(4lq) Molecular Simulations to Probe Dynamics and Interactions in Nucleic Acids and Nucleoprotein Systems

Research Interests: The focus of my past research has been the computational modeling and characterization of various biomolecular systems, including nucleic acids, proteins, and membrane systems. As part of my future work, I am interested in expanding my research work on RNA molecules by characterizing the energetic and structural effects of chemical modifications in DNA molecules by performing alchemical free energy calculations of these modifications. Results from these simulations will be useful in the design and functionalization of DNA nanostructures which can be further used in the drug delivery process. Furthermore, I am interested in applying computational modeling in understanding how the host-cell DNA strands are properly positioned prior to integration of the viral DNA genome in the viral intasome complex as well as the subsequent conformational changes which the intasome undergoes during the multistep integration process of the viral genome into the host-cell genome. Insights from these simulations will be useful in designing novel integrase strand transfer inhibitors (INSTIs). As my last project, I would like to develop coarse grained models of DNA molecules to characterize DNA packaging into chromatin fibers which is an essential biophysical process in cells.

Teaching Interests: During my doctoral and postdoctoral assignments, I had the opportunity of training several undergraduate and graduate students in developing skills and knowledge necessary to conduct molecular simulations. As a TA, I had the opportunity to teach both core chemical engineering courses such as unit operations and transport phenomena as well as an elective course to students with diverse backgrounds. As a chemical engineering faculty, I am ready to teach any core chemical engineering course or any other elective that fits my professional background. As an example of an elective course, I would like to introduce students to the fundamentals of bioengineering/biophysics while further emphasizing how molecular modeling, simulation, and visualization techniques can assist us in understanding biomolecular structures.