This paper deals with the hierarchy of simulation methods and theoretical analysis that may be used in understanding biomolecular function. The hierarchy proceeds from the most detailed and most difficult for large systems and long times—quantum mechanics—to the least detailed and most readily directly applicable to large systems and long times—integrated constitutive theory. Substantial advances in understanding biological systems can come from linking these different hierarchies into integrated comprehensive descriptions of biomolecular function. This paper critically reviews several recent and ongoing studies of biomolecular function in membranes that accomplish this linking. These studies are chosen to illustrate both the power of this approach and possible pitfalls in particular applications. © 1993 John Wiley & Sons, Inc.