Postdoctoral researcher Kamal Saha, left, and Associate Prof. Branislav Nikolic with UD’s high-speed Chimera computer that enabled them to conduct their research on DNA sequencing. Photo by Evan Krape |
Look
at the tip of that old pencil in your desk drawer, and what you’ll see
are layers of graphite that are thousands of atoms thick. Use the pencil
to draw a line on a piece of paper, and the mark you’ll see on the page
is made up of hundreds of one-atom layers.
But
when scientists found a way—using, essentially, a piece of ordinary
sticky tape—to peel off a layer of graphite that was just a single atom
thick, they called the two-dimensional material graphene and, in 2010,
won the Nobel Prize in physics for the discovery.
Now,
researchers at the University of Delaware have conducted
high-performance computer modeling to investigate a new approach for
ultrafast DNA sequencing based on tiny holes, called nanopores, drilled
into a sheet of graphene.
“Graphene
is a two-dimensional sheet of carbon atoms arranged in a honeycomb
pattern” Branislav Nikolic, associate professor of physics and
astronomy, said. “The mechanical stability of graphene makes it possible
to use an electron beam to sculpt a nanopore in a suspended sheet of
graphene, as demonstrated in 2008 by Marija Drndi? at the University of
Pennsylvania.”
Graphene
has been among the fastest-growing areas of study in nanoscience and
technology over the past five years, Nikolic said. He calls it a wonder
material that has remarkable mechanical, electronic and optical
properties and is being investigated for a variety of applications as
diverse as plastic packaging and next-generation gigahertz transistors.
In
the sequencing that he and other physicists have proposed, a tiny hole a
few nanometers in diameter is drilled into a sheet of graphene and DNA
is threaded through that nanopore. Then, a current of ions flowing
vertically through the pore or an electronic current flowing
transversely through the graphene is used to detect the presence of
different DNA bases within the nanopore.
“Since
graphene is only one atom thick, the nanopore through which DNA is
threaded has contact with only a single DNA base,” Nikolic said.
In
2010, three experimental teams—led by Jene Golovchenko of Harvard, Cees
Dekker of Delft and Drndi?—demonstrated DNA detection using nanopores
in large-area graphene. However, Nikolic said, the process moved too
quickly for the existing electronics to detect single DNA bases.
The
new device concept proposed by the UD researchers uses graphene
nanoribbons—thin strips of graphene that are less than 10 nm wide—with a
nanopore drilled in their interior. Chemists, engineers, materials
scientists and physicists have devised various methods over the past
three years to fabricate nanoribbons with a specific zigzag pattern of
carbon atoms along their edges, Nikolic said. Nanoribbons could enable
fast and low-cost (less than $1,000) DNA sequencing, he said, because of
the quantum-mechanically generated electronic currents that flow along
those edges.
Such quick and inexpensive DNA sequencing could usher in an era of personalized medicine, Nikolic said.
“We
used the knowledge acquired from several years of theoretical and
computational research on the electronic transport in graphene to
increase the magnitude of the detection current in our biosensor by a
thousand to million times when compared to other recently considered
devices,” Nikolic said. “Two years ago, scientists would have told me
our device was impossible, but there are so many people working on
graphene that nothing is impossible anymore.
“Every time physicists think something is impossible, materials scientists or chemists come to the rescue—and vice versa.”
Nikolic
said he and postdoctoral researcher Kamal Saha have employed their
home-grown massively parallel computational codes to simulate the
operation of the proposed nanoelectronic biosensor from first
principles, using the supercomputer Chimera that UD acquired with
support from a National Science Foundation grant.
“This
project has to run on 500-1,000 processors for several months
continuously,” he said. “We couldn’t have done it without UD Chimera
becoming fully operational in early 2011.”
Nikolic, Saha and Drndi? have recently published the results of this research in an article in the prestigious Nano Letters,
a journal with an impact factor of 12.219 published by the American
Chemical Society. Colleagues, led by Drndi? at the University of
Pennsylvania, will now seek to fabricate the biosensors in their lab,
guided by the simulations presented in the article. Nikolic said that
this research synergy will, in turn, allow for simulations of improved
device designs.
Nikolic
is also organizing an interdisciplinary workshop, sponsored by the
Centre Européen de Calcul Atomique et Moléculaire, to be held in June in
Pisa, Italy. The workshop will bring together some of the world’s
leading experts in computational modeling and in the experimental
investigation of nanodevices for third-generation DNA sequencing
technologies.
Source: University of Delaware
