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作者 Dewey, T. Gregory
書名 Fractals in Molecular Biophysics
出版項 Cary : Oxford University Press, Incorporated, 1998
©1997
國際標準書號 9780195359183 (electronic bk.)
9780195084474
book jacket
說明 1 online resource (289 pages)
text txt rdacontent
computer c rdamedia
online resource cr rdacarrier
系列 Topics in Physical Chemistry Ser
Topics in Physical Chemistry Ser
附註 Intro -- Contents -- 1 What Are Fractals? -- 1.1 Basic Concepts -- 1.2 Fractals and Set Theory -- 1.3 Self-Affine Fractals -- 1.4 Multifractals and the Partition Function -- 1.5 Fractals and the Renormalization Group -- 1.6 Summary -- 2 Fractal Aspects of Protein Structure -- 2.1 Polymers as Mass Fractals -- 2.1.1 The Radius of Gyration and the Fractal Dimension -- 2.1.2 Scaling of Excluded Volume, Ideal, and Collapsed Polymers -- 2.2 Fractal Dimension of the Protein Backbone -- 2.2.1 Measuring the Fractal Dimension -- 2.2.2 Significance of the Fractal Dimension -- 2.3 Scaling Properties of Protein Surfaces -- 2.4 Determining Fractal Dimensions by Scattering Techniques -- 2.4.1 Basic Concepts -- 2.4.2 Low-Angle Scattering from Proteins -- 2.5 Scaling Laws for Membrane Proteins -- 2.6 Summary -- 3 Loops, Polymer Statistics, and Helix-Coil Transitions -- 3.1 Random Walks and Loops -- 3.2 Real Space Renormalization Groups -- 3.2.1 The Self-Avoiding Walk -- 3.2.2 Ring Closure -- 3.3 The Entropy of Loop Formation -- 3.3.1 Loop Formation in Proteins -- 3.3.2 Loop Formation in Nucleic Acids -- 3.3.3 Comparison with Theory -- 3.4 Constraints on the Size of Enzymes and Receptors -- 3.5 The Statistical Mechanics of Biopolymers -- 3.5.1 Sequence-Generating Functions -- 3.5.2 Calculations on the Alpha Helix -- 3.5.3 The Finite Perfect Matching Double Strand -- 3.6 Summary -- 4 The Multifractality of Biomacromolecules -- 4.1 Origins of Multifractality -- 4.1.1 Random Multiplicative Processes -- 4.1.2 Random Walks on Random Media -- 4.2 Multifractal Behavior of the Generalized Cantor Set -- 4.3 Multifractality of Order-Disorder Transitions in Biopolymers -- 4.3.1 Sequence-Generating Functions and Multifractals -- 4.3.2 Alpha Helical Model -- 4.3.3 Perfect Matched Double Helix -- 4.4 Protein Structure and Multifractals
4.4.1 Algorithm for Calculating Multifractal Spectra -- 4.4.2 Multifractal Spectra of Solvent Accessibilities from Proteins -- 4.4.3 Origins of Multifractality in Proteins -- 4.5 Summary -- Appendix: Extraction Procedures and Comparison with Transfer Matrix Methods -- 5 Fractal Diffusion and Chemical Kinetics -- 5.1 Diffusion and Dimensionality -- 5.2 Fractal Chemical Kinetics -- 5.2.1 Fluctuations and Anomalous Scaling -- 5.2.2 Scaling of Depletion Zones -- 5.2.3 Anomalous Reaction Order -- 5.2.4 Scaling in Chemically Controlled Reactions -- 5.3 Isotope Exchange Kinetics in Proteins -- 5.3.1 Models of Exchange in Lysozyme -- 5.3.2 Reactions on Spheres and Surface Fractals -- 5.3.3 Reaction Widths in Proteins -- 5.3.4 Fractal Effects on Chemically Controlled Reactions -- 5.3.5 Summary of Hydrogen Exchange in Proteins -- 5.4 Diffusion and Reaction in an Archipelago -- 5.5 Other Diffusional Processes -- 5.6 Summary -- 6 Are Protein Dynamics Fractal? -- 6.1 Introduction to Protein Dynamics -- 6.2 The Origins of Nonexponential Behavior -- 6.2.1 Random Multiplicative Processes and the Log-Normal Distribution -- 6.2.2 Static and Dynamic Disorder Models -- 6.3 Fractal Time -- 6.3.1 Long Tail Distributions and Fractal Time -- 6.3.2 A Chemical Kinetic Model with Fractal Time -- 6.3.3 Hierarchical and Defect-Diffusion Models -- 6.4 Ion Channel Kinetics -- 6.5 Summary -- 7 Fractons and Vibrational Relaxation in Proteins -- 7.1 Lattice Diffusion and Fracton Dynamics -- 7.1.1 Lattice Dynamics and Scaling Arguments -- 7.1.2 Fractons -- 7.2 Experimental Techniques for Determining the Density of States -- 7.2.1 Heat Capacity Measurements on Biological Systems -- 7.2.2 Electron Spin Relaxation and Proteins with Iron Centers -- 7.2.3 Neutron Scattering from Proteins -- 7.3 Density of States of Simple Polymer Models
7.4 Random Walks on Multiply Connected Linear Arrays -- 7.5 Summary -- 8 Encoded Walks and Correlations in Sequence Data -- 8.1 Encoded Walks and Scaling Laws -- 8.2 Correlations in DNA Sequences -- 8.3 The Brownian Bridge and Protein Sequences -- 8.4 The Connection with Multifractals -- 8.5 Information Theory and the Ergodicity of Protein Sequences -- 8.6 Summary -- 9 Percolation -- 9.1 Introduction to Percolation Phenomena -- 9.1.1 Scaling Laws for Percolation -- 9.1.2 Real-Space Renormalization -- 9.1.3 Percolation Clusters as Fractals -- 9.2 Antibody-Receptor Clustering and the Cayley Tree -- 9.2.1 Clustering and the Immune Response System -- 9.2.2 Percolation on the Cayley Tree -- 9.3 Percolation in Biomembranes -- 9.3.1 Fluorescence Recovery after Photobleaching -- 9.3.2 Finite Size Scaling -- 9.3.3 Continuum and Correlated Percolation Thresholds -- 9.4 Percolation of Proton Transport in Hydrated Proteins -- 9.5 Summary -- Appendix: A Correlated Percolation Model for Biomembranes -- 10 Chaos in Biochemical Systems -- 10.1 Chaos in Chemical Systems -- 10.1.1 Chemical Kinetics in Simple Systems -- 10.1.2 Open Systems, Oscillations, and Chaos -- 10.1.3 Origins of Chaos -- 10.2 Theoretical Models of Enzymatic Chaos -- 10.2.1 Mechanisms involving Michaelis-Menten Enzymes -- 10.2.2 Mechanisms involving Allosteric Enzymes -- 10.3 Experimental Systems -- 10.3.1 Glycolytic Oscillations -- 10.3.2 Horseradish Peroxidase -- 10.4 Physiological Advantages of Chaos -- 10.5 Summary -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- P -- R -- S -- U -- V -- W
1. What Are Fractals?2. Fractal Aspects of Protein Structure3. Loops, Polymer Statistics, and Helix-Coil Transitions4. The Multifractality of Biomacromolecules5. Fractal Diffusion and Chemical Kinetics6. Are Protein Dynamics Fractal?7. Fractons and Vibrational Relaxation in Proteins8. Encoded Walks and Correlations in Sequence Data9. Percolation10. Chaos in Biochemical SystemsIndex
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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2020. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
鏈接 Print version: Dewey, T. Gregory Fractals in Molecular Biophysics Cary : Oxford University Press, Incorporated,c1998 9780195084474
主題 Molecular biology -- Mathematical models.;Biophysics -- Mathematical models.;Fractals
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