II-NEW: A Dedicated Computing Platform for Large Spatiotemporal-scale Atomistic Simulations of DNA Translocation and Self-Assembly

该奖项根据 2009 年美国复苏和再投资法案（公法 111-5）提供资助。该项目建立了一个用于微秒模拟的专用计算平台，以研究 DNA 通过固态纳米孔的自组装和易位。该项目使用预测分层千万亿级模拟框架来研究： DNA 通过固态纳米孔的易位动力学和动力学；用于核苷酸测序的易位 DNA 的电子特性；纳米孔表面电荷的离子筛选；压力驱动的 DNA 在有限的二氧化硅通道中运输；该计算平台还将支持此类模拟的并行化技术以及分子生物学和生物材料科学的多尺度、多现象模拟代码集成的计算机科学研究。通过固态纳米孔和纳米流体通道进行千万亿次 DNA 易位模拟是“芯片实验室”技术和用于分子结构和高速测序的固态纳米孔“显微镜”的基础。该基础设施将有助于培训新一代研究生。学生参加双学位课程，获得物理科学或工程学博士学位以及计算机科学硕士学位。该基础设施还加强了针对代表性不足群体的年度计算科学研讨会，来自历史悠久的黑人学院和大学以及少数族裔服务机构的本科生和教师导师在研讨会上获得了并行计算的实践经验。有关该项目的更多信息可以在项目网页上找到：http://cacs.usc.edu/cri/index.php

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).This project establishes a dedicated computing platform for microsecond simulations to study DNA self-assembly and translocation through solid-state nanopores. The project uses a predictive hierarchical petascale simulation framework to study: Translocation kinetics and dynamics of DNAs through solid state nanopores; electronic properties of translocating DNAs for sequencing nucleotides; ionic screening of surface charges in nanopores; pressure-driven DNA transport in confined silica channels; and shear-induced DNA self-assembly.The computing platform will also support computer science research in techniques for the parallelization of such simulations, and for the integration of multi-scale, multi-phenomena simulation codes for molecular biology and biological materials science.Petascale simulations of DNA translocation through solid-state nanopores and nanofluidic channels underlie "lab-on-a-chip" technology and solid-state nanopore "microscopy" for molecular structure and high-speed sequencing.The infrastructure will help in training a new generation of graduate students. Students participate in a dual-degree program in which they do a PhD in physical sciences or engineering and a master's degree in computer science. The infrastructure also strengthens the annual computational science workshops for underrepresented groups, in which undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions acquire hands-on experience in parallel computing. Further information on the project can be found at the project web page: http://cacs.usc.edu/cri/index.php