The roles of patchy attractions and Brownian motion in fundamental biological processes in a model cell

Microscopic forces and physical phenomena at the colloidal scale are involved with fundamental processes inside living cells. Examples of such phenomena include Brownian motion and deterministic forces between constituents of the cellular milieu. In order to faithfully represent interactions between proteins, in particular, computational models must take into account the orientation-dependence (i.e. “patchiness”) of attractions and binding events. To connect these microscopic forces to whole-cell functions, we use coarse-grained patchy simulations to study key biological processes, including translation elongation, in a model prokaryotic cell. We examine the relationship between the attractive potential strength relative to Brownian motion (used in colloidal simulations) and the equilibrium dissociation constant, K_d, a metric used to describe the binding affinity of biological macromolecules in experiments. Here, we present our results investigating the structure and dynamics of these coarse-grained systems, probing the inseparable connection between colloidal-scale transport and biological function.