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

该奖项是根据2009年美国复苏和再投资法案(公法111-5)资助的。该项目建立了一个专门的微秒模拟计算平台，用于研究通过固态纳米孔进行的DNA自组装和移位。该项目使用一个预测的分级千万亿级模拟框架来研究：DNA通过固态纳米孔的移位动力学和动力学；用于核苷酸测序的移位DNA的电子性质；纳米孔中表面电荷的离子筛选；受限二氧化硅通道中的压力驱动DNA传输；计算平台还将支持计算机科学研究，以实现此类模拟的并行化，以及分子生物学和生物材料科学的多尺度、多现象模拟代码的集成。通过固态纳米孔和纳米流体通道进行DNA转移的百万亿级模拟是分子结构和高速测序的“芯片实验室”技术和固态纳米孔“显微镜”的基础。基础设施将有助于培养新一代研究生。学生们参加了一个双学位项目，在这个项目中，他们获得了物理科学或工程学博士学位和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，在研讨会上，来自历史悠久的黑人学院和少数族裔服务机构的本科生和教师导师获得了并行计算的实践经验。有关该项目的更多信息，请访问该项目的网页：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