Small wonders

released 10.30.07

By James E. Kloeppel

Scientists tap NCSA resources to design a tunable semiconductor membrane that could be used for protein filtering or DNA sequencing.

A semiconductor membrane designed by researchers at the University of Illinois could offer more flexibility and better electrical performance than biological membranes. Built from thin silicon layers doped with different impurities, the solid-state membrane also could be used in applications such as single-molecule detection, protein filtering, and DNA sequencing.

"By creating nanopores in the membrane, we can use the membrane to separate charged species or regulate the flow of charged molecules and ions, thereby mimicking the operation of biological ion channels," says lead researcher Jean-Pierre Leburton, the Stillman Professor of Electrical and Computer Engineering at the University of Illinois at Urbana-Champaign.

Leburton and postdoctoral research associate Maria Gracheva used high-performance computers at NCSA to simulate the operation of the semiconductor membrane at a number of electrostatic potentials.

"We have a huge grid of two million grid points that we have to simulate in 3D," Leburton says. "It requires huge resources."

Previously, Leburton and his collaborators had been using workstations to carry out their simulations, but "we were working at the limits of the capabilities of these workstations," he explains. Moving their calculations to one of NCSA's high-performance computing systems enabled the researchers to get their results more quickly and easily.

The team currently simulates each membrane configuration in sequence, with each one of the hundreds of configurations taking up to four hours to compute, even on NCSA's powerful systems. Leburton says the team plans to parallelize their code in order to better leverage high-performance computing resources.

In the researchers' model, the nanopore-membrane structure is made of two layers of silicon, each 12 nanometers thick, with opposite (n- and p-) doping. The electrostatic potential is positive on the n-side and negative on the p-side of the membrane.

"The use of p-type semiconductor material in the p-n membrane opens up additional possibilities for ion current and biomolecule manipulation," Gracheva says. "With this membrane one can electrically block the current through the nanopore, even though the nanopore is physically open. One can also envision stretching biomolecules translocating through such a membrane."

The nanopore has an hourglass shape, with a neck one nanometer in diameter and openings on each side of the membrane six nanometers in diameter. The "size" of the nanopore can be changed by changing the electrostatic potential around it.

By controlling the flow of ions, the artificial nanopore offers a degree of tunability not found in biological ion channels, said Leburton. The findings are reported in a paper accepted for publication in the journal Nano Letters. In addition to serving as a substitute for biological ion channels, the solid-state nanopore and membrane could be used in other applications, including sequencing DNA.

"Using semiconductor technology to sequence the DNA molecule would save time and money," Leburton says. "By biasing the voltage across the membrane, we could pull DNA through the nanopore. Since each base pair carries a different electrical charge, we could use the membrane as a p-n junction to detect the changingelectrical signal."

For more information: http://www.beckman.uiuc.research/mens/ce.html

Support for this research was provided by the National Science Foundation and the National Institutes of Health.

James E. Kloeppel is a research editor with the University of Illinois News Bureau. Trish Barker, NCSA Public Information Officer, contributed to this article.