Molecular Switching Probed For Nanocomputers

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March 16, 1999 (2:23 PM EST)

Molecular Switching Probed For Nanocomputers

As chemists learn more about molecular behavior, the possibility of building nanocomputers -- both CPUs and memory systems -- is getting closer to reality.

Both the complex proteins manufactured by virtually all living systems and long-chain polymer molecules can act as bi-stable devices when their basic 3-D configurations change as a result of outside stimulation. Probing with tiny atomic-force microscope tips or simply using photons, researchers are getting a handle on molecular mechanisms that could form the basis of 21st-century nanocomputers.

Biologically produced molecules figured in a recent demonstration of a reversible protein switch in Seattle at the Center for Nanotechnology at the University of Washington. The molecules could be organized into molecular-scale switching arrays to perform basic computations. Meanwhile, researchers at the University of Arizona, in Tucson, are experimenting with polymers that respond to individual photons. Terabit 3-D optical memories the size of a sugar cube might some day result from the "designer" molecules created by two researchers there, Joseph Perry and Seth Marder. The team recently uncovered a molecule that initiates polymerization as well as causing "on" bits to fluoresce, yielding two ways to read out stored data.

Viola Vogel, associate professor of bioengineering at the University of Washington, uncovered the molecular switch operation while investigating fibronectin, a molecule that plays a role in the cell-binding functions of living proteins. Like untying a shoelace, a slight mechanical pull on the fibronectin protein unravels a segment, switching off its active capabilities. The molecular operation is nondestructive, so it can be "reset" to its active mode.

"Most people are concentrating on the chemical mechanisms of regulating living functions, so we were totally surprised when we discovered that this switch worked mechanically -- you tug on a strand of the protein to turn off its function, but it leaves the molecule intact for reactivation," said Vogel, who, is also director of the Center for Nanotechnology.

"This is the first time a tension-activated switching mechanism has been discovered on an atomic scale," she said. "Our discovery not only gives new insights into how nature regulates functions, but we hope will be the basis for a new family of biotechnology devices."

Vogel made the discovery after five years of work, not experimentally, but by using an advanced computer simulation designed by physics professor Klaus Schulten at the University of Illinois' Beckman Institute for Advanced Science and Technology. Schulten has pioneered a new computational approach to simulating molecules that is accurate enough to model a molecule's structural response to external forces.

"This tension-activated switching mechanism is very, very small-it takes place at the angstrom level-so we hope it will eventually result in a very elegant mechanical switch for nanotechnology devices," said Vogel.

The fibronectin molecule is a member of the family of glycoproteins, the building blocks that reinforce the surface of living cells. The extracellular matrix created by fibronectin is thought to regulate communication, gene expression, adhesion, and other interactions between living cells and their environment. For that reason, it is the focus of intense study by engineers designing artificial devices that interface with living tissue.

"There is an immense amount of research being directed at the fibronectin molecule, but not a single study has revealed that simple tension can be used to regulate its functions," said Vogel. "Only last year was the first study published about attempting to pull single molecules apart. This [newest] discovery could open up an entirely new field dedicated to studying single-molecule mechanics."

Though fibronectin is usually found in a long chain of repeating modules, only one of the loops in the chain is responsible for the switching mechanism. This active loop sticks out above the surface of the molecule from a slot between two strands, making Vogel curious as to its function. By gently tugging on the exposed loop, using Schulten's simulation program, Vogel determined that the function of the molecule could be turned on and off like an angstrom-size switch.

Schulten's simulation showed that tugging on the loop not only unraveled it, thereby switching off the molecule's active functions, but that the molecule remained intact enough to reassemble and restore its active functions. In living tissue, the molecule sometimes migrates to a new site before reactivation, but for nanotechnology devices it would remain stationary.

Next, Vogel plans to experimentally confirm the simulation using a combination of atomic-force microscopy and nanoscale optical tweezers to verify the accuracy of the results. After that she plans to begin engineering a new family of nanometer-size switches that could be used to create nanocomputers.

"This is a very exciting time," said Vogel. "Many different pieces of the puzzle are starting to come together to explain how living organisms regulate biological activities, which should in turn give us insights into how to design nanotechnology devices based on the same principles."

While Vogel's molecular switch is basically mechanical in nature, the University of Arizona researchers are working with molecules that modify the absorption of photons. The effect could lead to very high-density optical storage systems.

"We are very hopeful about densities-about a 1012 bits/cm3, or about two orders of magnitude denser than traditional 2-D optical media," said Seth Marder of the university's chemistry department.

The team's designer molecules absorb two photons when turned "on," jumping them up two notches on the energy scale making for a phenomenally high signal-to-noise ratio. And yet getting the molecule to change state can be performed with submicron precision by merely focusing a laser beam within the 3-D memory.

Supersensitive
Ordinarily two-photon absorption requires the square of the light intensity, but the team's molecules were designed from the ground up to be supersensitive. Two-photon absorption is also highly localized, occurring only at the focus of the laser-within a cube with sides the length of the laser's wavelength. The specific molecules created by the team were enhanced for two-photon absorptivity by harnessing donor-acceptor-donor (D-A-D) and acceptor-donor-acceptor (A-D-A) structural motifs.

Since the absorption of two photons can initiate polymerization in several monomers, making them polymers only where the laser was focused, the effect can be used to "etch" a complex structure within a 3-D solid for micromechanical nanotechnology applications. There are even biological applications on the drawing board to synthesize dyes that can be conjugated with antibodies through biotin-strepavidin interactions.

"Our molecules are sensitive enough to laser light that myriad applications in materials science and photonics are possible. The basic idea that a molecule can simultaneously absorb two photons goes back 70 years to Maria Goeppert-Mayer in 1931," said Marder. But it wasn't until 1995 that the team observed an orange (lower-energy) laser beam generating a blue (higher-energy) fluorescence in its experimental 3-D material.

"Fluorescence can only be explained by molecules simultaneously absorbing two photons, losing some energy and then emitting a photon still higher in energy than the ones being absorbed," said Marder.

The team's fluorescence-tending molecules are so sensitive to two-photon absorption, that the lasers used for read and write operations can be much lower power than those required today for current optical memory systems. The technique also brings access to the third dimension for photo lithography and fabricating microscopic molds, semiconductor materials and nanotechnology-sized micro-mechanical devices.

"We have provided the knowledge and the molecules that others can now really start using in two-photon absorption applications they previously would not have considered feasible," Marder said.

The team itself is pursuing several follow-on research directions, from faster writing methods to new materials, other than polymers, that can be fabricated with two-photon absorption molecules, especially semiconductors. Perry will additionally expand his development of nanotechnology-sized structures that have the correct periodicity to serve as photonic band-gap devices.

In polymers, the team plans to develop molecules that can serve as the molds for an inorganic semiconductor material with extremely high dielectric contrasts. In 3-D imaging of biological materials, the team plans to develop microscopy molecules that will fluoresce to pinpoint affected areas.