Computation Core (Greg Voth, Director)
Our Computation Core provides access to leading edge theory and simulation capability in atomistic molecular dynamics, coarse-graining, and multiscale modeling. The major current focus of this core facility is on modeling HIV capsid assembly and stability, but the Computation Core facility expertise is available to all Center participants. Molecular dynamics capabilities include force field development and access to all major biomolecular MD simulation packages. Coarse-graining and multiscale modeling studies are carried out using specialized methods and codes developed in the Voth group, with a particular focus on relating coarse-grained models to the underlying molecular-scale interactions. The Computation Core also has access to substantial computational resources, both in house and at the major national supercomputer centers. | |
| Fullerene Cone Model for the HIV-1 Capsid.
A) Thin sectioned EM image of an HIV-1 virion showing the conical capsid structure. B) Thin-sectioned image of a “synthetic” capsid assembled in vitro from recombinant CA-NC protein. Note the similarity between cones formed in vivo and in vitro. C) Schematic illustration of the capsid fullerene cone model. The hexameric net that forms the body of the cone is composed of CA hexamers, and the penton “defects” required to close the net are shaded red. |