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 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 research 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.

Includes supplementary material: sn.pub/extras

1 Mathematical Methods in BiophysicsRajiv R.P. Singh1.1. Functions of One Variable and Ordinary Differential Equations1.2. Functions of Several Variables: Diffusion Equation in One Dimension1.3. Random Walks and Diffusion1.4. Random Variables, Probability Distribution, Mean, and Variance1.5. Diffusion Equation in Three Dimensions1.6. Complex Numbers, Complex Variables, and Schrödinger's Equation1.7. Solving Linear Homogeneous Differential Equations1.8. Fourier Transforms1.9. Nonlinear Equations: Patterns, Switches and Oscillators2 Quantum Mechanics Basic to Biophysical MethodsWilliam Fink2.1. Quantum Mechanics Postulates2.2. One-Dimensional Problems2.3. The Harmonic Oscillator2.4. The Hydrogen Atom2.5. Approximate Methods2.6. Many Electron Atoms and Molecules2.7. The Interaction of Matter and Light3 Computational Modeling of Receptor¿Ligand Binding and Cellular Signaling ProcessesSubhadip Raychaudhuri, Philippos Tsourkas, and Eric Willgohs3.1. Introduction3.2. Differential Equation-Based Mean-Field Modeling3.3. Application: Clustering of Receptor¿Ligand Complexes3.4. Modeling Membrane Deformation as a Result of Receptor¿Ligand Binding3.5. Limitations of Mean-Field Differential Equation-Based Modeling3.6. Master Equation: Calculating the Time Evolution of a Chemically Reacting System3.7. Stochastic Simulation Algorithm (SSA) of Gillespie3.8. Application of the Stochastic Simulation Algorithm (SSA)3.9. Free Energy-Based Metropolis Monte Carlo Simulation3.10. Application of Metropolis Monte Carlo Algorithm3.11. Stochastic Simulation Algorithm with Reaction and Diffusion:Probabilistic Rate Constant¿Based Method3.12. Mapping Probabilistic and Physical Parameters3.13. Modeling Binding between Multivalent Receptors and Ligands3.14. Multivalent Receptor¿Ligand Binding and Multimolecule Signaling Complex Formation3.15. Application of Stochastic Simulation Algorithm with Reaction and Diffusion3.16. Choosing the Most Efficient Simulation Method3.17. Summary4 Fluorescence SpectroscopyYin Yeh, Samantha Fore, and Huawen Wu4.1. Introduction4.2. Fundamental Process of Fluorescence4.3. Fluorescence Microscopy4.4. Types of Biological Fluorophores4.5. Application of Fluorescence in Biophysical Research4.6. Dynamic Processes Probed by Fluorescence5 Electrophysiological Measurements of Membrane ProteinsTsung-Yu Chen, Yu-Fung Lin, and Jie Zheng5.1. Membrane Bioelectricity5.2. Electrochemical Driving Force5.3. Voltage Clamp versus Current Clamp5.4. Principles of Silver Chloride Electrodes5.5. Capacitive Current and Ionic Current5.6. Gating and Permeation Functions of Ion Channels5.7. Two-Electrode Voltage Clamp for Xenopus Oocyte Recordings5.8. Patch-Clamp Recordings5.9. Patch-Clamp Fluorometry6 Single-Particle TrackingMichael J. Saxton6.1. Introduction6.2. The Broader Field6.3. Labeling the Dots6.4. Locating the Dots6.5. Connecting the Dots6.6. Interpreting the Dots: Types of Motion6.7. Is It Really a Single Particle?6.8. Enhancing z-Resolution6.9. Can a Single Fluorophore Be Seen in a Cell?6.10. Colocalization6.11. Example: Motion in the Plasma Membrane Is More Complicated