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

University Of Southern California, Los Angeles CA

Investigators

Abstract

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