Sotiria Lampoudi's publications by topic

Computational Chemistry

E. S. Penev, S. Lampoudi, J.-E. Shea, TiRex: Replica Exchange Molecular Dynamics Using TINKER, Computer Physics Communications, October 2009, 180(10):2013-2019.

Stochastic Simulation

S. Lampoudi, D.T. Gillespie, L.R. Petzold, The Multinomial Simulation Algorithm for discrete stochastic simulation of reaction-diffusion systems, J Chem Phys, 2009 Mar; 130:194104.
S. Lampoudi, D.T. Gillespie, L.R. Petzold, Effect of excluded volume on 2D discrete stochastic chemical kinetics, J Comput Phys. 2009;228(10):3656-3668.
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.

Protein Folding

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.
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.

Systems

S. Lampoudi, D.M. Beazley, SWILL: A Simple Embedded Web Server Library, USENIX 2002, Monterey, CA, June 2002. (Best Student paper award)