EIGER FELLOW SINCE JULY 2006

EDUCATION

Virginia Tech, Blacksburg, VA
B.S., Physics, Minors in Math and Chemistry, May 2003

ADVISORS

Professor Rahul Kulkarni, Department of Physics
Professor Alexey Onufriev, Department of Computer Science

EIGER INTERNSHIP

March 2008 to May 2008
Lawrence Livermore National Lab
The primary goal of the trip was to study the effects of stochasticity on sRNA(s) regulation. The work was done with Dr. Eivind Almaas.

DISSERTATION RESEARCH

Applying physical models to biologically motivated problems at various length scales.

Certain bacteria are able to orchestrate the starting and stopping of critical functions depending on the size of the bacterial colony. These bacteria are known as quorum sensing bacteria. The bacteria are constantly producing, secreting, and detecting small signaling molecules called autoinducers. When the concentration of autoinducers reaches a critical amount, the cells in the colony turn on a particular function, for example the bacteria will produce light. My research involves modeling all the different interactions inside the cell corresponding to the quorum sensing regulatory network and then combining the insights gained from the model with experimental data.  

Many important interactions at the molecular level are directed by electrostatic forces. Since the introduction of atomic resolution structures from X-ray crystallography and the foundation of the Protein DataBank, a plethora of computation tools have been produced to analyze these freely available structures. One aspect of my research focuses on determining the electrostatic potential at and near the surface of large biomolecules. The potential can then be used to find electrostatic regions of interest across the surface that might be involved with the function of the biomolecule.

Eukaryotes store their DNA inside a nucleus, which is about one micron in diameter. However, the DNA itself can stretch to over a meter in length depending on the organism. The high level of compaction the DNA must undergo to fit inside the nucleus is critical for the cell. The first level of compaction consists of the DNA repeatedly wrapping a couple of times around beads of proteins called histones. The result looks like a string of pearls, where the pearls are called Nucleosomes (histones with wrapped DNA) and the string connecting the Nucleosomes are unwrapped DNA. Understanding how the DNA wraps and unwraps from the histones is important for studying the transcription of certain genes, for example those genes whose RNA polymerase binding sites would be occluded when wrapped around the histones. My research involves modeling the stability of the Nucleosome relative to changes in the system, where the changes are electrostatic in nature -- salt concentrations, total charge of the histones, etc.

CONTACT INFORMATION

Email: afenley@vt.edu

This page last updated 11/10/09