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This small book is a simplified, abbreviated, and updated version of the author's Free Energy Transduction in Biology, published in 1977 (Academic Press, New York). The present book is meant to be a textbook for a class or for self-study. The first chapter gives a self-contained and elementary discussion of the principles of free energy transduction in biology. Section 5 includes new material on the Onsager coefficients Lij (for systems near equilibrium) not avail­ able in 1977. Some readers may wish to study the first chapter only. The second chapteris a little more sophisticated, and deals with the so-called diagram method for calculating steady-state probabili­ ties and cycle fluxes. Although these concepts are useful in the analysis of free energy transduction systems, they have an intrinsic importance and interest. Section 8 summarizes quite recent new results not included in the 1977 book. The third chapter is again a step more sophisticated. Some readers may wish to omit it. Free energy levels of the states in a kinetic diagram are introduced. This topic is primarily of conceptual inter­ est for ordinary kinetic diagrams but it is essential in understanding muscle contraction (and related systems) at the molecular level. Contents Preface................................. vii................ Chapter 1 Survey of the Elements of Free Energy Transduction........................ 1 1. States, Diagrams, Cycles, and Free Energy Transduction...................... 2 2. Thermodynamic Forces................ 12.... 3. Operational, Cycle, and Transition Fluxes..... 20 4. Efficiency and the Rate of Free Energy Dissipation.................. 24......

This monograph provides a general introduction to advanced computational methods for free energy calculations, from the systematic and rigorous point of view of applied mathematics. Free energy calculations in molecular dynamics have become an outstanding and increasingly broad computational field in physics, chemistry and molecular biology within the past few years, by making possible the analysis of complex molecular systems. This work proposes a new, general and rigorous presentation, intended both for practitioners interested in a mathematical treatment, and for applied mathematicians interested in molecular dynamics.