I was a postdoc at UC Berkeley from 2000 to 2005, and I had a visiting scholar position in the mathematics department at UC Berkeley. There, I have been part of the Mathematical Radiobiology group led by Professor Rainer Sachs. Our group typically consists of one senior faculty member, two junior faculty, one graduate student and several undergraduate assistants. We developed mathematical and biophysical models of DNA repair in human cells by analyzing the aberrations induced on them by low-dose ionizing radiation. We used Monte-Carlo simulation to give a quantitative analysis of various models for chromosomal aberration production. This analysis is compared to experimental data given by mFISH (multiplex fluorescence in situ hybridization). Most of our results have been published; the relevant papers can be found in the list of publications.
I am very interested in understanding the mechanism of action of type-2 topoisomerases. I am currently modelling their DNA unknotting reaction. This project was inspired by our work on DNA packing in bacteriophages (Arsuaga et al. 2002) while working with Javier Arsuaga and Joaquim Roca (molecular biologist).
Jointly with John Luecke and Isabel Darcy, I have analyzed data from novel difference topology experiments to unveil the structure of the Mu transpososome. The technique was developed in Rasika Harshey’s and Makkuni Jayaram’s lab, and the experiments were done by Shailja Pathania.
The tangle model is a mathematical method due to De Witt Sumners and Claus Ernst [Sumners et al. Quart. Rev. Biophysics 28, 3 (1995), 253 - 313], which uses knot theory and low-dimensional topology to understand the mechanisms of binding and strand-exchange by site-specific recombinases. A web description of the tangle model can be found here.
The National Science Foundation began supporting ADVANCE initiatives in 2001, and has awarded over $130M in funding for a variety of programs. The most significant efforts seek to create permanent institutional transformation.