Department Highlights

Aaron Van Dyne '14, mathematics and physics

During the summer of 2013, I participated in an undergraduate research program in the Department of Computational and Systems Biology at the University of Pittsburgh. The program was both education and research based. I participated in a variety of seminars
related to computational biology and bioinformatics as well as conducting my
own research. The seminars provided me an overview that enriched both my
understanding of biology and my understanding of the research conducted by my
colleagues. Especially important was the fact that I began to understand the
practical applications of computational biology and bioinformatics including
screening drugs and looking for genes related to various diseases.

My research focused on improving simulations of interactions between proteins. I focused specifically on simulating the interactions between two proteins in bacteria, but the technique will be applicable across computational structural biology. I applied Monte
Carlo simulation as I have in previous work, but my work this summer focused on
making the simulation faster by calculating the energy associated with the
interaction between the proteins before the simulation and storing the energies
in a table. This accelerated the simulation because calculating the energy is
the most time-intensive step in the simulation. This acceleration came at the
cost of decreased accuracy because the table of energies could be infinitely
large. There is a limit to how small of an area can be represented by any one
cell in the table. I am continuing to work on the project, and I am currently
working on developing more accurate tables by using a finer resolution when the
proteins are close and calculating the energy due to more complex interactions
between the proteins.