Structural and Computational Biophysics Discussion Group meeting. Dr. Sam Cho, joint appointment in Computer Science and in Physics, will be the speaker.
Coarse-grained GPU optimized MD simulations of biomolecular folding and assembly
Molecular dynamics (MD) simulations provide a molecular resolution view of biomolecular dynamics, folding, and assembly mechanisms, but the computational demands of the underlying algorithms limit the length- and time-scales of the simulations one can perform. Recently, graphics processing units (GPUs) have been repurposed for high performance computing, and we have implemented a coarse-grained MD simulation code with novel parallel algorithms specifically optimized for the GPU architecture. As an application, we introduced protein-nanoparticle GPU-optimized MD simulation approach of a biocorona formation, a first in the field, that was inspired electron microscopy imagining. Consistent with CD spectra, we observe a decrease in α-helices coupled with an increase in β-sheets in apolipoprotein upon biocorona formation. If time permits, I will briefly outline some ongoing projects in our group to encourage future collaborations.
Meetings are at Foothills on 4th Street downtown. Free appetizers and drinks (paid for by the Graduate School). The group starts to assemble around 3:30 and the talk goes from 4-5pm.