Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells.

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Accurate evaluation of the performance of buildings participating in Demand Response (DR) programs is critical to the adoption and improvement of these programs. Typically, we calculate load sheds during DR events by comparing observed electric demand against counterfactual predictions made using statistical baseline models. Many baseline models exist and these models can produce different shed calculations. Moreover, modelers implementing the same baseline model can make different modeling implementation choices, which may affect shed estimates. In this work, using real data, we analyze the effect of different modeling implementation choices on shed predictions. We focused on five issues: weather data source, resolution of data, methods for determining when buildings are occupied, methods for aligning building data with temperature data, and methods for power outage filtering. Results indicate sensitivity to the weather data source and data filtration methods as well as an immediate potential for automation of methods to choose building occupied modes.

The performance of buildings participating in demand response (DR) programs is usually evaluated with baseline models, which predict what electric demand would have been if a DR event had not been called. Different baseline models produce different results. Moreover, modelers implementing the same baseline model often make different model implementation choices producing different results. Using real data from a DR program in CA and a regression-based baseline model, which relates building demand to time of week, outdoor air temperature, and building operational mode, we analyze the effect of model implementation choices on DR shed estimates. Results indicate strong sensitivities to the outdoor air temperature data source and bad data filtration methods, with standard deviations of differences in shed estimates of %20-30 kW, and weaker sensitivities to demand/temperature data resolution, data alignment, and methods for determining when buildings are occupied, with standard deviations of differences in shed estimates of %2-5 kW.

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