Our research is focused on modeling, analysis, simulation and software, applied to multiscale, networked systems in biology, materials and social networks. My group has been developing advanced algorithms for discrete stochastic simulation of systems where the fate of a few key molecules can make a big difference to important outcomes. We engage with experimentalists through the analysis of data and the development of mathematical models that yield insight and offer new directions for research. Current collaborations range from biology (circadian rhythm [jet lag] and cell polarization), to medicine (coagulopathy and post-traumatic stress disorder), to ecology (chytrid disease in frogs), to social networks (sentiment analysis and opinion dynamics), to materials. We are collaborating with Prof. Chandra Krintz on the development of an integrated, cloud-based environment called Stochastic Simulation Service (StochSS) for modeling and simulation of biological processes.

Announcements & News

Kasturi and Yuanyang successfully defended their Ph.D. theses this summer, and immediately started working in industry. Kasturi is employed at Target Corp., Sunnyvale, California as a data analyst ... Read more
StochSS: Stochastic Simulation Service, is an integrated development environment for modeling and simulation of discrete stochastic biochemical systems.  An easy to use GUI enables researchers to... Read more
Professor Petzold has been chosen to receive the 2016 SIAM Prize for Distinguished Service to the Profession. This prize is awarded to an applied mathematician who has made distinguished... Read more
We are pleased to announce the release of StochSS Version 1.6! StochSS: Stochastic Simulation Service, is an integrated development environment for modeling and simulation of discrete stochastic... Read more
Kirsten Meeker, Sheng Wu and Jin Fu received their PhDs in Computer Science in December 2014. Here they are, preparing to get hooded.

Recent Publications

aes_paper.pdf Lim, R. K., Petzold, L. R., & Koc, C. K. (2016). Bitsliced High-Performance AES-ECB on GPUs. LNCS 9100, pp. 125-133
pnas-2016-abel-1521178113.pdf Abel, J. H., Meeker, K., Granados-Fuentes, D., St. John, P. C., Wang, T. J., Bales, B. B., Doyle III, F. J., Herzog, E. D., & Petzold L. R. (2016). Functional Network Inference of the Suprachiasmatic Nucleus. Proceedings of the National Academy of Science.
15m1014784.pdf Drawert, B., Trogdon, M., Toor, S., Petzold, L., & Hellander, A. (2016). MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. SIAM J. Sci. Comput., 38(3), C179-C202
ec11568_final.pdf Hellander, S., & Petzold, L. (2016). Reaction Rates for a Generalized Reaction-Diffusion Master Equation. Phys. Rev. E 93, 013307.
interface_latex.pdf Lawson, M. J., Petzold, L., & Hellander, A. (2015). Accuracy of the Michaelis-Menten Approximation When Analysing Effects of Molecular Noise. J. R. Soc. Interface 12:20150054.