IMR: Acquisition of a Linux Cluster for Large-Scale Bio- and Nano-Materials Modeling and Student Training

该提案要求提供资金，用于购置一个64节点的Linux集群，用于生物和纳米材料模拟。该集群将成为物理学、材料科学与工程和化学工程四个跨学科研究小组的共享设施。它将与北卡罗来纳州立大学的高性能计算小组合作维护，主要由研究生和博士后学生在他们的研究要求的全过程中使用。该小组目前的研究跨越计算物理学，材料科学和结构生物学，重点是纳米技术和生物物理学应用。该集群将用于的研究项目包括生物分子的模拟，如溶剂化DNA和蛋白质，蛋白质聚集和分子识别现象的动力学，通过分子电子系统的量子传输的研究，纳米压痕，纳米流体，智能材料等的研究。研究跨越许多长度和时间尺度，因此通常需要多尺度方法。模拟技术的使用范围从最先进的量子化学方法在其最准确的，以有限元和相场的方法在连续长度尺度。这是一个仪器材料研究（IMR）的建议，旨在获得一个计算机集群，用于生物和纳米材料建模和学生培训的研究工具。该集群将由北卡罗来纳州的四个研究小组共享，并将保持和提高这些小组的研究竞争力。在期望使用该集群将带来的所有计算周期的同时，任何多余的周期将免费捐赠给更大的北卡罗来纳州研究社区，从而确保最大限度地影响和利用这一重要的计算资源。利用该设施进行的研究将对生物和纳米技术的新材料和模拟技术的发展产生广泛的影响。后者包括诸如优化的微观结构的材料，亚微米尺度的探针，与微电子工业相关的材料的机械性能，以及纳米电子应用的分子系统等主题。生物研究应用包括对蛋白质聚集、微阵列、DNA和溶剂化蛋白质的化学和机械性质的新理解，以及对分子识别现象的理解。

This proposal requests funds for the acquisition of a 64-node Linux cluster for bio- and nano-materials simulations. The cluster will be a shared facility to be used by four interdisciplinary research groups in Physics, Materials Science and Engineering, and Chemical Engineering. It will be maintained in partnership with NC State's High Performance Computing group, and used primarily by graduate and postdoctoral students in fullfillment of their research requirements. Current research of the group cuts across computational physics, materials science, and structural biology, with an emphasis on nanotechnology and biophysics applications. Research projects for which the cluster will be used include simulations of biomolecules such as solvated DNA and proteins, dynamics of protein aggregation and molecular recognition phenomena, investigation of quantum transport through molecular electronic systems, studies of nanoindentation, nanofluidics, smart materials, and many more. The research cuts across many length and time scales, and therefore typically requires a multiscale approach. Simulation technology in use ranges from state-of-the art quantum chemistry methods at its most accurate, to finite-element and phase-field approaches at the continuum length scale.This is an Instrumentation for Materials Research (IMR) proposal aimed at acquiring a computer cluster to be used as a research tool for bio- and nano-materials modeling and student training. The cluster is to be shared by four research groups at NC State, and will maintain and enhance the research competitiveness of the groups. While expecting to use all of the computational cycles that this cluster would bring, any excess cycles will be donated free of charge to the larger NC State research community, thereby ensuring maximum impact and utilization of this important computational resource. The research that will take advantage of this facility will have a broad impact on the development of new materials and simulation technology for bio- and nanotechnology. The latter include topics such as materials with optimized microstructures, probes for the sub-micron scale, mechanical properties of materials relevant for the microelectronics industry, and molecular systems for nanoelectronic applications. Biological research applications include new understanding of protein aggregation, microarrays, the chemical and mechanical properties of DNA and solvated proteins, and understanding of molecular recognition phenomena.