Nonlinear Cooperative Phenomena in Biological Systems

The Table of Contents for the book is as follows:

• Preface
• Chapter 1
  • Monte Carlo Simulations of Biological Ageing
    • 1. Introduction
    • 2. Azbel theory
    • 3. Penna model
    • 4. Generalization to sex
    • 5. Discussion
  • Why Do Cells Count?
    • 1. Introduction
    • 2. The biochemical explanation of the R point
    • 3. Why is cell cycle progression regulated in this way?
    • 4. Predictions
    • 5. Conclusions
  • Quantal DNA Replication and Hedgehog Cytoskeleton Induced by Lyotropic Harmonic-Liquid Crystal Like Membrane Dynamics
    • 1. Introduction
    • 2. Binding of ligands to the blast cell
    • 3. The quantal DNA replication
    • 4. Lyotropic self-duality
    • 5. Generalization to three spatial dimensions
    • 6. Analogy with superconductor
    • 7. Lyotropically induced order parameters, chirality and cytoskeleton dynamics
    • 8. Dynamic instability and variable length of growing microtubules
    • 9. Hedgehog cytoskeleton solution from nonabelian model
    • 10. Coherent light in a counting cell
  • Punctuated Equilibria vs Darwin?
    • 1. Introduction
    • 2. On self-organized criticality (SOC)
    • 3. The Fossil record
    • 4. Mathematical models
    • 5. Critical ecologies
    • 6. Concluding remarks
  • Evolution at Molecular Resolution
    • 1. Introduction
    • 2. Evolution of molecules
    • 3. Theory of molecular evolution
    • 4. Modeling evolutionary dynamics
    • 5. Genotype-phenotype mapping of RNA
    • 6. Optimization of RNA structures
    • 7. Statistical topology and evolution
  • Self-Organization of Colloids and Interfaces
    • 1. Introduction
    • 2. The morphology of wetting layers
    • 3. The morphology of membranes
    • 4. Self-assembly and bending elasticity
    • 5. Curvature arsing from dispersed particles
    • 6. Colloidal machines
• Chapter 2
  • Is Myoglobin Like a Swiss Watch?
    • 1. Introduction
    • 2. Conformation and Energy Landscapes
    • 3. Kinetics and the Reaction Coordinate
    • 4. Problems and Puzzles
    • 5. The Input Data
    • 6. The Model
    • 7. Conclusions
  • Collective Proton Freezing in Hydrated Protein Powders
    • 1. Introduction
    • 2. Experimental results
    • 3. Discussion
    • 4. Biological implications of the glassy transition
  • Energy Landscapes of Folding Proteins: The Effects of Nonlinearity and Cooperativity
  • Effects of Long-Range Dispersion in Nonlinear Dynamics of DNA Molecules
    • 1. Introduction
    • 2. System and equations of motion
    • 3. Tails of intrinsically localized states
    • 4. Switching between bistable states
    • 5. Conclusion
  • Investigations — A Beginning Draft
    • 1. Introduction
    • 2. Prolegomenon to a general biology
• Chapter 3
  • Spin Glasses, Random Boolean Networks and Simple Models of Evolution
    • 1. Introduction
    • 2. Mean field spin glasses
    • 3. Random boolean networks and random map models
    • 4. A simple model of evolution
    • 5. Conclusion
  • Mechanical Properties of Membranes and Cell Polarity
    • 1. Introduction
    • 2. Elastic properties of layered membranes with closed surfaces
    • 3. Shapes of unsupported cells and phospholipid vesicles
    • 4. Shapes of cells and phospholipid vesicles subject to axial force
    • 5. Discussion
  • Nonlinear Chemical Catalysis and Making of Molecular Ecosystems
  • Cooperative Interactions in DNA Systems
• Chapter 4
  • Collective Ratchet Effects Induced by Harmonic Forcing and Temperature
    • 1. Introduction
    • 2. Anisotropic substrate potentials and equations of motion
    • 3. Mobility of topological solitons
    • 4. Kink motion driven by a harmonic force
    • 5. Thermal kink dynamics in a bistable chain: analytical results
    • 6. Numerical results for the bistable chain
    • 7. Summary and outlook
  • Nonlinear Energy Localization in a Lattice: Applications in Biomolecular Physics
    • 1. Introduction
    • 2. Intrinsic localized modes
    • 3. A first step in the formation of intrinsic localized modes: modulational instability
    • 4. Growth of large amplitude breathers
    • 5. Nonlinear energy localization in complex lattices
    • 6. DNA thermal denaturation: nonlinear energy localization in a biological molecule
    • 7. Conclusion
  • Statistical Physics, Neural Networks, Brain Studies
    • 1. Introduction
    • 2. A trajectory through statistical physics
  • Ligand Gated Ion Channel Currents in Lyotropic, Chemically Open, Nonstationary System
    • 1. Introduction
    • 2. Independent channel ligandation
    • 3. From molecular interaction to macroscopic effect
    • 4. Phenomenology and discussion of results
• Abstracts
  • Vegetation Dynamics as a Nonlinear Cooperative Phenomenon
  • TDXanes Study of the Conformational Landscape of Trehalose Coated MbCO
  • Speciation by Competition in a Smooth Fitness Landscape
  • Interparticle Interactions and Subunit Dissociation from Light Scattering Experiment on Hemoglobin
  • Anomalous Flexibility of DNA Fragments from Stochastic Simulations and Dynamic Fluorescence Spectroscopy
  • Direction of Protein Biosynthesis and its Conformational Consequences
  • Immunization, Aging and Learning Process
  • The Evolution of HIV Infection: A Cellular Automaton Approach
• Summary of Panel Discussion