Katharina Wilkins

Biosketch

1999 Vordiplom in Process Engineering (a two-year university degree course) at the Fridericiana University of Karlsruhe, Germany

2002 Diplome d'ingénieur en Biotechnologie/ Diplom-Biotechnologin

3 year graduate degree in Biotechnology at the Ecole Supérieure de Biotechnologie de Strasbourg, France

01 – 09/2002 Thesis: 'Production and purification of an Endopeptidase GluC in high-density fed-batch fermentation of B.subtilis’, supervised by Dr. J. Benner, New England Biolabs, Inc. in Beverly, MA.

2002 - 2003 Production of different restriction enzymes in high-density fed-batch fermentation of E.Coli, purification using intein-mediated techniques. Supervised by Dr. Shaorong Chong, New England Biolabs, Inc.

Since 09/2003 PhD program in the Chemical Engineering Department at MIT Advisors: Prof. Paul I. Barton and Prof. Bruce Tidor ‘Dynamic Optimization Methods as Tools for the Analysis of Biological ` Networks’

Research Focus

Oscillations play many interesting roles in Biology. Processes like the cell cycle, a periodic process, are controlled by a machinery of cyclically expressed and activated proteins. In the circadian clock, the different proteins that are expressed in periodic manner help to guide our ‘internal clock’ through the changing conditions of our days.

Other biological systems are hypothesized to use oscillations, for example of Calcium or cAMP, to transmit information. In short, oscillations occur in different situations in different cells, and can play very different roles.

My research is focused on analyzing biological systems that exhibit oscillatory behavior. Due to their nonlinearity and their dynamic behavior, mathematical models of such systems cannot always be analyzed using traditional methods.

Dynamic optimization methods provide a means to analyze the behavior of complex systems in a ‘top down’ approach, by imposing a design goal on the system’s behavior and observing which parameterization or which network architecture can realize such a behavior. By analyzing the characteristics of oscillations, such as period, amplitude and phase shifting in the biological systems, I hope to gain insight on design principles for different oscillatory networks.