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Googling Molecules: Scientists Revamp The Search Engine, Unlock The Secrets Of Water

In a new twist on the search engine, scientists have reprogrammed it to look at chemistry: Each molecule is a website, each bond is a hyperlink, and PageRank can quickly sort through which ones are the most important. Research just got a lot faster.

Googling Molecules: Scientists Revamp The Search Engine, Unlock The Secrets Of Water
Bruce Amos/Shutterstock

Researchers at Washington State University and the University of Arizona have come up with an innovative use for Google’s ubiquitous PageRank algorithm that has nothing to do with finding a new toaster oven, or asking bet-settling trivia questions. Who knew Google could be so useful?

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The chemists have applied the same mathematical formulas that helps web searchers locate the most-cited pages to analyze the way molecules are organized. They say the research, once applied, could help clean up toxic dumps, speed drug experiments, and analyze proteins and crystals.

The software helps analyze hydrogen bonds in water, treating the interactions between molecules as if they were hyperlinks between pages. The PageRank software is useful because it can cope with huge amounts of data. Like the billions of pages on the web, the millions of molecules in a droplet of water are constantly shifting as they relate with one another.

The initial aim of the research, which is funded by the Department of Energy, is to come up with “environmental remediation” strategies for dealing with toxic heavy metals, such as uranium, plutonium, neptunium, and lead. WSU is nearby the Hanford waste repository, one of the original Manhattan Project sites, where several underground tanks are in danger of leaking.

“The idea is that if we understand how these ions impact the behavior of water, then we can design things to try and control that organization,” says Aurora Clark, an associate professor of chemistry at Washington State University. “If we can control that organization, then ultimately we can control the reactivity of these ions and water, which means we can design strategies to make these toxic metals stick to mineral surfaces, so they don’t travel in the groundwater.”

Clark worked on the project with a student named Barbara Mooney, who has a degree in computer science, and brought the technical chops necessary to use the algorithm.

“Traditionally computer science and chemistry are pretty separate disciplines and it’s very hard to cross fertilize. But I had a very talented student who had gotten a master’s degree in computer science, and so when she switched from computer science to chemistry, she brought all that familiarity with computer science into the chemical realm,” says Clark.

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The advantage of using computer modeling is that it is much faster than observing the molecules by sight, and much safer. The researchers don’t need to worry about the dangers of lab experiments, and there are fewer expenses and logistics issues, too.

Clark says advancing the basic science of water molecules has many potential uses. “Water is an active participant in most chemical reactions that are occurring in it. So if you can understand what the structure and network of water is, then you can get a lot of insight into chemical reactions and maybe even control those reactions more.” Toxic chemicals: Are you feeling lucky?

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About the author

Ben Schiller is a New York staff writer for Fast Company. Previously, he edited a European management magazine and was a reporter in San Francisco, Prague, and Brussels.

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