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