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We present an individual agent-based model of transcription factor binding to DNA. We explicitly represent every single transcription factor and every single binding site in our simulation. In order to obtain statistically significant results from our model, it is necessary to perform a large number of simulations. This has previously been hampered by the computational demands of individual agent-based models. Here we present an approach to make such simulations feasible using approaches related to dynamic memory allocations in computer systems.