Systems Biodynamics Lab

Sotiria Lampoudi
Postdoctoral Fellow

Email: slampoud@ucsd.edu
Phone: 858.822.3858
My CV

Education

Ph.D., Computer Science, University of California Santa Barbara (2008)
M.S. Computer Science, University of California Santa Barbara (2004)
B.A. Computer Science, University of Chicago (2002)

Research Interests

I work at the interface of computer science with physical chemistry and biology. On the one hand, I am interested in the impact of space, in various senses, on discrete stochastic chemical kinetics. I design algorithms for spatial stochastic simulation (most notably the Multinomial Simulation Algorithm), and conduct computational experiments to investigate the impact of various physical attributes of reactants (e.g. reactant size) on reaction kinetics. On the other hand, I collaborate with biologists to build mechanistic models of bacterial signal transduction. I am especially interested in phosphorelays, a type of unorthodox two-component system which tends to show up in quorum sensing, virulence control and other committing decision circuits.

Publications

[5] S. Lampoudi, D.T. Gillespie, L.R. Petzold, The Multinomial Simulation Algorithm for discrete stochastic simulation of reaction-diffusion systems, accepted to J Chem Phys.

[4] S. Lampoudi, D.T. Gillespie, L.R. Petzold, Effect of excluded volume on 2D discrete stochastic chemical kinetics, accepted to J Comp Phys.

[3] D.T. Gillespie, S. Lampoudi, L.R. Petzold, Effect of reactant size on discrete stochastic chemical kinetics, J Chem Phys, 2007 Jan; 126(3):034302.

[2] W. Guo W, S. Lampoudi, J.-E. Shea, Temperature dependence of the free energy landscape of the src-SH3 protein domain, Proteins, 2004 May; 55(2):395-406.

[1] W. Guo, S. Lampoudi, J.-E. Shea, Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain, Biophys J, 2003 Jul; 85(1):61-9.