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

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
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

Recent Publications

07843624.pdf Abel, J., Drawert, B., Hellander, A. & Petzold, L. R. (2017). GillesPy: A Python Package for Stochastic Model Building and Simulation. IEEE Life Sciences Letters, Vol. 2, No. 3, pp. 35-38.
1-s2.0-s0925231217305581-main.pdf Torshizi, A. D., Petzold, L., & Cohen, M. (2017). Multivariate Soft Repulsive System Identification for Constructing Rule-based Classification Systems: Application to Trauma Clinical Data. To appear Neurocomputing
main.pdf Hellander, S. & Petzold, L. (2017). Reaction Rates for Reaction-Diffusion Kinetics on Unstructured Meshes. J. Chem. Phys. 146, 064101
balesetal_2017_modelling_simul._mater._sci._eng._10.1088_1361-651x_aa67b9.pdf Bales, B., Pollock, T., & Petzold, L. (2017). Segmentation-Free Image Processing and Analysis of Precipitate Shapes in 2D and 3D. To appear Modelling Simul. Mater. Sci. Eng.
07887681.pdf Torshizi, A. D. & Petzold, L. (2017). Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases. To appear IEEE/ACM Transactions on Computational Biology and Bioinformatics