Foundations of Bioenergetics

Foundations of Bioenergetics provides an introduction to the physical foundations of bioenergetics and the methods of applying these constructs to biological problems. It combines parts of thermal physics, biochemistry, ecology, and cellular and organismic biology into a single coherent work. Much of the material in this volume comes from ""Entropy for Biologists,"" an introductory thermodynamics book aimed particularly at life scientists. Some of the topics originally appeared in the monograph ""Energy Flow in Biology."" The current volume expands on that material with respect to biological applications and attempts to bridge the gap between physics and biology. The book explains basic concepts such as energy, temperature, the second law of thermodynamics, entropy, information theory, and statistical mechanics. It discusses the relations between thermodynamics and statistical mechanics, free-energy functions, radiant energy, the free energy of cells and tissue, chemical kinetics, and cyclic flows. It examines the relationships between energy flows and biological processes; applications of the concepts of Gibbs free energy, chemical potential, and activity; and measurements of temperature, energy, and thermochemical quantities. The book also includes chapters that deal with irreversible dynamics, irreversible theory, and osmotic flow.

Table of Contents:
PrefaceList of Symbols1 Energy A. Introduction B. Conservation of Mechanical Energy C. Thermal Energy Transition Bibliography2 Temperature A. Empirical Thermometers B. Gas-Law Thermometers C. Temperature in Biology D. Kinetic Theory Transition Bibliography3 The Measurability of Energy A. Energy Changes in a System B. The First Law of Thermodynamics C. Energy Units D. Generalization of the Conservation of Energy E. Energy Conservation in Living Organisms Transition Bibliography4 The Second Law of Thermodynamics A. Heat Engines and Refrigerators B. Statements of the Second Law C. Cycles D. Carnot Theorems E. The Thermodynamic Temperature Scale F. Equivalence of the Ideal Gas and Thermodynamic Temperature G. Life at Absolute Zero Transition Bibliography5 Entropy A. State Function B. Integrating Factors C. Integrals of dQ D. Properties of the Entropy Function E. The Measurability of Entropy F. The Third Law of Thermodynamics G. Entropy and Chemical Reactions H. Limitations of the Formulation Transition Bibliography6 Information A. Probability B. Information Theory Transition Bibliography7 Statistical Mechanics A. The Statistical Point of View B. The Quantum Mechanical Description of Systems C. Ensemble Approach D. The Most Probable Distribution E. The Maxwell-Boltzmann Distribution Transition Bibliography8 Connecting Thermodynamics and Statistical Physics A. Equivalent Formulations B. The Partition Function C. Helmholtz Free Energy D. Classical Statistical Mechanics E. Velocity Distribution Function F. Internal Degrees of Freedom Transition Bibliography9 Information Theory Considerations A. Information and Entropy B. Maxwell's Demon Transition Bibliography10 Free-Energy Functions A. Gibbs Free Energy B. Helmoltz Free Energy C. Generalized Energy Function D. Enthalpy and Standard States E. The Euler Equation F. Activity G. Alternative Methods of Solving a Problem H. Chemical Reactions Transition Bibliography11 Radiant Energy A. The Flow of Thermal Energy B. Black-Body Radiation C. Spectral Distribution Transition Bibliography12 The Free Energy of Cells and Tissue A. Solar Radiation B. Photosynthesis and Global Ecology C. Thermodynamic Calculations Transition Bibliography13 Kinetics and Cycles A. Chemical Kinetics B. Absolute Reaction Rate Theory C. Reaction Networks D. Cyclic Flows E. Model Systems with Cycling Behavior Transition Bibliography14 Ecological Energetics A. Biochemical Outlines B. Heats of Combustion C. Trophic Levels D. Energy Utilization E. Energy Flow Transition Bibliography15 Applications of the Gibbs Free Energy A. Electrochemistry B. Oxidation-Reduction C. Surface Chemistry D. The Phase Rule E. Osmotic Pressure Transition Bibliography16 Thermal Energy A. Order and Disorder B. Diffusion C. Brownian Motion D. Equipartition of Energy Transition Bibliography17 Thermal Measurements Transition Bibliography18 Information-Entropy Formalism in Biology Transition Bibliography19 Irreversible Thermodynamics A. Nonequilibrium Systems B. Local Variables C. Continuum Formulation D. Entropy Flow and Entropy Production E. Phenomenological Equations Transition Bibliography20 Fluctuations A. Fluctuating Variables B. Light Scattering C. Fluctuation Analysis of an Isomerization Reaction D. Entropy in Nonequilibrium Systems E. The Onsager Reciprocal Relations Transition Bibliography21 Applications of Irreversible Theory A. Thermoelectric Effects B. Analysis Using the Reciprocal Relations Transition Bibliography22 Osmotic Flow A. Irreversible Thermodynamics and Osmosis B. A Kinetic Model BibliographyAppendix I Standard International Units (SI) A. Names of International Units B. Prefixes C. Definitions of International Units D. Physical ConstantsAppendix II Conservation of Mechanical Energy: General TreatmentAppendix III Entropy of an Ideal GasAppendix IV Stirling's ApproximationAppendix V The Geometry and Intuition of Lagrange Multipliers A. Motivation and Pictures B. Mathematical Formulation C. Cautionary Examples on Existence and Uniqueness of Solutions D. Lagrange Multipliers Are an Extension of the Condition f'(x) = 0 from Calculus E. A Special Case in Which Solutions Are Unique and Maximal F. Interpretation of Lagrange Multipliers as Sensitivity to Changes in the Constraints G. The Relation between the Lagrange Multiplier and Thermodynamic Temperature in the Maxwell-Boltzmann EquationAppendix VI Evaluation of the Partition Function of an Ideal GasIndex