Table Of Contents:
Introduction v

Building Blocks and Structure 1(16)

Atoms and Ions 1(3)

Subatomic Particles 1(2)

Atomic Constituents of Life 3(1)

Ions 3(1)

Molecules Essential for Life 4(7)

Water 4(1)

Proteins 5(3)

Lipids 8(2)

Carbohydrates 10(1)

Cholesterol 10(1)

Nucleic Acid 11(1)

What Is Life? 11(6)

Requirements for Life 12(1)

Domains of Life 12(1)

Characteristics of Living Cells 12(1)

Structure of Living Cells 13(1)

Boundary of Life 13(4)

Living State Interactions 17(12)

Forces and Molecular Bonds 17(3)

Ionic Bonds 18(1)

Covalent Bonds 19(1)

Hydrogen Bonds 19(1)

Van der Waal Forces 20(1)

Electric and Thermal Interactions 20(1)

Electric Dipoles 21(3)

Polarization and Induced Dipoles 23(1)

Casimir Interactions 24(2)

Domains of Physics in Biology 26(3)

Exercises 27(2)

Heat Transfer in Biomaterials 29(10)

Heat Transfer Mechanisms 29(3)

Conduction 30(1)

Convection 30(1)

Radiation 31(1)

The Heat Equation 32(3)

Transient Heat Flow 32(2)

Steady State Heat Flow 34(1)

Joule Heating of Tissue 35(4)

Exercises 37(2)

Living State Thermodynamics 39(22)

Thermodynamic Equilibrium 40(1)

First Law of Thermodynamics and Conservation of Energy 40(1)

Entropy and the Second Law of Thermodynamics 41(2)

Does Life Violate the Second Law? 41(1)

Measures of Entropy? 42(1)

Free Expansion of a Gas 42(1)

Physics of Many Particle Systems 43(6)

How Boltzmann Factors in Biology 44(1)

Canonical Partition Function 45(1)

Average Energy 46(1)

Entropy and Free Energy 47(1)

Heat Capacity 48(1)

Two-State Systems 49(1)

Continuous Energy Distribution 50(1)

Composite Systems 50(3)

DNA Stretching 51(2)

Casimir Contribution to the Free Energy 53(2)

Lipid Bilayer Tubes 53(1)

Rouleax 53(2)

Protein Folding and Unfolding 55(6)

Protein Unfolding 55(1)

Levinthal's Paradox 55(1)

Energy Landscape 56(1)

Folding on a Lattice 57(1)

Monte Carlo Methods 58(1)

Folding @home 59(1)

Exercises 59(2)

Open Systems and Chemical Thermodynamics 61(18)

Enthalpy, Gibbs Free Energy, and Chemical Potential 61(3)

Chemical Reactions 64(2)

First-Order Reactions 64(1)

Second-Order Reactions 65(1)

Activation Energy and Rate Constants 66(4)

Detailed Balance 68(1)

Nitrogen Fixation 69(1)

Enzymatic Reactions 70(3)

ATP Hydrolysis and Synthesis 73(1)

Entropy of Mixing 74(1)

The Grand Canonical Ensemble 74(2)

Hemoglobin 76(3)

Exercises 77(2)

Diffusion and Transport 79(22)

Maxwell-Boltzmann Statistics 79(2)

Brownian Motion 81(3)

Fick's Laws of Diffusion 84(4)

Fick's First Law 84(1)

Fick's Second Law 85(1)

Quantum Diffusion 86(1)

Time-Independent Concentrations 86(1)

Fick's Law for Growing Bacterial Cultures 87(1)

Sedimentation of Cell Cultures 88(1)

Diffusion in a Centrifuge 89(2)

Diffusion in an Electric Field 91(1)

Lateral Diffusion in Membranes 92(1)

Navier---Stokes Equation 93(2)

Reynolds Number 94(1)

Low Reynolds Number Transport 95(2)

Purcell's ``Life at Low Reynolds Number'' 95(1)

Coasting Distance of a Bacterium 95(2)

Active and Passive Membrance Transport 97(4)

Exercises 98(3)

Fluids 101(10)

Laminar and Turbulent Fluid Flow 101(1)

Bernoulli's Equation 102(1)

Equation of Continuity 103(1)

Venturi Effect 104(2)

Fluid Dynamics of Circulatory Systems 106(3)

Viscous Flow 106(1)

Vessel Constriction and Aneurysm 107(1)

Variation of Blood Pressure with Depth 108(1)

Microgravity Effects 108(1)

Capillary Action 109(2)

Exercises 110(1)

Bioenergetics and Molecular Motors 111(16)

Kinesins, Dyneins, and Microtubule Dynamics 111(2)

Brownian Motors 113(3)

Feynman Ratchet 113(2)

Kinesin Brownian Dynamics 115(1)

Myosin Brownian Dynamics 115(1)

ATP Synthesis in Mitochondria 116(2)

Electron Transport Chain 116(1)

ATP Synthase 117(1)

Torque Generation in ATP Synthase 118(1)

Photosynthesis in Chloroplasts 118(2)

Photosystem II 120(1)

Photosystem I 120(1)

Light Absorption in Biomolecules 120(2)

Vibrational Spectra of Biomolecules 122(5)

Square Well Potential 122(1)

Harmonic Oscillator Potential 122(3)

Exercises 125(2)

Passive Electrical Properties of Living Cells 127(26)

Poisson---Boltzmann Equation 127(4)

One---One Valent Electrolytes 129(1)

Low Field Limit 130(1)

Spherical Solution 130(1)

Intrinsic Membrane Potentials 131(1)

Induced Membrane Potentials 132(6)

Plasma Membrane 132(2)

Liposome in a Static Electric Field 134(1)

Spherical Cell in an Alternating Electric Field 135(1)

Inertial Effects in Field-Induced Counterion Motion 136(1)

Induced Potentials in Organelle Membranes 136(1)

Mitochondrion in an Alternating Electric Field 137(1)

Bioimpedance 138(7)

Time Harmonic Current Flow 138(1)

Dielectric Spectroscopy 139(3)

Deybe Relaxation Model 142(1)

Cole Equation 142(1)

Maxwell---Wagner Effect 143(1)

Skin Impedance 144(1)

Electrode Polarization 144(1)

Bioimpedance Simulator 145(3)

Nonlinear Effects 148(5)

Exercises 149(4)

Nerve Conduction 153(16)

Nerve Impulses 153(1)

Neurotransmitters and Synapses 154(1)

Passive Transport in Dendrites 155(1)

Active Transport and the Hodgkin---Huxley Equations 156(4)

Simulation of Action Potential 160(3)

Excitation Threshold 160(1)

Neuronal Refactoriness 160(1)

Repetitive Spiking 161(2)

FitzHugh---Nagumo Model 163(3)

Action Potentials in the Earthworm Nerve Fiber 166(3)

Exercises 168(1)

Mechanical Properties of Biomaterials 169(8)

Elastic Moduli 169(3)

Young's Modulus 169(1)

Shear Modulus 170(1)

Poisson's Ratio 171(1)

Electric Stresses in Biological Membranes 172(1)

Mechanical Effects of Microgravity During Spaceflight 172(5)

Exercises 173(4)

Biomagnetism 177(18)

Biomagnetic Field Sources 177(3)

Current Dipole Model 179(1)

Vector Potential Formulation 180(1)

Nerve Impulses 180(1)

Magnetotactic Bacteria 181(1)

SQUID Magnetometry 182(7)

Josephson Effect 184(2)

Flux-Locked Loop 186(1)

Intrinsic Noise Factors 187(1)

Extrinsic Noise Factors 187(2)

Digital Filters 189(1)

Magnetocardiography 189(1)

Fetal Magnetocardiography 190(1)

Magnetoencephalography 191(4)

Exercises 193(2)

Nonlinearity and Chaos in Biological Systems 195(30)

Chaotic Dynamics 195(7)

Characteristics of Chaotic Dynamics 196(1)

Sensitive Dependence on Initial Conditions 197(1)

Phase Space 197(1)

Phase Space Reconstruction 198(1)

Poincare Sections 199(1)

Lyapunov Exponents 200(1)

Power Spectra 200(2)

Population Growth in a Limited Environment 202(1)

Predator---Prey Models of Population Dynamics 203(1)

Discrete Logistic Equation 204(11)

Period-Doubling Route to Chaos 206(4)

Bifurcation Diagrams 210(2)

Lyapunov Exponent of the Logistic Equation 212(1)

Shannon Entropy 213(2)

Chaos in the Heart 215(1)

Reaction Diffusion Equations 216(1)

Action Potentials 216(1)

Fertilization Calcium Waves 216(1)

Pattern Formation 217(1)

Dynamics of the Driven Hodgkin---Huxley System 217(1)

Models of DNA Motility 218(7)

Exercises 221(4)

Fractals and Complexity in the Life Sciences 225(22)

Fractal Geometry 225(6)

Computing Fractal Dimension 228(3)

Fractal Structures in Biology 231(2)

Fractal Ferns 231(2)

Diffusion-Limited Aggregation 233(1)

Power Laws in Biology 233(2)

Self-Organized Criticality 235(3)

BTW Sandpile Model 236(2)

Extinction in the Bak---Sneppen Model 238(1)

Power Law Behavior in Chemical Reactions 239(2)

The Game of Life 241(6)

SOC in the Game of Life 244(1)

Exercises 245(2)

Life and the Universe 247(26)

Astrobiology 247(1)

Extremophiles 248(1)

Primordial Soup, Interstellar Gas, and Dust 249(2)

The Miller Experiment 249(1)

Chemistry of the Interstellar Medium 250(1)

Searches for Life in the Solar System 251(7)

Mars 251(5)

Europa 256(1)

Lake Vostok 257(1)

Search for Life Outside the Solar System 258(5)

Extrasolar Planets 258(1)

SETI Initiatives 258(1)

Anticoded Signals 259(1)

Frequency Domain Searches 259(1)

Radio Interferometry 260(1)

The Drake Equation 261(2)

Implications for Life in the Multiverse Picture 263(10)

The Multiverse 263(1)

The Anthropic Principle 264(1)

Multiverse Cosmological Models 265(4)

Exercises 269(4)

Appendix 1: Mathematical Formulas 273(8)

Appendix 2: Overview of MATLAB® 281(8)

Appendix 3: Derivation of the Heat Equation 289(2)

Appendix 4: Derivation of Shannon's Entropy Formula 291(4)

Exercises 294(1)

Appendix 5: Thermodynamic Identities 295(2)

Appendix 6: Kramers---Kronig Transformations 297(2)

Appendix 7: Solution to the One-Dimensional Schrodinger Equation 299(4)

Exercises 302(1)

Appendix 8: Biophysical Applications of QuickField™ 303(6)

Appendix 9: Biological Material Properties 309(4)

Appendix 10: Solutions of the Linearized Poisson---Boltzmann Equation 313(12)

Exercises 323(2)
References and Further Reading 325(14)
Index 339