Caltech Chemical Engineer Frances Arnold Awarded National Medal of Technology and Innovation

PASADENA, Calif.—Frances H. Arnold, a leader in the field of protein engineering and a member of the faculty at the California Institute of Technology (Caltech) has been named one of 11 inventors who are the recipients of the 2011 National Medal of Technology and Innovation. The announcement was made by the White House on December 21.

Arnold, who is the Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering, and Biochemistry at Caltech, pioneered methods of "directed evolution" that are now widely used to create biological catalysts for use in industrial processes, including the production of fuels and chemicals from renewable resources. In a process akin to breeding by artificial selection, directed evolution uses mutation and screening to optimize the amino-acid sequence of a protein and give it new capabilities or improve its performance. 

Arnold says her work is strongly motivated by a desire to find ways to produce fuels that can help lower carbon dioxide emissions. "I would like my children to grow up in a world that is even better than the one that I grew up in," she says. "For that to happen, we have to stop wasting precious resources and learn to live in a sustainable fashion. Biology can and should be one of the solutions."

Arnold's award brings to 13 the number of Caltech faculty members, alumni, and trustees who have received the National Medal of Technology and Innovation.

"Professor Arnold's work has led to a radical transformation in the way people understand protein engineering and what it can accomplish," says Caltech president Jean-Lou Chameau. "We are very proud of all that Professor Arnold has achieved and celebrate this recognition of her contributions." 

The National Medal of Technology and Innovation was established by Congress in 1980, and complements the older National Medal of Science. The U.S. Department of Commerce's Patent and Trademark Office administers the medal on behalf of the White House.

The White House also announced the winners of the 2011 National Medal of Science. A Caltech alumnus and former chair of the Division of Biology, Leroy Hood, was among the 12 awardees. His citation brings the number of Caltech faculty members and alumni to have received the National Medal of Science to 57.

"I am proud to honor these inspiring American innovators," said President Barack Obama in the press release. "They represent the ingenuity and imagination that has made this Nation great—and they remind us of the enormous impact a few good ideas can have when these creative qualities are unleashed in an entrepreneurial environment."

Arnold says her discoveries and accomplishments were made possible by her position at Caltech, whose structure encourages work that crosses traditional disciplinary boundaries. Indeed, her work spans chemistry, bioengineering, biochemistry, molecular biology, microbiology, and chemical engineering.

She also thanks her colleagues and students. "I'm thrilled because this is a recognition not just of my work, but of the work of many people around the world who have developed and applied these methods," Arnold says. "I've also been privileged to work with a brilliant and enthusiastic group of young people over the years."

Arnold received her undergraduate degree in mechanical and aerospace engineering at Princeton University in 1979. She became interested in protein engineering during graduate school at UC Berkeley at the beginning of the biotechnology revolution, when she realized that the then-new methods of genetic engineering offered a path to solving pressing human problems using biology.

"It was clear that being able to rewrite the code of life signified a future full of fantastic technological possibilities," she says. "I wanted to be on board."

Arnold received her PhD in 1985 and arrived at Caltech as a visiting associate in 1986. She joined the faculty as an assistant professor the following year and became associate professor in 1992, professor in 1996, and Dickinson Professor in 2000. She has been honored with many awards, including the 2011 Charles Stark Draper Prize, and holds the rare distinction of having been elected to all three branches of the National Academies—the National Academy of Engineering (2000), the Institute of Medicine (2004), and the National Academy of Sciences (2008).

"Frances has made critically important contributions through her development of directed evolution," says Jacqueline Barton, chair of the Division of Chemistry and Chemical Engineering at Caltech. "It is outstanding that this work is being recognized through the National Medal."

Arnold and her fellow medal recipients will receive their awards at a White House ceremony in early 2013. 

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Unlocking New Talents in Nature

Caltech protein engineers create new biocatalysts

PASADENA, Calif.—Protein engineers at the California Institute of Technology (Caltech) have tapped into a hidden talent of one of nature's most versatile catalysts. The enzyme cytochrome P450 is nature's premier oxidation catalyst—a protein that typically promotes reactions that add oxygen atoms to other chemicals. Now the Caltech researchers have engineered new versions of the enzyme, unlocking its ability to drive a completely different and synthetically useful reaction that does not take place in nature. 

The new biocatalysts can be used to make natural products—such as hormones, pheromones, and insecticides—as well as pharmaceutical drugs, like antibiotics, in a "greener" way.

"Using the power of protein engineering and evolution, we can convince enzymes to take what they do poorly and do it really well," says Frances Arnold, the Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry at Caltech and principal investigator on a paper about the enzymes that appears online in Science. "Here, we've asked a natural enzyme to catalyze a reaction that had been devised by chemists but that nature could never do."

Arnold's lab has been working for years with a bacterial cytochrome P450. In nature, enzymes in this family insert oxygen into a variety of molecules that contain either a carbon-carbon double bond or a carbon-hydrogen single bond. Most of these insertions require the formation of a highly reactive intermediate called an oxene.

Arnold and her colleagues Pedro Coelho and Eric Brustad noted that this reaction has a lot in common with another reaction that synthetic chemists came up with to create products that incorporate a cyclopropane—a chemical group containing three carbon atoms arranged in a triangle. Cyclopropanes are a necessary part of many natural-product intermediates and pharmaceuticals, but nature forms them through a complicated series of steps that no chemist would want to replicate.

"Nature has a limited chemical repertoire," Brustad says. "But as chemists, we can create conditions and use reagents and substrates that are not available to the biological world."

The cyclopropanation reaction that the synthetic chemists came up with inserts carbon using intermediates called carbenes, which have an electronic structure similar to oxenes. This reaction provides a direct route to the formation of diverse cyclopropane-containing products that would not be accessible by natural pathways. However, even this reaction is not a perfect solution because some of the solvents needed to run the reaction are toxic, and it is typically driven by catalysts based on expensive transition metals, such as copper and rhodium. Furthermore, tweaking these catalysts to predictably make specific products remains a significant challenge—one the researchers hoped nature could overcome with evolution's help.

Given the similarities between the two reaction systems—cytochrome P450's natural oxidation reactions and the synthetic chemists' cyclopropanation reaction— Arnold and her colleagues argued that it might be possible to convince the bacterial cytochrome P450 to create cyclopropane-bearing compounds through this more direct route.  Their experiments showed that the natural enzyme (cytochrome P450) could in fact catalyze the reaction, but only very poorly; it generated a low yield of products, didn't make the specific mix of products desired, and catalyzed the reaction only a few times. In comparison, transition-metal catalysts can be used hundreds of times. 

That's where protein engineering came in. Over the years, Arnold's lab has created thousands of cytochrome P450 variants by mutating the enzyme's natural sequence of amino acids, using a process called directed evolution. The researchers tested variants from their collections to see how well they catalyzed the cyclopropane-forming reaction. A handful ended up being hits, driving the reaction hundreds of times. 

Being able to catalyze a reaction is a crucial first step, but for a chemical process to be truly useful it has to generate high yields of specific products. Many chemical compounds exist in more than one form, so although the chemical formulas of various products may be identical, they might, for example, be mirror images of each other or have slightly different bonding structures, leading to dissimilar behavior. Therefore, being able to control what forms are produced and in what ratio—a quality called selectivity—is especially important.

Controlling selectivity is difficult. It is something that chemists struggle to do, while nature excels at it. That was another reason Arnold and her team wanted to investigate cytochrome P450's ability to catalyze the reaction.

"We should be able to marry the impressive repertoire of catalysts that chemists have invented with the power of nature to do highly selective chemistry under green conditions," Arnold says.

So the researchers further "evolved" enzyme variants that had worked well in the cyclopropanation reaction, to come up with a spectrum of new enzymes. And those enzymes worked—they were able to drive the reaction many times and produced many of the selectivities a chemist could desire for various substrates.  

Coelho says this work highlights the utility of synthetic chemistry in expanding nature's catalytic potential. "This field is still in its infancy," he says. "There are many more reactions out there waiting to be installed in the biological world."

The paper, "Olefin cyclopropanation via carbene insertion catalyzed by engineered cytochrome P450 enzymes," was also coauthored by Arvind Kannan, now a Churchill Scholar at Cambridge University; Brustad is now an assistant professor at the University of North Carolina at Chapel Hill. The work was supported by a grant from the U.S. Department of Energy and startup funds from UNC Chapel Hill.

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Credit: Benjamin Deverman/Caltech

Gene therapy for boosting nerve-cell repair

Caltech scientists have developed a gene therapy that helps the brain replace its nerve-cell-protecting myelin sheaths—and the cells that produce those sheaths—when they are destroyed by diseases like multiple sclerosis and by spinal-cord injuries. Myelin ensures that nerve cells can send signals quickly and efficiently.

Credit: L. Moser and P. M. Bellan, Caltech

Understanding solar flares

By studying jets of plasma in the lab, Caltech researchers discovered a surprising phenomenon that may be important for understanding how solar flares occur and for developing nuclear fusion as an energy source. Solar flares are bursts of energy from the sun that launch chunks of plasma that can damage orbiting satellites and cause the northern and southern lights on Earth.

Coincidence—or physics?

Caltech planetary scientists provided a new explanation for why the "man in the moon" faces Earth. Their research indicates that the "man"—an illusion caused by dark-colored volcanic plains—faces us because of the rate at which the moon's spin rate slowed before becoming locked in its current orientation, even though the odds favored the moon's other, more mountainous side.

Choking when the stakes are high

In studying brain activity and behavior, Caltech biologists and social scientists learned that the more someone is afraid of loss, the worse they will perform on a given task—and that, the more loss-averse they are, the more likely it is that their performance will peak at a level far below their actual capacity.

Credit: NASA/JPL-Caltech

Eyeing the X-ray universe

NASA's NuSTAR telescope, a Caltech-led and -designed mission to explore the high-energy X-ray universe and to uncover the secrets of black holes, of remnants of dead stars, of energetic cosmic explosions, and even of the sun, was launched on June 13. The instrument is the most powerful high-energy X-ray telescope ever developed and will produce images that are 10 times sharper than any that have been taken before at these energies.

Credit: CERN

Uncovering the Higgs Boson

This summer's likely discovery of the long-sought and highly elusive Higgs boson, the fundamental particle that is thought to endow elementary particles with mass, was made possible in part by contributions from a large contingent of Caltech researchers. They have worked on this problem with colleagues around the globe for decades, building experiments, designing detectors to measure particles ever more precisely, and inventing communication systems and data storage and transfer networks to share information among thousands of physicists worldwide.

Credit: Peter Day

Amplifying research

Researchers at Caltech and NASA's Jet Propulsion Laboratory developed a new kind of amplifier that can be used for everything from exploring the cosmos to examining the quantum world. This new device operates at a frequency range more than 10 times wider than that of other similar kinds of devices, can amplify strong signals without distortion, and introduces the lowest amount of unavoidable noise.

Swims like a jellyfish

Caltech bioengineers partnered with researchers at Harvard University to build a freely moving artificial jellyfish from scratch. The researchers fashioned the jellyfish from silicon and muscle cells into what they've dubbed Medusoid; in the lab, the scientists were able to replicate some of the jellyfish's key mechanical functions, such as swimming and creating feeding currents. The work will help improve researchers' understanding of tissues and how they work, and may inform future efforts in tissue engineering and the design of pumps for the human heart.

Credit: NASA/JPL-Caltech

Touchdown confirmed

After more than eight years of planning, about 354 million miles of space travel, and seven minutes of terror, NASA's Mars Science Laboratory successfully landed on the Red Planet on August 5. The roving analytical laboratory, named Curiosity, is now using its 10 scientific instruments and 17 cameras to search Mars for environments that either were once—or are now—habitable.

Credit: Caltech/Michael Hoffmann

Powering toilets for the developing world

Caltech engineers built a solar-powered toilet that can safely dispose of human waste for just five cents per use per day. The toilet design, which won the Bill and Melinda Gates Foundation's Reinventing the Toilet Challenge, uses the sun to power a reactor that breaks down water and human waste into fertilizer and hydrogen. The hydrogen can be stored as energy in hydrogen fuel cells.

Credit: Caltech / Scott Kelberg and Michael Roukes

Weighing molecules

A Caltech-led team of physicists created the first-ever mechanical device that can measure the mass of an individual molecule. The tool could eventually help doctors to diagnose diseases, and will enable scientists to study viruses, examine the molecular machinery of cells, and better measure nanoparticles and air pollution.

Splitting water

This year, two separate Caltech research groups made key advances in the quest to extract hydrogen from water for energy use. In June, a team of chemical engineers devised a nontoxic, noncorrosive way to split water molecules at relatively low temperatures; this method may prove useful in the application of waste heat to hydrogen production. Then, in September, a group of Caltech chemists identified the mechanism by which some water-splitting catalysts work; their findings should light the way toward the development of cheaper and better catalysts.

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In 2012, Caltech faculty and students pursued research into just about every aspect of our world and beyond—from understanding human behavior, to exploring other planets, to developing sustainable waste solutions for the developing world.

In other words, 2012 was another year of discovery at Caltech. Here are a dozen research stories, which were among the most widely read and shared articles from Caltech.edu.

Did we skip your favorite? Connect with Caltech on Facebook to share your pick.

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Theodor Agapie Wins American Chemical Society Award

Theodor Agapie, assistant professor of chemistry at Caltech, has received the 2013 Award in Pure Chemistry from the American Chemical Society (ACS). The award will be presented at the national meeting of the ACS in New Orleans in April.

ACS is recognizing Agapie for his laboratory research on inorganic compounds. According to Agapie, his lab is working toward developing catalysts for artificial photosynthesis, a promising area of research into sustainable energy.

"I am very honored and thrilled to have received this award, particularly because I think it provides recognition for the efforts of my entire research team," says Agapie. "I have been lucky to work with a group of very talented young scientists who made the discoveries noted in this award."

Agapie, a native of Romania, received his bachelor's degree from MIT in 2001 and his PhD from Caltech in 2007. He has been an assistant professor at Caltech since early 2009. Since joining Caltech's faculty, Agapie has been named a Searle Scholar, a Sloan Research Fellow, and the recipient of a National Science Foundation CAREER Award. The Award in Pure Chemistry comes with a $5,000 prize and travel expenses for the upcoming national meeting of the American Chemical Society.

 

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Spring Teaching Assistant Orientation

Caltech Modeling Feat Sheds Light on Protein Channel's Function

PASADENA, Calif.—Chemists at the California Institute of Technology (Caltech) have managed, for the first time, to simulate the biological function of a channel called the Sec translocon, which allows specific proteins to pass through membranes. The feat required bridging timescales from the realm of nanoseconds all the way up to full minutes, exceeding the scope of earlier simulation efforts by more than six orders of magnitude. The result is a detailed molecular understanding of how the translocon works.

Modeling behavior across very different timescales is a major challenge in modern simulation research. "Computer simulations often provide almost uselessly detailed information on a timescale that is way too short, from which you get a cartoon, or something that might raise as many questions as it answers," says Thomas Miller, an assistant professor of chemistry at Caltech. "We've managed to go significantly beyond that, to create a tool that can actually be compared against experiments and even push experiments—to predict things that they haven't been able to see."

The new computational model and the findings based on its results are described by Miller and graduate student Bin Zhang in the current issue of the journal Cell Reports.

The Sec translocon is a channel in cellular membranes involved in the targeting and delivery of newly made proteins. Such channels are needed because the proteins that are synthesized at ribosomes must travel to other regions of the cell or outside the cell in order to perform their functions; however, the cellular membranes prevent even the smallest of molecules, including water, from passing through them willy-nilly. In many ways, channels such as the Sec translocon serve as gatekeepers—once the Sec translocon determines that a given protein should be allowed to pass through, it opens up and allows the protein to do one of two things: to be integrated into the membrane, or to be secreted completely out of the cell.

Scientists have disagreed about how the fate of a given protein entering the translocon is determined. Based on experimental evidence, some have argued that a protein's amino-acid sequence is what matters—that is, how many of its amino acids interact favorably with water and how many clash. This argument treats the process as one in equilibrium, where the extremely slow rate at which a ribosome adds proteins to the channel can be considered infinitely slow.  Other researchers have shown that slowing down the rate of protein insertion into the channel actually changes the outcome, suggesting that kinetic effects can also play a role.

"There was this equilibrium picture, suggesting that only the protein sequence is really important. And then there was an alternative picture, suggesting that kinetic effects are critical to understanding the translocon," Miller says. "So we wondered, could both pictures, in some sense, be right? And that turns out to be the case."

In 2010 and earlier this year, Miller and Zhang published papers in the Proceedings of the National Academy of Sciences and the Journal of the American Chemical Society describing atomistic simulations of the Sec translocon. These computer simulations attempt to account for every motion of every single atom in a system—and typically require so much computing time that they can only model millionths of seconds of activity, at most. Meanwhile, actual biological processes involving proteins in the translocon last many seconds or minutes.

Miller and Zhang were able to use their atomistic simulations to determine which parts of the translocon are most important and to calculate how much energy it costs those parts to move in ways that allow proteins to pass through. In this way, they were able to build a simpler version of the simulation that modeled important groupings of atoms, rather than each individual atom. Using the simplified simulation, they could simulate the translocon's activity over the course of more than a minute.

The researchers ran that simplified model tens of thousands of times and observed the different ways in which proteins move through the channel. In the simulation, any number of variables could be changed—including the protein's amino-acid sequence, its electronic charge, the rate at which it is inserted into the translocon, the length of its tail, and more. The effect of these alterations on the protein's fate was then studied, revealing that proteins move so slowly within the tightly confined environment of the translocon that the pace at which they are added to the channel during translation—a process that might seem infinitely slow—can become important. At the same time, Miller and Zhang saw that other relatively fast processes give rise to the results associated with the equilibrium behavior.

"In fact, both equilibrium and kinetically controlled processes are happening—but in a way that was not obvious until we could actually see everything working together," Miller says.

Beyond elucidating how the translocon works and reconciling seemingly disparate experimental results, the new simulation also lets the researchers perform experiments computationally that have yet to be tried in the lab. For example, they have run simulations with longer proteins and observed that at such lengths—unlike what has been seen with shorter proteins—the equilibrium picture begins to be affected by kinetic effects.  "This could bring the two experimental camps together, and to have led that would be kind of exciting," Miller says.

The new Cell Reports paper is titled "Long-timescale dynamics and regulation of Sec-facilitated protein translocation." The work was supported by the U.S. Office of Naval Research and the Alfred P. Sloan Foundation, with computational resources provided by the U.S. Department of Energy, the National Science Foundation, and the National Institute of General Medical Sciences.

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Barton Elected to Institute of Medicine

Jacqueline K. Barton, Arthur and Marian Hanisch Memorial Professor and professor of chemistry and chair of the Division of Chemistry and Chemical Engineering at Caltech, has been elected to membership in the Institute of Medicine (IOM), one of the highest honors in the fields of health and medicine. As the health arm of the National Academies, the IOM is recognized as "a national resource for independent, scientifically informed analysis and recommendations on human health issues."

"The Institute of Medicine selects as members those individuals who are at the top of their fields; this is certainly true of Professor Barton," says Caltech president Jean-Lou Chameau. "This highly prestigious appointment is a reflection of the respect Professor Barton has earned among leaders in medicine, science, and academia."

"I am honored to have been elected to join this prestigious group of colleagues," says Barton. "It is also nice to consider that the research in my group, which started out as quite fundamental research, may have implications and applications that touch the medical community."

In particular, Barton's research group examines the chemical and physical properties of DNA. Her lab has made fundamental discoveries with regard to the way electrical charges travel through DNA structures. This basic research has led to the development of novel DNA diagnostics and to insights into how DNA is damaged and repaired, an important issue with respect to aging and cancer. Barton has also designed a range of transition metal complexes as probes of DNA damage.  Her work provides a foundation for the design of new chemotherapeutics.

Barton joined the Caltech faculty as a professor of chemistry in 1989 and was named Hanisch Memorial Professor in 1997. She was appointed division chair in 2009.

Barton is the recipient of numerous awards, including the National Medal of Science in 2011, as well as the American Chemical Society Award in Pure Chemistry, the National Science Foundation's Waterman Award, and a MacArthur Fellowship, among others. Barton was elected a fellow of the American Philosophical Society in 2000 and to the National Academy of Sciences in 2002.

Barton is one of 70 individuals and 10 foreign associates invited to join the IOM in 2012. Each year, the full membership of the IOM elects new members from the medical profession, research institutions, and universities. To diversify its pool of experts, a quarter of the membership is drawn from fields such as the natural, social, and behavioral sciences; law; engineering; and the humanities.

In addition to advising Congress on health-related policy matters, the IOM, which was established in 1970 by the National Academy of Sciences, generates reports to inform the public about issues as wide ranging as electronic health records, diet and obesity, AIDS treatment and prevention, and vaccine side effects. The Institute also hosts events and speaking engagements throughout the year to disseminate information on health topics and stimulate discussion.

With her election, Barton becomes the ninth member of the Caltech community (faculty and trustees) elected to the IOM.

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Caltech's Sarah Reisman Wins Arthur C. Cope Scholar Award

Sarah Reisman, assistant professor of chemistry at Caltech, is one of 10 winners of 2013 Arthur C. Cope Scholar Award from the American Chemistry Society. Winning in the "early career scholar" category, Reisman will accept the award at the annual meeting of the American Chemistry Society in Indianapolis in September 2013.

According to the award citation, Reisman was recognized for her Caltech research group's original contributions to the understanding of complex molecule synthesis and reaction development.

"It is a wonderful honor in recognition of our research program," says Reisman. "I am very proud of my students and post-doctoral fellows whose dedication and hard work helped to make this award possible."

The award includes a certificate, a $5,000 cash prize, a $40,000 unrestricted research grant, and up to $2,500 in travel expenses for Reisman to deliver a lecture at the American Chemical Society's meeting in Indianapolis next year.

 

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Caltech Again Named World's Top University in <i>Times Higher Education</i> Global Ranking

PASADENA, Calif.—The California Institute of Technology (Caltech) has been rated the world's number one university in the 2012–2013 Times Higher Education global ranking of the top 200 universities.

Oxford University, Stanford University, Harvard University, and MIT round out the top five.

"We are pleased to be among the best, and we celebrate the achievements of all our peer institutions," says Caltech president Jean-Lou Chameau. "Excellence is achieved over many years and is the result of our focus on extraordinary people. I am proud of our talented faculty, who educate outstanding young people while exploring transformative ideas in an environment that encourages collaboration rather than competition."

Times Higher Education compiled the listing using the same methodology as in last year's survey. Thirteen performance indicators representing research (worth 30 percent of a school's overall ranking score), teaching (30 percent), citations (30 percent), international outlook (which includes the total numbers of international students and faculty and the ratio of scholarly papers with international collaborators, 7.5 percent), and industry income (a measure of innovation, 2.5 percent) make up the data. Included among the measures are a reputation survey of 17,500 academics; institutional, industry, and faculty research income; and an analysis of 50 million scholarly papers to determine the average number of citations per scholarly paper, a measure of research impact.

In addition to placing first overall in this year's survey, Caltech came out on top in the teaching indicator as well as in subject-specific rankings for engineering and technology and for the physical sciences.

"Caltech held on to the world's number one spot with a strong performance across all of our key performance indicators," says Phil Baty, editor of the Times Higher Education World University Rankings. "In a very competitive year, when Caltech's key rivals for the top position reported increased research income, Caltech actually managed to widen the gap with the two universities in second place this year—Stanford University and the University of Oxford. This is an extraordinary performance."

Data for the Times Higher Education's World University Rankings were provided by Thomson Reuters from its Global Institutional Profiles Project, an ongoing, multistage process to collect and validate factual data about academic institutional performance across a variety of aspects and multiple disciplines.

The Times Higher Education site has the full list of the world's top 400 schools and all of the performance indicators.

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John Brady Wins Fluid Dynamics Prize

John Brady, Chevron Professor of Chemical Engineering and professor of mechanical engineering at Caltech, will receive the 2012 Fluid Dynamics Prize from the American Physical Society at the Division of Fluid Dynamics annual meeting in November. Brady was cited for his contributions to the study of the deformation and flow of complex fluids, for developing a computational model known as Stokesian Dynamics, and for his contributions to the field of fluid dynamics through his role as a journal editor.

"I am honored to receive this award from the American Physical Society," Brady says. "The mechanics of complex fluids is a very exciting field right now. While we gained a great deal of understanding of these materials over the past few decades, there is still so much yet to be discovered. That's what keeps me and my research group going."

 

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