Study seeks ways to block the action of viruses

Researchers can track the movements of molecules as they hop, skip and jump across a surface

SCIENTISTS IN Cork and the Netherlands are watching two-legged molecules while out on a “stroll” as they walk, hop or fly over a surface. Being able to control how molecules move could lead to the development of new medical devices and of ways to block the action of viruses. The work represents a blend of actual experimental work and matching this with computer modelling, according to Dr Damien Thompson of the Tyndall National Institute in Cork.

The experimentalists in the University of Twente in the Netherlands make the lanky molecules and track their movements, while Dr Thompson, in Tyndall’s theory, modelling and design centre, models the molecular motion in detail so that the experimenters can interpret what they are seeing.

“The experiments and simulations show you can control the movement of molecules on a surface,” says Thompson. They move in a range of predictable ways but walk, hop or fly over the surface in response to their local environment, he adds. Details of the work were published online in Nature Chemistry and is in the current print edition of the journal.

Experimenters can now almost see down to the level of a molecule, but it is not like watching a film. Normal physics can act very differently once at the scale of atoms and molecules, Thompson says. For this reason the EU- funded collaboration needed the computer simulations to help work out what was happening.

Thompson used Science Foundation Ireland-supported computing clusters at Tyndall and also the more powerful computer systems at the Irish Centre for High End Computing.

Although the various “steps” taken by the molecules could vary, the experimenters were in control. This is because they could define the layout of the surface that the molecules traversed.

The molecules were hydrophobic, meaning they would shun water. They were then sent across a wet surface that had small hydrophobic cavities dotted over it.

The molecules were sent across the surface, with hydrophobic molecular “feet” latching on to the hydrophobic cavities in a kind of “molecular hopscotch”, says Thompson. This produced the three movements detected: walking, hopping and flying.

“It is an exciting time for research as experiments and simulations are finally on the same page,” Thompson says. “The experiments can finally drill down far enough to see molecule-scale features, while advances in computing mean we can routinely model systems composed of hundreds of thousands and even millions of atoms.”

This is not research for the sake of research, but something Thompson feels can be useful in practical terms. “The example we have used is applicable to medical devices,” he says.

It could be used as a laboratory on a chip to measure molecules in or adjacent to cells. It could be used to identify important biomarkers in the diagnosis of diseases. Viruses use similar attachments when latching on to cells, and this work could help find ways to block their connections by developing new drugs, Thompson suggests.

The initial system can also readily be changed to deliver different kinds of sensor systems. The molecules can be synthesised in the lab to include different atoms to simulate different applications.