DescriptionThis proposal requests CPU time on XSEDE resources for research aimed at understanding assembly and pattern formation in biological and biomimetic systems. The first two subprojects will use coarse-grained simulations to explore two processes which are essential for replication of many viruses: the assembly of capsid proteins around RNA and the simultaneous assembly and budding of capsid proteins through lipid bilayers. The third subproject will study pattern formation and spontaneous flow in a far-from-equilibrium system containing microtubules and motor proteins studied by our experimental collaborators, the Dogic Lab at Brandeis. A common goal in each of the three subprojects is to reveal structural and dynamical information about key intermediates which are not accessible to experiments. The simulations of capsid assembly around RNA will be performed with the program HOOMD which enables great computational speedups on GPUs. The simulations of capsids assembling on lipid bilayers will use LAMMPS which affords excellent scaling for the large membranes being considered. The simulations of microtubules and motor proteins will use a self-written code optimized to characterize high aspect ratio, extensile bundles. Funding for Subprojects 1 & 2 is provided by NIH NIAID (R01AI080791) and Subproject 3 is funded by the NSF (NSF-MRSEC-0820492).
OrganizationBrandeis University
Sponsor Campus GridOSG-XSEDE
Principal Investigator
Michael Hagan
Field Of ScienceMolecular and Structural Biosciences