The inside of cells is highly crowded with bio-macromolecules, such as proteins, DNA, RNA. This environment is quite different from the conditions in a test tube that we usually use for analysis of biomolecular functions, where the macromolecular concentration is ~100 times less than inside cells. This crowding significantly alters motions (kinetics) and stability (thermodynamics) of those molecules. Therefore, modeling of the intracellular environment is an important first step towards whole cell simulation.
Recently, we simulated a virtual cytoplasmic system of E. coli to elucidate the nature of motions of macromolecules inside cells by using a Brownian dynamics method. Our simulation study showed that hydrodynamic interactions play an important role in macromolecular motions in cells: Hydrodynamic interactions greatly reduce the diffusion coefficient and create collective motions at cellular concentrations.
Reference: T. Ando and J. Skolnick. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Science 2010, 107:18457-18462. PDF