Approaches to Protein Dynamics written by Monika Fuxreiter and published by CRC Press. This book was released on 2014-12-24 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
Download or read book Physics at the Biomolecular Interface written by Ariel Fernández and published by Springer. This book was released on 2016-05-11 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines.
Download or read book Thermodynamics and Kinetics of Drug Binding written by György Keserü and published by John Wiley & Sons. This book was released on 2015-07-28 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: This practical reference for medicinal and pharmaceutical chemists combines the theoretical background with modern methods as well as applications from recent lead finding and optimization projects. Divided into two parts on the thermodynamics and kinetics of drug-receptor interaction, the text provides the conceptual and methodological basis for characterizing binding mechanisms for drugs and other bioactive molecules. It covers all currently used methods, from experimental approaches, such as ITC or SPR, right up to the latest computational methods. Case studies of real-life lead or drug development projects are also included so readers can apply the methods learned to their own projects. Finally, the benefits of a thorough binding mode analysis for any drug development project are summarized in an outlook chapter written by the editors.
Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.
