Understanding the connection between mechanics and cell structure requires a critical exploration of molecular structure. One of these molecular bridges is known to be the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational simulation that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic scheme with both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, these inert monomers have a limiting effect based upon their relative density ratios, which alter the polymerization process. Finally, by introducing localized mobility parameters, we are able to set up molecular gradients that are found in non-homogeneous protein distributions in vitro. This method and results have potential applications in cell and molecular biology as well as self assembly in inorganic systems.

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