Thermodynamically Calibrated RNA Simulations to Decode Mechanisms of RNAMolecular Recognition

这是一份行政补充申请，要求采购一台高性能 Dell，Inc.的计算（HPC）群集对于包含1，664个CPU内核的13节点仪器 加上进行大规模并行分子动力学所需的低延迟网络 PI Alan Chen的父母NIH R35资助中提出的模拟。实质性进展 在开发改进的RNA折叠模拟方法，特别是一种新的2D- 复制-交换-分子动力学算法，已经产生了令人印象深刻的初步 结果然而，目前将这种方法应用于生物学相关的RNA是困难的。 由于PI现有仪器缺乏足够的计算能力而受到质疑。PI的 2014年购买的现有仪器由38个节点组成，采用双核8核至强“桑迪 桥接”CPU。2019年保修到期，不再提供更换零件; 因此，该仪器已达到“寿命终点”，将作为单个仪器退役 组件失效。这是一笔太大的开支，无法从父母补助金中取代， 补充申请将使父母补助金的高目标顺利完成， 分辨率3D折叠75-100 nt RNA的原子细节，这将显着推进 生物医学研究

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.