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Biological cells are remarkably structured. Rather than being the well-mixed slurries of proteins and nucleic acids that are often envisioned, they are actually highly organized with specific locations, or co-localizations, for most of the biochemical components. My research on intracellular organization has two main aspects. First, I am developing a computer program called Smoldyn, which is a general purpose tool for simulating biochemical reaction networks with high spatial accuracy and single molecule detail. Smoldyn is open source, freely available, and reasonably easy to use. Second, I use Smoldyn and other software to model specific examples of biochemical organization. One recently completed project was on the shapes of membrane-bound protein polymers such as the E. coli MinD helices, FtsZ ring, and MreB coils. In a current project, I am using Smoldyn to study diffusion and reaction rates in crowded systems. This work will help us connect in vitro and in vivo rate measurements. This is useful because it will allow significantly improved quantitative biochemical models which are used for drug discovery and other medical research.
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