Download or read book A Mathematical Approach to Protein Biophysics written by L. Ridgway Scott and published by Springer. This book was released on 2017-12-04 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores quantitative aspects of protein biophysics and attempts to delineate certain rules of molecular behavior that make atomic scale objects behave in a digital way. This book will help readers to understand how certain biological systems involving proteins function as digital information systems despite the fact that underlying processes are analog in nature. The in-depth explanation of proteins from a quantitative point of view and the variety of level of exercises (including physical experiments) at the end of each chapter will appeal to graduate and senior undergraduate students in mathematics, computer science, mechanical engineering, and physics, wanting to learn about the biophysics of proteins. L. Ridgway Scott has been Professor of Computer Science and of Mathematics at the University of Chicago since 1998, and the Louis Block Professor since 2001. He obtained a B.S. degree (Magna Cum Laude) from Tulane University in 1969 and a PhD degree in Mathematics from the Massachusetts Institute of Technology in 1973. Professor Scott has published over 130 papers and three books, extending over biophysics, parallel computing and fundamental computing aspects of structural mechanics, fluid dynamics, nuclear engineering, and computational chemistry. Ariel Fernández (born Ariel Fernández Stigliano) is an Argentinian-American physical chemist and mathematician. He obtained his Ph. D. degree in Chemical Physics from Yale University and held the Karl F. Hasselmann Endowed Chair Professorship in Bioengineering at Rice University. He is currently involved in research and entrepreneurial activities at various consultancy firms. Ariel Fernández authored three books on translational medicine and biophysics, and published 360 papers in professional journals. He holds two patents in the field of biotechnology.

Download or read book Fractal Symmetry of Protein Interior written by Anirban Banerji and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: The essential question that fractal dimensions attempt to answer is about the scales in Nature. For a system as non-idealistic and complex as a protein, studying scale-invariance becomes particularly important. Fractal Symmetry of Protein Interior investigates the diverse facets of the various scales at which we describe protein biophysical and biochemical phenomena. Following a thorough introduction to fractal dimensions, fractal-dimension-based approaches, that have been employed to study protein interior biophysical properties, are described. The focus is on the question “which scales are scale-invariant?” Investigations related to scaling of biophysical and biochemical behaviors may one day help us to formulate a fundamental theory about protein biophysics; which, in turn, may help us to understand fundamental principles of proteins.

Download or read book Mathematical Modeling of Protein Complexes written by Tatiana Koshlan and published by Springer. This book was released on 2018-09-06 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is devoted to the physical and mathematical modeling of the formation of complexes of protein molecules. The models developed show remarkable sensitivity to the amino acid sequences of proteins, which facilitates experimental studies and allows one to reduce the associated costs by reducing the number of measurements required according to the developed criteria. These models make it possible to reach a conclusion about the interactions between different amino acid chains and to identify more stable sites on proteins. The models also take the phosphorylation of amino acid residues into account. At the end of the book, the authors present possible directions of application of their physical and mathematical models in clinical medicine.

Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2010-12-17 with total page 623 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the tools and techniques of structural biophysics assume greater roles in biological research and a range of application areas, learning how proteins behave becomes crucial to understanding their connection to the most basic and important aspects of life. With more than 350 color images throughout, Introduction to Proteins: Structure, Function, and Motion presents a unified, in-depth treatment of the relationship between the structure, dynamics, and function of proteins. Taking a structural–biophysical approach, the authors discuss the molecular interactions and thermodynamic changes that transpire in these highly complex molecules. The text incorporates various biochemical, physical, functional, and medical aspects. It covers different levels of protein structure, current methods for structure determination, energetics of protein structure, protein folding and folded state dynamics, and the functions of intrinsically unstructured proteins. The authors also clarify the structure–function relationship of proteins by presenting the principles of protein action in the form of guidelines. This comprehensive, color book uses numerous proteins as examples to illustrate the topics and principles and to show how proteins can be analyzed in multiple ways. It refers to many everyday applications of proteins and enzymes in medical disorders, drugs, toxins, chemical warfare, and animal behavior. Downloadable questions for each chapter are available at CRC Press Online.

Download or read book Lectures on Statistical Physics and Protein Folding written by Kerson Huang and published by World Scientific. This book was released on 2005-05-30 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: ' This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestions on possible research directions, as developed by the author in collaboration with C C Lin. The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes. The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix. Contents:EntropyMaxwell–Boltzmann DistributionFree EnergyChemical PotentialPhase TransitionsKinetics of Phase TransitionsThe Order ParameterCorrelation FunctionStochastic ProcessesLangevin EquationThe Life ProcessSelf-AssemblyKinetics of Protein FoldingPower Laws in Protein FoldingSelf-Avoiding Walk and TurbulenceConvergent Evolution in Protein Folding Readership: Graduate students, researchers and academics interested in statistical physics and molecular biology. Keywords:Statistical Physics;Protein Folding;BiophysicsReviews:“My particularly favorite is the chapter on order parameters, explaining with simplicity and clarity this subject so frequently difficult and confusing for the beginning students … the book makes a strong attempt to place the protein folding problem where it really belongs — in the context of fundamental statistical mechanics. Whether the attempt is successful or not is a matter of a reader's opinion, but the very direction is both timely and welcome.”Professor Alexander Grosberg University of Minnesota '

Download or read book Mathematical Biophysics written by Andrew Rubin and published by Springer Science & Business Media. This book was released on 2013-11-26 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents concise descriptions and analysis of the classical and modern models used in mathematical biophysics. The authors ask the question "what new information can be provided by the models that cannot be obtained directly from experimental data?" Actively developing fields such as regulatory mechanisms in cells and subcellular systems and electron transport and energy transport in membranes are addressed together with more classical topics such as metabolic processes, nerve conduction and heart activity, chemical kinetics, population dynamics, and photosynthesis. The main approach is to describe biological processes using different mathematical approaches necessary to reveal characteristic features and properties of simulated systems. With the emergence of powerful mathematics software packages such as MAPLE, Mathematica, Mathcad, and MatLab, these methodologies are now accessible to a wide audience.

Download or read book Fractal Symmetry of Protein Exterior written by Anirban Banerji and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 62 pages. Available in PDF, EPUB and Kindle. Book excerpt: The essential question that fractal dimensions attempt to answer is about the scales in Nature. For a system as non-idealistic and complex as a protein, studying scale-invariance becomes particularly important. Fractal Symmetry of Protein Exterior investigates the diverse facets of the various scales at which we describe protein biophysical and biochemical phenomena. Although these ideas are entirely mathematical, mathematical expositions have been avoided, unless the use of some expressions becomes absolutely obligatory. A first chapter introduce into fractal dimensions, protein exteriors and to methods to study the roughness of surfaces. The main topics covered in the following chapters include: protein-protein interaction interfaces; protein surface-roughness and local shape as well as adhesion on protein and other rough biomolecular surfaces.

Download or read book Water in Biomechanical and Related Systems written by Adam Gadomski and published by Springer Nature. This book was released on 2021-04-21 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: The contributed volume puts emphasis on a superior role of water in (bio)systems exposed to a mechanical stimulus. It is well known that water plays an extraordinary role in our life. It feeds mammalian or other organism after distributing over its whole volume to support certain physiological and locomotive (friction-adhesion) processes to mention but two of them, both of extreme relevance. Water content, not only in the mammalian organism but also in other biosystems such as whether those of soil which is equipped with microbiome or the ones pertinent to plants, having their own natural network of water vessels, is always subjected to a force field.The decisive force field applied to the biosystems makes them biomechanically agitated irrespective of whether they are subjected to external or internal force-field conditions. It ought to be noted that the decisive mechanical factor shows up in a close relation with the space-and-time scale in which it is causing certain specific phenomena to occur.The scale problem, emphasizing the range of action of gravitational force, thus the millimeter or bigger force vs. distance scale, is supposed to enter the so-called macroscale approach to water transportation through soil or plants’ roots system. It is merely related to a percolation problem, which assumes to properly inspect the random network architecture assigned to the biosystems invoked. The capillarity conditions turn out to be of prior importance, and the porous-medium effect has to be treated, and solved in a fairly approximate way.The deeper the scale is penetrated by a force-exerting and hydrated agent the more non-gravitational force fields manifest. This can be envisaged in terms of the corresponding thermodynamic (non-Newtonian) forces, and the phenomena of interest are mostly attributed to suitable changes of the osmotic pressure. In low Reynolds number conditions, thus in the (sub)micrometer distance-scale zone, they are related with the corresponding viscosity changes of the aqueous, e.g. cytoplasmatic solutions, of semi-diluted and concentrated (but also electrolytic) characteristics. For example, they can be observed in articulating systems of mammals, in their skin, and to some extent, in other living beings, such as lizards, geckos or even insects. Through their articulating devices an external mechanical stimulus is transmitted from macro- to nanoscale, wherein the corresponding osmotic-pressure conditions apply. The content of the proposed work can be distributed twofold. First, the biomechanical mammalian-type (or, similar) systems with extraordinary relevance of water for their functioning will be presented, also including a presentation of water itself as a key physicochemical system/medium. Second, the suitably chosen related systems, mainly of soil and plant addressing provenience, will be examined thoroughly. As a common denominator of all of them, it is proposed to look at their hydrophobic and/or (de)hydration effects, and how do they impact on their basic mechanical (and related, such as chemo-mechanical or piezoelectric, etc.) properties. An additional tacit assumption employed throughout the monograph concerns statistical scalability of the presented biosystems which is equivalent to take for granted a certain similarity between local and global system’s properties, mostly those of mechanical nature. The presented work’s chapters also focus on biodiversity and ecological aspects in the world of animals and plants, and the related systems. The chapters’ contents underscore the bioinspiration as the key landmark of the proposed monograph.

Download or read book Biophysics for Therapeutic Protein Development written by Linda O. Narhi and published by Springer Science & Business Media. This book was released on 2013-02-26 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.

Download or read book Protein Geometry Classification Topology and Symmetry written by William R. Taylor and published by CRC Press. This book was released on 2004-10-01 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure. The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

Download or read book Structural Bioinformatics written by Forbes J. Burkowski and published by CRC Press. This book was released on 2008-10-30 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Beauty of Protein Structures and the Mathematics behind Structural BioinformaticsProviding the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure.Helps Students Go Further in Their Study of Structural Biolog

Download or read book Protein Physics written by Alexei V. Finkelstein and published by Elsevier. This book was released on 2016-06-22 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Physics: A Course of Lectures covers the most general problems of protein structure, folding and function. It describes key experimental facts and introduces concepts and theories, dealing with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states. The book systematically summarizes and presents the results of several decades of worldwide fundamental research on protein physics, structure, and folding, describing many physical models that help readers make estimates and predictions of physical processes that occur in proteins. New to this revised edition is the inclusion of novel information on amyloid aggregation, natively disordered proteins, protein folding in vivo, protein motors, misfolding, chameleon proteins, advances in protein engineering & design, and advances in the modeling of protein folding. Further, the book provides problems with solutions, many new and updated references, and physical and mathematical appendices. In addition, new figures (including stereo drawings, with a special appendix showing how to use them) are added, making this an ideal resource for graduate and advanced undergraduate students and researchers in academia in the fields of biophysics, physics, biochemistry, biologists, biotechnology, and chemistry. Fully revised and expanded new edition based on the latest research developments in protein physics Written by the world's top expert in the field Deals with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states Summarizes, in a systematic form, the results of several decades of worldwide fundamental research on protein physics and their structure and folding Examines experimental data on protein structure in the post-genome era

Download or read book A Mathematical Approach to Multilevel Multiscale Health Interventions written by Rodrick Wallace and published by World Scientific. This book was released on 2013 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, based on published studies, takes a unique perspective on the 30-year collapse of pharmaceutical industry productivity in the search for small molecule OC magic bulletOCO interventions. The relentless escalation of inflation-adjusted cost per approved medicine in the United States OCo from $200 million in 1950 to $1.2 billion in 2010 OCo has driven industry giants to, at best, slavish imitation in drug design, and at worst, abandonment of research and embracing of widespread fraud in consumer marketing.The book adapts formalism across a number of disciplines to the strategy for design of mutilevel interventions, focusing first on molecular, cellular, and larger scale examples, and then extending the argument to the simplifications provided by the dominant role of social and cultural structures and processes in individual and population patterns of health and illness.In place of OC magic bulletsOCO, we must now apply OC magic strategiesOCO that act across both the scale and level of organization. This book provides an introductory roadmap to the new tools that will be needed for the design of such strategies."

Download or read book Protein Folding Kinetics written by Bengt Nölting and published by Springer Science & Business Media. This book was released on 2005-12-05 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: First methods book which includes many detailed descriptions Absolutely needed and thus timely for the scientific community Comprises 15% more content and includes the mentioned special features

Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2007-08-24 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.

Download or read book A Mathematical Approach to Multilevel Multiscale Health Interventions written by Rodrick Wallace and published by World Scientific. This book was released on 2013-01-28 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, based on published studies, takes a unique perspective on the 30-year collapse of pharmaceutical industry productivity in the search for small molecule “magic bullet” interventions. The relentless escalation of inflation-adjusted cost per approved medicine in the United States — from $200 million in 1950 to $1.2 billion in 2010 — has driven industry giants to, at best, slavish imitation in drug design, and at worst, abandonment of research and embracing of widespread fraud in consumer marketing. The book adapts formalism across a number of disciplines to the strategy for design of mutilevel interventions, focusing first on molecular, cellular, and larger scale examples, and then extending the argument to the simplifications provided by the dominant role of social and cultural structures and processes in individual and population patterns of health and illness. In place of “magic bullets”, we must now apply “magic strategies” that act across both the scale and level of organization. This book provides an introductory roadmap to the new tools that will be needed for the design of such strategies. Contents:Beyond Magic BulletsExpanding the TheoryDynamic ‘Regression Models’An Evolutionary ExcursionExample: Mental DisordersExample: Protein FoldingExample: Glycome DeterminantsExample: Glycan/Lectin Logic GatesExample: IDP Logic GatesTreatmentHistory and HealthBeyond GlasperlenspielMathematical Appendix Readership: Undergraduate, graduate, researchers and professionals in biomathematics, biostatistics, mathematical modeling, complex systems and pharmaceuticals. Keywords:Cognition;Information Theory;Mathematical Model;Social EpidemiologyKey Features:The book synthesizes published, peer-reviewed articles to make explicit the complexity of human biology that underlies the catastrophic failure of the pharmaceutical industryIt develops a formalism of statistical tools for modeling and data analysis to explicitly address that multiscale and multilevel complexityIt uses the formalism to explore case histories at a number of scales

Download or read book BIOMAT 2006 written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: