Top NSF petascale supercomputer and expert staff accelerate discoveries for nation's scientists

Published on May 27, 2014 by Aaron Dubrow

A sequence of still images illustrate the temporal evolution of synthetic DNA nanostructures imaged through all-atom molecular dynamics simulations. Credits: Jejoong Yoo and Aleksei Aksimentiev, Department of Physics, University of Illinois-Urbana Champaign

Cutting-Edge DNA Sequencing

The Stampede supercomputer enabled Aleksei Aksimentiev at the University of Illinois-Urbana Champaign to explore a cutting-edge method of DNA sequencing that uses an electric field to drive a strand of DNA through a small hole, or "nanopore," either in silicon or a biological membrane. By controlling this process, the sequencer can read each base pair in order by measuring the change in ionic current as the DNA strands moves through the pore of the membrane.

"Being able to routinely obtain 40-80 nanoseconds of molecular dynamic simulations in 24 hours, regardless of the systems' size, has been essential for us to make progress with rapidly evolving projects," he explained.

Aksimentiev showed that localized heating can be used to stretch DNA, which significantly increases the accuracy of nanopore DNA sequencing. In addition, he and his team used an all-atom molecular dynamics method to accurately describe DNA origami objects, making it possible to engineer materials for future applications in biosensing, drug delivery and nano-electronics. These results were published in ACS Nano and the Proceedings of the National Academy of Sciences.

"Stampede is by far the best computer systems my group has used over the past 10 years," said Aksimentiev.

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