We model, design, construct and test synthetic biological systems. We are focusing on therapeutic molecules, such as antimicrobial peptides, and on gene regulatory modules, such as logical AND gates. With mathematical models we can understand the complex behavior of biological systems and reduce their complexity in networks of molecules interacting according to laws of thermodynamics and kinetics.

News:

Professor Kaznessis' textbook "Statistical Thermodynamics and Stochastic Kinetics: An Introduction for Engineers" is published by Cambridge University Press www.cambridge.org/9780521765619

Recent Research Highlights:

Katherine Volzing built ProTeOn and ProTeOff, two molecular devices that precisely control the expression of proteins in bacteria. Her work is published in ACS Chemical Biology. Click here for the article.

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Recent Research Highlights:

How do antimicrobial peptides work? Dr. Dan Bolintineanu, Dr. Allison Langham and Professor Yiannis Kaznessis, Department of Chemical Engineering and Materials Science, simulated the pore that is formed by protegrin-1, a potent antimicrobial peptide, in the lipid bilayer membrane of bacteria. Molecular dynamics simulations coupled with Poisson-Nernst-Planck electrodiffusion equations show exactly how a protegrin pore allows ions and other cell contents to leak out of the bacterion, causing its death. In the picture, the cross sectional view of a protegrin-1 pore (in green) in a lipid bilayer is shown (lipid chains in grey and lipid heads in red; water is cyan). The movement of ions through the pore was visualized using molecular dynamics simulations (in yellow, a chloride ion is shown as it moves through the pore). This information helps to elucidate the mechanism of action by which this antimicrobial peptide kills bacteria and rationalizes engineering of novel, potent antibiotic molecules. The top view of the full system is shown in the insert. With a clear picture of the physical interactions that underlie biological function we set out to engineer new antibiotics.For more information visit our publications webpage and consult the following:

•  Langham A., Sayyed-Ahmad A, Kaznessis YN, “On the nature of antimicrobial activity: a model for Protegrin-1 pores”, JACS, 2008, 130(13): 4338-4346.

•  Bolintineanu D, Hazrati E, Davis HT, Lehrer RI, Kaznessis YN. “Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli.” Peptides. 2010.

•  D. Bolintineanu, HT. Davis, YN. Kaznessis, “Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore”, PLoS Computational Biology, 2009.