Washington State Magazine

Washington State Magazine :: Spring 2014

Spring 2014

Points of views

In This Issue...


Mountains and Rivers and Prairies Without End—Recollecting Washington’s landscapes :: “The whole concept has burgeoned ... to one where the landscape is part of why people select to live in certain locations, has political meaning, has religious meaning, has all of these other kinds of meaning.” by Tim Steury

{ WEB EXCLUSIVE–Trips: Washington road trips from Tim Steury and Kathleen Flenniken}

A True Story Fraught with Peril :: Buried in hundreds of layers of rock are tales of fire, brimstone, destruction, and fragility. by Eric Sorensen

{ WEB EXCLUSIVE–Trips: Flood Basalts and Glacier Floods: Roadside Geology of Parts of Walla Walla, Franklin, and Columbia Counties, Washington }

A Dose of Reason—Pediatric specialists advocate for vaccines :: In 2011, Washington’s vaccination rate was dangerously low. According to the CDC, 6.2 percent of children in kindergarten had not been fully immunized. by Hannelore Sudermann

An inquiring mind :: Ken Alexander ’82, chief of pediatric infectious diseases at the University of Chicago’s Comer Children’s Hospital.


On the Road :: Washington’s Poet Laureate brings poetry to, and discovers it in, each of the state’s 39 counties. by Kathleen Flenniken ’83


:: Backyard boarders

:: Google ranking molecules

:: Music to a closed country

:: The calculus of caring and cooperation

:: Sorting debitage from rubble

:: A wider canvas

:: Predictive software helps communication

{ WEB EXCLUSIVE–Video: WSU chemist applies Google software to webs of the molecular world }


:: First Words

:: Posts

:: Sports: After the games

:: In Season: What about buckwheat?

:: Last Words: Everyone could use a lift

{ WEB EXCLUSIVE–Recipe: Sonoko Sakai’s Nihachi Soba Noodles }

{ WEB EXCLUSIVE–Video: Campus shortcuts }


:: Robert Franklin ’75, ’76, ’79—A new leash on life

:: Pavlo Rudenko ’09—As fast as he can go

:: Nancy Gillett ’78—The business of science

:: Alumni news: Two alumni recognized for their contributions to food and agriculture

{ WEB EXCLUSIVE–Guide: A Guide to TriboTeX Nano-based Lubricant }

New Media

Soldiers of Paint by Doug Gritzmacher ’98 and Michael DeChant Jr.

Civility and Democracy in America: A Reasonable Understanding edited by Cornell W. Clayton and Richard Elgar

A Yankee on Puget Sound by Karen L. Johnson ’78 and Dennis M. Larsen ’68

New & Noteworthy: Operation Cody: An Undercover Investigation of Illegal Wildlife Trafficking in Washington State by Todd A. Vandivert ’79; Isaiah Shembe’s Prophetic Uhlanga by Joel E. Tishken; The Business of Android Apps Development/Taking Your Kindle Fire to the Max/LEGO Technic Robotics/Practical LEGO Technics by Mark Rollins ’94

On the cover: “Washington Road Trips” by John S. Dykes

“Molecular” typeface <em>by Mithila Shafiq</em>

“Molecular” typeface by Mithila Shafiq

Google ranking molecules

by | © Washington State University

When Aurora Clark likened water molecules to webpages, and the hydrogen bonds that connect them to hyperlinks, she knew she was onto something. As she thought about it on a larger scale, billions of water molecules began resembling the World Wide Web. And where else could Clark, an associate professor of chemistry, turn to make sense of such a vast network?

Google, of course.

By adapting Google’s PageRank to determine how molecules are shaped and organized, Clark started her journey of importing concepts from computer science into her work in chemistry. First she used Google, but recently Clark has employed digital mapping principles and ideas behind social networks to understand the life of molecules.

“I think that is a fundamentally neat concept,” says Clark. “You can take all the technology you use in your day-to-day life, and use it in chemistry.”

Google’s PageRank assigns a number to every page on the web—a numerical rank determined by how many other pages link or point to it. The more links, the better the ranking. With this ranking system, a vast and otherwise chaotic network was given order.

Google was happy to lend Clark its PageRank algorithm, which was developed in the 1990s while the company’s founders, Sergey Brin and Larry Page, were doctoral students at Stanford University. They published their algorithm in 1998, the year they dropped out of school and started Google. The Silicon Valley giant eventually began using techniques alongside PageRank to improve its search engine, and Clark has done the same.

Her motivation to expand and improve on her program came when she wanted her work to look at more than just water molecules and the relatively well-understood hydrogen bonds that connect them. She and her team devised ChemNetworks, a further iteration of Clark’s original program, moleculaRnetworks. The new software program will be discussed in an article written by Clark and Abdullah Ozkanlar, a postdoctoral fellow in chemistry at WSU, in the Journal of Computational Chemistry.

The software will help chemists better understand how the physical properties of a chemical system are related to intermolecular interactions—those fleeting but ever-present forces that molecules feel when they come close to each other.

“It’s like the seven degrees of Kevin Bacon, but between molecules,” says Clark. “How many pathways of interaction do you have? You’re finding the shortest path, the linkage, between entities. What’s the shortest way to get from here to here?”

Clark’s work is helping researchers better understand how the organization of liquid-liquid interfaces influences the ability to purify water and separate complex mixtures of materials.

Typically chemists separate metals by dissolving a molecule that is selective for a specific metal in the mixture, and then bringing it across the interface, or membrane. But they don’t really know why this process works. If they did, which Clark’s work promises to do, the nuclear and mining industries could be transformed.

Another area of research for Clark and her team deals with biofuel purification.

Understanding solvent organization in a confined environment would help researchers better separate the water and alcohol involved in the manufacture of biofuel. When distilling a mixture of the two, you reach a point where they have the same boiling points and can no longer be separated by distillation. To get around this problem, scientists have begun using porous and hydrophobic materials to force the alcohol and water apart. Clark says her research shows it’s not a matter of repelling something from water, but the size of the area into which it is repelled.

“We’re showing that the confinement effect itself is contributing to the mechanism behind separation,” she says. “That’s important. It will change how people design these materials.”

Her work could have other implications, she says. In a time when high school and college chemistry labs compete with other school programs for funding, she hopes her program could be used in a virtual lab, allowing students who don’t have access to a full laboratory to experience some of the complexity of chemistry.

Categories: Chemistry | Tags: Molecules, Google, Networks

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