Contents
Cover
Title page
Copyright page
Introduction
Part I: Biophysics of Complex Systems
I. Kinetics of Biological Processes
Chapter 1: Qualitative Methods for Studying Dynamic Models of Biological Processes
1.1 General Principles of Description of Kinetic Behavior of Biological Systems
1.2 Qualitative Analysis of Elementary Models of Biological Processes
Chapter 2: Types of Dynamic Behavior of Biological Systems
2.1 Biological Triggers
2.2 Oscillatory Processes in Biology. Limit Cycles
2.3 Time Hierarchy in Biological Systems
Chapter 3: Kinetics of Enzyme Processes
3.1 Elementary Enzyme Reactions
3.2 Multiplicity of Stationary States in Enzyme Systems
3.3 Oscillations in Enzyme Systems
3.4 Mathematical Modeling of Metabolic Pathways
Chapter 4: Self-Organization Processes in Distributed Biological Systems
4.1 General Characteristics of Autowave Processes
4.2 Mathematical Models of Self-Organized Structures
4.3 Chaotic Processes in Determined Systems
II. Thermodynamics of Biological Processes
Chapter 5: Thermodynamics of Irreversible Processes in Biological Systems Near Equilibrium (Linear Thermodynamics)
Chapter 6:
Thermodynamics of Systems Far From Equilibrium (Nonlinear Thermodynamics)
Part II: Molecular Biophysics
III. Three-dimensional Organization of Biopolymers
Chapter 7: Three-dimensional Configurations of Polymer Molecules
7.1 Statistical Character of Polymer Structure
7.2 Volumetric Interactions and Globule–Coil Transitions in Polymer Macromolecules
7.3 Phase Transitions in Proteins
Chapter 8: Different Types of Interactions in Macromolecules
8.1 Van-der-Waals Interactions
8.2 Hydrogen Bond. Charge–Dipole Interactions
8.3 Internal Rotation and Rotational Isomerism
Chapter 9: Conformational Energy and Three-dimensional Structure of Biopolymers
9.1 Conformational Energy of Polypeptide Chains
9.2 Numerical Methods for Estimation of Conformational Energy of Biopolymers
9.3 Predictions of Three-dimensional Structure of Proteins
9.4 Peculiarities of Three-dimensional Organization of Nucleic Acids
9.5 State of Water and Hydrophobic Interactions in Biostructures
9.6 Protein Folding
IV. Dynamic Properties of Globular Proteins
Chapter 10: Protein Dynamics
10.1 Structural Changes in Proteins
10.2 Conformational Mobility of Proteins by the Data of Different Methods
Chapter 11: Physical Models of Dynamic Mobility of Proteins
11.1 General Characteristic of Molecular Dynamics of Biopolymers
11.2 Model of Limited Diffusion (Brownian Oscillator with Strong Damping)
11.3 Numerical Modeling of Molecular Dynamics of Proteins
11.4 Molecular Dynamics of Protein Myoglobin
11.5 Dynamic Models of DNA
11.6 Direct Modeling of Interactions of Proteins
Further Reading
Part III: Biophysics of Membrane Processes
V. Structure-functional Organization of Biological Membranes
Chapter 12: Molecular Organization of Biological Membranes
12.1 Composition and Structure of Biological Membranes
12.2 Formation of Membrane Structures
12.3 Thermodynamics of Membrane Formation and Stability
12.4 Mechanical Properties of Membranes
12.5 Effect of Electric Fields on Cells
Chapter 13: Conformational Properties of Membranes
13.1 Phase Transitions in Membrane Systems
13.2 Lipid – Lipid Interactions in Membranes
13.3 Lipid – Protein and Protein – Protein Interactions in Membranes
13.4 Peroxidation of Biomembrane Lipids
VI. Transport of Substances and Bioelectrogenesis
Chapter 14: Nonelectrolyte Transport
14.1 Diffusion
14.2 Facilitated Diffusion
14.3 Water Transport. Aquaporins
Chapter 15: Ion Transport. Ionic Equilibria
15.1 Electrochemical Potential
15.2 Ion Hydration
15.3 Ionic Equilibrium on the Phase Interface
15.4 Profiles of Potential and Concentrations at the Interface
15.5 Double Electric Layer
Chapter 16: Electrodiffusion Theory of Ion Transport Across Membranes
16.1 The Nernst – Planck Equation of Electrodiffusion
16.2 Constant Field Approximation
Chapter 17: Induced Ion Transport
17.1 Bilayer Lipid Membranes
17.2 Mobile Carriers
17.3 Channel-forming Reagents
17.4 Effect of Surface and Dipole Potentials on the Ion Transport Rate
Chapter 18: Ion Transport in Channels
18.1 Discrete Description of Transport
18.2 Channel Blocking and Saturation
18.3 General Properties of Ion Channels in Nervous Fibers
18.4 Molecular Structure of Channels
18.5 Electric Fluctuations of Membrane Properties
Chapter 19: Ion Transport in Excitable Membranes
19.1 Action Potential
19.2 Ion Currents in the Axon Membrane
19.3 Description of Ionic Currents in the Hodgkin – Huxley Model
19.4 Gating Currents
19.5 Impulse Propagation
Chapter 20: Active Transport
20.1 Calcium Pump
20.2 Sodium-Potassium Pump
20.3 Electrogenic Ion Transport
20.4 Proton Transport
VII. Energy Transformation in Biomembranes
Chapter 21: Electron Transport and Energy Transformation in Biomembranes
21.1 General Description of Energy Transformation in Biomembranes
21.2 Mechanisms of Proton Translocation and Generation of ΔμH+ in Respiratory and Photosynthetic Chains of Electron Transport
21.3 ATPase Complex
21.4 ATPase Complex as a Molecular Motor
Chapter 22: Physics of Muscle Contraction, Actin-Myosin Molecular Motor
22.1 General Description of Energy Transformation in Systems of Biological Motility
22.2 Basic Information on Properties of Cross-striated Muscles
22.3 Structural Organization of Muscle Contractile and Regulatory Proteins
22.4 Mechanochemical Transformation of Energy in Muscles. Lymn – Taylor Scheme
22.5 Three-dimensional Structure of Actin and the Myosin Head
22.6 Mechanism of the Work Cycle of the Actin-Myosin Motor
Chapter 23: Biophysics of Processes of Intracellular Signaling
23.1 General Regularities of Intracellular Signaling
23.2 Biophysics of Cellular Signaling
23.3 Methods for Studying Cell Signaling
Further Reading
VIII. Electronic Properties of Biopolymers
Chapter 24: Fundamentals of Quantum Description of Molecules
24.1 Introduction
24.2 Stationary and Non-stationary States of Quantum Systems. Principle of Superposition of States
24.3 Theory of Non-stationary Excitations — Theory of Transitions
24.4 Model of a Hydrogen Molecule Ion. Nature of Chemical Bonds
24.5 Method of Molecular Orbitals
24.6 Manifestation of Electronic Properties of Biopolymers
Chapter 25: Mechanisms of Charge Transfer and Energy Migration in Biomolecular Structures
25.1 Tunneling Effect
25.2 The Charge Transfer Theory
25.3 Role of Hydrogen Bonds in Electron Transport in Biomolecular Systems
25.4 Dynamics of Photoconformational Transfer
25.5 Mechanisms of Energy Migration
Chapter 26: Ion Transport in Excitable Membranes
26.1 Physicochemical Description and Biophysical Models of Enzyme Processes
26.2 Electron Conformational Interactions upon Enzyme Catalysis
26.3 Electronic Interactions in the Enzyme Active Center
26.4 Molecular Modeling of the Structure of an Enzyme – Substrate Complex
Part IV. Biophysics of Photobiological Processes
IX. Primary Processes of Photosynthesis
Chapter 27: Energy Transformation in Primary Processes of Photosynthesis
27.1 General Characteristic of Initial Stages of Photobiological Processes
27.2 General Scheme of Primary Processes of Photosynthesis
27.3 Structural Organization of Pigment–Protein Antenna Complexes
27.4 Mechanisms of Transformation of Excitation Energy in Photosynthetic Membrane
27.5 Reaction Centers in Purple Photosynthesizing Bacteria
27.6 Pigment – Protein Complex of Photosystem I
27.7 Pigment – Protein Complex of Photosystem II
27.8 Variable and Delayed Fluorescence
Chapter 28: Electron-Conformational Interactions in Primary Processes of Photosynthesis
28.1 Studies of Superfast Processes in Reaction Centers of Photosynthesis
28.2 Initial Charge Separation in RCs
28.3 Mechanisms of Cytochrome Oxidation in Reaction Centers
28.4 Conformational Dynamics and Electron Transfer in Reaction Centers
28.5 Electron Transfer and Formation of Contact States in the System of Quinone Acceptors (
PQ
A
Q
B
)
28.6 Mathematical Models of Primary Electron Transport Processes in Photosynthesis
X. Primary Processes in Biological Systems
Chapter 29: Photo-conversions of Bacteriorhodopsin and Rhodopsin
29.1 Structure and Functions of Purple Membranes
29.2 Photocycle of Bacteriorhodopsin
29.3 Primary Act of Bacteriorhodopsin Photoconversions
29.4 Model Systems Containing Bacteriorhodopsin
29.5 Molecular Bases of Visual Reception. Visual Cells (Rods)
29.6 Primary Act of Rhodopsin Photoconversion
Chapter 30: Photoregulatory and Photodestructive Processes
30.1 General Characteristics of Photoregulatory Processes
30.2 Photoreceptors and Molecular Mechanisms of Photoregulatory Processes. Phytochromes
30.3 General Characteristics of Photodestructive Processes
30.4 Photochemical Reactions in DNA and Its Components
30.5 Effects of High-intensity Laser UV Irradiation on DNA (Two-quantum Reactions)
30.6 Photoreactivation and Photoprotection
30.7 Ultraviolet Light Action on Proteins
30.8 Sensitized Damage of Biomolecules in Photodynamic Reactions
30.9 Photosensitized Effects in Cell Systems
Further Reading
Index
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Guide
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