Molecular thermodynamics finds application in biological systems in a number of areas, including separation and purification of biological molecules, and drug delivery mediated by hydrogels; and in understanding a variety of intracellular events, including signal transduction, protein-protein interactions, membrane transport and maintenance and regulation of the cytoskeleton. A particular challenge lies in describing and quantifying interactions of biological macromolecules. An important example from bioprocessing is the separation and subsequent purification of proteins. Protein precipitation by salts is the first and most common step in protein isolation from microbial, plant and animal sources. Subsequent purification by chromatographic means relies on protein interactions with charged or hydrophobic solid phases. In order to obtain protein crystals for X-ray diffraction, solution conditions that favor crystallization can often be identified from thermodynamic measurements at high dilution. Protein-protein intermolecular forces are generally short-ranged. Their specific nature is governed by such factors as pH, protein surface charge, charge distribution, surface hydrophobicity and the nature of the intervening electrolyte solution. These effects require quantification to develop useful molecular thermodynamic models for the processes described above. The role of specific salts on protein-protein interactions has been examined using static light scattering with lysozyme, ovalbumin, and a D101F mutant of lysozyme. These experiments provide insight concerning solvation forces that contribute to the interprotein potential. A statistical-mechanical description of protein crystallization is developed, based on the favorable interactions due to the protein-protein contacts in the crystal and the unfavorable entropy loss resulting from constraining the protein in the crystal. The intracellular environment is crowded, and at high rates of recombinant protein synthesis, protein-protein interactions can form inclusion bodies, presenting purification challenges. Protein aggregation can result in misfolding, while molecular chaperones within the cell can assist in protein folding. The competition between desired folding to a native structure and undesired aggregation is examined by Monte Carlo simulations in the presence and absence of chaperone analogs at finite protein concentrations. Aggregates are favored over native, folded proteins when the protein volume fraction exceeds 10%. Presence of a chaperone enhances the formation of native configurations.