Overview

An essential property of all living systems is that they operate in states of flux, transporting and transforming mass, transducing free energy between chemical, electrical, and mechanical forms, and delivering signals and information in terms of biochemical activities. Consequently, the principles governing the behavior of biochemical systems are the principles of physical chemistry. As an introduction to background material necessary for describing and understanding the behavior of biochemical systems, this chapter covers the concepts of chemical thermodynamics including temperature, entropy, chemical potential, free energy, and Boltzmann statistics.

In the early nineteenth century Carnot gave birth to the field that came to be known as thermodynamics, with the first theoretical treatise on mechanical work and efficiency in heat engines. Over the course of that century, a complete physical theory of how changes in heat, mechanical work, and internal energy of molecular systems are related – in short the theory of thermodynamics – was assembled by Clausius, Helmholtz, Boltzmann, Gibbs, and others. As part of the thermodynamic theory a number of familiar physical quantities were introduced, including entropy, enthalpy, and free energy. We shall see that understanding these quantities and how they are related is essential for building physically realistic simulations of biochemical systems.