Essentially all cellular processes depend on spatially localized proteins. Some proteins localize to cell poles, others to the particular cell membranes, and yet others to specific cytoplasmic regions. This localization is often dynamic, with proteins shuttling between different regions. The Smoldyn biochemical simulator helps researchers study this intracellular organization; Smoldyn represents each protein as an individual point-like particle that diffuses, reacts, and interacts with membranes, all in continuous space. It was surprisingly difficult to make these processes quantitative, such as for finding the "binding radius" for bimolecular reactions and the adsorption probability for molecules that adsorb to membranes. Smoldyn has enabled a variety of research projects over the last several years. In one example, Smoldyn simulations showed that yeast cells appear to secrete a protease (called Bar1) which degrades extracellular pheromone so that, paradoxically, they can sense the pheromone gradient more accurately. This helps cells improve their mating success.

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