Research Scientist
jalberts@u.washington.edu
Here at the CCD I build computational and mathematical models of cellular processes. My research is currently focused on cytoskeletal polymers, specifically actin and bactin (bacterial actin, e.g. ParM). A more detailed description of two behaviors I'm investigating, the actin-based motility of L. monocytogenes and the ParM mediated plasmid segregation in some bacteria, can be found in the Research Projects page. I'm also interested in building frameworks to make it easier for others to build these types of computational models. To that end I've devised one efficient and biophysically realistic scheme for representing flexible biological filaments. This work is encapsulated in the code package SimFil, which can be found in the Tutorials -> Java Tutorials page. On that tutorials page you'll also find Sim2D and Sim3D, which are intended as starting points for 2D and 3D Java simulations, respectively. These starting points encode a simple predator-prey model which might easily be modified/extended to represent real biological interactions. Let me know if I can help get you going...
The philosophy behind the computer modeling I do is this: encoding simply interactions rules between agents in a simulation most closely parallels the facts discernible from experiment, thus requiring the least human intuition or guessing about the outcome of the many dynamic interactions. Encoding interactions at this level comes at the price of greater computational cost, but computers are fast and getting faster. Ideally, these complex computer models will instruct us in constructing simpler, encapsulating mathematical models that are more amenable to human understanding, and that build a meaningful intuition for the system under study.
