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Quantitative Understanding of Biosystems

An Introduction to Biophysics

Thomas M. Nordlund, Thomas Nordlund, Peter M. Hoffmann
Publication Date:
March 04, 2011
Content Details:
588 pages

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  • About the Book

    Book Summary

    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:

    1. Mathematical and computational tools—graphing, calculus, simple differential equations, diagrammatic analysis, and visualization tools
    2. Randomness, variation, statistical mechanics, distributions, and spectra
    3. The biological micro- and nanoworld—structures, processes, and the physical laws
    4. 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.


      • Provides a hands-on understanding of the movement of microorganisms, enabling students to analyze positions, velocities, and forces of real microorganisms
      • Reviews the necessary mathematics, including geometry, calculus, and differential equations
      • Discusses quantum mechanics in biosystems, covering photosynthesis and micro and chemical reactions
      • Describes the transition from discreet random walks to continuum diffusive motion
      • Contains standard exercises, advanced problems, and miniprojects
      • Includes a CD-ROM with "active" versions of Excel graphs and diagrams from the text, along with links to mathematical and biological/biochemical source data

      Solutions manual and presentation-quality diagrams available with qualifying course adoption


      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

  • Contents

    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
    Two- and Three-Dimensional Geometry
    Differential Equations

    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
    Small Molecules
    Medium-Sized Molecules: Components of Large Biomolecules
    Forces and Free Energies
    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

    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

    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
    Points to Remember

    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

    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


    Further Resources


    Problem Solving and References appear at the end of each chapter.