Department of Physics
Colloquium for Friday, April 15
Apr 11, 2011
Speaker: Dr. J C Gumbart
Date: April 15, 2011 (Friday)
Time: 4 PM
Room: 205 Currens Hall
Realizing Feynman's dream with the computational microscope
Much as physical microscopes allow us to glimpse the inner workings of biological and physical systems, a computational microscope also provides unique insight into the complexity of the world at the nanoscale. By combining the classical equations of motion derived by Newton, the laws of electromagnetism from Maxwell, and the statistical mechanics of Boltzmann, we can simulate biological processes in full atomic detail. These so-called molecular dynamics simulations provide tremendous power to visualize the workings of individual proteins and protein complexes, although they require also tremendous amounts of computing resources, including public-sector commodity supercomputers as well as private special-purpose ones. I will highlight the application of simulations and related methodologies to questions of protein synthesis by the ribosome, a large, dynamic molecular machine whose structure led to a Nobel Prize in 2009, and the subsequent extrusion and trafficking of the nascent protein through the membrane-bound protein-conducting channel. The results presented are the modern-day realization of Feynman's belief that "everything that living things do can be reduced to wiggling and jiggling of atoms."
About the speaker:
Dr. James (JC) Gumbart is currently a Director's Postdoctoral Fellow at Argonne National Laboratory. A physicist by training and a biophysicist by trade, his work focuses on understanding the biological functions of proteins at the atomic level using large-scale molecular dynamics simulations.