Monte Carlo and molecular dynamics simulations are being used in combination with statistical mechanical theories to understand thermodynamics, structure, and kinetics of biomolecules in aqueous solutions. Special emphasis is placed on understanding and relating water structure near different solutes and in different environments to resulting interactions (e.g., hydrophilic and hydrophobic interactions). Theory and molecular simulations are also used to study the effects of geometrical and chemical heterogeneity on molecular transport and reaction in porous catalysts, sorbents and membranes, and to apply this knowledge to their rational design.