Computational biology has developed rapidly during the last two decades following the genomic revolution which culminated in the sequencing of the human genome. More than ever it has developed into a field which embraces computational methods from different branches of the exact sciences: pure and applied mathematics, computer science, theoretical physics. This Second Edition provides a solid introduction to the techniques of statistical mechanics for graduate students and researchers in computational biology and biophysics. Material has been reorganized to clarify equilbrium and nonequilibrium aspects of biomolecular systems Content has been expanded, in particular in the treatment of the electrostatic interactions of biomolecules and the application of non-equilibrium statistical mechanics to biomolecules New network-based approaches for the study of proteins are presented. All treated topics are put firmly in the context of the current research literature, allowing the reader to easily follow an individual path into a specific research field. Exercises and Tasks accompany the presentations of the topics with the intention of enabling the readers to test their comprehension of the developed basic concepts.

The mechanics underlying the form and structure of biological tissues is being increasingly investigated and appreciated, with new results appearing at a fast pace. Cellular Patterns covers the salient elements of this thriving field of research in a textbook style, including both historic landmark results and recent achievements. By building on concepts such as packing, confinement, surface tension, and elastic instabilities, the book explains the structure and the shape of sheet-like and bulk tissues by adapting the mechanics of continuous media to living matter. It reviews experimental results and empirical laws, and wherever possible, it discusses more than a single theoretical interpretation of a given phenomenon. The in-depth treatment of technical details, the many boxes summarizing essential physical and biological ideas, and an extensive set of problems make this book suitable as a complementary textbook for a graduate course in biophysics and as a standalone reference for students and researchers in biophysics, bioengineering, and mathematical biology interested in the mechanics of tissue. Features: Provides an overview of patterns and shapes seen in animal tissues in addition to an interpretation of these structures in terms of physical forces and processes Contains detailed analysis and a critical comparison of mechanical models of cells, tissues, and morphogenetic movements Presents a visually rich style which is accessible to physicists and biologists alike

Recent years have witnessed an increasing number of theoretical and experimental contributions to cancer research from different fields of physics, from biomechanics and soft-condensed matter physics to the statistical mechanics of complex systems. Reviewing these contributions and providing a sophisticated overview of the topic, this is the first book devoted to the emerging interdisciplinary field of cancer physics. Systematically integrating approaches from physics and biology, it includes topics such as cancer initiation and progression, metastasis, angiogenesis, cancer stem cells, tumor immunology, cancer cell mechanics and migration. Biological hallmarks of cancer are presented in an intuitive yet comprehensive way, providing graduate-level students and researchers in physics with a thorough introduction to this important subject. The impact of the physical mechanisms of cancer are explained through analytical and computational models, making this an essential reference for cancer biologists interested in cutting-edge quantitative tools and approaches coming from physics.

Quantum Mechanics, Cell-Cell Signaling, and Evolution offers a detailed accounting of the latest research and theorizing on the integration of quantum physics with biological action to produce a novel perspective on evolution. The book advocates for a paradigm shift towards understanding biology and medicine causally as predictive sciences, presenting quantum mechanics and physiology as vertically integrated. The author has taken a unique approach to the question of how and why evolution occurred. The account is based on extensive knowledge of lipid physical chemistry, and its role in the evolution of the lung under the influence of hormonal effects on structure and function. The title arranges lipid biochemistry and biophysics into an integrated explanation, guiding readers from the immersion of lipids in water as the origin of life, to lung surfactant in alveolar homeostasis, and leading to a new understanding of how consciousness interacts with the laws of nature. This volume argues for a novel understanding of evolutionary processes based on fundamental science and positions itself as seeking consilience among research disciplines. Starting from the origins of the cosmos, the author proceeds through nucleosynthesis and Endosymbiosis Theory, to finally describe consciousness in relation to natural law.

Herbal Biomolecules in Healthcare Applications presents extensive detailed information on all the vital principles, basics and fundamental aspects of multiple herbal biomolecules in the healthcare industry. This book examines important herbal biomolecules including alkaloids, glycosides, flavonoids, anthraquinones, steroids, polysaccharides, tannins and polyphenolic compounds, terpenes, fats and waxes, proteins and peptides, and vitamins. These herbal biomacromolecules are responsible for different bioactivities as well as pharmacological potentials. A systematic understanding of the extraction, purification, characterization, applications of these herbal biomolecules and their derivatives in healthcare fields is developed in this comprehensive book. Chapters explore the key topics along with an emphasis on recent research and developments in healthcare fields by leading experts. They include updated literature review of the relevant key topics, good quality illustrations, chemical structures, flow charts, well-organized tables and case studies. Herbal Biomolecules in Healthcare Applications will be useful for researchers working on natural products and biomolecules with bioactivity and nutraceutical properties. Professionals specializing in scientific areas such as biochemistry, pharmacology, analytical chemistry, organic chemistry, clinics, or engineering focused on bioactive natural products will find this book useful.

A sound knowledge of biology, mathematics, physics and chemistry in needed to understand how excitable cells function and the many basic concepts involved in acquiring this knowledge are described from first principles in this book. As these principles equally apply to other biological fields such as the study of membrane transport, artificial membranes, signal capturing, analysis in biological systems and general applications of mathematics and physics to biology, they are of general interest. An important feature of the book is the appendices, in which mathematical functions are derived, and which ensure the usefulness of the volume as a reference manual.

Principles of Nucleic Acid Structure, Second Edition, provides the most complete and concise summary of underlying principles and approaches to studying nucleic acid structure, including discussions of X-ray crystallography, NMR, molecular modelling and databases. The book's focus is on a survey of structures that are especially important for biomedical research and pharmacological applications. This updated edition includes the latest advances relevant to recognition of DNA and RNA by small molecules and proteins, including sections on RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes and short interfering RNA (siRNA). This reference is a must-have for those seeking an authoritative, comprehensive and up-to-date source on all aspects of nucleic acid structure, from basic first principles to details of recent research results.

Biochemistry of Lipids, Lipoproteins and Membranes, Seventh Edition serves as a comprehensive, general reference book for scientists and students studying lipids, lipoproteins and membranes. Here, across 19 chapters, leaders in the field summarize fundamental concepts, recent research developments, data analysis, and implications for human disease and intervention. Topics discussed include lipid biology in both prokaryotes and eukaryotes, fatty acid synthesis, desaturation and elongation, and pathways leading to synthesis of complex phospholipids, sphingolipids and their structural variants. Chapters also examine how bioactive lipids are involved in cell signaling, with an emphasis on disease implications and pathological consequences. As the field advances, each chapter in this new edition has been fully revised to address emerging topics, with all-new coverage of lipid droplets and their role as regulatory organelles for energy homeostasis, as well as their relationship to obesity, liver disease and diabetes. Evolving research in fatty acid handling and storage in eukaryotes is also discussed in-depth, with new sections addressing fatty acid uptake, activation and lipolysis.

These are exciting times for the field of optical imaging of brain function. Rapid developments in theory and technology continue to considerably advance understanding of brain function. Reflecting changes in the field during the past five years, the second edition of In Vivo Optical Imaging of Brain Function describes state-of-the-art techniques and their applications for the growing field of functional imaging in the live brain using optical imaging techniques. New in the Second Edition: Voltage-sensitive dyes imaging in awake behaving animals Imaging based on genetically encoded probes Imaging of mitochondrial auto-fluorescence as a tool for cortical mapping Using pH-sensitive dyes for functional mapping Modulated imaging Calcium imaging of neuronal activity using 2-photon microscopy Fourier approach to optical imaging Fully updated chapters from the first edition Leading Authorities Explore the Latest Techniques Updated to reflect continuous development in this emerging research area, this new edition, as with the original, reaches across disciplines to review a variety of non-invasive optical techniques used to study activity in the living brain. Leading authorities from such diverse areas as biophysics, neuroscience, and cognitive science present a host of perspectives that range from a single neuron to large assemblies of millions of neurons, captured at various temporal and spatial resolutions. Introducing techniques that were not available just a few years ago, the authors describe the theory, setup, analytical methods, and examples that highlight the advantages of each particular method.

This updated and up-to-date version of the first edition continues with the really interesting stuff to spice up a standard biophysics and biophysical chemistry course. All relevant methods used in current cutting edge research including such recent developments as super-resolution microscopy and next-generation DNA sequencing techniques, as well as industrial applications, are explained. The text has been developed from a graduate course taught by the author for several years, and by presenting a mix of basic theory and real-life examples, he closes the gap between theory and experiment. The first part, on basic biophysical chemistry, surveys fundamental and spectroscopic techniques as well as biomolecular properties that represent the modern standard and are also the basis for the more sophisticated technologies discussed later in the book. The second part covers the latest bioanalytical techniques such as the mentioned super-resolution and next generation sequencing methods, confocal fluorescence microscopy, light sheet microscopy, two-photon microscopy and ultrafast spectroscopy, single molecule optical, electrical and force measurements, fluorescence correlation spectroscopy, optical tweezers, quantum dots and DNA origami techniques. Both the text and illustrations have been prepared in a clear and accessible style, with extended and updated exercises (and their solutions) accompanying each chapter. Readers with a basic understanding of biochemistry and/or biophysics will quickly gain an overview of cutting edge technology for the biophysical analysis of proteins, nucleic acids and other biomolecules and their interactions. Equally, any student contemplating a career in the chemical, pharmaceutical or bio-industry will greatly benefit from the technological knowledge presented. Questions of differing complexity testing the reader's understanding can be found at the end of each chapter with clearly described solutions available on the Wiley-VCH textbook homepage under: www.wiley-vch.de/textbooks

This book provides a selection of essential knowledge on the image-based quantification of biophysical parameters for the purpose of clinical diagnosis. The authors regard clinical imaging scanners as physical measurement systems capable of quantifying intrinsic parameters for depiction of the constitution and biophysical properties of in vivo tissue. On the one hand, this approach supports the development of new methods of imaging highly reproducible, system-independent, and quantitative biomarkers, and these methods receive detailed attention in the book. On the other hand, the reader will also gain a deeper understanding of how physical tissue properties interact with the generation of signals in medical imaging, opening new windows on the intricate and fascinating relationship between the structure and function of living tissues. The book will be of interest to all who recognize the limitations of basing clinical diagnosis primarily on visual inspection of images and who wish to learn more about the diagnostic potential of quantitative and biophysics-based medical imaging markers and the challenges that the paucity of such markers poses for next-generation imaging technologies.

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.

What neurobiology and artificial intelligence tell us about how the brain builds itself How does a neural network become a brain? While neurobiologists investigate how nature accomplishes this feat, computer scientists interested in artificial intelligence strive to achieve this through technology. The Self-Assembling Brain tells the stories of both fields, exploring the historical and modern approaches taken by the scientists pursuing answers to the quandary: What information is necessary to make an intelligent neural network? As Peter Robin Hiesinger argues, "the information problem" underlies both fields, motivating the questions driving forward the frontiers of research. How does genetic information unfold during the years-long process of human brain development-and is there a quicker path to creating human-level artificial intelligence? Is the biological brain just messy hardware, which scientists can improve upon by running learning algorithms on computers? Can AI bypass the evolutionary programming of "grown" networks? Through a series of fictional discussions between researchers across disciplines, complemented by in-depth seminars, Hiesinger explores these tightly linked questions, highlighting the challenges facing scientists, their different disciplinary perspectives and approaches, as well as the common ground shared by those interested in the development of biological brains and AI systems. In the end, Hiesinger contends that the information content of biological and artificial neural networks must unfold in an algorithmic process requiring time and energy. There is no genome and no blueprint that depicts the final product. The self-assembling brain knows no shortcuts. Written for readers interested in advances in neuroscience and artificial intelligence, The Self-Assembling Brain looks at how neural networks grow smarter.

Presenting a detailed, hands-on approach to fluorescence spectroscopy, this book describes experiments that cover basic spectroscopy and advanced aspects of fluorescence spectroscopy. It emphasizes practical guidance, providing background on fundamental concepts as well as guidance on how to handle artifacts, avoid common errors, and interpret data. Nearly 150 experiments from biophysics, biochemistry, and the biomedical sciences demonstrate how methods are applied in practical applications. The result is a hands-on guide to the most important aspects of fluorescence spectroscopy, from steady-state fluorescence to advanced time-resolved fluorescence. Provides a complete overview of nearly 150 experiments using fluorescence spectroscopy, from basic to advanced applications Presents laboratory methods using a variety of instrumental setups with detailed discussion of data analysis and interpretations Covers steady-state phenomena, time-resolved phenomena, and advanced methods Spans biophysical, biochemical, and biomedical applications Describes related concepts, theory, and mathematical background as well as commercially available instruments used for measurements

Essentials of Medical Biochemistry, Third Edition offers a condensed, yet detailed overview of clinical biochemistry, spanning fundamentals and relevant physiologic and pathophysiologic concepts. Pivotal clinical case studies aid in understanding basic science in the context of diagnosis and treatment of human diseases, and the text illuminates key topics in molecular immunology and hemostasis. Users will find fundamental concepts aiding students and professionals in biochemistry, medicine, and other healthcare disciplines. The text is a useful refresher that will help users meet USMLE and other professional licensing examination requirements, providing thorough introductions, key points, multicolored illustrations of chemical structures and figures, fact-filled tables, and recommended reading lists. This Third Edition has been fully updated to address evolving techniques in the biological sciences, including genomics, metabolomics, transcriptomics, epigenomics, proteomics, and gene therapy, among other methods. In addition, each chapter has been fully revised for current science and now features learning objectives and chapter summaries, supplemental reading, and 5 clinical case based multiple choice questions. New clinical cases have been added throughout.

Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.

Fluid dynamics plays a crucial role in many cellular processes, including the locomotion of cells such as bacteria and spermatozoa. These organisms possess flagella, slender organelles whose time periodic motion in a fluid environment gives rise to motility. Sitting at the intersection of applied mathematics, physics and biology, the fluid dynamics of cell motility is one of the most successful applications of mathematical tools to the understanding of the biological world. Based on courses taught over several years, it details the mathematical modelling necessary to understand cell motility in fluids, covering phenomena ranging from single-cell motion to instabilities in cell populations. Each chapter introduces mathematical models to rationalise experiments, uses physical intuition to interpret mathematical results, highlights the history of the field and discusses notable current research questions. All mathematical derivations are included for students new to the field, and end-of-chapter exercises help consolidate understanding and practise applying the concepts.

Ubiquitous and fundamental in cell mechanics, multiscale problems can arise in the growth of tumors, embryogenesis, tissue engineering, and more. Cell Mechanics: From Single Scale-Based Models to Multiscale Modeling brings together new insight and research on mechanical, mathematical, physical, and biological approaches for simulating the behavior of cells, specifically tumor cells. In the first part of the text, the book discusses the powerful tool of microrheology for investigating cell mechanical properties, multiphysics and multiscale approaches for studying intracellular mechanisms in cell motility, and the role of subcellular effects involving certain genes for inducing cell motility in cancer. Focusing on models based on physical, mathematical, and computational approaches, the second section develops tools for describing the complex interplay of cell adhesion molecules and the dynamic evolution of the cell cytoskeleton. The third part explores cell interactions with the environment, particularly the role of external mechanical forces and their effects on cell behavior. The final part presents innovative models of multicellular systems for developmental biology, cancer, and embryogenesis. This book collects novel methods to apply to cells and tissues through a multiscale approach. It presents numerous existing tools while stimulating the discovery of new approaches that can lead to more effective and accurate predictions of pathologies.

Interactions between the fields of physics and biology reach back over a century, and some of the most significant developments in biology--from the discovery of DNA's structure to imaging of the human brain--have involved collaboration across this disciplinary boundary. For a new generation of physicists, the phenomena of life pose exciting challenges to physics itself, and biophysics has emerged as an important subfield of this discipline. Here, William Bialek provides the first graduate-level introduction to biophysics aimed at physics students.

Bialek begins by exploring how photon counting in vision offers important lessons about the opportunities for quantitative, physics-style experiments on diverse biological phenomena. He draws from these lessons three general physical principles--the importance of noise, the need to understand the extraordinary performance of living systems without appealing to finely tuned parameters, and the critical role of the representation and flow of information in the business of life. Bialek then applies these principles to a broad range of phenomena, including the control of gene expression, perception and memory, protein folding, the mechanics of the inner ear, the dynamics of biochemical reactions, and pattern formation in developing embryos.

Featuring numerous problems and exercises throughout, "Biophysics" emphasizes the unifying power of abstract physical principles to motivate new and novel experiments on biological systems. Covers a range of biological phenomena from the physicist's perspective Features 200 problems Draws on statistical mechanics, quantum mechanics, and related mathematical concepts Includes an annotated bibliography and detailed appendixes Instructor's manual (available only to teachers)

Biosurfactants: Research and Development provides a thorough overview of biosurfactant research and development across a range of settings and industries, highlighting the novel use of enzymes, metabolic and genetic engineering in biosurfactant production and showcasing diverse experimental models and approaches. Sections discuss fundamental characteristics of biosurfactants, their physio-chemical properties, and their differences from chemically synthesize surfactants, different research approaches for the study of known biosurfactants, and the genetic manipulation of microorganisms to increase biosurfactant productivity, or to produce molecules with improved characteristics. Throughout the book, methods and approaches are discussed in easy-to-digest formats, with methods discussed, ranging from in silico approaches to classical biocatalysis omics analysis and metabolic engineering.

Mechanobiology: From Molecular Sensing to Disease will provide a review of the current state of understanding of mechanobiology and its role in health and disease. It covers: Current understanding of the main molecular pathways by which cells sense and respond to mechanical stimuli, A review of diseases that with known or purported mechanobiological underpinnings; The role of mechanobiology in tissue engineering and regenerative medicine; Experimental methods to capture mechanobiological phenomena; Computational models in mechanobiology.

GPCRS: Structure, Function, and Drug Discovery provides a comprehensive overview of recent discoveries and our current understanding of GPCR structure, signaling, physiology, pharmacology and methods of study. In addition to the fundamental aspects of GPCR function and dynamics, international experts discuss crystal structures, GPCR complexes with partner proteins, GPCR allosteric modulation, biased signaling through protein partners, deorphanization of GPCRs, and novel GPCR-targeting ligands that could lead to the development of new therapeutics against human diseases. GPCR association with, and possible therapeutic pathways for, retinal degenerative diseases, Alzheimer's disease, Parkinson's disease, cancer and diabetic nephropathy, among other illnesses, are examined in-depth.

In considering ways that physics has helped advance biology and medicine, what typically comes to mind are the various tools used by researchers and clinicians. We think of the optics put to work in microscopes, endoscopes, and lasers; the advanced diagnostics permitted through magnetic, x-ray, and ultrasound imaging; and even the nanotools, that allow us to tinker with molecules. We build these instruments in accordance with the closest thing to absolute truths we know, the laws of physics, but seldom do we apply those same constants of physics to the study of our own carbon-based beings, such as fluidics applied to the flow of blood, or the laws of motion and energy applied to working muscle. Instead of considering one aspect or the other, Handbook of Physics in Medicine and Biology explores the full gamut of physics' relationship to biology and medicine in more than 40 chapters, written by experts from the lab to the clinic. The book begins with a basic description of specific biological features and delves into the physics of explicit anatomical structures starting with the cell. Later chapters look at the body's senses, organs, and systems, continuing to explain biological functions in the language of physics. The text then details various analytical modalities such as imaging and diagnostic methods. A final section turns to future perspectives related to tissue engineering, including the biophysics of prostheses and regenerative medicine. The editor's approach throughout is to address the major healthcare challenges, including tissue engineering and reproductive medicine, as well as development of artificial organs and prosthetic devices. The contents are organized by organ type and biological function, which is given a clear description in terms of electric, mechanical, thermodynamic, and hydrodynamic properties. In addition to the physical descriptions, each chapter discusses principles of related clini

Intrinsically Disordered Proteins: Dynamics, Binding, and Function thoroughly examines and ties together the fundamental biochemical functions of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs), including signaling, binding, and regulation, with the methodology for study and the associated pathways for drug design and therapeutic intervention. The role of new mechanistic, computational, and experimental approaches in IDP study are explored in depth, with methods for the characterization of IDP dynamics; models, simulations, and mechanisms of IDP and IDR binding; and biological and medical implications of IDP dynamics prominently featured. Written and edited by leading scientists in the field, this book explores groundbreaking areas such as ensemble descriptions of IDPs and IDRs, single-molecule studies of IDPs and IDRs, IDPs and IDRs in membraneless organelles, and molecular mechanisms of fibrillation of IDPs. Intrinsically Disordered Proteins provides students and researchers in biochemistry, molecular biology, and applied microbiology with a comprehensive and updated discussion of the complex dynamics of IDPs and IDRs.

A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation? Cell Biology by the Numbers explores these questions-and dozens of others-providing a richly illustrated and handy reference for students and researchers in molecular and cell biology, chemistry, and biophysics. The book features question-driven vignettes and "back of the envelope" calculations that investigate some of the key numbers in cell biology. Readers will learn about the sizes, concentrations, rates, energies, and other numbers that describe and drive the living world.