Thermodynamically Calibrated RNA Simulations to Decode Mechanisms of RNAMolecular Recognition

State University Of New York At Albany, Albany NY

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Abstract

This is an administrative supplement request for the acquisition of a High-Performance Computing (HPC) cluster from Dell, Inc. for a 13 nodes instrument containing 1,664 CPU cores plus low-latency networking necessary to carry out the massively parallel molecular dynamics simulations proposed in PI Alan Chen’s parent NIH R35 grant. Substantial progress has been made in developing improved simulation methods for RNA folding, in particular, a novel 2D- Replica-Exchange-Molecular Dynamics algorithm which has yielded impressive preliminary results. However, the application of this method to biologically relevant RNAs is currently bottlenecked by the lack of sufficient computing power of the PI’s existing instrument. The PI’s existing instrument, purchased in 2014, consists of 38 nodes with dual, 8-core Xeon “Sandy Bridge” CPUs. The warranty expired in 2019, and replacement parts are no longer available; therefore, this instrument has reached “end of life” and is being retired as individual components fail. This is too large an expense to replace from the parent grant, and this supplement request would enable the successful completion of the parent grant’s goal of high- resolution 3D folding of 75-100 nt RNAs in atomistic detail, which would significantly advance biomedical research.