Research

I work on computational biophysics projects and on education projects. I collaborate with colleagues from Physics, Chemistry and Mathematics and work with undergraduate students whenever possible.

Computational Biophysics

Mission statement: Our goal is to understand and be able to predict the physico-chemical mechanisms by which molecules, including mutagens, carcinogens, and drugs interact with DNA molecules. The ultimate goals are to achieve a molecular-level understanding of carcinogenesis, to help develop strategies that prevent carcinogenesis, and to help develop better therapies.

A vibrational entropy term for DNA docking with autodock

In this paper we showed that adding a vibrational entropy term to a popular physics-based scoring function improves the predicted geometries of how small molecules bind to DNA.

Non-covalent interactions of the carcinogen (+)-anti-BPDE with exon 1 of the human K-ras proto-oncogene

A highly mutagenic and carcinogenic metabolite of the tobacco smoke carcinogen benzo[a]pyrene, (+)-anti-BPDE, physically binds to and then subsequently damages DNA. In this work, we found that the initial non-covalent binding of the carcinogen to the human proto-oncogene K-ras, promotes DNA damage by brining the reactive atom of the carcinogen and DNA in proximity.

Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA

Prior to using a computational methodology to study how carcinogens (small molecules) interact with DNA macromolecules, we need to validate it against experimental results. In this work, we showed that a popular computational methodology used in drug discovery (with protein as targets) also works relatively well for predicting how small molecules physically bind to DNA.

Correction to DFT interaction energies by an empirical dispersion term valid for a range of intermolecular distances

Implementations of Kohn-Sham Density Functional Theory (KS-DFT) were problematic in predicting physical binding of two molecules when there was significant dispersion interactions. Here, we present a computational approach that significantly improves the performance of three widely used density functionals without adding a significant computational cost. The KS-DFT with the added correction we developed can be used to calculate the interaction energies between carcinogens and DNA.

Education

A Classroom Activity for Teaching Electric Polarization of Insulators and Conductors

Here we present an activity physics instructors can implement during class in order to have students understand the theory of polarization. The activity includes embodied activities and group work using whiteboards. Our study results suggest that students enjoy the activity and learn from it.