Foundations of Biochemistry and Biophysics – serie

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.

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.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. This book describes the building blocks of understanding from a reasonable but not high-level technical language viewpoint, employing the perspective of a clinical physician. It brings together concepts from five specific branches of physics relevant to biology and medicine, namely, biophysics, classical electromagnetism, thermodynamics, systems biology and quantum mechanics. Key Features: Broad and up-to-date overview of the field of metabolism, especially connecting the spectrum of topics that range from modern physical underpinnings with cell biology to clinical practice. Provides a deeper basic science and interdisciplinary understanding of biological systems that broaden the perspectives and therapeutic problem solving. Introduces the concept of the Physiological Fitness Landscape, which is inspired by the physics of phase transitionsThis first volume in a two-volume set, primarily targets an audience of clinical and science students, biomedical researchers and physicians who would benefit from understanding each other’s language.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. This book connects these insights to what causes them to go awry in the context of unhealthy human behaviors and aging, aiming to buttress scientific creativity. It also provides links between the art and science of medicine that strengthens problem-solving in patient care. New and important discoveries in the area of metabolic health and metabolic diseases are discussed in exquisite detail.Key Features:Broad and up-to-date overview of the field of metabolic aspects of health and chronic disease development, especially connecting the spectrum of topics that range from molecular clocks to stress response to nuclear hormone receptors and the role of microbiota in human healthProvides a deeper basic science and interdisciplinary understanding of biological systems that broaden the perspectives and therapeutic problem solving by elaborating on the usefulness of the Physiological Fitness LandscapeDescribes the importance of insulin resistance in metabolic disease, especially diabetes but also includes links to cancer and Alzheimer’s diseaseExamines the process of aging from the perspective of metabolic decline illustrating it with the Physiological Fitness LandscapeThis book, the second volume in a two-volume set, primarily targets an audience of clinical and science students, biomedical researchers and physicians who would benefit from understanding each other’s language.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. This book describes the building blocks of understanding from a reasonable but not high-level technical language viewpoint, employing the perspective of a clinical physician. It brings together concepts from five specific branches of physics relevant to biology and medicine, namely, biophysics, classical electromagnetism, thermodynamics, systems biology and quantum mechanics. Key Features: Broad and up-to-date overview of the field of metabolism, especially connecting the spectrum of topics that range from modern physical underpinnings with cell biology to clinical practice. Provides a deeper basic science and interdisciplinary understanding of biological systems that broaden the perspectives and therapeutic problem solving. Introduces the concept of the Physiological Fitness Landscape, which is inspired by the physics of phase transitionsThis first volume in a two-volume set, primarily targets an audience of clinical and science students, biomedical researchers and physicians who would benefit from understanding each other’s language.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. This book connects these insights to what causes them to go awry in the context of unhealthy human behaviors and aging, aiming to buttress scientific creativity. It also provides links between the art and science of medicine that strengthens problem-solving in patient care. New and important discoveries in the area of metabolic health and metabolic diseases are discussed in exquisite detail.Key Features:Broad and up-to-date overview of the field of metabolic aspects of health and chronic disease development, especially connecting the spectrum of topics that range from molecular clocks to stress response to nuclear hormone receptors and the role of microbiota in human healthProvides a deeper basic science and interdisciplinary understanding of biological systems that broaden the perspectives and therapeutic problem solving by elaborating on the usefulness of the Physiological Fitness LandscapeDescribes the importance of insulin resistance in metabolic disease, especially diabetes but also includes links to cancer and Alzheimer’s diseaseExamines the process of aging from the perspective of metabolic decline illustrating it with the Physiological Fitness LandscapeThis book, the second volume in a two-volume set, primarily targets an audience of clinical and science students, biomedical researchers and physicians who would benefit from understanding each other’s language.

Praise for the prior edition"The author has done a magnificent job… this book is highly recommended for introducing biophysics to the motivated and curious undergraduate student."―Contemporary Physics"a terrific text … will enable students to understand the significance of biological parameters through quantitative examples―a modern way of learning biophysics." ―American Journal of Physics"A superb pedagogical textbook… Full-color illustrations aid students in their understanding" ―Midwest Book ReviewThis new edition provides a complete update to the most accessible yet thorough introduction to the physical and quantitative aspects of biological systems and processes involving macromolecules, subcellular structures, and whole cells. It includes two brand new chapters covering experimental techniques, especially atomic force microscopy, complementing the updated coverage of mathematical and computational tools. The authors have also incorporated additions to the multimedia component of video clips and animations, as well as interactive diagrams and graphs.Key Features:Illustrates biological examples with estimates and calculations of biophysical parameters.Features two brand-new chapters on experimental methods, a general overview and focused introduction to atomic force microscopy.Includes new coverage of important topics such as measures of DNA twist, images of nanoparticle assembly, and novel optical and electron nanoscopy. Provides a guide to investigating current expert biophysical research.Enhanced self-study problems and an updated glossary of terms.

"Taken together, the body of information contained in this book provides readers with a bird’s-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." –Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USANew experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined.Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.

This landmark collective work introduces the physical, chemical, and biological principles underlying photosynthesis: light absorption, excitation energy transfer, and charge separation. It begins with an introduction to properties of various pigments, and the pigment proteins in plant, algae, and bacterial systems. It addresses the underlying physics of light harvesting and key spectroscopic methods, including data analysis. It discusses assembly of the natural system, its energy transfer properties, and regulatory mechanisms. It also addresses light-harvesting in artificial systems and the impact of photosynthesis on our environment. The chapter authors are amongst the field’s world recognized experts.Chapters are divided into five main parts, the first focused on pigments, their properties and biosynthesis, and the second section looking at photosynthetic proteins, including light harvesting in higher plants, algae, cyanobacteria, and green bacteria. The third part turns to energy transfer and electron transport, discussing modeling approaches, quantum aspects, photoinduced electron transfer, and redox potential modulation, followed by a section on experimental spectroscopy in light harvesting research. The concluding final section includes chapters on artificial photosynthesis, with topics such as use of cyanobacteria and algae for sustainable energy production.Robert Croce is Head of the Biophysics Group and full professor in biophysics of photosynthesis/energy at Vrije Universiteit, Amsterdam. Rienk van Grondelle is full professor at Vrije Universiteit, Amsterdam.Herbert van Amerongen is full professor of biophysics in the Department of Agrotechnology and Food Sciences at Wageningen University, where he is also director of the MicroSpectroscopy Research Facility.Ivo van Stokkum is associate professor in the Department of Physics and Astronomy, Faculty of Sciences, at Vrije Universiteit, Amsterdam.

Introductory Science of Alcoholic Beverages provides readers an engaging introduction to the science behind beer, wine, and spirits. It illustrates not only the chemical principles that underlie what alcoholic beverages are, why they are the way they are and what they contain, but also frames them within the context of historical and societal developments.Discussed chapter topics include introductions to beer, wine, and spirits; the principles behind fermentation and distillation; and overviews of how each beverage class is made. The chapters highlight the unique chemistries that lend beer, wine, and spirits their individuality, as well as the key chemicals that impart their characteristic aroma and flavor profiles. This book goes beyond focused descriptions of individual alcoholic beverages by summarizing their common chemical lineage and illuminating the universal scientific principles that underpin them. It will be of interest to students of physics and chemistry, as well as enthusiasts and connoisseurs of beer, wine, and spirits.

Introductory Science of Alcoholic Beverages provides readers an engaging introduction to the science behind beer, wine, and spirits. It illustrates not only the chemical principles that underlie what alcoholic beverages are, why they are the way they are and what they contain, but also frames them within the context of historical and societal developments.Discussed chapter topics include introductions to beer, wine, and spirits; the principles behind fermentation and distillation; and overviews of how each beverage class is made. The chapters highlight the unique chemistries that lend beer, wine, and spirits their individuality, as well as the key chemicals that impart their characteristic aroma and flavor profiles. This book goes beyond focused descriptions of individual alcoholic beverages by summarizing their common chemical lineage and illuminating the universal scientific principles that underpin them. It will be of interest to students of physics and chemistry, as well as enthusiasts and connoisseurs of beer, wine, and spirits.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. The first volumeconnects these insights to what causes them to go awry in the context of unhealthy human behaviors and aging, aiming to buttress scientific creativity. It also provides links between the art and science of medicine that strengthens problem-solving in patient care. New and important discoveries in the area of metabolic health and metabolic diseases are discussed in exquisite detail.The second volume describes the building blocks of understanding from a reasonable but not high-level technical language viewpoint, employing the perspective of a clinical physician. It brings together concepts from five specific branches of physics relevant to biology and medicine, namely, biophysics, classical electromagnetism, thermodynamics, systems biology and quantum mechanics.

Chronic disease states of aging should be viewed through the prism of metabolism and biophysical processes at all levels of physiological organization present in the human body. The first volumeconnects these insights to what causes them to go awry in the context of unhealthy human behaviors and aging, aiming to buttress scientific creativity. It also provides links between the art and science of medicine that strengthens problem-solving in patient care. New and important discoveries in the area of metabolic health and metabolic diseases are discussed in exquisite detail.The second volume describes the building blocks of understanding from a reasonable but not high-level technical language viewpoint, employing the perspective of a clinical physician. It brings together concepts from five specific branches of physics relevant to biology and medicine, namely, biophysics, classical electromagnetism, thermodynamics, systems biology and quantum mechanics.

The Compressible Fluid Physics of the Human Respiratory System provides a comprehensive exploration of the principles of fluid dynamics, classical mechanics, and their applications to complex systems such as human respiration. It dives into foundational concepts like Newtonian mechanics and stress-strain relationships while also addressing advanced topics such as compressible fluid flow, viscosity, and energy conservation. It uniquely combines classical principles with real-world phenomena, such as the behavior of gases, liquids, and solids under various forces and pressures. The inclusion of detailed mathematical derivations, historical context, and empirical models adds depth to the discussion. Its interdisciplinary approach makes it valuable for readers interested in physics, engineering, and biological sciences. This book is designed for a general audience with an interest in science and medicine irrespective of mathematical background.

The Compressible Fluid Physics of the Human Respiratory System provides a comprehensive exploration of the principles of fluid dynamics, classical mechanics, and their applications to complex systems such as human respiration. It dives into foundational concepts like Newtonian mechanics and stress-strain relationships while also addressing advanced topics such as compressible fluid flow, viscosity, and energy conservation. It uniquely combines classical principles with real-world phenomena, such as the behavior of gases, liquids, and solids under various forces and pressures. The inclusion of detailed mathematical derivations, historical context, and empirical models adds depth to the discussion. Its interdisciplinary approach makes it valuable for readers interested in physics, engineering, and biological sciences. This book is designed for a general audience with an interest in science and medicine irrespective of mathematical background.

"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 BristolThis 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.

"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. LouisThis 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.

This book gives an accessible, detailed overview on techniques of single molecule biophysics (SMB), showing how they are applied to numerous biological problems associated with understanding the molecular mechanisms of DNA replication, transcription, and translation, as well as functioning of molecular machines. It covers major single molecule imaging and probing techniques, highlighting key strengths and limitations of each method using recent examples. The chapters begin with a discussion of single molecule fluorescence techniques followed by an overview of the atomic force microscope and its use for direct time-lapse visualization of dynamics of molecular complexes at the nanoscale, as well as applications in measurements of interactions between molecules and mechanical properties of isolated molecules and their complexes. The next chapters address magnetic tweezers and optical tweezers, including instrumentation, fundamentals of operation, and applications. A final chapter turns to nanopore transport and nanopore-based DNA sequencing technology that will play a major role in next-generation genomics and healthcare applications.

Praise for the prior edition"The author has done a magnificent job… this book is highly recommended for introducing biophysics to the motivated and curious undergraduate student."―Contemporary Physics"a terrific text … will enable students to understand the significance of biological parameters through quantitative examples―a modern way of learning biophysics." ―American Journal of Physics"A superb pedagogical textbook… Full-color illustrations aid students in their understanding" ―Midwest Book ReviewThis new edition provides a complete update to the most accessible yet thorough introduction to the physical and quantitative aspects of biological systems and processes involving macromolecules, subcellular structures, and whole cells. It includes two brand new chapters covering experimental techniques, especially atomic force microscopy, complementing the updated coverage of mathematical and computational tools. The authors have also incorporated additions to the multimedia component of video clips and animations, as well as interactive diagrams and graphs.Key Features:Illustrates biological examples with estimates and calculations of biophysical parameters.Features two brand-new chapters on experimental methods, a general overview and focused introduction to atomic force microscopy.Includes new coverage of important topics such as measures of DNA twist, images of nanoparticle assembly, and novel optical and electron nanoscopy. Provides a guide to investigating current expert biophysical research.Enhanced self-study problems and an updated glossary of terms.

"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. LouisThis 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.

This book gives an accessible, detailed overview on techniques of single molecule biophysics (SMB), showing how they are applied to numerous biological problems associated with understanding the molecular mechanisms of DNA replication, transcription, and translation, as well as functioning of molecular machines. It covers major single molecule imaging and probing techniques, highlighting key strengths and limitations of each method using recent examples. The chapters begin with a discussion of single molecule fluorescence techniques followed by an overview of the atomic force microscope and its use for direct time-lapse visualization of dynamics of molecular complexes at the nanoscale, as well as applications in measurements of interactions between molecules and mechanical properties of isolated molecules and their complexes. The next chapters address magnetic tweezers and optical tweezers, including instrumentation, fundamentals of operation, and applications. A final chapter turns to nanopore transport and nanopore-based DNA sequencing technology that will play a major role in next-generation genomics and healthcare applications.

This landmark collective work introduces the physical, chemical, and biological principles underlying photosynthesis: light absorption, excitation energy transfer, and charge separation. It begins with an introduction to properties of various pigments, and the pigment proteins in plant, algae, and bacterial systems. It addresses the underlying physics of light harvesting and key spectroscopic methods, including data analysis. It discusses assembly of the natural system, its energy transfer properties, and regulatory mechanisms. It also addresses light-harvesting in artificial systems and the impact of photosynthesis on our environment. The chapter authors are amongst the field’s world recognized experts.Chapters are divided into five main parts, the first focused on pigments, their properties and biosynthesis, and the second section looking at photosynthetic proteins, including light harvesting in higher plants, algae, cyanobacteria, and green bacteria. The third part turns to energy transfer and electron transport, discussing modeling approaches, quantum aspects, photoinduced electron transfer, and redox potential modulation, followed by a section on experimental spectroscopy in light harvesting research. The concluding final section includes chapters on artificial photosynthesis, with topics such as use of cyanobacteria and algae for sustainable energy production.

"Taken together, the body of information contained in this book provides readers with a bird’s-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." –Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USANew experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined.Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.