Quantitative Understanding of Biosystems: An Introduction to Biophysics(Foundations of Biochemistry and Biophysics)

Quantitative Understanding of Biosystems: An Introduction to Biophysics focuses on the behavior and properties of microscopic structures that underlie living systems. It clearly describes the biological physics of macromolecules, subcellular structures, and whole cells, including interactions with light. Providing broad coverage of physics, chemistry, biology, and mathematics, this color text features: Mathematical and computational tools—graphing, calculus, simple differential equations, diagrammatic analysis, and visualization tools Randomness, variation, statistical mechanics, distributions, and spectra The biological micro- and nanoworld—structures, processes, and the physical laws Quantum effects—photosynthesis, UV damage, electron and energy transfer, and spectroscopic characterization of biological structures Through its active learning approach, the text encourages practical comprehension of the behavior of biosystems, rather than knowledge of the latest research. The author includes graph- and diagram-centered physics and mathematics, simple software, frequent checks of understanding, and a repetition of important ideas at higher levels or from different points of view. After completing this book, students will gain significant computational and project experience and become competent at quantitatively characterizing biosystems. CD-ROM Resource The accompanying CD contains multimedia learning tools, such as video clips and animations, that illustrate intrinsically dynamic processes. For students inexperienced in the application of mathematics and physical principles to naturally occurring phenomena, this multimedia component emphasizes what is most obvious about biological systems: living things move. Students can also manipulate and re-program the included Excel graphs.

Table of Contents:
INTRODUCTION, APPROACH, AND TOOLS Introduction to a New World Biological and Nonliving Worlds Contrasted Hierarchical Structure and Function Some Important Quantities to Get Started Biophysics and Biochemistry Operate in Water (Water 1) Important or "Hot" Issues in Biophysics, or How to Be Out-of-Date Quickly Is There a Career Here Somewhere? Read Appendix A How (Most) Physicists Approach Biophysics Dealing with Nonspherical Cows: Drive for Simplicity Two Approaches to Biosystems Comparison of "Physics" and "Biology" Approaches to Organisms Memorization: Its Advantages and Dangers Math Tools: First Pass What Math Do We Need? Notation: Mathematics vs. Physics Notations Approximations Vectors Two- and Three-Dimensional Geometry Calculus Differential Equations Distributions STRUCTURE AND FUNCTION Water Introduction Structure Unusual Physical Properties Summary of Important Physical Properties Bulk vs. Local Structures Diffusion and Chemical Reactions in Water Solutes and the Solvent Power of Water Points to Remember Structures: From 0.1 to 10 nm and Larger Software to Display and Analyze Biological Structures Solvents Small Molecules Medium-Sized Molecules: Components of Large Biomolecules Forces and Free Energies Biopolymers Macromolecules: When Does a Molecule Become a Macroscopic Object? Points to Remember First Pass at Supramolecular Structures: Assemblies of Biomolecules Measuring Properties of Three-Dimensional Aggregates Small Aggregates Large Aggregates Two-Dimensional Aggregates: Membranes Points to Remember Putting a Cell Together: Physical Sketch Minimal, Prokaryotic, and Eukaryotic Cells Physiology: Selective Overview Reproduction, DNA, and the Cell Nucleus Sensors and Recognition: Responding to the Outside World without Eyes BIOLOGICAL ACTIVITY: QUANTUM MICROWORLD Quantum Primer Quantum Glossary Schrödinger Equation and Other Tools of Quantum Mechanics Pauli Exclusion Principle From Atoms to Molecules Collisions of Atoms and Molecules Classical vs. Quantum: Is a 1-mm-Long Molecule of DNA a Quantum Object? Points to Remember Light and Life Light: Our Energy Source Crucial Differences between One 5-eV and Two 2.5-eV Photons Properties of Photons Scattering and Refraction Absorption Spectra Emission Spectra Einstein Relations between Absorption and Emission of Atoms (Graduate Section) Intersystem Crossing: Singlets (S = 0) to Triplets (S = 1) Energy Transfer (FRET) Points to Remember Photosynthesis Global Numbers Overall Process Structural Organization of Photosynthetic Units Light-Harvesting (Antenna) Proteins: Arrays of Absorbers Reaction Centers and Charge Separation: Purple Bacteria and Cyanobacteria Artificial Models and Nonpolluting Energy Production Points to Remember Direct Ultraviolet Effects on Biological Systems Types and Sources of UV Light Divisions of the UV for Health Purposes: UV-A, UV-B, and UV-C UV Damage to Organisms: "Action Spectra" Wavelength-Dependent Photochemical Yields and Protein Damage UV Damage to DNA Optical Properties of the Skin Sunscreens Points to Remember BIOLOGICAL ACTIVITY: (CLASSICAL) MICROWORLD Mechanics and Dynamics Conservation Laws, Newton’s Laws, Forces, and Torques Friction: Familiar and Less Familiar Examples of Motion Gravitational Forces Volume Changes and Compressibility Stress and Strain Force of Friction, Dissipation, Inertia, and Disorder Fluids and Turbulence Points to Remember Random Walks, Diffusion, and Polymer Conformation Review of Kinetic Theory of Gases: Implications for Biomolecular Averaging One-Dimensional Random Walk: Probabilities and Distributions Spreadsheet Model for a One-Dimensional Random Walk Three-Dimensional Random Walk Diffusion in the Bulk Reprise of Photosynthetic Light Harvesting Biopolymers—A Random Reprise Points to Remember Statistical Physics and Thermodynamics Primer Important Quantities: Temperature, Pressure, Density, and Number Statistical Mechanical View and Distributions Equipartition of Energy "Internal" Energy: Kinetic (K) and Potential (U) Heat, Internal Energy, Work, and Enthalpy Conservative and Nonconservative Forces: DNA Example Ideal Gas Law Entropy: Gases and Polymers Free Energy (Gibbs) Energy Diagrams Boltzmann Distribution if Numbers Vary: Gibbs Distribution Equilibrium Constants in Ideal, Uniform Solutions Free Energy: Enthalpy, Entropy, Mixing, Gradients, Potential, and ATP Points to Remember Reactions: Physical View Energy, Entropy, and Free Energy Diagrams Rate Theory I: Activation-Energy Model Diffusion-Controlled Rates (Bimolecular) Effects of Temperature on Rate Constants Quantum Tunneling A ⇌ B: Unimolecular Reactions A + B → C Binding Reactions: Free-Solution Reactions Complex Reactions: Rate-Determining Steps and Michaelis–Menten Analysis Driving Forces Reversibility and Detailed Balance Single-Molecule Behavior Points to Remember Molecular Machines: Introduction Basic Considerations for Motors DNA-Manipulating Motors Points to Remember Assembly Overview of Assembly Issues Kinetics and Equilibrium Restricted Space for Assembly Entropic Drive: Ordered Structures Can Be Driven by Random Processes Nucleosomes and Nucleosome-Like Structures Points to Remember Appendix A: Reading Skills and Information Sources Appendix B: Snapshot of the Supporting CD Glossary Further Resources Index Problem Solving and References appear at the end of each chapter.

About the Author :
Thomas M. Nordlund is an associate professor in the Department of Physics at the University of Alabama at Birmingham. A Fellow of the American Physical Society, Dr. Nordlund has performed research in biomolecular dynamics for 30 years. He earned his Ph.D. in physics from the University of Illinois at Urbana-Champaign, under the supervision of Hans Frauenfelder.

Review :
The author has done a magnificent job in writing an easy-to-follow, intriguing and well-written introductory section. … the chapter referring to `Direct ultraviolet effects on biological systems’ is probably my favourite. Exceptionally written, it contains informative material found only in specialised textbooks and is equally attractive for science and medical students. … the text is stimulatingly and well written for the focused student. Apart from the scientific content, the artwork of the book is of high quality, aiding significantly the understanding of the concepts presented. … this book is highly recommended for introducing biophysics to the motivated and curious undergraduate students. —Nikolaos Kourkoumelis, Contemporary Physics, June 2012 This terrific text offers a broad range of learning opportunities for many undergraduate majors. It is filled with a wide range of analogies that facilitate understanding of fundamental biophysics, thus making abstract concepts easier to comprehend. It uses a friendly language that avoids unnecessary technicalities and terminologies. … Almost all sections of the book illustrate conceptual examples supplemented by estimates and calculations of biophysical parameters, describing biological problems in depth. This characteristic marks the fundamental distinction between this biophysics book and others. It will enable students to understand the significance of biological parameters through quantitative examples—a modern way of learning biophysics. —American Journal of Physics, February 2012 The book contains a beautiful review of essential physics for understanding biological systems, particularly at the molecular scale, emphasizing that which is rarely taught in standard physics classes: how to think like a physicist. The chapters on quantum mechanics and the interaction of photons with biological systems are particularly welcome, and set this book apart. I believe that the progression through to the effects of UV radiation and sunscreens will be popular with students. —Ernest Barreto, George Mason University This book is so far the best on the market in terms of an undergraduate biophysics textbook. It is very likely that I will adopt this textbook for my next year! The book is quite an equilibrated comprehensive description of the basic mechanisms that govern biological systems. This textbook is indeed a great example of a quantitative approach for teaching undergraduate students from physics and biological sciences. The material offers conceptual examples and broad lists of key references. The textbook will have great success not only for the clarity of presentation, but also for its structure and numerous examples … . —Liviu Movileanu, Department of Physics and Syracuse Biomaterials Institute, Syracuse University This is an excellent book for the physics or bioengineering undergraduate student. It is approachable at the junior level and it is written in a very clear style with plenty of useful and colorful figures. Particularly, it is nice how the book builds up toward the main equations to make them intuitive from basic principles… . The accompanying CD is very useful as well. The glossary section is an excellent tool for the student not familiar with biology. —Diego Krapf, School of Biomedical Engineering, Colorado State University Biology is complex, but teaching it may be even more complicated. Modern biology integrates a traditional biology perspective with a deeper look into mechanisms that require perspectives from physics and chemistry. However, many instructors who want to teach courses that bridge these fields often are confronted with the problem that no good text exists. We therefore need textbooks that can function as the basis for courses that will train students to integrate these diverse disciplines. Quantitative Understanding of Biosystems is a text geared toward starting a student along this path. The book provides a good introduction into a broad range of biology and physics topics and shows how physics can explain aspects of biological mechanisms at many different length scales. The text also provides a nice exposition on the differences between how a biologist approaches a problem and how a physicist does. This discussion is important for helping to bring these two communities together, and will aid in making a course developed using this text applicable to students from biology as well as from physics, chemistry, math, or engineering. —Charles Wolgemuth, University of Connecticut Health Center A superb pedagogical textbook about the behavior and properties of the microscopic structures that form the essential building blocks of living systems. … Full-color illustrations aid students in their understanding of how to use mathematical tools (graphing, calculus, simple differential equations, diagrammatic analysis, and more) to better grasp, analyze, and project solutions to problems involving the quantitative characterization of biosystems. An accompanying CD-ROM offers `active’ versions of Excel graphs and diagrams listed in the text, and links to mathematical, biological, and biochemical source data. … an excellent college text or self-instruction manual for advanced biophysics science students. —Midwest Book Review, May 2011 Combines a nice balance of topics with important basic material … . The emphasis on problems, projects, and tools is very helpful. —Stephen J. Hagen, University of Florida A versatile textbook that also serves as a good introduction to quantitative biology … strikes a balance between `not too difficult’ for life science students and `conceptually rich and challenging’ for physics and math students. —Yuri Gartstein and Stephen Levene, The University of Texas at Dallas