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The National Institute for Computational Sciences

Article Co-Authored by JICS and ORNL Researchers Earns Recognition from One of the World’s Top Scientific Publishers

by Scott Gibson

Collaborative research led by a senior scientist from the Joint Institute for Computational Sciences (JICS) is the subject of an article recently highlighted by one of the world’s most prominent and best-known publishers of scientific information.

The publisher, IOP Science, chose as Publisher’s Pick of October for its Nanotechnology section the article, “DNA translocating through a carbon nanotube can increase ionic current,” by Predrag Krstic of JICS, Jae Hyun Park of the Physics Division at Oak Ridge National Laboratory (ORNL), and Jin He, Brett Gyarfas, and Stuart Lindsay of the Biodesign Institute of Arizona State University in Tempe.

The article conveys details of the research team’s investigation of a physics-based method of DNA sequencing, which is intended to read the hereditary traits coded in human DNA.

The method they explored, known as nanopore sequencing, uses a narrow, single-walled carbon nanotube and electric field to thread a strand of DNA from one reservoir with solvent to another, allowing for the electrical detection of DNA sequences.

 

A follow-up to the published results of the researchers’ previous experimental investigation, this article explains, using computer simulations, the existence of surprising conditions during the DNA translocation through the carbon nanotube. Contrary to the anticipated outcome, measured ionic current was enhanced rather than blocked.

“Nanopore sequencing is of particular interest to researchers because it is intrinsically faster and potentially less expensive than existing DNA sequencing methods,” Krstic said.

The National Institutes of Health, through its “$1,000 Genome Initiative,” is driving the development of new sequencing technologies toward the creation of affordable doctor’s office instruments that could be used to quickly analyze segments of DNA for disease-causing traits.

The research performed by Krstic, Park, and the team from Arizona State was both theoretical and experimental. Krstic and Park performed computational work using resources provided by the University of Tennessee’s National Institute for Computational Sciences and the U.S. Department of Energy’s National Center for Computational Sciences at ORNL. The researchers from Arizona State, led by Biodesign Institute Director Lindsay, conducted the experiments.

“The development of this DNA sequencing technology is a collective effort in nanoscience,” Krstic said. “It integrates biology, chemistry, physics, and engineering, through interlaced experimental and theoretical/computational efforts, which makes it very attractive for our multi-institutional, multidisciplinary research team.”

  The Joint Institute for Computational Sciences was established by the University of Tennessee and Oak Ridge National Laboratory (ORNL) to advance scientific discovery and state-of-the-art engineering, and to further knowledge of computational modeling and simulation. JICS pursues its mission by taking full advantage of petascale-and-beyond computers housed at ORNL, and by educating a new generation of scientists and engineers well-versed in the application of computational modeling and simulation for solving the most challenging scientific and engineering problems.

The National Institute for Computational Sciences is a joint effort of the University of Tennessee and Oak Ridge National Laboratory and is funded in part by the National Science Foundation. Located on the campus of ORNL, NICS is a major partner in NSF’s Extreme Science and Engineering Discovery Environment, known as XSEDE.