Simulation tools for non-homogeneous molecular systems

As circuit feature size approaches the limits for Moore's law, new technologies are needed to enable continued performance improvements. Computing with biomolecular devices is one promising direction. To support this technology, new simulation tools to model effects at the molecular level are needed. One approach is agent based modeling (ABM). In previous work we showed that ABM gives good qualitative results for molecular-level simulations. Here we present an improved ABM tool, ABMSim, which models a wider range of molecular-level phenomena, including nonhomogeneous configurations, crowding, and a range of molecule-specific properties, and produces quantitative results comparable to those of simulation tools based on the traditional stochastic approach.

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