| ORIGINS AND EVOLUTION OF LIFE |
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| Initiation |
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| Machinery of prokaryotic cells |
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| The Photosynthetic revolution |
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| Origins of diploidal eukaryotic cells |
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| Summary: Further stages of evolution |
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| STRUCTURE OF BIOMOLECULES |
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| Elementary building blocks |
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| Generalized ester bonds |
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| Directionality of chemical bonds |
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| Weaker intratomic interactions |
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| Hydrogen bonds and hydrophobic interactions |
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| Amphipatic molecules in water environments |
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| Structure of proteins |
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| Structures of nucleic acids |
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| DYNAMICS OF BIOMOLECULES |
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| Diffusion |
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| Vibration versus conformational transitions |
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| Stochastic theory of reaction rates |
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| Conformational transitions of proteins |
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| Models of random walks on fractal lattices |
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| Introduction to polymer biophysics |
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| Cellular automata |
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| Bioenergetics: The Davydov model |
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| Biological coherence: The Froehlich model |
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| Ionic currents through electrolytes |
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| Electron conduction and tunneling |
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| Proton transport |
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| Interactions with electromagnetic radiation |
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| STRUCTURE OF A BIOLOGICAL CELL |
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| General characteristics of a cell |
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| Membrane and membrane proteins |
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| Ion channels and ion pumps |
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| Cytoplasm |
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| Cytoskeleton: The proteins participating in cytoskeletal organization |
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| Networks, stress fibers, and tensegrity |
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| Motor proteins and their roles in cellular processes |
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| Centrioles, basal bodies, cilia, and flagella |
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| Cell energetics: Chloroplasts and mitochondria |
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| Other organelles |
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| Nucleus: Nuclear chromatin, chromosomes, and nuclear lamina |
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| Cell division |
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| Cell intelligence |
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| Biological signaling |
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| NONEQUILIBRIUM THERMODYNAMICS AND BIOCHEMICAL REACTIONS |
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| Second law of thermodynamics |
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| Nonequilibrium thermodynamics |
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| Rates of nonequilibrium thermodynamics processes |
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| Single unimolecular chemical reaction |
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| Bimolecular reactions: Protolysis |
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| Redox reactions |
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| The steady state approximation: The theory of reaction rates |
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| Chemical mechanisms of enzymatic catalysis |
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| Michaelis-Menten kinetics |
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| Control of enzymatic reactions |
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| MOLECULAR AND BIOLOGICAL MACHINES |
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| Biological motion |
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| Free energy transduction |
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| Chemo-chemical machines |
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| Biological machines as biased Maxwell's demons |
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| Pumps and motors as chemochemical machines |
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| Flux-force dependence |
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| Overview of motor protein biophysics |
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| Biochemical energy currency: ATP molecules |
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| Assembly of microtubules |
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| Assembly of actin filaments |
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| Muscle contraction: Biophysical mechanisms, contractile proteins |
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| NERVE CELLS |
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| Anatomy of a nerve cell |
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| Conducting properties of neurons |
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| Action potential generation, Huxley-Hodgkin equations |
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| Structure and function of synapse |
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| Neural network models |
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| TISSUE AND ORGAN BIOPHYSICS |
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| Introduction |
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| Anatomy and physiology of human circulatory system |
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| Heart dynamics |
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| Energy management in the human body |
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| Respiration biophysics |
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| Kidney physiology and dialysis |
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| Muscle biophysics |
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| Bone stiffness and strength |
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| Vision biophysics |
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| Sound perception biophysics |
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| Gross features of the nervous system |
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| Bioelectricity and biomagnetism |
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| Immune system and its models |
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| BIOLOGICAL SELF-REGULATION AND SELF-ORGANIZATION |
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| Introduction |
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| Self-organization |
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| Homeostasis |
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| First law of thermodynamics and living organisms |
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| Physics of animal thermoregulation |
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| Allometric laws in physiology |
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| Entropy and information |
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| Entropy reduction in living systems |
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| Biological information |
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| Evolutionary theories |
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| Epilogue: Toward New Physics and New Biology |
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| APPENDIX 1 - Random Walks and Diffusion |
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| APPENDIX 2 - Models of Phase Transitions and Criticality |
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| APPENDIX 3 - Foundations of Nonlinear Physics |
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