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新书资源(2010年8月)

Fundamental concepts in biophysics / Thomas Jue, editor. — New York : Humana, 2009. – (58.171/F981)

Contents

    CONTENTS
    
    1 Mathematical Methods in Biophysics
    1.1. Functions of One Variable and Ordinary Differential Equations 1
    1.2. Functions of Several Variables: Diffusion Equation in One Dimension 2
    1.3. Random Walks and Diffusion 4
    1.4. Random Variables, Probability Distribution, Mean, and Variance 7
    1.5. Diffusion Equation in Three Dimensions 8
    1.6. Complex Numbers, Complex Variables, and Schrodinger's Equation 9
    1.7. Solving Linear Homogeneous Differential Equations 10
    1.8. Fourier Transforms 13
    1.9. Nonlinear Equations: Patterns, Switches and Oscillators 14
    2 Quantum Mechanics Basic to Biophysical Methods
    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
    3.1. Introduction 41
    3.2. Differential Equation-Based Mean-Field Modeling 42
    3.3. Application: Clustering of Receptor-Ligand Complexes 45
    3.4. Modeling Membrane Deformation as a Result of Receptor-Ligand Binding 46
    3.5. Limitations of Mean-Field Differential Equation-Based Modeling 47
    3.6. Master Equation: Calculating the Time Evolution of a Chemically Reacting System 47
    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
    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
    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
    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
    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 201
    Index 233