Statistical Physics for Biological Matter

Statistical Physics for Biological Matter
Author: Wokyung Sung
Publisher: Springer
Total Pages: 444
Release: 2018-10-19
Genre: Science
ISBN: 940241584X

This book aims to cover a broad range of topics in statistical physics, including statistical mechanics (equilibrium and non-equilibrium), soft matter and fluid physics, for applications to biological phenomena at both cellular and macromolecular levels. It is intended to be a graduate level textbook, but can also be addressed to the interested senior level undergraduate. The book is written also for those involved in research on biological systems or soft matter based on physics, particularly on statistical physics. Typical statistical physics courses cover ideal gases (classical and quantum) and interacting units of simple structures. In contrast, even simple biological fluids are solutions of macromolecules, the structures of which are very complex. The goal of this book to fill this wide gap by providing appropriate content as well as by explaining the theoretical method that typifies good modeling, namely, the method of coarse-grained descriptions that extract the most salient features emerging at mesoscopic scales. The major topics covered in this book include thermodynamics, equilibrium statistical mechanics, soft matter physics of polymers and membranes, non-equilibrium statistical physics covering stochastic processes, transport phenomena and hydrodynamics. Generic methods and theories are described with detailed derivations, followed by applications and examples in biology. The book aims to help the readers build, systematically and coherently through basic principles, their own understanding of nonspecific concepts and theoretical methods, which they may be able to apply to a broader class of biological problems.

Equilibrium and Nonequilibrium Statistical Mechanics: Principles and Concepts

Equilibrium and Nonequilibrium Statistical Mechanics: Principles and Concepts
Author: Avijit Lahiri
Publisher: Avijit Lahiri
Total Pages: 1623
Release: 2023-10-14
Genre: Science
ISBN:

Equilibrium and Non-equilibrium Statistical Mechanics is a source-book of great value to college and university students embarking upon a serious reading of Statistical Mechanics, and is likely to be of interest to teachers of the subject as well. Written in a lucid style, the book builds up the subject from basics, and goes on to quite advanced and modern developments, giving an overview of the entire framework of statistical mechanics. The equilibrium ensembles of quantum and classical statistical mechanics are introduced at length, indicating their relation to equilibrium states of thermodynamic systems, and the applications of these ensembles in the case of the ideal gas are worked out, pointing out the relevance of the ideal gas in respect of a number of real-life systems. The application to interacting systems is then taken up by way of explaining the virial expansion of a dilute gas. The book then deals with a number of foundational questions relating to the existence of the thermodynamic limit and to the equivalence of the various equilibrium ensembles. The relevance of the thermodynamic limit in explaining phase transitions is indicated with reference to the Yang-Lee theory and the Kirkwood-Salsburg equations for correlation functions. The statistical mechanics of interacting systems is then taken up again, with reference to the 1D and 2D Ising model and to the spin glass model of disordered systems. Applications of the Mean field theory are worked out, explaining the Landau-Ginzburg theory, which is then followed by the renormalization group approach to phase transitions. Interacting systems in the quantum context are referred to, addressing separately the cases of interacting bosons and fermions. The case of the weakly interacting bosons is explained in details, while the Landau theory for fermi liquids is also explained in outline. The book then goes on to a modern but readable account of non-equilibrium statistical mechanics, explaining the link with irreversible thermodynamcs. After an exposition of the Boltzmann equations and the linear response theory illustrated with reference to the hydrodynamic model, it explains the statistical mechanics of reduced systems, in the context of a number of reduction schemes. This is followed by an account of the relevance of dynamical chaos in laying down the foundations of classical statistical mechanics, where the SRB distributon is introduced in the context of non-equilibrium steady states, with reference to which the principle of minimum entropy production is explaned. A number of basic fluctuation relations are then worked out, pointing out their relation to irreversible thermodynamics. Finally, the book explains the relevance of quantum chaos in addressing foundational issues in quantum statistical mechanics, beginning with Berry’s conjecture and then going on to an exposition of the eigenstate thermalization (ETH) hypothesis, indicating how the latter is relevant in explaining the processes of equilibriation and thermalization in thermodynamic systems and their sub-systems.

Computational Biology

Computational Biology
Author: Ralf Blossey
Publisher: CRC Press
Total Pages: 276
Release: 2006-05-25
Genre: Computers
ISBN: 1420010786

Quantitative methods have a particular knack for improving any field they touch. For biology, computational techniques have led to enormous strides in our understanding of biological systems, but there is still vast territory to cover. Statistical physics especially holds great potential for elucidating the structural-functional relationships in bi

Entropy and Free Energy in Structural Biology

Entropy and Free Energy in Structural Biology
Author: Hagai Meirovitch
Publisher: CRC Press
Total Pages: 348
Release: 2020-08-14
Genre: Computers
ISBN: 1000072320

Nuclear Structure Physics connects to some of our fundamental questions about the creation of the universe and its basic constituents. At the same time, precise knowledge on the subject has led to the development of many important tools for humankind such as proton therapy and radioactive dating, among others. This book has chapters on some of the crucial and trending research topics in nuclear structure, including the nuclei lying on the extremes of spin, isospin and mass. A better theoretical understanding of these topics is important beyond the confines of the nuclear structure community. Additionally, the book will showcase the applicability and success of the different nuclear effective interaction parameters near the drip line, where hints for level reordering have already been seen, and where one can test the isospin-dependence of the interaction. The book offers comprehensive coverage of the most essential topics, including: • Nuclear Structure of Nuclei at or Near Drip-Lines • Synthesis challenges and properties of Superheavy nuclei • Nuclear Structure and Nuclear models - Ab-initio calculations, cluster models, Shell-model/DSM, RMF, Skyrme • Shell Closure, Magicity and other novel features of nuclei at extremes • Structure of Toroidal, Bubble Nuclei, halo and other exotic nuclei These topics are not only very interesting from a theoretical nuclear physics perspective but are also quite complimentary for ongoing nuclear physics experimental programs worldwide. The book chapters, written by experienced and well-known researchers/experts, will be helpful for master students, graduate students and researchers and serve as a standard and up-to-date research reference book on the topics covered.

Statistical Physics for Biological Matter

Statistical Physics for Biological Matter
Author: Wokyung Sung
Publisher:
Total Pages: 435
Release: 2018
Genre: Biophysics
ISBN: 9789402415858

This textbook covers a broad range of topics in statistical physics, including statistical mechanics (equilibrium and non-equilibrium), soft matter and fluid physics, for applications to biological phenomena at both cellular and macromolecular levels. Typical statistical physics courses cover ideal gases (classical and quantum) and interacting units of simple structures. In contrast, even simple biological fluids are solutions of macromolecules, the structures of which are very complex. This book fills this wide gap by providing appropriate content as well as by explaining the theoretical method that typifies good modeling, namely, the method of coarse-grained descriptions that extract the most salient features emerging at mesoscopic scales. The major topics covered in this book include thermodynamics, equilibrium statistical mechanics, soft matter physics of polymers and membranes, non-equilibrium statistical physics covering stochastic processes, transport phenomena and hydrodynamics. Generic methods and theories are described with detailed derivations, followed by applications and examples in biology. By systematically and coherently covering the basic principles, this book helps the readers to build up their understanding of nonspecific concepts and theoretical methods, which they may be able to apply to a broader class of biological problems. While intended as a graduate level textbook, it can also address the interested senior level undergraduate. In addition, it is suitable for those involved in research on biological systems or soft matter based on physics, particularly on statistical physics.

Statistical Physics of Biomolecules

Statistical Physics of Biomolecules
Author: Daniel M. Zuckerman
Publisher: CRC Press
Total Pages: 356
Release: 2010-06-02
Genre: Mathematics
ISBN: 1420073796

From the hydrophobic effect to protein-ligand binding, statistical physics is relevant in almost all areas of molecular biophysics and biochemistry, making it essential for modern students of molecular behavior. But traditional presentations of this material are often difficult to penetrate. Statistical Physics of Biomolecules: An Introduction brin

Non-equilibrium Statistical Mechanics - Satellite Meeting To Statphys 17 And 4th Medyfinol Conference

Non-equilibrium Statistical Mechanics - Satellite Meeting To Statphys 17 And 4th Medyfinol Conference
Author: Susana Hernandez
Publisher: World Scientific
Total Pages: 203
Release: 1990-05-01
Genre:
ISBN: 9814535451

This text provides a pedagogical tour through mechanics from Newton to Einstein with detailed explanations and a large number of worked examples. From the very beginning relativity is kept in mind, along with its relation to concepts of basic mechanics, such as inertia, escape velocity, Newton's potential, Kepler motion and curvature. The Lagrange and Hamilton formalisms are treated in detail, and extensive applications to central forces and rigid bodies are presented. After consideration of the motivation of relativity, the essential tensor calculus is developed, and thereafter Einstein's equation is solved for special cases with explicit presentation of calculational steps. The combined treatment of classical mechanics and relativity thus enables the reader to see the connection between Newton's gravitational potential, Kepler motion and Einstein's corrections, as well as diverse aspects of mechanics. The text addresses students and others pursuing a course in classical mechanics, as well as those interested in a detailed course on relativity.

Encyclopedia of Nonlinear Science

Encyclopedia of Nonlinear Science
Author: Alwyn Scott
Publisher: Routledge
Total Pages: 2881
Release: 2006-05-17
Genre: Reference
ISBN: 1135455570

In 438 alphabetically-arranged essays, this work provides a useful overview of the core mathematical background for nonlinear science, as well as its applications to key problems in ecology and biological systems, chemical reaction-diffusion problems, geophysics, economics, electrical and mechanical oscillations in engineering systems, lasers and nonlinear optics, fluid mechanics and turbulence, and condensed matter physics, among others.

Entropy and Free Energy in Structural Biology

Entropy and Free Energy in Structural Biology
Author: Hagai Meirovitch
Publisher: CRC Press
Total Pages: 374
Release: 2020-08-14
Genre: Computers
ISBN: 1000072304

Computer simulation has become the main engine of development in statistical mechanics. In structural biology, computer simulation constitutes the main theoretical tool for structure determination of proteins and for calculation of the free energy of binding, which are important in drug design. Entropy and Free Energy in Structural Biology leads the reader to the simulation technology in a systematic way. The book, which is structured as a course, consists of four parts: Part I is a short course on probability theory emphasizing (1) the distinction between the notions of experimental probability, probability space, and the experimental probability on a computer, and (2) elaborating on the mathematical structure of product spaces. These concepts are essential for solving probability problems and devising simulation methods, in particular for calculating the entropy. Part II starts with a short review of classical thermodynamics from which a non-traditional derivation of statistical mechanics is devised. Theoretical aspects of statistical mechanics are reviewed extensively. Part III covers several topics in non-equilibrium thermodynamics and statistical mechanics close to equilibrium, such as Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed as well. Part IV presents advanced simulation methods for polymers and protein systems, including techniques for conformational search and for calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating the absolute entropy, and methodologies for calculating the absolute free energy of binding are evaluated. Enhanced by a number of solved problems and examples, this volume will be a valuable resource to advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry biophysics, pharmacology, and computational biology.

A First Course in Systems Biology

A First Course in Systems Biology
Author: Eberhard Voit
Publisher: Garland Science
Total Pages: 480
Release: 2017-09-05
Genre: Computers
ISBN: 1351332945

A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.