Biomolecular Thermodynamics

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Biomolecular Thermodynamics

Author : Douglas Barrick
Publisher : CRC Press
Page : 553 pages
File Size : 47,5 Mb
Release : 2017-09-11
Category : Medical
ISBN : 9781315363028

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Biomolecular Thermodynamics by Douglas Barrick Pdf

"an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologically-relevant systems along with a practical focus.... the ample problems and tutorials throughout are much appreciated." –Tobin R. Sosnick, Professor and Chair of Biochemistry and Molecular Biology, University of Chicago "Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels." –Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University "a masterful tour de force.... Barrick's rigor and scholarship come through in every chapter." –Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis This book provides a comprehensive, contemporary introduction to developing a quantitative understanding of how biological macromolecules behave using classical and statistical thermodynamics. The author focuses on practical skills needed to apply the underlying equations in real life examples. The text develops mechanistic models, showing how they connect to thermodynamic observables, presenting simulations of thermodynamic behavior, and analyzing experimental data. The reader is presented with plenty of exercises and problems to facilitate hands-on learning through mathematical simulation. Douglas E. Barrick is a professor in the Department of Biophysics at Johns Hopkins University. He earned his Ph.D. in biochemistry from Stanford University, and a Ph.D. in biophysics and structural biology from the University of Oregon.

Biomolecular Thermodynamics

Author : Douglas Barrick
Publisher : CRC Press
Page : 954 pages
File Size : 50,7 Mb
Release : 2017-09-11
Category : Medical
ISBN : 9781439800201

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Biomolecular Thermodynamics by Douglas Barrick Pdf

"an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologically-relevant systems along with a practical focus.... the ample problems and tutorials throughout are much appreciated." –Tobin R. Sosnick, Professor and Chair of Biochemistry and Molecular Biology, University of Chicago "Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels." –Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University "a masterful tour de force.... Barrick's rigor and scholarship come through in every chapter." –Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis This book provides a comprehensive, contemporary introduction to developing a quantitative understanding of how biological macromolecules behave using classical and statistical thermodynamics. The author focuses on practical skills needed to apply the underlying equations in real life examples. The text develops mechanistic models, showing how they connect to thermodynamic observables, presenting simulations of thermodynamic behavior, and analyzing experimental data. The reader is presented with plenty of exercises and problems to facilitate hands-on learning through mathematical simulation. Douglas E. Barrick is a professor in the Department of Biophysics at Johns Hopkins University. He earned his Ph.D. in biochemistry from Stanford University, and a Ph.D. in biophysics and structural biology from the University of Oregon.

Biological Thermodynamics

Author : Donald T. Haynie
Publisher : Cambridge University Press
Page : 369 pages
File Size : 44,8 Mb
Release : 2008-02-14
Category : Science
ISBN : 9781139470896

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Biological Thermodynamics by Donald T. Haynie Pdf

This inter-disciplinary guide to the thermodynamics of living organisms has been thoroughly revised and updated to provide a uniquely integrated overview of the subject. Retaining its highly readable style, it will serve as an introduction to the study of energy transformation in the life sciences and particularly as an accessible means for biology, biochemistry and bioengineering undergraduate students to acquaint themselves with the physical dimension of their subject. The emphasis throughout the text is on understanding basic concepts and developing problem-solving skills. The mathematical difficulty increases gradually by chapter, but no calculus is required. Topics covered include energy and its transformation, the First Law of Thermodynamics, Gibbs free energy, statistical thermodynamics, binding equilibria and reaction kinetics. Each chapter comprises numerous illustrative examples taken from different areas of biochemistry, as well as a broad range of exercises and references for further study.

Biothermodynamics

Author : Urs von Stockar,Luuk A. M. van der Wielen
Publisher : CRC Press
Page : 632 pages
File Size : 45,5 Mb
Release : 2013-05-30
Category : Science
ISBN : 9781466582163

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Biothermodynamics by Urs von Stockar,Luuk A. M. van der Wielen Pdf

This book covers the fundamentals of the rapidly growing field of biothermodynamics, showing how thermodynamics can best be applied to applications and processes in biochemical engineering. It describes the rigorous application of thermodynamics in biochemical engineering to rationalize bioprocess development and obviate a substantial fraction of this need for tedious experimental work. As such, this book will appeal to a diverse group of readers, ranging from students and professors in biochemical engineering, to scientists and engineers, for whom it will be a valuable reference.

Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics

Author : Prakash Saudagar,Timir Tripathi
Publisher : Elsevier
Page : 560 pages
File Size : 50,8 Mb
Release : 2022-09-28
Category : Science
ISBN : 9780323993661

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Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics by Prakash Saudagar,Timir Tripathi Pdf

Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics presents the latest emerging technologies in spectroscopy and advances in established spectroscopic methods. The book presents a guide to research methods in biomolecular spectroscopy, providing comprehensive coverage of developments in the spectroscopic techniques used to study protein structure and dynamics. Seventeen chapters from leading researchers cover key aspects of spectroscopic methods, with each chapter covering structure, folding, and dynamics. This title will help researchers keep up-to-date on the latest novel methods and advances in established methods. Presents current, emerging, and evolving advances and applications of spectroscopic techniques in the study of biomolecules, including proteins and nucleic acids Discusses contemporary spectroscopic techniques used to study biomolecular structure, interaction, and dynamics

Introduction to Biomolecular Energetics

Author : Irving Klotz
Publisher : Elsevier
Page : 152 pages
File Size : 47,9 Mb
Release : 2012-12-02
Category : Science
ISBN : 9780323160995

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Introduction to Biomolecular Energetics by Irving Klotz Pdf

Introduction to Biomolecular Energetics Including Ligand-Receptor Interactions focuses on the concepts of energetics and their biological applications, including the study of ligand-receptor interactions. The book provides quantitative calculations and addresses topics that have become more prominent in the biochemical and related sciences in recent years, including the first and second laws of thermodynamics, the concept of entropy, free energy or chemical potential, group-transfer potential, physicochemical behavior, and enzyme kinetics. This volume is organized into 10 chapters, and it begins with an overview of the scope of energetics and two general approaches to the field: the classical or phenomenological approach and the statistical-molecular approach. The chapters that follow explore the concepts of energy and entropy in the context of the first and second laws of thermodynamics, along with the relationships between work, heat, energy and entropy as an index of exhaustion. The discussion then shifts to the free energy function and general procedures for computing standard free energies. The book also introduces the reader to the fundamental relationship between chemical potential (free energy) and concentration; high-energy bond and the concept of group-transfer potential; the use of thermodynamic methods in the analysis of physicochemical behavior; and statistical thermodynamics. The final chapter examines the number of ligands that are bound by the receptor entity, how strongly the ligands are held, and the molecular nature of the forces of ligand-receptor interaction. This book will be of interest to biologists and those who want to understand the principles of energetics governing biochemical changes.

The Thermodynamic Machinery of Life

Author : Michal Kurzynski
Publisher : Springer Science & Business Media
Page : 438 pages
File Size : 41,8 Mb
Release : 2006-07-09
Category : Science
ISBN : 9783540336549

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The Thermodynamic Machinery of Life by Michal Kurzynski Pdf

Thermodynamics was created in the ?rst half of the 19th century as a theory designed to explain the functioning of heat engines converting heat into mechanical work. In the course of time, while the scope of research in this ?eld was being extended to a wider and wider class of energy transformations, thermodynamics came to be considered as a general theory of machines identi?ed with energy transducers. Imp- tant progress in biochemistry in the ?rst half of the 20th century, and in molecular biology in the second half, made it possible to think of treating even living organisms as machines, at least on the subcellular level. However, success in applying thermodynamics to elucidate the phenomenon of life has been rather mitigated. Two reasons seem to be responsible for this unsatisfactory s- uation. Nineteenth century thermodynamics dealt only with simple (homogeneous) systems in complete equilibrium. Although during the 20th century a nonequilibrium thermodynamics was developed, sta- ing with the Onsager theory of linear response and ending with the Prigogine nonlinear theory of dissipative structures, these theories still concern the originally homogeneous systems. Because living organisms are complex systems with a historically frozen spatial and functional structure, a thermodynamics of both nonequilibrium and complex s- tems is needed for their description. The ?rst goal of the present book is to formulate the foundations of such a thermodynamics.

Biomolecular Kinetics

Author : Clive R. Bagshaw
Publisher : CRC Press
Page : 883 pages
File Size : 54,8 Mb
Release : 2017-10-04
Category : Medical
ISBN : 9781351646666

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Biomolecular Kinetics by Clive R. Bagshaw Pdf

"a gem of a textbook which manages to produce a genuinely fresh, concise yet comprehensive guide" –Mark Leake, University of York "destined to become a standard reference.... Not just a ‘how to’ handbook but also an accessible primer in the essentials of kinetic theory and practice." –Michael Geeves, University of Kent "covers the entire spectrum of approaches, from the traditional steady state methods to a thorough account of transient kinetics and rapid reaction techniques, and then on to the new single molecule techniques" –Stephen Halford, University of Bristol This illustrated treatment explains the methods used for measuring how much a reaction gets speeded up, as well as the framework for solving problems such as ligand binding and macromolecular folding, using the step-by-step approach of numerical integration. It is a thoroughly modern text, reflecting the recent ability to observe reactions at the single-molecule level, as well as advances in microfluidics which have given rise to femtoscale studies. Kinetics is more important now than ever, and this book is a vibrant and approachable entry for anyone who wants to understand mechanism using transient or single molecule kinetics without getting bogged down in advanced mathematics. Clive R. Bagshaw is Emeritus Professor at the University of Leicester, U.K., and Research Associate at the University of California at Santa Cruz, U.S.A.

Thermodynamics and Kinetics of Drug Binding

Author : György Keserü,David C. Swinney
Publisher : John Wiley & Sons
Page : 360 pages
File Size : 53,6 Mb
Release : 2015-03-09
Category : Medical
ISBN : 9783527673056

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Thermodynamics and Kinetics of Drug Binding by György Keserü,David C. Swinney Pdf

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.

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

Author : Adam Liwo
Publisher : Springer
Page : 851 pages
File Size : 54,7 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.

Nonequilibrium Thermodynamics

Author : Yasar Demirel
Publisher : Newnes
Page : 792 pages
File Size : 40,5 Mb
Release : 2013-12-16
Category : Technology & Engineering
ISBN : 9780444595812

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Nonequilibrium Thermodynamics by Yasar Demirel Pdf

Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, Third Edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapter on stochastic approaches to include the statistical thermodynamics, mesoscopic nonequilibrium thermodynamics, fluctuation theory, information theory, and modeling the coupled biochemical systems in thermodynamic analysis. This new addition also comes with more examples and practice problems. Informs and updates on all the latest developments in the field Contributions from leading authorities and industry experts A useful text for seniors and graduate students from diverse engineering and science programs to analyze some nonequilibrium, coupled, evolutionary, stochastic, and dissipative processes Highlights fundamentals of equilibrium thermodynamics, transport processes and chemical reactions Expands the theory of nonequilibrium thermodynamics and its use in coupled transport processes and chemical reactions in physical, chemical, and biological systems Presents a unified analysis for transport and rate processes in various time and space scales Discusses stochastic approaches in thermodynamic analysis including fluctuation and information theories Has 198 fully solved examples and 287 practice problems An Instructor Resource containing the Solution Manual can be obtained from the author: [email protected]

Structural Bioinformatics

Author : Jenny Gu,Philip E. Bourne
Publisher : John Wiley & Sons
Page : 1105 pages
File Size : 48,7 Mb
Release : 2011-09-20
Category : Science
ISBN : 9781118210567

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Structural Bioinformatics by Jenny Gu,Philip E. Bourne Pdf

Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics

Thermodynamics and Biophysics of Biomedical Nanosystems

Author : Costas Demetzos,Natassa Pippa
Publisher : Springer
Page : 475 pages
File Size : 42,7 Mb
Release : 2019-03-04
Category : Technology & Engineering
ISBN : 9789811309892

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Thermodynamics and Biophysics of Biomedical Nanosystems by Costas Demetzos,Natassa Pippa Pdf

This book highlights the recent advances of thermodynamics and biophysics in drug delivery nanosystems and in biomedical nanodevices. The up-to-date book provides an in-depth knowledge of bio-inspired nanotechnological systems for pharmaceutical applications. Biophysics and thermodynamics, supported by mathematics, are the locomotive by which the drug transportation and the targeting processes will be achieved under the light of the modern pharmacotherapy. They are considered as scientific tools that promote the understanding of physicochemical and thermotropic functionality and behavior of artificial cell membranes and structures like nanoparticulate systems. Therefore, this book focusses on new aspects of biophysics and thermodynamics as important elements for evaluating biomedical nanosystems, and it correlates their physicochemical, biophysical and thermodynamical behaviour with those of a living organism. In 2018, Prof. Demetzos was honored with an award by the Order of Sciences of the Academy of Athens for his scientific contribution in Pharmaceutical Nanotechnology.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 380 pages
File Size : 40,8 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.

Introduction to Macromolecular Binding Equilibria

Author : Charles P. Woodbury
Publisher : CRC Press
Page : 272 pages
File Size : 53,8 Mb
Release : 2007-11-08
Category : Science
ISBN : 9781420052992

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Introduction to Macromolecular Binding Equilibria by Charles P. Woodbury Pdf

Macromolecules in the body form noncovalent associations, such as DNA-protein or protein-protein complexes, that control and regulate numerous cellular functions. Understanding how changes in the concentration and conformation of these macromolecules can trigger physiological responses is essential for researchers developing drug therapies to treat diseases affected by these imbalances. Introduction to Macromolecular Binding Equilibria gives students in medicinal chemistry, pharmaceuticals, and bioengineering the necessary background in biophysical chemistry for research applications in drug discovery and development. Building upon a fundamental knowledge of calculus and physical chemistry, this compact, graduate-level text prepares students for advanced work in solution thermodynamics and binding phenomena and applying methods in this book to their own research. This book describes the underlying theory of binding phenomena and explains how to apply the binding polynomial approach for building models and interpreting data. It also covers practical considerations for setting up binding experiments and describes how to obtain true thermodynamic isotherms unbiased by model assumption via model-free analysis of binding data.