Main description:

Over the past several years, I have organized and taught a core course in Modern Biophysics Techniques at the University of California Davis. Graduate students in biophysics, chemistry, physics, and engineering enroll in the class to survey the physical techniques that scientists use to study biology.

Introducing the diverse and complex field of biophysics in an academically rigorous but in-teresting way poses daunting challenges. Indeed, the course has undergone many transforma-tions and has tried on many styles: seminar/journal club, lecture/lab, and just plain didactic lec-ture formats. These, however, have achieved limited success, because they either assume a strong mathematics/physical-science background or reduce the physical science to a pedestrian level of knowledge, or demand that students trudge along with the expert researchers. None have attracted the interest of biology, physiology, or medical students, who must search for the biological meaning within biophysics.

One major obstacle to developing an attractive but scholarly course centers on the balance between formalism and perspective. Each biophysics technique requires a mastery of a chal-lenging set of physical-science/mathematics formalism. Yet even with mastery the reader may still not gain a biomedical perspective. How will these biophysical techniques help clarify the complex issues in biology? Moreover, how will the course deal with biomedical students’ reluc-tance to overcome the imposing physical-science/mathematical formalism in order to gain new perspectives on biology?

These considerations have given rise to the series Handbook of Modern Biophysics. The books in this series will bring current biophysics topics into focus and expand as the field of biophysics expands, so that biology and physical-science students or researchers can learn fun-damental concepts and apply new biophysics techniques to address biomedical questions. How-ever, the chapter structure will recognize the demand for explicating the conceptual framework of the underlying physics formalism and for casting perspectives on the biomedical applica-tions. Each chapter will have a bipartite structure: the first part establishes the fundamental physics concepts and describes the instrumentation or technique, while the second illustrates current applications in addressing complex questions in biology. With the addition of problem sets, further study, and references, the interested reader will be able to further explore the ideas presented.

In the first volume, Fundamental Concepts in Biophysics, the authors lay down a foundation for biophysics study. Rajiv Singh opens the book by pointing to the central importance of "Mathematical Methods in Biophysics." William Fink follows with a discussion on "Quantum Mechanics Basic to Biophysical Methods." Together, these two chapters establish some of the principles of mathematical physics underlying many biophysics techniques. Because computer modeling forms an intricate part of biophysics research, Subhadip Raychaudhuri and colleagues introduce the use of computer modeling in "Computational Modeling of Receptor–Ligand Bind-ing and Cellular Signaling Processes." Yin Yeh and coworkers bring to the reader’s attention the physical basis underlying the common use of fluorescence spectroscopy in biomedical re-search in their chapter "Fluorescence Spectroscopy." Electrophysiologists have also applied biophysics techniques in the study of membrane proteins, and Tsung-Yu Chen et al. explore stochastic processes of ion transport in their "Electrophysiological Measurements of Membrane Proteins." Michael Saxton takes up a key biophysics question about particle distribution and behavior in systems with spatial or temporal inhomogeneity in his chapter "Single-Particle Tracking." Finally, in "NMR Measurement of Biomolecule Diffusion," Thomas Jue explains how magnetic resonance techniques can map biomolecule diffusion in the cell to a theory of respiratory control .

This book thus launches the Handbook of Modern Biophysics series and sets up for the reader some of the fundamental concepts underpinning the biophysics issues to be presented in future volumes.

Back cover:

HANDBOOK OF MODERN BIOPHYSICS

Series Editor Thomas Jue, PhD

Handbook of Modern Biophysics brings current biophysics topics into focus, so that biology, medical, engineering, mathematics, and physical-science students or researchers can learn fundamental concepts and the application of new techniques in addressing biomedical challenges. Chapters explicate the conceptual framework of the physics formalism and illustrate the biomedical applications. With the addition of problem sets, guides to further study, and references, the interested reader can continue to explore independently the ideas presented.

Volume I: Fundamental Concepts in Biophysics

Editor Thomas Jue, PhD

In Fundamental Concepts in Biophysics, prominent professors have established a foundation for the study of biophysics related to the following topics:

Mathematical Methods in Biophysics

Quantum Mechanics Basic to Biophysical Methods

Computational Modeling of Receptor–Ligand Binding and Cellular Signaling Processes

Fluorescence Spectroscopy

Electrophysiological Measurements of Membrane Proteins

Single-Particle Tracking

NMR Measurement of Biomolecule Diffusion

About the Editor

Thomas Jue is a Professor in the Department of Biochemistry and Molecular Medicine at the University of California Davis. He is an internationally recognized expert in developing and applying magnetic resonance techniques to study animal as well as human physiology in vivo and has published extensively in the field of magnetic resonance spectroscopy and imaging, near-infrared spectroscopy, bioenergetics, cardiovascular regulation, exercise, and marine biology. Over the past several years, he has led the way as a Chair of the Biophysics Graduate Group Program to establish attractive but scholarly approaches to educate graduate students with a balance of physical-science/mathematics formalism and biomedical perspective in order to promote interest at the interface of physical science, engineering, mathematics, biology, and medicine. The Handbook of Modern Biophysics represents one approach.

Contents:

1 Mathematical Methods in Biophysics
Rajiv R.P. Singh
1.1. Functions of One Variable and Ordinary Differential Equations
1.2. Functions of Several Variables: Diffusion Equation in One Dimension
1.3. Random Walks and Diffusion
1.4. Random Variables, Probability Distribution, Mean, and Variance
1.5. Diffusion Equation in Three Dimensions
1.6. Complex Numbers, Complex Variables, and Schrödinger's Equation
1.7. Solving Linear Homogeneous Differential Equations
1.8. Fourier Transforms
1.9. Nonlinear Equations: Patterns, Switches and Oscillators
2 Quantum Mechanics Basic to Biophysical Methods
William Fink
2.1. Quantum Mechanics Postulates
2.2. One-Dimensional Problems
2.3. The Harmonic Oscillator
2.4. The Hydrogen Atom
2.5. Approximate Methods
2.6. Many Electron Atoms and Molecules
2.7. The Interaction of Matter and Light
3 Computational Modeling of Receptor–Ligand Binding and Cellular Signaling Processes
Subhadip Raychaudhuri, Philippos Tsourkas, and Eric Willgohs
3.1. Introduction
3.2. Differential Equation-Based Mean-Field Modeling
3.3. Application: Clustering of Receptor–Ligand Complexes
3.4. Modeling Membrane Deformation as a Result of Receptor–Ligand Binding
3.5. Limitations of Mean-Field Differential Equation-Based Modeling
3.6. Master Equation: Calculating the Time Evolution of a Chemically Reacting System
3.7. Stochastic Simulation Algorithm (SSA) of Gillespie
3.8. Application of the Stochastic Simulation Algorithm (SSA)
3.9. Free Energy-Based Metropolis Monte Carlo Simulation
3.10. Application of Metropolis Monte Carlo Algorithm
3.11. Stochastic Simulation Algorithm with Reaction and Diffusion:Probabilistic Rate Constant–Based Method
3.12. Mapping Probabilistic and Physical Parameters
3.13. Modeling Binding between Multivalent Receptors and Ligands

3.14. Multivalent Receptor–Ligand Binding and Multimolecule Signaling Complex Formation
3.15. Application of Stochastic Simulation Algorithm with Reaction and Diffusion
3.16. Choosing the Most Efficient Simulation Method
3.17. Summary
4 Fluorescence Spectroscopy
Yin Yeh, Samantha Fore, and Huawen Wu
4.1. Introduction
4.2. Fundamental Process of Fluorescence
4.3. Fluorescence Microscopy
4.4. Types of Biological Fluorophores
4.5. Application of Fluorescence in Biophysical Research

4.6. Dynamic Processes Probed by Fluorescence
5 Electrophysiological Measurements of Membrane Proteins
Tsung-Yu Chen, Yu-Fung Lin, and Jie Zheng
5.1. Membrane Bioelectricity
5.2. Electrochemical Driving Force
5.3. Voltage Clamp versus Current Clamp
5.4. Principles of Silver Chloride Electrodes
5.5. Capacitive Current and Ionic Current
5.6. Gating and Permeation Functions of Ion Channels
5.7. Two-Electrode Voltage Clamp for Xenopus Oocyte Recordings
5.8. Patch-Clamp Recordings
5.9. Patch-Clamp Fluorometry
6 Single-Particle Tracking
Michael J. Saxton
6.1. Introduction
6.2. The Broader Field
6.3. Labeling the Dots
6.4. Locating the Dots
6.5. Connecting the Dots
6.6. Interpreting the Dots: Types of Motion
6.7. Is It Really a Single Particle?
6.8. Enhancing z-Resolution
6.9. Can a Single Fluorophore Be Seen in a Cell?
6.10. Colocalization
6.11. Example: Motion in the Plasma Membrane Is More Complicated