Protocols for Calculating Reaction Kinetics and Thermodynamics

Abstract

Thermodynamics is central to our understanding of the ecology and physiology of microbial ecosystems. In physiological research, thermodynamics is used to determine the directionality of a reaction or the feasibility of a pathway. In ecological research, thermodynamics is used to determine the feasibility of a process and to rationalize the sequence of redox reactions in both natural environments and engineered biological systems and increasingly also as a basis to describe microbial activities as a function of environ- mental factors. This protocol provides a detailed annotated description of how to calculate change in Gibbs free energy values and redox potentials and a brief discussion on linking thermodynamics and kinetics for reactions of biological interest.