The three researchers who share the 2013 Nobel Prize in Chemistry. From left: Martin Karplus of Harvard, Michael Levitt of Stanford, and Arieh Warshel of the University of Southern California. (Getty Images)
The three researchers who share the 2013 Nobel Prize in Chemistry. From left: Martin Karplus of Harvard, Michael Levitt of Stanford, and Arieh Warshel of the University of Southern California. (Getty Images)

Stanford biologist Michael Levitt is one of three scientists to share the Nobel Prize in chemistry for developing powerful, computer-aided tools to model the complex chemical processes at the foundation of life. Levitt’s co-winners are Martin Karplus of the University of Strasbourg in France and Harvard University, and Arieh Warshel of the University of Southern California.

When the three men started studying chemistry, scientists built models of atoms and molecules with sticks and balls. As you can imagine, that made it cumbersome to portray complex molecules, and nigh impossible to create a model of the light-speed chemical reactions by which cells consume food, say, or drugs battle bacteria.

Levitt, Karplus and Warshel won the Nobel prize for figuring out how to model these chemical reactions in cyberspace, at a time when computers still ran on punch cards, and didn’t have the power to run the complex calculations needed. In his fascinating blog post, NPR’s Michaeleen Doucleff explains how the work of each man dovetailed precisely with the others, to break open whole new possibilities for scientific research that had previously seemed out of reach.

Their work “led to such practical applications such as the production of human antibodies for modern anticancer therapy and catalysts to clean car exhaust fumes,” Mercury News reporter Lisa M. Krieger explains.

Levitt said on a Stanford website honoring his award that he got the news early this morning.

“Like everyone else, one is surprised,” said Levitt of the early morning call. “Now I just hope to get through the day and make sure that, in the end, my life doesn’t change very much. Because I really have a wonderful life.

“My phone never rings,” he added. “Everyone sends me texts and email. So when the phone first rang, I was sure it was a wrong number. When it rang a second time, I picked it up. I immediately heard a Swedish accent and got very excited. It was like having five double espressos.”

All three of today’s winners are immigrants who came to the United States early in their research careers: Levitt is a U.S.-U.K.-Israeli citizen born in South Africa; Karplus is a dual U.S.-Austrian citizen; and Warshel is a dual national of Israel and the United States.

Levitt gave an overview of his research to KQED’s Joshua Johnson this morning:

It’s research that started in 1967, so it’s research that’s been going on ever since I was 20 years old, so for 46 years. Basically, it tries to simulate the molecules of life. And simulation is now quite common — flight simulators and for bridges. I’m sure the Bay Bridge was simulated to pieces before it was built. So simulation is a very important tool. We started doing simulations on molecules back in the late ‘60s, principally because it had become clear that molecules had very well-defined shapes. They were complicated, they consisted of a thousand spheres, or a thousand atoms, and all these atoms were very precisely arranged.

This Stanford video explains how the work of Levitt and his Nobel colleagues benefits medicine, as researchers observe how protein molecules come together in ways that are healthy, or that promote disease. (Courtesy of Stanford University)
This Stanford video explains how the work of Levitt and his Nobel colleagues benefits medicine, as researchers observe how protein molecules come together in ways that are healthy, or that promote disease. (Courtesy of Stanford University)

The molecules are much like the inside of a clock … they were all highly arranged in space. Once things are very arranged in space, you can do very precise calculations. You can simulate how they move, how they will behave under stress and so on. So it becomes a rather mechanical calculation, not exactly the same as simulating a jet airliner or a bridge or a nuclear explosion, but it’s a similar principal where you have a system and you see how it changes over time.

… This is something which ties in very closely to experiment because the shapes of these molecules were actually determined experimentally by crystallography, and that resulted in many Nobel Prizes–I guess in the early 1960s. Since then, it took a long, long time for people to appreciate that computation had a role to play. For me, the big excitement is to see computational biology honored in this way, because computers have had such a massive impact on everything else we do.

He also said simplicity in models remains crucial even though computer time, once a crushing research expense, has “become cheaper by a factor of 100 million or so.” Levitt said the computational representations of chemical processes he employs now are very similar to those he and his colleagues pioneered in the late ‘60s and early ‘70s.

Here’s the summary of the trio’s groundbreaking work from the Royal Swedish Academy of Sciences, which awards the Nobel in chemistry:

Chemical reactions occur at lightning speed. In a fraction of a millisecond, electrons jump from one atomic nucleus to the other. Classical chemistry has a hard time keeping up; it is virtually impossible to experimentally map every little step in a chemical process. Aided by the methods now awarded with the Nobel Prize in Chemistry, scientists let computers unveil chemical processes, such as a catalyst’s purification of exhaust fumes or the photosynthesis in green leaves.

The work of Karplus, Levitt and Warshel is groundbreaking in that they managed to make Newton’s classical physics work side by side with the fundamentally different quantum physics. Previously, chemists had to choose to use either or. The strength of classical physics was that calculations were simple and could be used to model really large molecules. Its weakness, it offered no way to simulate chemical reactions. For that purpose, chemists instead had to use quantum physics. But such calculations required enormous computing power and could therefore only be carried out for small molecules.

This year’s Nobel Laureates in chemistry took the best from both worlds and devised methods that use both classical and quantum physics. For instance, in simulations of how a drug couples to its target protein in the body, the computer performs quantum theoretical calculations on those atoms in the target protein that interact with the drug. The rest of the large protein is simulated using less demanding classical physics.

Joshua Johnson and Kat Snow of KQED News contributed to this report.

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Author

Dan Brekke

Dan Brekke (Twitter: @danbrekke) has worked in media ever since Nixon's first term, when newspapers were still using hot type. He had moved on to online news by the time Bill Clinton met Monica Lewinsky. He's been at KQED since 2007, is an enthusiastic practitioner of radio and online journalism and will talk to you about absolutely anything. Reach Dan Brekke at dbrekke@kqed.org.

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