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Fall 2013 Newsletter


Summer Research


Rebeckah Johnson '14, chemistry
This summer I had the opportunity to work at the University of Rochester on a research project entitled “Cytochrome c Constructs for Carbon Nanotubes." The research is part of a project focused on alternative energy sources. Ideally, a chromophore (like cytochrome c proteins) would absorb light, exciting electrons that could be transferred to carbon nanotubes. These nanotubes would shuttle electrons to hydrogen catalysts, resulting in hydrogen gas production. I was involved in studying electron transfer between various cytochrome c peptides and carbon nanotubes. Daily, I spent most of my time learning biochemistry and molecular biology. We used E. Coli to express the desired proteins, so I grew E. Coli and harvested the cells for protein on a regular basis. I made microperoxidase-11 (a peptide fragment of cyotchrome c) from horse heart cytochrome c via proteolysis using pepsin. The peptides resulting from these two procedures were suspended with carbon nanotubes, and fluorescence spectroscopy was used to study electron transfer. Altogether, this experience gave me a better understanding of graduate school and what its like to be an active participant in current research.


Aaron VanDyne '14, mathematics, physics, biochemistry
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.

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