Quantitative Understanding of Biosystems
An Introduction to Biophysics
 Edition:
 1st
 Author(s):
 Thomas M. Nordlund, Thomas Nordlund, Peter M. Hoffmann
 ISBN:
 9781420089721
 Format:
 Hardback
 Publication Date:
 March 04, 2011
 Content Details:
 588 pages
 Language:
 English
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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:
 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 diagramcentered 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.
CDROM 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 reprogram the included Excel graphs.
Features
 Provides a handson 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 CDROM with "active" versions of Excel graphs and diagrams from the text, along with links to mathematical and biological/biochemical source data
Solutions manual and presentationquality diagrams available with qualifying course adoption
Reviews
The author has done a magnificent job in writing an easytofollow, intriguing and wellwritten 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 2012This 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 2012The 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 UniversityThis 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 UniversityThis 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 UniversityBiology 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 CenterA superb pedagogical textbook about the behavior and properties of the microscopic structures that form the essential building blocks of living systems. … Fullcolor 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 CDROM 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 selfinstruction manual for advanced biophysics science students.
—Midwest Book Review, May 2011Combines a nice balance of topics with important basic material … . The emphasis on problems, projects, and tools is very helpful.
—Stephen J. Hagen, University of FloridaA 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, 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 OutofDate Quickly
Is There a Career Here Somewhere?
Read Appendix AHow (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 DangersMath Tools: First Pass
What Math Do We Need?
Notation: Mathematics vs. Physics Notations
Approximations
Vectors
Two and ThreeDimensional Geometry
Calculus
Differential Equations
DistributionsSTRUCTURE 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 RememberStructures: From 0.1 to 10 nm and Larger
Software to Display and Analyze Biological Structures
Solvents
Small Molecules
MediumSized Molecules: Components of Large Biomolecules
Forces and Free Energies
Biopolymers
Macromolecules: When Does a Molecule Become a Macroscopic Object?
Points to RememberFirst Pass at Supramolecular Structures: Assemblies of Biomolecules
Measuring Properties of ThreeDimensional Aggregates
Small Aggregates
Large Aggregates
TwoDimensional Aggregates: Membranes
Points to RememberPutting 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 EyesBIOLOGICAL 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 1mmLong Molecule of DNA a Quantum Object?
Points to RememberLight and Life
Light: Our Energy Source
Crucial Differences between One 5eV and Two 2.5eV 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 RememberPhotosynthesis
Global Numbers
Overall Process
Structural Organization of Photosynthetic Units
LightHarvesting (Antenna) Proteins: Arrays of Absorbers
Reaction Centers and Charge Separation: Purple Bacteria and Cyanobacteria
Artificial Models and Nonpolluting Energy Production
Points to RememberDirect Ultraviolet Effects on Biological Systems
Types and Sources of UV Light
Divisions of the UV for Health Purposes: UVA, UVB, and UVC
UV Damage to Organisms: "Action Spectra"
WavelengthDependent Photochemical Yields and Protein Damage
UV Damage to DNA
Optical Properties of the Skin
Sunscreens
Points to RememberBIOLOGICAL 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 RememberRandom Walks, Diffusion, and Polymer Conformation
Review of Kinetic Theory of Gases: Implications for Biomolecular Averaging
OneDimensional Random Walk: Probabilities and Distributions
Spreadsheet Model for a OneDimensional Random Walk
ThreeDimensional Random Walk
Diffusion in the Bulk
Reprise of Photosynthetic Light Harvesting
Biopolymers—A Random Reprise
Points to RememberStatistical 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 RememberReactions: Physical View
Energy, Entropy, and Free Energy Diagrams
Rate Theory I: ActivationEnergy Model
DiffusionControlled Rates (Bimolecular)
Effects of Temperature on Rate Constants
Quantum Tunneling
A ⇌ B: Unimolecular Reactions
A + B → C Binding Reactions: FreeSolution Reactions
Complex Reactions: RateDetermining Steps and Michaelis–Menten Analysis
Driving Forces
Reversibility and Detailed Balance
SingleMolecule Behavior
Points to RememberMolecular Machines: Introduction
Basic Considerations for Motors
DNAManipulating Motors
Points to RememberAssembly
Overview of Assembly Issues
Kinetics and Equilibrium
Restricted Space for Assembly
Entropic Drive: Ordered Structures Can Be Driven by Random Processes
Nucleosomes and NucleosomeLike Structures
Points to RememberAppendix A: Reading Skills and Information Sources
Appendix B: Snapshot of the Supporting CDGlossary
Further Resources
Index
Problem Solving and References appear at the end of each chapter.