Our efforts in constructing a general continuum description of solvent effects for use in biomolecular simulations is centered on the idea of making a transition from a microscopic to a macroscopic formulation. This is difficult since macroscopic descriptions are traditionally the first ones to emerge because they involve phenomenological approaches. Therefore, it has been a common trend to apply those purely macroscopic concepts directly to the macromolecular realm. However, biomolecules are truly mesoscopic systems for which purely macroscopic approaches are not justified (actually, incorrect; see references). At the same time, a purely microscopic approach may not be necessary (e.g., when describing the effects of the aqueous solutions). Therefore, simplified models are needed that can be derived from the microscopic view. Specific examples of this kind of approach come from our earlier work on pattern formation and self-organization in model systems. In particular, we were interested in the propagation in time and spatial steady states in systems described by reaction-diffusion equations. These systems include the general case of multiple interacting chemical species that react and also propagate in space according to classical diffusion processes. These kinds of interactions are typical in all biochemical processes where the systems are open and out of equilibrium (most likely far away from the linear regime). In this case feedback mechanisms, where the products of a reaction control the rate and extent of the reaction itself, are the most important processes, and are characteristic of the chemical reactions occurring in the cell interior. We studied how the permeability of the system in its borders, expressed mathematically by appropriate boundary conditions, affects the structures and spatial propagation of the final products. The differential equations describing these kinds of processes can be highly non-linear (giving origin to the so-called non-linear dynamics) and no general mathematical formalism is available for solving the general problem. We have addressed the problem of macroscopic pattern-formation process in simple, open non-equilibrium systems, described by reaction-diffusion equations. Although the models considered are necessarily simple for mathematical convenience, the concepts involved are typical of the general case found in virtually any phenomenon in nature and it is central for understanding the macroscopic complexity of the cellular world. 

Biologists and biochemists have only recently began to pay more attention to these topics in the form of the emerging discipline known as Systems Biology. Theoretical progress in this field is unlikely unless that a deeper undersanding of the processes mentioned above is pursued.