WFU Physics Colloquium

TITLE: Simple computational solutions to complex biological problems

SPEAKER: Professor Alexey Onufriev,

TIME: Thursday Dec. 10, 2009 at 4:30 PM*

PLACE: Room 101 in Olin Physical Laboratory

^* Note: late starting time.

In this presentation I will argue that it is the very simple theoretical/computational approaches that may be robust enough to provide insights into complex biological phenomena. I will exemplify my point with several recent research projects of my group: 1) Computational identification of pathways of ligand migration in myoglobin. Exactly how do small non-polar ligands such as O2 or CO travel from the solvent to the buried binding site in myoglobin? I will show how this 50 year old puzzle in structural biology can be addressed by conceptually simple computational means. 2) Nucleosome stability control in vivo: a simple model. The primary level of DNA compaction in living cells is the nucleosome. Modulation of the nucleosome's stability is one of the key aspects of chromatin regulation, which in turn is vital for the fundamental cellular processes such as DNA replication, repair, transcription, and epigenetic inheritance. Yet, exactly how this modulation is accomplished in Nature remains unclear. I will demonstrate how a model based on basic electrostatics may provide an answer. 3) If time permits, I will touch upon the use of simple charge representations and hierarchical partitioning to develop novel Nlog(N) algorithms for computation of long-range forces in molecular dynamics.