Our efforts in constructing a general continuum description of solvent effects for use in biomolecular simulations are motivated by the need of a smooth transition between a microscopic and a macroscopic formulation. This is difficult since macroscopic descriptions are traditionally the first ones to emerge because they involve phenomenological approaches. Therefore, it is natural to apply these purely macroscopic concepts directly to the macromolecular realm. However, biomolecules are truly mesoscopic systems for which purely macroscopic approaches are not justified. At the same time, a purely microscopic approach may not be necessary, e.g., when describing the effects of the bulk medium, including long-range correlations. Therefore, simplified models are useful if they can be derived from microscopic view using statistical mechanics formalisms.

These simplified approaches are needed if computer simulations are used to represent explicitely the propagation in time and space of many body systems, e.g., 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 diffusion processes. These kinds of interactions are typical of all biochemical processes in the cell, where the systems are open and out of equilibrium. 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. For example, morphological developments in embryo, including the formation of the central nervous system, skull, limbs, lungs, etc, are determined by a complex network of interactions of proteins, nucleic acids, small organic molecules, ions and cosolutes, etc, in different compartments of the cells and also in the intercellular space of the growing tissues. We have studied some of these processes theoretically, and showed 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 mathematical formalism is available for solving the general problem. 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. Computer simulations may be of great help to address these problems without the need of simplified mathematical assumptions, as long as a physically realistic continuum representation of water forces is available. 

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.