Scientists have created the world’s first nanoscale electric motor, according to research published in the journal Nature Nanotechnology. The team designed a turbine made of DNA powered by hydrodynamic flow inside a nanopore, a nanometer-sized hole in a solid-state silicon nitride membrane.
The tiny engine could help research for future applications, such as making molecular factories for useful chemicals or medical detectors of molecules in the bloodstream to detect diseases like cancer.
“Common macroscopic machines become inefficient at the nanoscale,” said study co-author Professor Aleksei Aksimentiev, professor of physics at the University of Illinois at Urbana-Champagne. “We need to develop new principles and physical mechanisms to realize electric motors on a very, very small scale.”
Experimental work on the tiny motor was carried out by Cees Dekker of Delft University of Technology and Hendrik Dietz of Technical University of Munich.
Dietz is a world expert on DNA origami. His lab manipulated DNA molecules to make the turbine of the tiny motor, which consisted of 30 DNA double-helix helices built into a shaft and three blades about 72 base pairs long. Decker’s laboratory work showed that the turbine can indeed be rotated by applying an electric field. Aksimentiev’s lab performed molecular dynamics simulations with all the atoms in a system of five million atoms to characterize the physical phenomena of how the motor works.
The system was the smallest representation that could yield meaningful results about the experiment. However, “it was one of the largest ever simulated in terms of DNA origami,” Aksimentiev said.
Mission Impossible to Mission Possible
The Texas Advanced Computing Center (TACC) awarded Aksimentiev a Leadership Resource Allocation to support the study of mesoscale biological systems at the National Science Foundation (NSF)-funded Frontera, the leading academic supercomputer in the US.
“Frontera played a key role in this DNA nanoturbine project,” Aksimentiev said. “We got microsecond simulation trajectories in two to three weeks instead of waiting a year or more on smaller computing systems. The big simulations were done on Frontera using about a quarter of the machine — over 2,000 knots,” Aksimentiev said. “However, it’s not just the hardware, it’s also the interaction with the TACC staff. It’s extremely important that we make the best use of the resources once we have the opportunity.”
Aksimentiev was also awarded supercomputing allocations for this project from the NSF-funded Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) at the Expanse of the San Diego Supercomputer Center and Anvil of Purdue University.
“We had up to 100 different nanomotor systems to simulate. We had to run them for different conditions and in a fast way, which the ACCESS supercomputers helped perfectly,” said Aksimentiev. “Many thanks to NSF for their support — we couldn’t do the science we do without these systems.”
DNA as a building block
The success with the functional DNA nanovortex builds on a previous study that also used Frontera and ACCESS supercomputers. The study showed that a DNA helix is the tiniest electric motor anyone can make — it can spin up to a billion revolutions per minute.
DNA has emerged as a nanoscale building material, according to Aksimentiev.
“The way DNA base pairs is a very powerful programming tool. We can program geometric, three-dimensional objects from DNA using Cadnano software simply by programming the sequence of letters that make up the steps of the double helix,” he explained.
Another reason for using DNA as a building block is that it carries a negative charge, a key feature for building the electric motor.
“We wanted to replicate one of the most spectacular biological machines — ATP synthase, which is driven by an electric field. We chose to make our engine out of DNA,” Akhismediev said.
“This new work is the first nanoscale motor where we can control the speed and direction of rotation,” he added. It is done by adjusting the electric field across the solid-state nanopore membrane and the salt concentrations of the fluid surrounding the rotor.
“In the future, we might be able to synthesize a molecule using the new nanoscale electric motor, or use it as a component of a larger molecular factory, where things move. Or we could imagine it as a vehicle for soft propulsion, where synthetic systems they can enter a bloodstream and detect molecules or cells one at a time,” Aksimentiev said.
If you think this sounds like something out of a 1960s sci-fi movie, you’re right. In the movie Fantastic Voyage, a group of Americans in a nuclear submarine are shrunk and injected into a scientist’s body to fix a blood clot, and they have to work fast before the miniature runs out.
As far-fetched as this may sound, Aksimentiev says the concept and components of the machines we’re developing today could allow this to happen.
“We were able to achieve this thanks to supercomputers,” Aksimentiev said. “Supercomputers are becoming more and more necessary as the systems we build grow in complexity. They are computational microscopes, which at the ultimate resolution can see the movement of individual individuals and how it connects to a larger system.”
Funding came from ERC Advanced Grant no. 883684 and the NanoFront and BaSyC programs. ERC Consolidator Grant to HD (GA no. 724261), the Deutsche Forschungsgemeinschaft through the Gottfried-Wilhelm-Leibniz Program (to HD) and SFB863 Project ID 111166240 TPA9. National Science Foundation Grant DMR-1827346; of the Max Planck School Matter to Life and the MaxSynBio Consortium. Supercomputer time is provided through TACC Leadership resource allocation MCB20012 to Frontera and through ACCESS allocation MCA05S028.