The laws of thermodynamics dictate the behavior of biotic and abiotic systems. Simulation methods based on statistical thermodynamics can provide a fundamental understanding of how biological systems function and are coupled to their environment. While mass action kinetic simulations are based on modeling reactions using rate constants, in many cases analogous thermodynamic simulations of mass action dynamics can be based on modeling states using chemical potentials. The latter have the advantage that standard free energies of formation and reaction are much easier to determine than rate parameters, allowing one to model across a large range of scales. Bridging theory and experiment, statistical thermodynamics simulations allow us to both predict activities of metabolites and enzymes, and use experimental measurements of metabolites and proteins as input data.