ARCHIVED: Petascale computing on the TeraGrid: Metalloproteins - Computational Challenges, Methods, and Tools

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Note: The project described in this document is funded by the National Science Foundation (NSF) Office of Cyberinfrastructure (OCI) to use TeraGrid's petascale environments for highly advanced scientific analysis and simulations that advance the frontiers of scientific and engineering research. For more, see ARCHIVED: Petascale computing on the TeraGrid.

This focused research group investigates key issues related to the structure and function of selected metalloproteins and metalloenzymes. The group will develop a set of computational tools for large-scale biomolecular simulations as part of its work.

The research team will build on achievements made under prior National Science Foundation (NSF) awards, including:

The development of the highly parallel Particle Mesh Ewald Molecular Dynamics (PMEMD) code currently incorporated into AMBER
A fast implementation of higher-order electrostatic multipoles that is the basis of an efficient coding of the AMOEBA force fields in AMBER
A new partitioning of the molecular electrostatic potential
The development of pfaffian wavefunctions for quantum Monte Carlo simulations
The coupling of ab initio molecular dynamics
The establishment of the new quantum Monte Carlo open source package, QWalk

The team will focus on investigating:

Signal transduction Ras proteins
Vitamin K-dependent coagulation proteins
Select DNA repair enzymes
The folding/unfolding of metallopeptides and metalloprotein domains

Methods developed by this research will be incorporated into the above packages and tested on multiple architectures, including petaFLOPS machines.

For more, see award abstract #0804549 on the National Science Foundation (NSF) web site.