If you have ever tried to build something as a kid, with a kid, or for a kid with the tiniest of Legos, you might have an idea of the challenge in creating at the small scale. Scientists at the University of Illinois Urbana Champaign face this type of challenge regularly in their study of how to create tiny motors inspired by DNA. The added challenge for them, though, is the level of tiny at which they work – the nanoscale. This is better understood by thinking about the thickness of one sheet of paper or the width of a single strand of human hair – both equal to about 100,000 nanometers.

To study at this scale, ACCESS resources like the Expanse supercomputer at the San Diego Supercomputer Center at UC San Diego come in handy for researchers such as those led by Aleksei Aksimentiev, professor of biological physics at the University of Illinois Urbana Champaign and principal investigator for a recent study with findings titled DNA double helix, a tiny electromotor, published in Nature Nanotechnology.

A supercomputer such as Expanse enables researchers to peer deeper into elements of what they are studying by creating simulations that use a mathematical description, or model, of a real system embodied in a computer program. Aksimentiev explained that the first step in creating the Expanse simulations was to place DNA molecules in water, apply electric field flow and then observe the rotation or measure the torque generated. 

Supercomputers like SDSC’s Expanse are essential to the development of nanotechnology as they provide a window into the nanoscale world that is otherwise not accessible to experiments.

Aleksei Aksimentiev, professor of biological physics and principal investigator for the study

For this study, a typical simulation took a little longer than a week to complete, which allowed the researchers to carefully create their simulations and measure the torque, enabling them to see the rotation. Once they carefully analyzed the results, they submitted their work to be published in the journal so that the broader research community had access to their findings.

“People have thought about this for a while and gone back and forth—could it work or not,” Aksimentiev said. “We thought that maybe the water doesn’t have enough traction to produce torque, but it did, and we were excited to see the DNA spin in the direction prescribed by its helicity despite significant fluctuations.”

Aksimentiev said that he and the Illinois team plan to use lessons learned from this study to build systems at a nanoscale level that will be used as components in self-propelled systems or for nanoscale energy conversion.

You can read more about this story here (published April 28, 2023): Expanse Supercomputer Used for Tiny Torque Simulations of DNA Molecules

Project Details

Institution: SDSC (San Diego Supercomputer Center)
University: University of Illinois at Urbana Champaign
Funding Agency: NSF
Allocation Number: MCA05S028

The science story featured here, allocated through August 31, 2022, was enabled through Extreme Science and Engineering Discovery Environment (XSEDE) and supported by National Science Foundation grant number #1548562. Projects allocated September 1, 2022 and beyond are enabled by the ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.