WSU chemist applies Google software to webs of the molecular world

February 13, 2012
Aurora Clark, an associate professor of chemistry at Washington State University, has adapted Google's PageRank software to determine the way molecules are shaped and organized. Credit: Washington State University photo

The technology that Google uses to analyze trillions of Web pages is being brought to bear on the way molecules are shaped and organized.

Aurora Clark, an associate professor of chemistry at Washington State University, has adapted Google's software to create moleculaRnetworks, which scientists can use to determine molecular shapes and without the expense, logistics and occasional danger of lab experiments.

"What's most cool about this work is we can take technology from a totally separate realm of science, computer science, and apply it to understanding our natural world," says Clark.

Clark and colleagues from the University of Arizona discuss the software in a recent online article in The Journal of Computational Chemistry. Their work is funded by the U.S. Department of Energy's Basic Energy Sciences program.

The software focuses on in water, earth's most abundant solvent and a major player in most every .

"From a biological or chemical standpoint, water is where it's at," says Clark.

In living things, water can perform key functions like helping proteins fold or organizing itself around the things it dissolves so molecules stay apart in a fluid state. But the processes are dazzlingly complex, changing in fractions of a second and in myriad possible forms.

Much like the trillion-plus Web domains on the Internet.

Google's PageRank software, developed by its founders at Stanford University, uses an algorithm—a set of mathematical formulas—to measure and prioritize the relevance of various to a user's search. Clark and her colleagues realized that the interactions between molecules are a lot like links between Web pages. Some links between some molecules will be stronger and more likely than others.

"So the same algorithm that is used to understand how Web pages are connected can be used to understand how molecules interact," says Clark.

The PageRank algorithm is particularly efficient because it can look at a massive amount of the Web at once. Similarly, it can quickly characterize the interactions of millions of molecules and help researchers predict how various chemicals will react with one another.

Ultimately, researchers can use the software to design drugs, investigate the roles of misfolded proteins in disease and analyze radioactive pollutants, Clark says.

"Computational chemistry is becoming the third leg in the stool of chemistry," the other two being experimental and analytical chemistry, says Clark. "You can call it the ultimate green chemistry. We don't produce any waste. No one gets exposed to anything harmful."

Clark, who uses Pacific Northwest National Laboratories supercomputers and a computer cluster on WSU's Pullman campus, specializes in the remediation and separation of radioactive materials. With computational and her Google-based , she says, she "can learn about all those really nasty things without ever touching them."

Explore further: Quantum physics predict chemical reactions

Related Stories

Quantum physics predict chemical reactions

September 15, 2005

Purdue University scientists say chemists trying to predict how complex biological molecules react with others may soon get help from quantum physics.

Computational actinide chemistry: Are we there yet?

August 21, 2007

Ever since the Manhattan project in World War II, actinide chemistry has been essential for nuclear science and technology. Yet scientists still seek the ability to interpret and predict chemical and physical properties of ...

Orange peels could be made into biodegradable plastic

September 26, 2011

Plastic waste is one of the worst forms of trash because it takes so long to degrade, thus overflowing our landfills and polluting our oceans and waterways. But what if we could make plastic from a recycled, natural, biodegradable ...

Madrid duo fire up quantum contender to Google search

December 14, 2011

(PhysOrg.com) -- Two Madrid scientists from The Complutense University think they have an algorithm that may impact the nature of the world's leading search engine. In essence, they are saying Hey, world, Google This. "We ...

Recommended for you

Findings illuminate animal evolution in protein function

July 27, 2015

Virginia Commonwealth University and University of Richmond researchers recently teamed up to explore the inner workings of cells and shed light on the 400–600 million years of evolution between humans and early animals ...

New polymer able to store energy at higher temperatures

July 30, 2015

(Phys.org)—A team of researchers at the Pennsylvania State University has created a new polymer that is able to store energy at higher temperatures than conventional polymers without breaking down. In their paper published ...

How to look for a few good catalysts

July 30, 2015

Two key physical phenomena take place at the surfaces of materials: catalysis and wetting. A catalyst enhances the rate of chemical reactions; wetting refers to how liquids spread across a surface.

Yarn from slaughterhouse waste

July 29, 2015

ETH researchers have developed a yarn from ordinary gelatine that has good qualities similar to those of merino wool fibers. Now they are working on making the yarn even more water resistant.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.