Lays the foundations for the study of biophysics. 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 Binding 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.
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 Schrodinger'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 than is Often Assumed 6.12. Example: From DNA to Protein 6.13. Example: Infection of a Cell by a Virus 7 NMR Measurement of Biomolecule Diffusion Thomas Jue 7.1. Introduction 7.2. Relaxation and Field Gradient Measurement of Diffusion 7.3. Frequency Encoding of Spatial Position with Field Gradient 7.4. Phase Encoding by the Field Gradient 7.5. Diffusion and Pulsed Field Gradient Signal Intensity 7.6.Fick's Laws of Diffusion 7.7. Biomolecule Diffusion in the Cell 7.8. Stimulated Echo and Biomolecule Diffusion in the Cell 7.9. Myoglobin Function in the Cell 7.10. Perfused Heart Model 7.11. O2 Diffusion in Muscle Cell 7.12. Translational Diffusion of Mb in Vitro 7.13. Translational Diffusion of Mb In Vivo 7.14. Mb Contribution to O2 transport in Vivo 7.15. Mb-Facilitated Diffusion and Myocardial Function 7.16. Mb-Facilitated Diffusion and Skeletal Muscle Function 7.17. Cytoplasmic Properties and Architecture 7.18. Summary Problem Solutions Index
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.
From the reviews: "Thomas Jue from the University of California Davis, has introduced a new series of books under the title Handbook of Modern Biophysics. ! Reading of the first volume of the series Handbook of Modern Biophysics leads to the conclusion that this form of presentation of modern biophysical problems is very useful from the educational point of view. ! very helpful for students and young scientists working in molecular biology, biochemistry or molecular physics." (Genowefa A'losarek, Acta Biochimica Polonica, December, 2009) "The book 'Fundamental Concepts in Biophysics' launches new book series, which shall be dedicated to exploration of physical techniques that are used to study biological systems. ! Problems solutions are listed at the end of the book. Suggestions for further reading are included, as well. The book represents a very welcomed text for graduated students, their mentors, or for advanced researchers planning an excursion into a new experimental field." (A ubica Lacinova, General Physiology and Biophysics, Vol. 29, April, 2010)