Introduction to Experimental Biophysics, Second Edition

Biological Methods for Physical Scientists

Author: Jay L. Nadeau

Publisher: CRC Press

ISBN: 1351000926

Category: Medical

Page: 764

View: 5240

Praise for the First Edition “essential reading for any physical scientist who is interested in performing biological research.” ?Contemporary Physics "an ambitious text.... Each chapter contains protocols and the conceptual reasoning behind them, which is often useful to physicists performing biological experiments for the first time." –Physics Today This fully updated and expanded text is the best starting point for any student or researcher in the physical sciences to gain firm grounding in the techniques employed in molecular biophysics and quantitative biology. It includes brand new chapters on gene expression techniques, advanced techniques in biological light microscopy (super-resolution, two-photon, and fluorescence lifetime imaging), holography, and gold nanoparticles used in medicine. The author shares invaluable practical tips and insider’s knowledge to simplify potentially confusing techniques. The reader is guided through easy-to-follow examples carried out from start to finish with practical tips and insider’s knowledge. The emphasis is on building comfort with getting hands "wet" with basic methods and finally understanding when and how to apply or adapt them to address different questions. Jay L. Nadeau is a scientific researcher and head of the Biomedical Engineering in Advanced Applications of Quantum, Oscillatory, and Nanotechnological Systems (BEAAQONS) lab at Caltech and was previously associate professor of biomedical engineering and physics at McGill University.

An Introduction to Environmental Biophysics

Author: Gaylon S. Campbell,John M. Norman

Publisher: Springer Science & Business Media

ISBN: 1461216265

Category: Science

Page: 286

View: 6932

From reviews of the first edition: "well organized . . . Recommended as an introductory text for undergraduates" -- AAAS Science Books and Films "well written and illustrated" -- Bulletin of the American Meteorological Society

Methods in Molecular Biophysics

Author: Nathan R. Zaccai,Igor N. Serdyuk,Joseph Zaccai

Publisher: Cambridge University Press

ISBN: 1107056373

Category: Medical

Page: 702

View: 497

A comprehensive graduate textbook explaining key physical methods in biology, reflecting the very latest research in this fast-moving field.


Searching for Principles

Author: William Bialek

Publisher: Princeton University Press

ISBN: 1400845572

Category: Science

Page: 640

View: 5585

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)

A Practical Introduction to the Simulation of Molecular Systems

Author: Martin J. Field

Publisher: Cambridge University Press

ISBN: 1139465813

Category: Science

Page: N.A

View: 8528

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through

NMR Probeheads for Biophysical and Biomedical Experiments

Theoretical Principles and Practical Guidelines Second Edition

Author: Joël Mispelter,Mihaela Lupu,André Briguet

Publisher: World Scientific Publishing Company

ISBN: 1783268042

Category: Technology & Engineering

Page: 756

View: 8176

NMR Probeheads for Biophysical and Biomedical Experiments 2nd Edition is essential reading for anyone in the field of NMR or MRI, from students to medical or biological scientists performing experiments under certain physical and/or geometrical conditions, unattainable by conventional or available probes. The material guides the reader through the most basic and comprehensive stages in accomplishing a correct probe design, from a very basic oscillating circuit to much more elaborate designs. This new edition has been revised and updated to include a chapter dedicated to RF components, which are commonly used for probes realization and their frequency-dependent characteristics. Another completely revised chapter concerns the multiple coil systems and discusses arrays coils, different decoupling methods, and some principles for interfacing coils with low-noise preamplifiers. The principles of linear circuit analysis are presented in a dedicated chapter. Last but not least, accompanying files containing updated software for probe design have been made available from the publisher's website. Request Inspection Copy


Tools and Techniques

Author: Mark C. Leake

Publisher: CRC Press

ISBN: 1498702465

Category: Medical

Page: 410

View: 6046

An Up-to-Date Toolbox for Probing Biology Biophysics: Tools and Techniques covers the experimental and theoretical tools and techniques of biophysics. It addresses the purpose, science, and application of all physical science instrumentation and analysis methods used in current research labs. The book first presents the historical background, concepts, and motivation for using a physical science toolbox to understand biology. It then familiarizes students from the physical sciences with essential biological knowledge. The text subsequently focuses on experimental biophysical techniques that primarily detect biological components or measure/control biological forces. The author describes the science and application of key tools used in imaging, detection, general quantitation, and biomolecular interaction studies, which span multiple length and time scales of biological processes both in the test tube and in the living organism. Moving on to theoretical biophysics tools, the book presents computational and analytical mathematical methods for tackling challenging biological questions. It concludes with a discussion of the future of this exciting field. Future innovators will need to be trained in multidisciplinary science to be successful in industry, academia, and government support agencies. Addressing this challenge, this textbook educates future leaders on the development and application of novel physical science approaches to solve complex problems linked to biological questions.

Systems Immunology

An Introduction to Modeling Methods for Scientists

Author: Jayajit Das,Ciriyam Jayaprakash

Publisher: CRC Press

ISBN: 1351646141

Category: Mathematics

Page: 326

View: 1181

"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, USA New 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.

Light Harvesting in Photosynthesis

Author: Roberta Croce,Rienk van Grondelle,Herbert van Amerongen,Ivo van Stokkum

Publisher: CRC Press

ISBN: 1351242873

Category: Science

Page: 611

View: 5509

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.

A Mathematical Approach to Protein Biophysics

Author: L. Ridgway Scott,Ariel Fernández

Publisher: Springer

ISBN: 3319660322

Category: Mathematics

Page: 290

View: 9558

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.

Introduction to Marine Biology

Author: George Karleskint,Richard Turner,James W. Small

Publisher: Brooks/Cole Publishing Company


Category: Science

Page: 460

View: 6543

INTRODUCTION TO MARINE BIOLOGY distinguishes itself from other texts at this introductory level by taking an ecological approach to the study of marine biology, by providing succinct coverage of key topics, and through the use of the best illustrations and photos currently available. In this edition two co-authors have joined George KarleskintJames Small from Rollins College in Winter Park, Florida, and Richard Turner from the Florida Institute of Technology. Their experience in coastal environments nicely compliments Karleskint's clear, concise student-friendly writing style. Users will also discover that the level of the text has been broadened with additional coverage of plant, microbial, planktonic, and animal biology. In support of this emphasis, new "In Perspective" summary tables have been added to each of the marine organism chapters to provide a summary of important ecological and biological aspects of various marine organisms. Even with this broadened emphasis, this edition of INTRODUCTION TO MARINE BIOLOGY remains exceptionally readable. The textual material has been broken into small paragraph sections with more headings for ease of navigation, and "In Summary" statements have been added to the end of each main heading within the chapter, making it easy for students to check their understanding before reaching the end of the chapter. Furthermore, the authors have added more words to the glossary, many new illustrations, and over one hundred new photos. This second edition also boasts an increased "ecological focus" through the addition of discussions on "ecological roles and relationships."

Introduction to Proteins

Structure, Function, and Motion

Author: Amit Kessel,Nir Ben-Tal

Publisher: N.A

ISBN: 9781498747172

Category: Medical

Page: 988

View: 2641

Introduction to Proteins shows how proteins can be analyzed in multiple ways. It refers to the roles of proteins and enzymes in diverse contexts and everyday applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. This edition includes a brand-new chapter on enzymatic catalysis and biochemistry, an in-depth discussion of G-protein-coupled receptors (GPCRs), and a wider-scale description of methods for studying proteins.

Biomolecular Thermodynamics

From Theory to Application

Author: Douglas Barrick

Publisher: CRC Press

ISBN: 1439800200

Category: Medical

Page: 524

View: 4691

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

From Molecules to Networks

An Introduction to Cellular and Molecular Neuroscience

Author: John H. Byrne,Ruth Heidelberger,M. Neal Waxham

Publisher: Academic Press

ISBN: 0123982677

Category: Science

Page: 694

View: 4185

An understanding of the nervous system at virtually any level of analysis requires an understanding of its basic building block, the neuron. The third edition of From Molecules to Networks provides the solid foundation of the morphological, biochemical, and biophysical properties of nerve cells. In keeping with previous editions, the unique content focus on cellular and molecular neurobiology and related computational neuroscience is maintained and enhanced. All chapters have been thoroughly revised for this third edition to reflect the significant advances of the past five years. The new edition expands on the network aspects of cellular neurobiology by adding new coverage of specific research methods (e.g., patch-clamp electrophysiology, including applications for ion channel function and transmitter release; ligand binding; structural methods such as x-ray crystallography). Written and edited by leading experts in the field, the third edition completely and comprehensively updates all chapters of this unique textbook and insures that all references to primary research represent the latest results. The first treatment of cellular and molecular neuroscience that includes an introduction to mathematical modeling and simulation approaches 80% updated and new content New Chapter on "Biophysics of Voltage-Gated Ion Channels" New Chapter on "Synaptic Plasticity" Includes a chapter on the Neurobiology of Disease Highly referenced, comprehensive and quantitative Full color, professional graphics throughout All graphics are available in electronic version for teaching purposes

Biophysical Chemistry

Author: Alan Cooper

Publisher: Royal Society of Chemistry

ISBN: 1782625100

Category: Science

Page: N.A

View: 8618

Biophysical Chemistry covers the physical chemistry of biological macromolecules and the experimental techniques used to study them. Topics covered include: an introduction to biological molecules; spectroscopy, mass spectrometry and hydrodynamics of macromolecules; a ""bluffer's guide"" to molecular thermodynamics; biomolecular kinetics; chromatography and electrophoresis; and single-molecule methods. The easily digestible, pragmatic approach captures the reader with the fascinating challenges the subject poses for theoretical and experimental scientists. This book will be ideal for early undergraduates studying chemical or physical sciences and will act as a basis for more advanced study. Students in other areas of biological sciences will appreciate the less intimidating approach to physical chemistry as demonstrated here. Ideal for the needs of undergraduate chemistry students, Tutorial Chemistry Texts is a major series consisting of short, single topic or modular texts concentrating on the fundamental areas of chemistry taught in undergraduate science courses. Each book provides a concise account of the basic principles underlying a given subject, embodying an independent-learning philosophy and including worked examples.


A Practical Introduction to Structure, Mechanism, and Data Analysis

Author: Robert A. Copeland

Publisher: John Wiley & Sons

ISBN: 0471461857

Category: Science

Page: 416

View: 1277

Fully updated and expanded-a solid foundation for understanding experimental enzymology. This practical, up-to-date survey is designed for a broad spectrum of biological and chemical scientists who are beginning to delve into modern enzymology. Enzymes, Second Edition explains the structural complexities of proteins and enzymes and the mechanisms by which enzymes perform their catalytic functions. The book provides illustrative examples from the contemporary literature to guide the reader through concepts and data analysis procedures. Clear, well-written descriptions simplify the complex mathematical treatment of enzyme kinetic data, and numerous citations at the end of each chapter enable the reader to access the primary literature and more in-depth treatments of specific topics. This Second Edition of Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis features refined and expanded coverage of many concepts, while retaining the introductory nature of the book. Important new features include: A new chapter on protein-ligand binding equilibria Expanded coverage of chemical mechanisms in enzyme catalysis and experimental measurements of enzyme activity Updated and refined discussions of enzyme inhibitors and multiple substrate reactions Coverage of current practical applications to the study of enzymology Supplemented with appendices providing contact information for suppliers of reagents and equipment for enzyme studies, as well as a survey of useful Internet sites and computer software for enzymatic data analysis, Enzymes, Second Edition is the ultimate practical guide for scientists and students in biochemical, pharmaceutical, biotechnical, medicinal, and agricultural/food-related research.

Introduction to Experimental Biophysics - A Laboratory Guide

Author: Jay L. Nadeau

Publisher: CRC Press

ISBN: 1466557664

Category: Medical

Page: 197

View: 3936

Easily Get Started with Biological Experiments Introduction to Experimental Biophysics - A Laboratory Guide presents wet lab methods for courses in biophysics or molecular biology. A companion to the author’s highly praised An Introduction to Experimental Biophysics: Biological Methods for Physical Scientists, this manual offers a flexible course plan that permits completion of the labs in either a full term or intensive summer course. Tested in a pedagogical setting, the experiments follow a logical progression beginning with a DNA construct. The book starts with the basics of molecular cloning: amplifying and purifying plasmid, plasmid mapping, and using restriction enzymes. Later experiments deal with more advanced, emerging techniques, such as the synthesis and characterization of quantum dots and gold nanoparticles, protein crystallization, and spectroscopic techniques. This accessible guide will help both students and instructors in molecular biology, biophysics, and biomedical engineering. Students will understand how to use a variety of techniques in biological experiments while instructors will get practical guidance on preparing the experiments.

Biofluid Mechanics

An Introduction to Fluid Mechanics, Macrocirculation, and Microcirculation

Author: David Rubenstein,Wei Yin,Mary D. Frame

Publisher: Academic Press

ISBN: 0128011696

Category: Science

Page: 544

View: 8336

Biofluid Mechanics: An Introduction to Fluid Mechanics, Macrocirculation, and Microcirculation shows how fluid mechanics principles can be applied not only to blood circulation, but also to air flow through the lungs, joint lubrication, intraocular fluid movement, renal transport among other specialty circulations. This new second edition increases the breadth and depth of the original by expanding chapters to cover additional biofluid mechanics principles, disease criteria, and medical management of disease, with supporting discussions of the relevance and importance of current research. Calculations related both to the disease and the material covered in the chapter are also now provided. Uses language and math that is appropriate and conducive for undergraduate learning, containing many worked examples and end-of-chapter problems Develops all engineering concepts and equations within a biological context Covers topics in the traditional biofluids curriculum, and addresses other systems in the body that can be described by biofluid mechanics principles Discusses clinical applications throughout the book, providing practical applications for the concepts discussed NEW: Additional worked examples with a stronger connection to relevant disease conditions and experimental techniques NEW: Improved pedagogy, with more end-of-chapter problems, images, tables, and headings, to better facilitate learning and comprehension of the material

Introduction to Molecular Biology

Author: S Bresler

Publisher: Elsevier

ISBN: 0323145590

Category: Science

Page: 572

View: 8245

Introduction to Molecular Biology focuses on the principles of polymer physics and chemistry and their applications to fundamental phenomena in biological sciences. It examines the structure, synthesis, and function of nucleic acids and proteins, as well as the physicochemical techniques necessary in determining the macromolecular structure, the kinetics and mechanism of enzyme action, the genetics of bacteria and their viruses, and the genetic code. It also considers the importance of precise quantitative analysis in biochemistry and biophysics, the architecture and function of biological macromolecules, and the unique mechanisms that regulate the cell's biological activity. Organized into five chapters, this book begins with an overview of proteins and their functional activity, from contractility and enzymatic catalysis to immunological activity, formation of selectively permeable membranes, and reversible binding and transport. It explains how such functions are related to molecular interactions and therefore fall within the purview of molecular biology. The book then proceeds with a discussion on the chemical structure of proteins and nucleic acids, the physicochemical techniques in measuring molecular size and shape, the mechanism of enzymatic reactions, the functions of DNA and RNA, and the mechanism of phase transition in polynucleotides. This book is intended for both biologists and non-biologists who want to be acquainted with the advances made in molecular biology, molecular genetics, and molecular biophysics during the 1950s and 1960s.

Computational Approaches to Protein Dynamics

From Quantum to Coarse-Grained Methods

Author: Monika Fuxreiter

Publisher: CRC Press

ISBN: 1482297868

Category: Science

Page: 479

View: 4656

The Latest Developments on the Role of Dynamics in Protein Functions Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles. The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues: Is there a quantitative relationship between enzymatic catalysis and protein dynamics? Which are the functionally relevant motions of proteins? How can structural properties and partner recognition mechanisms of IDPs be simulated? How can we speed up molecular dynamics? How can we describe conformational ensembles by the synergistic effort of computations and experiments? While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.