EQuad News Summer 2014 Volume 26, Number 1 School of Engineering and Applied Science Princeton, NJ 08544-5263 www.princeton.edu/engineering
2 EQuad News Summer 2014 DEAN’S Volume 26, Number 1 NOTE Dean H. Vincent Poor Ph.D. ’77 Vice Dean N. Jeremy Kasdin Engineering and biology: Associate Dean, Undergraduate Affairs A vital connection Peter Bogucki What is it that makes crossing borders between academic Associate Dean, Graduate Affairs fields so appealing? The way Eric Wieschaus, Princeton Brandi Jones biologist and Nobel laureate, describes it on page 9 of this Associate Dean, Development magazine, emerging outposts of research and teaching that Jane Maggard span multiple fields are like cities that arise at the border Director of Engineering Communications
of two countries. The sometimes chaotic mix of cultures and Steven Schultz Photo by Danielle Alio ideas creates a nexus of creativity and progress. The rich Senior New Media Editor opportunities, in turn, attract more people who might not Teresa Riordan Staff Writer even be from the originating areas. John Sullivan So it is with engineering and biology. The articles in this Contributors magazine describe work that can be hard to classify. In Anna Azvolinksy NEWS Stacey Huang ’15 some cases engineers are using their expertise in complex John Greenwald Catherine Shen systems or mechanics to make fundamental discoveries Catherine Zandonella about growth and structure in living organisms; in others, Additional editing MIGHTY MATH: VALEDICTORIAN POGREBNIAK ADVANCES Morgan Kelly engineers are creating tools that will bring needed advances MEDICINE THROUGH COMPUTATION Graphic Designer for human health. The bottom line is that it exemplifies what Matilda Luk By her own account, when Katherine “She is very intelligent and she also has Katherine Pogrebniak (left), Dan Fernandez I see as the best in engineering: bringing together whatever Pogrebniak first arrived at the National Eye a superb work ethic,” said Mona Singh, a worked with Mona Singh Web Designer expertise is needed to solve a problem, whether a funda- (right), a professor of com- Neil Adelantar Institute in the summer before her sophomore professor of computer science and the Lewis- puter science and the Lewis- mental question of science or an immediate societal need. EQuad News is published year at Princeton, she knew relatively little Sigler Institute for Integrative Genomics. Sigler Institute for Integrative I want to take a moment here to highlight and congratulate twice a year by the Office of about the highly complex research in Singh, who advised Pogrebniak for her inde- Genomics, on a computational Engineering Communica- method for evaluating how our 2014 valedictorian, Katherine Pogrebniak (the second BSE tions in collaboration with the national laboratory. pendent project, said her contribution to the Princeton University Of- certain substances bind student in a row to receive this honor). Her research fits fice of Communications. It By the end of the summer, she had her lab was akin to that from an advanced with proteins, a fundamental perfectly the theme of this magazine, combining the tools serves the alumni, faculty, students, staff, corporate sketched out the framework of a model to graduate student. question of modern biology. of computer science and “big data” to bring fresh insight to affiliates and friends of the analyze a protein that researchers believe In a second internship at the NIH last “I started with math,” said Princeton University School Pogrebniak, “but I have always medicine and biology. of Engineering and Applied could be a critical factor in the development summer, Pogrebniak helped a team of re- Science. been interested in biomedi- The collaborative spirit of engineering includes you – of an eye disease that affects children. searchers develop a new method of using cal problems because I was alumni, colleagues and friends. Please stay in touch and EQuad News MRI excited about their real-world C-222, EQuad, “She has this tremendous ability to learn,” magnetic resonance imaging ( ) in the let’s find ways to work together. Princeton University said Yuri Sergeev, a senior researcher at treatment of patients with multiple sclerosis applications.” Princeton, NJ 08544 the Bethesda, Maryland, institute, which is (MS). Daniel Reich, a principal investigator at T 609 258 4597 F 609 258 6744 a branch of the National Institutes of Health NIH and the team leader, called Pogrebniak “an [email protected] H. Vincent Poor Ph.D. ’77 (NIH). He said Pogrebniak brought an intense outstanding young star,” and said that through About the cover Dean www.princeton.edu/ engineering/eqnews focus to her work, first learning biological her work the lab was able to achieve The scientific images represent a range of work Michael Henry Strater University from molecules to whole organisms: in the L, aspects of the project and then bringing her a major goal in imaging research. Professor of Electrical Engineering Copyright © 2014 by a model of an enzyme studied in the lab of The Trustees of computational skills to bear on working out In May, the results of Pogrebniak’s work A. James Link BSE ’00; in the I, nucleoli from Princeton University egg cells of the African clawed frog from the lab In the Nation’s Service and a solution. at the NIH were presented at the annual of Cliff Brangwynne; in the F, bearded dragon in the Service of All Nations Pogrebniak’s peers and professors speak embryo lung tissue from the lab of Celeste meeting of the International Society for Nelson (exhibited in “Art of Science” 2011). 450456 of the intellect and determination that have Magnetic Resonance in Medicine in Milan. led her to the top of her class. A computer “Katherine made quite an impression on science major from Jacksonville, Florida, she me and all my colleagues,” Reich said in a 1 9 22 26 28 30 32 is the valedictorian of the Princeton Class of letter to the University. He noted that in apply- News LIFE Faculty Undergraduate Graduate Alumni Ideas 2014, and delivered an address at the Uni- ing computation to solve biological problems, Engineering News News News News Illustrated versity’s Commencement ceremony on June 3. “none of us has any doubt that Katherine will and Biology become a world leader.” 2 3 NEWS NEWS MIGHTY MATH: VALEDICTORIAN POGREBNIAK ADVANCES MEDICINE THROUGH COMPUTATION (continued from page 1) MODERN EXPERTISE BUILDS BRIDGE TO ANCIENT MARVEL Understanding the big picture Computation and health Many engineering lectures concern themselves available materials Pogrebniak is the first woman earning a Colleagues uniformly speak of Pogrebniak’s with cutting-edge technology but at a recent and historic records Bachelor of Science in Engineering at Prince- consideration for fellow students and co- talk on bridge construction, Princeton profes- of Roman construction eton to be named valedictorian. She also workers. She has served for two years as a sor Branko Gliši asked his audience to go techniques, to draw received a certificate in engineering biology. residential college adviser at Wilson College; back nearly 2,000 years. their conclusions, For her independent research, Pogrebniak Eduardo Cadava, an English professor and the “You have to think like a Roman,” Gliši some of which run joined a group in Singh’s lab, which is studying college master, spoke of her “wild intelligence told students and faculty gathered for a counter to historical how proteins bind with other molecules, – which she wears with grace and humility.” brown-bag lunch. He gestured to a schematic assumptions. called ligands. These binding interactions Pogrebniak said she has long wanted to diagram of an arch on the screen behind him. Mehrotra majored in are a fundamental process and understand- work in medicine. “You minimize connections because they add civil and environmental ing them could lead to new drugs and medical “I started with math,” Pogrebniak said. complication.” engineering and graduated in 2013. A carving from Trajan’s therapies. “But I have always been interested in biomedi- Gliši , an assistant professor of civil and Built under the Emperor Trajan, the bridge Column in Rome (at left and Pogrebniak assisted the effort by finding upper right) and a contem- cal problems because I was excited about environmental engineering, was speaking has inspired wonder for centuries. porary Roman coin provided ways to find repeated measurements in mas- their real-world applications.” about Trajan’s Bridge, a wood-and-masonry “Brilliant, indeed, as are his other achieve- clues to the bridge’s form. sive data sets that could skew an analysis by Pogrebniak will attend the University of structure that the Romans constructed be- ments, yet this surpasses them,” wrote Cas- (Images courtesy of Branko suggesting that certain interactions are more Cambridge as a Churchill Scholar in the fall tween 103 and 105 A.D. to span the Danube sius Dio, the Roman consul and historian. Gliši ) common than they really are. and plans to obtain a master’s degree in River between what is now Serbia and The researchers reviewed historic repre- “I was very impressed with Katherine’s computational biology. After that, she intends Romania. At more than a kilometer long sentations of the bridge that were proposed degree of scientific maturity in dealing with the to pursue a medical degree and a doctorate at (six-tenths of a mile), it is considered a wonder by scientists over the past two centuries, but problems and coming up with alternatives,” Stanford University. of the ancient world, but nearly all details rejected all or elements of various analyses said Dario Ghersi, a postdoctoral researcher The summer before her senior year at of its form and construction have been lost. either because of instability issues or the use who worked with her on the project. “We tried the NIH’s National Institute of Neurological Gliši and former undergraduate Anjali of techniques that the Romans were unlikely to many things to reduce the redundancy in this Disorders and Stroke, she assisted with ways Mehrotra have reconstructed the engineering have mastered, such as fixed joints. data set. Her persistence was key.” to formulate treatments for people with MS. behind the bridge and published their findings Examinations of the remaining masonry Reich, the lead researcher, said in his letter in the Journal of Cultural Heritage. piers at the site, carried out in 1979 by to Princeton that Pogrebniak came up with a Gliši and Mehrotra used modern engi- Serbian archaeologists Milutin Garašanin and method to use errors in scan data to identify neering analysis, coupled with a review of Miloje Vasi , showed that the Romans drove lesions in the cortex – “a major but hitherto support beams into the piers to strengthen unachieved goal of contemporary MS-imaging Photo by Frank Wojciechowski the arches. research.” “The holes gave us the most probable “In imaging, there is a lot of physics and positions for the ends of the arches,” he said. Photo by Denise Applewhite Photo by math, but most of the people who do imaging The support beams also would have given can’t deal with massive amounts of data,” he sufficient stability to the bridge. said. “Katherine is certainly someone who can Gliši said without a definitive historical do that.” –John Sullivan record, there is no way to be sure how the bridge looked. But he said that applying engineering analyses can narrow the Pogrebniak, a computer possibilities. science major from Jacksonville, Florida, gives “We cannot say it really was like this,” the valedictory oration, telling Researchers led by Branko Gliši , an assistant he said, “but we can say it very likely was her peers that it is their time professor of civil and environmental engineering like this.” –JS to “venture into the unknown at Princeton, used modern engineering analysis to and create a new path.” determine the materials and techniques that ancient Roman engineers used to build Trajan’s Bridge over the Danube River. 4 5 NEWS A FAREWELL TO ARMS? NOVEL TECHNIQUE NEWS COULD FACILITATE NUCLEAR DISARMAMENT HACKPRINCETON DRAWS 500 STUDENTS TO BRAINSTORM AND BUILD Photo by Frank Wojciechowski A key step in nuclear disarma- Their system would compare a warhead to A robotic insect that waves hello, a calculator ing entrepreneurial ventures, among ment requires solving a co- be inspected with a known true warhead to controlled by a few pokes in midair, an alarm undergraduates. nundrum: how to verify that a see if the weapons matched. This would be clock that sprays water and posts embar- The Princeton event was organized by weapon slated for destruction done by beaming high-energy neutrons into rassing social media statuses — not ordinary electrical engineering major Adam Yabroudi contains a true warhead, yet not each warhead and recording how many neu- products of a college student’s weekend. and Hansen Qian, a computer science major. A Photo by Elle Starkman Photo by reveal any information whatso- trons passed through to detectors positioned But this was no ordinary weekend — it was panel of experienced technologists in busi- ever about the device. Using a on the other side. Neutrons that passed HackPrinceton. ness and academia judged the best projects, concept borrowed from computer through would be added to those already “pre- For 36 hours culminating March 30, Prince- which were awarded prize money and “swag” science – a so-called “zero-know- loaded” into the detectors by the warheads’ ton’s Jadwin Gym was packed with roughly 500 from sponsors such as Google and Facebook. ledge proof” – a Princeton owner – and if the total number of neutrons undergraduates from more than 40 univer- The students came from all around the engineer has collaborated with were the same for each warhead, the weapons sities working furiously on programming and East Coast and beyond. Yi Qin and Jian Zhang HackPrinceton, a weekend-long event held in Jadwin Gym scientists at the Princeton would be found to match. But different totals hardware projects. Such “hackathons” have of Purdue University drove 13 hours, picking March 28-30, brought roughly Plasma Physics Laboratory (PPPL) would show that the putative warhead was grown in popularity in recent years providing up teammate Paul Wong from the University 500 college students to campus to invent such a system. really a spoof. Prior to the test, the inspector students with food, camaraderie and a loca- of Pittsburgh. The three developed SmartCar, to build hardware and software The researchers published would decide which preloaded detector would an inexpensive accident-avoidance system for tools and toys. The event was tion to devote a weekend to developing ideas organized by Princeton under- their approach in the June 26 go with which warhead. for products or services. older cars that combines turn-by-turn naviga- graduates Hansen Qian (left) issue of the journal Nature. Glaser hit upon the idea over a lunch HackPrinceton received support from tion with tools that issue a warning if a driver and Adam Yabroudi (right) with The secrecy is required to hosted by David Dobkin, a computer scien- the Stephen C. Johnson ’64 Slingshot Fund leaves a lane or risks a collision. a committee of student volunteers. avoid revealing classified details tist who was dean of the Princeton faculty at for Innovation, which was established by “We just really wanted to build something about materials or design that the time. Glaser described the inspectors’ the Johnson family to foster innovation, includ- cool,” Qin said. –Stacey Huang ’15 must remain off-limits to inspec- dilemma and Dobkin immediately recognized tors, the authors said. Most it as a problem requiring a zero-knowledge TATTOO REMOVAL TO CRUDE OIL EXTRACTION: disarmament efforts so far have proof, which are widely used in applications RESEARCH WITH COMMERCIAL APPEAL Photo by Frank Wojciechowski Assistant Professor Alex relied on counting missile silos, such as verifying online passwords. Glaser Glaser displays a device Graduate student George Khoury said he pitch to a panel of judges consisting of inves- known as the “British submarines or other deployment then turned to Barak, an expert in such proofs, must have practiced a hundred times prior tors and business leaders. After each presen- Test Object,” which simu- vehicles that are easily identified. and to Goldston, whose work at PPPL involves to taking the stage at this year’s Innovation tation, the judges were allotted five minutes lates the materials used Future rounds, however, will place limits on powerful neutron sources that could simulate Forum at Princeton. to ask questions on details such as potential in a nuclear warhead tactical or non-deployed weapons, which must a nuclear device. and is used for testing “I’ve never done anything like this risks and competitors and how they would use methods of verifying be identified and counted individually. A project to test the researchers’ approach before,” said Khoury, whose group took home the funding. the authenticity of the “What we really want to do is count war- is now under construction at PPPL. the $10,000 second prize with a method of The first prize, of $15,000 in funding, weapons. heads,” said Alex Glaser, an assistant profes- The project was launched with a seed grant discovering HIV inhibitors. “It was a once-in-a- was won by a team that developed a tech- sor of mechanical and aerospace engineering from the Simons Foundation of Vancouver, lifetime opportunity.” nology for mass production of “Janus The panel of judges for the and international affairs and an author of the Canada, that came to Princeton through Global Khoury’s group – led by Christodoulos particles,” tiny spheres with two distinct sides Nature paper. Zero, a nonprofit organization. Support was Innovation Forum is made up of Floudas, the Stephen C. Macaleer ’63 composed of typically incompatible materials investors and business leaders. Glaser co-wrote the article with Robert also provided by the U.S. Department of State, Professor in Engineering and Applied Science, such as plastics and metals. Vikram Pansare, Goldston Ph.D. ’77, a physicist at PPPL, and the Department of Energy and, most recently, and including fellow graduate student James a Ph.D. student, presented the idea for a team Boaz Barak, a computer scientist formerly a $3.5 million grant from the National Nuclear Smadbeck – was one of 10 teams that pitched including Professors Robert Prud’homme and at Princeton and now at Microsoft Research. Security Administration. –John Greenwald the commercial potential of research ranging Rodney Priestley and graduate students Chris PPPL is a U.S. Department of Energy national from advances in medicine to painless Sosa and Chuan Zhang. Pansare said the lab administered by Princeton University. tattoo removal. program honed his business, as well as his The ninth annual event, sponsored by technical, skills. Princeton’s Keller Center, took place on “You’re not just working with one thing,” he Feb. 26 before an audience of nearly 200 said. “Dealing with both simultaneously, you people in the University’s Fields Center. A learn so much.” –Catherine Shen member of each team delivered a three-minute “clean rooms” that have ultra-low dust levels window of his classroom, in the Engineering 6 7 and labs that house some of the world’s Quadrangle, overlooks the project, and he tries NEWS NEWS most sophisticated imaging and analytical to end every class with a look through the equipment. window at progress on the construction site. Emily Carter, the Gerhard R. Andlinger Garlock, an associate partner with the New Professor in Energy and the Environment and York-based firm Leslie E. Robertson Associates founding director of the center, stressed the and the project manager for the new 4 World importance of “the Andlinger Center as a living Trade Center Tower project, said it is important laboratory, both as it is being built and upon for engineering students to get into the field occupancy.” during their studies. Added Carter, “Students will have the op- “You have to set their sense of scale and portunity to not only witness and learn about you can’t do it in the classroom alone,” he the creation and operation of this building ded- said. “They have to see and smell the materi- icated to sustainability but also to participate als and the space – you have to get their eyes in cutting-edge research aimed at preserving used to seeing what is going on.” the planet for future generations.” Garlock usually takes his students on tours Rozycki, who estimates that he has given of several sites during a term. He said one of about 18 class tours of the site since con- the benefits of touring Princeton projects is struction began, said he is continually im- that Rozycki and his colleagues at the Office of pressed by the questions he receives from Design and Construction go out of their way to
Photos by Denise Applewhite Photos by students. be helpful. –JS EVEN UNDER CONSTRUCTION, ANDLINGER LAB TEACHES Richard Garlock, a visiting lecturer in civil and environmental engineering, has brought The Andlinger construction The class walked into a cavernous construc- addressed by the flanges,” he said. “Shear several of his classes to the site. In fact, the site gives students the op- tion site that is becoming the Andlinger Center strength is more of a concern at the end of portunity to take a close look at how materials and for Energy and the Environment at Princeton the beam.” engineering help shape University. Light, filtering from the open floors Leading student groups through construc- Students study a model the emerging structure. above, lined the gray concrete floors and the tion sites is not typically part of a construc- of the Andlinger Center, steel beams that cross the high ceiling. Con- tion manager’s job, but the Andlinger project scheduled to open in sum- mer 2015. Emily Carter, struction crews had knocked off a few minutes on Olden Street offers student engineers an the Gerhard R. Andlinger earlier. Sound in the space, far below street opportunity for firsthand observation of the Professor in Energy and level, was muted. fundamentals they are learning in class. On the Environment and Sam Rozycki, leading the small group of one recent tour, Claire White, an assistant pro- founding director of the center, described it as a students, pointed to open spaces cut from the fessor of civil and environmental engineering “living laboratory, both as middle of a nearby beam. and the Andlinger Center for Energy and the it is being built and upon “A lot of that beam is missing,” said Environment, used the site to demonstrate to occupancy.” Rozycki, senior project manager at the Univer- the students in her class “Materials in Engi- sity’s Office of Design and Construction. “Can neering” how concrete and steel were used in anyone tell me why it still works?” various ways to shape the emerging structure. Dennis Smith, a sophomore majoring in “The week before, we were in a cement civil and environmental engineering, spoke up, plant,” said White. “It is very important to give “Most of the strength for resisting bending is the students real-world experience.” in the flanges.” The new building, scheduled to open in Rozycki agreed. summer 2015, will hold lecture and laboratory “The engineer is more concerned about classrooms, office space, a lecture hall, con- bending in the center of the beam, which is ference rooms, and research labs, including Images from Princeton University’s 2014 “Art of Science” exhibit, clockwise from lower left: “#5” by Nathan Tyrell BSE ’14 (Mechanical and Aerospace Engineering); “Vitamin C” by Nathan Myhrvold Ph.D. ’83 (Applied Mathematics); “Cave of Crystals” by Hyoungsoo Kim, François Boulogne and Howard Stone (MAE); “Ring of Fire” by Clara O’Farrell BSE ’08 (MAE); “Watermarks” by Sara Sadri (Civil and Environ- mental Engineering); and “Elodea leaf cell” by Nicolas Pegard and Jason Fleischer (Electrical Engineering).
The winning print entries chosen by the panel of judges were: first place went to “Wa- termarks” by Sara Sadri, postdoctoral researcher, civil and environmental engi- neering; second place for “Fungus among us” by James Waters, postdoctoral researcher, ecology and evolutionary biology; and third place went to “Portrait of the artist in the air shower” by Yasmin Afsar, a graduate student in electrical engineering. Photo by Denise Applewhite The top video award went to Sabine Petry, Eric Wieschaus had a question. assistant professor of molecular biology, for at PIZZA It was Friday afternoon, and Stephanie Weber her video “Microtubules branch out.” ‘ART OF SCIENCE’ EXHIBIT the BORDER: was well into her presentation on cellular structure when Wieschaus, a molecular biolo- SPANS ENGINEERING AND People’s choice NATURAL SCIENCES gist and Nobel laureate, politely raised his Of 185 ballots cast for People’s Choice, first ‘NOVEL hand and gave the talk a nudge in a different place for still images went to “Fruit fly factory” The 2014 “Art of Science” exhibit, INTERACTIONS’ direction. by graduate students Yogesh Goyal and Bomyi featuring 44 images and 12 videos created “We’d been thinking about the problem Lim, postdoctoral researcher Miriam Osterfield SPUR BIOLOGICAL during the course of scientific research, from a physics perspective,” said Weber, a Faculty members, graduate students and postdoctoral and Stasnislav Shvartsman, a professor of opened May 8 at Princeton University’s Friend post-doctoral researcher in chemical and bio- researchers from across the University gather every chemical and biological engineering and the DISCOVERY Friday to discuss current research at the intersection of Center. An online gallery of the current and logical engineering. “Eric’s question was about Lewis-Sigler Institute for Integrative Genom- biology and engineering. Participants say they value the past “Art of Science” exhibits can be viewed at the biology – about transcriptional regulation.” exchange of perspectives in these informal sessions. ics. The People’s Choice award for video went http://artofsci.princeton.edu. by John Sullivan For a few minutes, the question bounced to “Plenty of fish” by graduate student Colin More than 200 people attended the open- back and forth among the group gathered in Twomey and postdoctoral researcher Haishan ing reception at which the top awards in a a large conference room in Hoyt Laboratory. In what has become a Friday afternoon Wu of ecology and evolutionary biology. juried competition were announced and visitors Grad students, postdocs, junior and senior tradition, the bioengineering faculty orders Zach Donnell, a graduate student in voted on People’s Choice awards. The images professors ran with the new thought for a pizza and offers a rolling series of lectures on molecular biology and one of the 2014 and videos exhibited were selected for their while until Weber resumed her talk. After, ongoing research. Whether the participants organizers, noted that, as in past years, the artistic merit from more than 300 submissions Weber and Wieschaus arranged to talk further are, like Weber, postdocs making their first winners selected by the jury and those from undergraduates, graduate students, about the approach. formal presentation or senior scientists like selected by visitors to the opening reception postdocs, staff and alumni representing more “Science is essentially social,” Wieschaus, Wieschaus, the atmosphere is democratic. were completely different. “It reminds us than 25 departments. the Squibb Professor in Molecular Biology, It is also eclectic; the gatherings frequently that art is quite a subjective thing,” he said. “So much of science and engineering said later. “Somehow you have to think of include representatives from a wide range of The exhibit at the Friend Center is free involves video or animation these days that it a way for people who are truly scientists – scientific disciplines. and open to the public through April 2015. was inevitable we would include it in ‘Art of whether they are grad students, postdocs or That makes sense; bioengineering is a –Teresa Riordan Science,’” said Dan Quinn, a graduate student professors – to participate. How do you do hybrid by its very nature. Wieschaus calls the in mechanical and aerospace engineering who that? One way is to serve pizza.” field a scientific “border city.” It is a deliberate is one of the 2014 exhibit organizers. 8 9 ‘NOVEL INTERACTIONS’ SPUR BIOLOGICAL DISCOVERY (continued from page 9) Modern medicine, from cardiac surgery to chemo- therapy, rests on a foundation of reliable antibiotics. BACK merger of two well-settled scientific disciplines TO and, as a result, attracts people who are But health authorities around the world warn that the comfortable working outside their normal effectiveness of antibiotics is under increasing threat BASICS framework. from resistant bacteria. Mark Brynildsen, an assistant professor of chemical and biological engineering, is LASER REVEALS “It is not just the confrontation of the health clues in border,” he said. “Immigrants from all over the seeking solutions to this problem through new ways to world are attracted to border cities. People combat dangerous bacteria. Researchers in his lab are HUMAN BREATH who are in other areas see it as a place where combining several approaches: disrupting bacteria’s novel interactions and ideas can occur.” ability to infect people; unravelling bacteria’s ability Bonnie Bassler, the Squibb Professor in to survive anti-biotics and other forms of stress; and Molecular Biology and chair of the Depart- preventing formations called biofilms, which some ment of Molecular Biology, said Princeton has bacteria use to protect themselves from outside long had the philosophy that the borders of threats such as antibiotics. The lab is also pursuing academic disciplines should not become an fundamental research into the interaction between bacteria and their hosts. “Antibiotics work anywhere obstacle to scientific inquiry. In fact, today’s High levels of the molecule they come in contact with bacteria, which means pres- students are not only comfortable working nitric oxide can alert doctors sure to develop resistance occurs both within sick across different fields, they expect it. In Eyewire, an online game, science enthusiasts to inflammation in critical people and outside in the environment,” Brynildsen “Students come here expecting open around the world interact with computer-generated areas of the body such as said. “To prevent illness, we only need agents that are feedback to map the convoluted paths of neurons, mindedness,” she said. “Someone might be the cardiovascular system. effective against infections in the host, which is a depicted above, through the retina. trained in engineering but they want to EYEWIRE: In a short video, Gerard more targeted approach with a potentially longer time immerse themselves in biology.” A game helps map the brain Wysocki, an assistant profes- Richard Register, the Eugene Higgins Pro- of effective use than conventional antibiotics.” –JS In a much-cited talk at a 2010 TED conference, Sebastian Seung sor of electrical engineering fessor of Chemical and Biological Engineering Photo by Frank Wojciechowski at Princeton, explains how and the department chair, said that bioengi- introduced the proposition, “I am my connectome.” his lab is developing a single neering at Princeton “tends to focus on the Seung, a computational neuroscientist then “We need an army of people to go out and system that measures levels fundamental, rather than the clinical, level.” at MIT, suggested that what makes a person explore that jungle,” Seung told NPR’s “Morn- of nitric oxide isotopes in “A particular strength that we have, and unique is more than their collection of genes, ing Edition” in May. “What could be more breath, as well as nitrites that makes Princeton distinctive, is that we or genome. Rather it is their connectome, exciting than exploring the brain? Much more and nitrates in blood and have a very strong life sciences presence at the connections between all their neurons, exciting than any artificial video game.” urine. Wysocki’s device uses the University, and a strong commitment to that arises from genetics but is shaped by Called Eyewire, the game has engaged a magnetic field and a biological engineering within the engineering experience. 120,000 people from 140 countries. Their on- high-frequency modulated school,” he said. In his department alone, “The connectome is where nature meets line “play” already has contributed to a paper laser to detect levels of nitric Register added, “We have very high-quality nurture,” Seung said. published in May in the journal Nature sug- oxide isotopes as low as one people from a range of backgrounds but all Seung joined the Princeton faculty in gesting how the perception of motion arises part per billion in samples of whom fit within chemical and biological January, jointly appointed in the Department from the structure of neuronal connections in from patients. The measure- engineering.” of Computer Science and the Princeton the retina. ment takes only one second. The diversity of backgrounds, and the Neuroscience Institute. With him, he brings At Princeton, Seung plans to collaborate “The analyzer has to be very commonality of interest, is valued by the his ambitious plan to map the human connec- with neuroscientists who have developed sensitive to look at such a participants. In many ways, the research focus tome, which includes a popular online game he sophisticated methods of recording neural minute amount of nitric oxide is represented by the Friday afternoon pizza. created to enlist people from around the world activity associated with behavior and decision- so quickly,” he said. “That is “It’s a formal presentation but at the same in tracing the interwoven tangle of neurons in making in animals. “The retina is a great way the main difficulty in measur- time it’s a discussion among colleagues,” the retina of the eye. to understand perception,” Seung said. “We ing important reactive spe- Weber said. want to move beyond perception to cognition cies such as nitric oxide.” Assistant Professor Mark Brynildsen (left) talks with graduate http://bit.ly/WysockiVideo student Jonathan Robinson. and learning and memory.” –Steve Schultz
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in Photo by Frank Wojciechowski MAPPING FIRST LIFE STEPS
, , is believed is believed , MAPK . “There is still much to MAPK The image below shows thin slices of The image below shows thin slices of but the journey from that tiny grouping to a to a grouping tiny from that journey but the complex and organism is fully developed a pro- Shvartsman, Stanislav mysterious. engineering chemical and biological fessor of for Integrative Institute and the Lewis-Sigler engineering perspective brings an Genomics, in tissue involved to studying mechanisms form. and development In one promising - lab is using math Shvartsman’s approach, and experiments on fruitematical modeling fly embryosbetter understand to reactions chain cellular behavior. of enzymes that control One enzyme currently being studied by called team, Shvartsman’s learn but our understanding of these very complex systems is growing steadily,” Shvartsman said. “It is a very time.” exciting a part of fruit fly embryoswhere stem cells turn into mature eggs. Created by graduate students Yogesh Lim and Bomyi Goyal and postdoctoral researcher Miriam the Osterfield, image was selected for in display Princeton’s of 2014 “Art Science” competition. to control the development of structuresto control the development rang- to the mam- insect eyes ing from compound malian brain. Shvartsman key has discovered mechanisms in cells that affect and are affected by –JS Life begins as a collection of cells as a collection begins Life - devel a mechanical perspective, “From advantage of a novel The team also takes to control the “This platform creates a way The researchers are extending their The researchers that understand believe - “This field is particularly exciting because systems. Often, the complexity of embryonic the complexity Often, systems. under - intuitive a simple, prevents tissues broader and math’s their behavior, standing of investigate to quantitatively gaze is needed them. that un- are soft materials oping tissues deformationsdergo large that are -- materials in response to different constantly growing said Varner. cues,” biochemical and physical help us decompose “Mathematical models due these deformations into the part that’s due to and the partto biological growth that’s of the tissue – how it the inherent elasticity mechanical loads.” responds to applied Using a tech- approach in experimentation. as a developed nique that Nelson originally Berkeley postdoctoral fellow at the Lawrence the researchers etch pat- National Laboratory, which are then into collagen, wells terns of tiny into filled with epithelial cells. The cells grow three-dimensional tissues that researchers molds. the shape of the collagen control by The researchers are able to use the shapes to pat- study how mechanical stress affects the tern of branching of the tissue. in a way in culture tissue microenvironment said. Varner that you cannot in an embryo,” have technique to examine other tissues that mam- implications for cancer research. The also has branches, mary for example, gland, the how and the researchers are investigating branched structure is formed during gland’s development. growth ing the cues that drive these invasive whether in mammarypatterns, or gland tissue - devel toward hold the keys could in cancer, oping more effective therapies for cancer patients. we and anything there is so much to learn, strategies lead to promising new may uncover Nelson said. human health,” to improve
Photo by Frank Wojciechowski Johnson Space Center before coming to “Before branches form, the cells in the “Before branches form, The conclusions in the experiment are “Understanding how these complex the investigating approach to Nelson’s whose undergraduate degree is in Varner, said Victor tube are roughly cube-shaped,” in Nelson’s a postdoctoral researcher Varner, lab. “These cells then become wedge-shaped branch points.” at new but the lab is pursuing avian lungs, specific to said. Varner similar work in mammals, tissues form will help us recreate their structure and treat problems related to their Nelson said. “These blueprints development,” might allow us to build replacement organs as and treat congenital diseases as well certain cancers.” of tissues integrates several development branches of engineering and biology. mechanical engineering and who worked at the NASA Princeton, said an importantPrinceton, tool for the lab is mathematical modeling – writing sets of equa- of biological tions that describe the behavior In one experiment, for example, Nelson’s Nelson’s for example, In one experiment, Their results challenged the generally Until recently, biologists believed this complex, complex, this biologists believed Until recently, localized formed by yet exacting shape was which bud regions of rapidly dividing cells, branches. to produce new collectively outward an Celeste Nelson, But research led by associate professor of chemical and bio- indicates that logical engineering at Princeton, branching is driven by in some types of lungs, cells changing shape rather than dividing. of the embryteam examined the development - lung. The lung begins as a tube onic chicken which sprouts buds that grow into of tissue, The researchers the branches that conduct air. modeling used a combination of mathematical and experimental analysis to determine the mechanisms that initiate and cellular physical branches. airway new that localized patternsaccepted view of the cell division drive branching; instead, researchers determined that changes in the initiates new shape of cells in the airway branches. Like a tree sprouting from an acorn, a lung grows from a small tube of a tree sprouting from an acorn, Like which assume trees, of branches and stems. But unlike cells into an array in the branched network of airways sizes, a dizzying variety of shapes and predictable form in each species. a single, the lung takes
Celeste Nelson and graduate student Victor the investigate Varner unrecognized previously mechanical factors that control how organs, develop. such as lungs, by John Sullivan John by
12 FORM ORGANS HOW SHAPING UP: SHAPING DISCOVERING izes in renal pathology. “I believe this novel cation of genes linked to podocytes was The photo illustration technique, which is a significant improvement verified by staining the cell samples with (opposite) depicts a in cell lineage-specific gene-expression analy- antibodies – each of which reacts to a specific specialized type of cell within the kidneys, sis, will not only help us understand the patho- protein constructed from the RNA instructions. podocytes, and a mathe- physiology of kidney diseases better through The researchers found that the computer’s matical concept that biopsy studies, but also provides a strong tool predictions were 65 percent accurate. The Professor Olga Troyanskaya for discovery or validation of cell-specific urine accuracy of the best existing method, which (inset) devised to virtually dissect those cells from Image courtesy of Olga Troyanskya or plasma biomarkers.” involves experimentally isolating the podocyte others in a complex The researchers focused on the glomeru- cells in mice and measuring their expression tissue sample. lus, an area of the kidney where the podocyte patterns, is only 23 percent. cells filter the waste from blood that will even- Troyanskaya said the goal is to train the tually leave the body as urine. One of the main computer to come up with a mathematical for- reasons the researchers chose to track the mula that identifies links between similar pat- podocytes is that the tiny cells are frequently terns and what distinguishes them from other,
Photo by Frank Wojciechowski involved in kidney disease. The researchers unrelated patterns. It is essentially the general wanted to identify genes active in the podo- type of approach that companies use to evalu- cytes and thus determine which genes cause ate customers’ buying habits to suggest new the cell to be able to perform the podocyte’s movies or purchases. filtering function, differentiating it from other “The genes that we know are specifically cell types in the kidneys. active in podocytes – they are the movies that It is not an easy job: even a biopsy precise we like,” Troyanskaya said. enough to sample only the glomerulus leaves Although the researchers used kidney doctors with a mix of four cell types including cells, Troyanskaya said the program also will the podocyte. This yields activity measure- work with other cell types, including other solid ments for tens of thousands of molecular tissues that cannot be experimentally micro- markers, called RNA. dissected in humans. The program is available “It’s a little more complicated than this, free to researchers on Princeton’s website. but you can think of RNA as the instructions In addition to Greene, Troyanskaya’s team that come from the DNA, and we need to at Princeton included Young-suk Lee and identify which of these instructions are Qian Zhu, graduate students in computer active in the podocytes” said Casey Greene, science and genomics. The group collaborated Olga Troyanskaya and her colleagues are making great strides in who worked on the project as a postdoctoral with Kretzler’s team at Michigan as well as MATCH dissecting tiny collections of human cells, but they are not using scalpels. researcher with Troyanskaya and is now an researchers at the University of Zurich and at assistant professor of genetics at Dartmouth Fondazione IRCCS Ca’ Grande Ospedale MAKING: They are using data. The method has proven to be far faster College. Maggiore Policlinico in Milan. Troyanskaya, a postdoctoral fellow and and significantly more effective than current Kretzler, a professor of internal medicine COMPUTER graduate students at Princeton have developed techniques. In findings published recently in and computational medicine, and his team in SCIENCE a system that allows computers to “virtually the journal Genome Research, Troyanskaya’s Michigan first obtained data from the biopsies dissect” a kidney in a way that surgery group and a team of researchers at the Uni- of 452 patients, each containing RNA from versity of Michigan led by Matthias Kretzler CONNECTS cannot. The computer uses data from an roughly 20,000 genes. The more RNA found in GENES TO TISSUES array of measurements in kidney biopsies to reported that they had identified 136 genes the sample from a particular gene, the more separate cells mathematically and identify involved in the creation of a critical kidney cell active that gene. genes that are turned on in a specific cell type. called a podocyte. In decades of research, only by John Sullivan By searching for patterns among the “We call it in-silico nano-dissection,” said 46 had been previously identified. patients’ data, the team identified 136 genes Troyanskaya, a professor of computer science “The potential for this is huge,” said linked to the podocytes. Two of those genes and the Lewis-Sigler Institute for Integrative Behzad Najafian, a University of Washington have been shown experimentally to be able to Genomics. assistant professor of pathology who special- cause kidney disease. The computer’s identifi-
14 15 Photo by Frank Wojciechowski diameter, but examples of such large cells are and require support to stay buoyed. not frequent. Scientists have attributed this Feric and Brangwynne plan to repeat the size limit to the difficulty that large-volume experiments in different-sized cells and explore WHY cells have obtaining nutrients, an explanation the properties of the actin network in the nu- Brangwynne said is not backed by substantial cleus to understand the limits of its strength. ARE CELLS evidence. The researchers said a rewarding aspect Brangwynne and Feric were not thinking of the study was its surprising turns, which at small? about gravity when they began their investi- one point led them to calculate the viscosity of gation. Brangwynne wanted to find out why the nucleus to understand the behavior of the certain types of large particles within cells beads they injected. fuse together upon contact, like water droplets, “We had absolutely no intention of trying to by Anna Azvolinsky when floating freely in a cell but not when they learn about gravity,” said Brangwynne. are in the cell’s nucleus. By injecting various “That you need to know the viscosity of size plastic beads into the nucleus of the frog the cell nucleus to figure out that gravity could egg cells, Branwynne and Feric found evidence be important for setting the upper limits of for an invisible scaffold that might keep the cell size? It’s hard to imagine how one could particles from fusing. predict such a connection.” Feric next discovered that this matrix could In an undergraduate course Brangwynne be made up of fibers of the protein actin, teaches, students have previously performed which was known to form a cytoskeleton in the calculations suggesting gravity is a negligible parts of cells outside of the nucleus but whose force on cells. Brangwynne said he will now role in the nucleus was not clear. To test the have to change the exercise. “This is where role of this actin scaffold, the researchers rid the research ends up influencing the class the nuclei of the actin polymers, either by treat- work.” ing the nuclei with drugs against the protein, or The research was supported by a New by making the nucleus pump out the protein. Innovator Award from the National Institutes From left, postdoctoral What goes up must come down – even inside the miniscule world of cells. “When we did this experiment we found the of Health and a Searle Scholar Award, both researcher Stephanie large particles sank like pebbles to the bottom awarded to Brangwynne in recognition of out- Weber, Assistant Professor Biologists have generally discounted gravity’s folding inside the cells was disturbed. of the nucleus. That was genuinely shocking,” standing work as a young scientist. Clifford Brangwynne and effect on cells because it was thought that the The researchers, who published their find- graduate student Marina said Brangwynne. Feric study the physical average cell is too small for gravity to play a ings in the journal Nature Cell Biology, con- Noting that actin is less abundant and and chemical characteris- role in its structure. But Princeton researchers cluded that when a cell reaches a certain size, does not appear to form an extensive mesh Researchers in the Brangwynne lab captured tics of important clusters Clifford Brangwynne and Marina Feric have it becomes subject to gravitational forces that in smaller cells, Feric’s experiments led the of molecules within cell microscope images of nuclei. Their work led to found that gravity helps constrain how large require a scaffolding to stabilize the internal researchers to deduce that larger cells have particles called nucleoli a fundamental discovery cells can grow. The results provide a novel components. Below that threshold size, the the actin mesh to protect against gravity. (shown in red) within the about the likely role of reason why most animal cells are small and of internal components of a cell float freely, They propose that gravity becomes impor- nucleus of a frog egg. When they disrupted a gravity in limiting the size similar size. buoyed by smaller chemical forces. tant at a certain particle density and a cell size of cells. chemical scaffold within “Gravity becomes really important at a “The research is really elegant and novel,” of roughly 10 microns – the size limit of most the cell, their images smaller scale than you might have guessed,” said Zemer Gitai, an associate professor of animal cells. The actin in these large nuclei showed the nucleoli fell to said Brangwynne, an assistant professor of molecular biology at Princeton, who was not in- keeps the particles in place as a support the bottom of the nucleus. chemical and biological engineering who led volved in the research. “Cells almost certainly In small cells, the particles against gravity. likely would not need the the research. evolved to be [small enough] to ignore the Particles in a cell become proportionally scaffold because other While studying what makes large particles effects of gravity.” larger with increasing cell size. A particle in chemical forces would in the nucleus of the African clawed frog’s egg The typical animal cell has a diameter a small cell is like a single piece of dust – it keep them afloat; in bigger cells the effects of gravity cells stay in place, Brangwynne and Feric, a of about 10 microns (10 millionths of a floats well, unhindered by gravity. But particles become significant. graduate student, observed the particles fall- meter). Larger cells, like the egg cells of the in larger cells are like many pieces of dust ing to the bottom of the nuclei when a scaf- African clawed frog, are up to 1 millimeter in clustered together that have a greater mass
16 17 A new technology for 3-D imaging A new, fast-focusing microscope lens at the nanoscale developed by Arnold’s research group will be Electronic technologies of the future as employed to help solve this problem. TRANSFORMATIVE well as investigations of cells and other bio- One of the first tasks in the two-year logical materials depend on parts that are just program will be to engineer a system that can nanometers – billionths of a meter – in size. rapidly – or even simultaneously – acquire TECHNOLOGIES Supported by the Schmidt Fund, Princeton scans of the nanomarkers at varying depths
Photos by Denise Applewhite researchers are developing an instrument for embedded in plastics. The team will also by Catherine Zandonella measuring the nanoscale properties of thin integrate a second imaging system to films of plastic and biological materials known enhance the results, and develop a computer generally as “soft matter,” which are neither program to combine the scans into images of simple liquids nor crystalline solids. the nanomarkers’ movements. The instrument will measure the flow of In the second year of the program, the small amounts of soft matter in three dimen- researchers will expand the use of the 3-D sions, including structures in living cells. NanoRheometer to study structures in living Called a 3-D NanoRheometer – a rheometer is cells and explore how these relate to cellular Princeton researchers, Princeton engineers are part of the two research teams awarded funding a device that measures flow – the instrument health, said Brangwynne, whose group studies from left, Ned Wingreen, Bonnie Bassler and in 2014 through the University’s Eric and Wendy Schmidt Transformative will help researchers explain the behavior of the self-assembly of biological materials. Howard Stone have Technology Fund. The fund aims to foster technologies that have the plastics and other soft matter restricted to Register and Priestley also will use the Princeton researchers, from left, Craig Arnold, received a Schmidt confined environments. technology to gain insight into the properties Fund for developing a capacity to transform entire fields of inquiry but may be considered too Richard Register, The device will fill an important gap in the of new types of polymers, which have many microscope to explore risky or forward-looking to obtain funding from traditional sources. Rodney Priestley and bacterial biofilms. needs of researchers, explained project leader industrial uses. “The Schmidt Fund is invalu- Clifford Brangwynne have The existing microscope has enabled the Rodney Priestley, an assistant professor of able in making this project possible,” Register received a Schmidt Fund A microscope for probing bacterial films for developing a techno- Experts of self-preservation, bacteria can grow researchers to observe how biofilms develop, chemical and biological engineering. said. “These sorts of opportunities make it logy for 3-D imaging at into sheets known as biofilms that evade an- cell by cell, when fluids are flowing past the “Nanostructured materials behave differ- great to be at Princeton.” the nanoscale. tibiotics, clog medical devices, and foul water cells. In nature, biofilms are influenced by the ently than the same materials in a larger quan- filters and pipes. To counter these negative forces that fluids exert on bacterial cells as tity,” he said. “To advance technology, there effects, a team of Princeton researchers is de- they gather to form the biofilm and communi- is a need to develop experimental techniques veloping a microscope to peer inside the slimy cate with each other. that allow us to find out why that is.” mantle and find the genes that make biofilms The improved microscope should allow the Along with Priestley, the team members so successful. researchers to find whether cells from certain are Craig Arnold, professor of mechanical and “We want to ask, at the single-cell level, parts of the biofilm, such as the edge that aerospace engineering; Clifford Brangwynne, what chemical and physical and mathematical faces the fluid, have special attributes. assistant professor of chemical and biological rules are underpinning the assembly of these “It is like taking a city apart, one high-rise engineering; and Richard Register, the Eugene films, and then we want to do something about at a time,” said Stone, whose expertise is on Higgins Professor of Chemical and Biological it,” said Bonnie Bassler, the Squibb Professor fluid dynamics. “We want to know what struc- Engineering. The four professors are associ- in Molecular Biology. Bassler is co-leading the tures are there, and what their functions are.” ated with the Princeton Center for Complex project with Ned Wingreen, the Howard A. Prior The researchers will apply two techniques Materials. Professor of the Life Sciences, and Howard for interrogating cells: optogenetics, which Researchers currently use microscopes Stone, the Donald R. Dixon ’69 and Elizabeth involves using laser light to turn on and off to track nanomarkers (particles 9,000 times W. Dixon Professor of Mechanical and Aero- individual genes, and deep sequencing of the smaller than a human hair’s width) in soft space Engineering. cellular genes. matter, but this method performs poorly at An early version of the microscope “There are very strong hints that the cells tracking particles in three dimensions. was developed by Princeton postdoctoral re- in biofilms take on different roles depending “If the nanomarkers move toward or away searcher Knut Drescher, who is jointly advised on their locations, but imaging alone cannot from the microscope, they will move out of by Bassler, Stone and Wingreen. The Schmidt tell you that,” said Wingreen. “The beauty of focus and you won’t be able to detect them,” Fund will enable the team to add to the micro- optogenetics is that we can manipulate indi- Arnold said. scope’s capabilities. vidual genes in specific cells to unpack what 18 all of these different interactions are doing.” 19 “The possibilities are endless,” said identified, with more than half discovered in Mikhail Maksimov, a graduate student in the the last two years. Partly, that is because lab who has written several papers on lasso the molecules are produced by bacteria, peptides with Link and won a Dodds Fellow- and only under the right conditions. So LASSOING ship for his fifth year of study at Princeton. researchers not only need to know which bac- The downside, for medical science, is that teria will make the molecules, they also need A UNIQUE most large molecules’ complexity leads to to know how to stimulate their production. instability. Storing and working with peptides Link’s lab, however, has developed an alter- FOR and proteins is formidably difficult and in many native approach to discovery. SHAPE cases impractical because of their innate “Right now, we don’t understand enough fragility. about the limitations of lasso peptides or That is where the lasso peptide stands out. how far we can push the scaffold,” Maksimov It is far larger than small molecules typically said. “We are trying to find more examples in NEW used in medicine, but far more stable than nature.” MEDICINES conventional peptides and proteins. The secret To accomplish this, the researchers have to its stability is its knotted shape. studied the DNA sequence of bacteria known by John Sullivan “Enzymes called proteases, which slice to produce lasso peptides in search of charac- up peptides and proteins, are a main cause teristics that could be mirrored in other of instability for molecules inside the organisms. In a series of recent publications, body,” Link said. “The knotted shape of the the team has identified 98 potential lasso lasso peptide renders them largely resistant peptide producers from 78 gene clusters on to proteases.” different organisms. Some particularly resistant lasso peptides The next step is to stimulate the organisms Photo by Frank Wojciechowski can even stand up to the protease-rich environ- to produce the lasso peptides in a lab – “not ment of the digestive tract, an area normally a trivial task,” according to Maksimov. Often, off-limits to therapeutic proteins and peptides. the researchers will take a genetic sample Graduate students Among the baroque shapes of molecular biology, with its twisting Mikhail Maksimov “Lasso peptides have multiple benefits – from a lasso-peptide producer and graft it into The Link lab investigates a (standing) and Alan proteins and spiraling nucleic acids, the lasso peptide stands out: like they are small enough to work with and they a microbe like E. coli that is easy to work type of molecule called “lasso peptides,” named for their Futran work in the lab a rope spun by a tiny cowboy, it is a trailing whip of amino acid are stable,” Maksimov said. “At the same with. Using this technique, Link’s lab has of Associate Professor resemblance to a rope lasso James Link BSE ’00 topped with a distinct lasso. time, they have a degree of complexity that produced a number of previously unknown – a ring at the top with a tail where they investigate allows us to do many things with them.” lasso peptides. extending beneath. These The shape is not just aesthetically inter- Peptides – and their larger cousins, protein segments Link’s lab is conducting several projects At the same time, the lab is working on molecules play important esting. Scientists like James Link BSE ’00 proteins – are long chains of amino acids. biological functions in bacteria called lasso peptides, looking into “grafting” molecules with identifying the functions of the new lasso which promise to have believe that the lasso peptide might serve as The large size of these molecules provides and show promise as a known therapeutic effects onto a lasso- peptides. structure for making new multiple uses in a scaffold upon which entirely new drugs and a critical functional benefit in biology. Their medicine. peptide scaffold. “We have developed robust tools to generations of medicines. medical therapies can be constructed. In fact, complexity allows them to perform highly “Since nature has already used the discover and produce new lasso peptides,” several lasso peptides naturally have thera- specialized tasks for organisms such as lasso-peptide scaffold for therapeutic Link said. “Based on our analysis, there peutic effects: some kill a specific type of fighting infection, copying DNA and carrying purposes, we are excited about the possi- are dozens more to find. Our next goals are bacteria; another binds to a part of liver and out chemical reactions in cells. bility of re-engineering lasso peptides to make to find the role of these lasso peptides in kidney cells that controls glucagon, which is This complexity also holds great potential completely new drugs that nature has not bacterial physiology and to turn them into important in diabetes. for medicine. Currently, most drugs are made explored,” Link said. new ways to combat disease.” “This structure is something that nature of small molecules that perform relatively Link also is looking for additional lasso seems to have used to carry out a lot of differ- simple tasks within the body. But Link and his peptides to serve as potential scaffolds. ent functions that are medically relevant,” said co-researchers believe that larger molecules Since they were discovered in 1991, only Link, an associate professor of chemical and can eventually be harnessed to create drugs 30 distinct lasso molecules have been biological engineering. “Among other things, that perform far more complex actions. our research is looking into whether they may lead to an entirely new way of making drugs.” 20 21 22 ENGINEERS ELECTED TO NATIONAL ACADEMIES SHELL STRUCTURES 23 FOR ARCHITECTURE: FACULTY Two members of the engineering faculty, com- made of members Photos by Frank Wojciechowski FACULTY NEWS puter science professors Jennifer Rexford elected by their peers FORM FINDING AND OPTIMIZATION NEWS BSE ’91 and Robert Schapire, were elected based on outstanding In a volume that combines art-book images this year to the National Academy of Engineer- contributions to and rigorous engineering, Sigrid Adriaens- ing. Membership in the academy is among scientific research. sens and an international team of colleagues the highest honors bestowed on engineers Stone’s research introduce professionals and students to shell in the United States. has explored funda- structures and the techniques needed to make Rexford, the mental problems in these complex and elegantly thin surfaces. Gordon Y.S. Wu fluid motion and evalu- Beautiful forms often emerge from underlying Professor in ated a wide range mathematics and physics, said Adriaenssens, Engineering, was of affects including an assistant professor of civil and environmen- recognized for her surface tension, Sergio Verdú tal engineering. “The context of gravity is our “contributions to the buoyancy, fluid playground,” she and colleague Laurent Ney operational stability rotation and surfactants. His work combines write. “This design driver is a hard constraint of large computer theory, modeling, computer simulation and but gives birth to a realm of networks,” the experimentation to examine flow phenomena. intriguing complex spatial STARTUP LEADERSHIP: HOW SAVVY academy said in Verdú, an expert in information theory, structural shapes.” ENTREPRENEURS TURN THEIR IDEAS a news release. examines the fundamental limits of informa- INTO SUCCESSFUL ENTERPRISES Jennifer Rexford An expert in tion transmission and compression. Among Derek Lidow BSE ’73, a lecturer in electrical Internet routing and network management, many other areas, his work has contributed to Faculty, students and staff from across engineering and at the Keller Center, offers Robert Schapire Rexford is a member of the Federal Communi- multi-user detection, which is used in commu- the University gathered May 30 in the his experience from a distinguished business cations Commission’s Open Internet Advisory nications to distinguish a signal from Engineering Quadrangle courtyard to career to help guide entrepreneurs through the Committee and coordinates the committee’s background interference. celebrate the publication of the book difficult stage of moving from a startup to a “Shell Structures for Architecture.” On group on mobile broadband networks. display during the event was a dome self-sustaining business. A founder must have Schapire, the David M. Siegel ’83 Profes- Robert Socolow, senior research scholar structure designed by graduate student a very personal “fire in the belly” as well as sor in Computer Science, was honored for and professor emeritus of mechanical and Yousef Anastas and assembled by four genuine empathy that makes it worthwhile for students in one day. “contributions to machine learning through aerospace engineering, was elected to the others to follow the vision, Lidow said. “There invention and development of boosting algo- American Academy of Arts and Sciences. has to be a balance between tremendous rithms,” the academy said. Founded in 1780, the academy’s membership selfishness and A specialist in machine learning, Schap- of roughly 5,000 includes some of the also selflessness ire is best known as a primary developer of world’s foremost scholars. on the part of a technique called boosting in which many Socolow’s the founder if weak and inaccurate prediction methods are current work focuses they really want combined to form a highly accurate predictor. on global carbon to take it all Since it was first proposed by Schapire and management and the way.” his colleague Yoav Freund, now a computer fossil-carbon science professor at the University of sequestration. He California-San Diego, boosting algorithms have is the co-director of Photo by Denise Applewhite Photo by been used in a wide variety of applications. Princeton’s Carbon The Keller Center Mitigation Initiative hosted a reception Howard Stone, the Donald R. Dixon ’69 and co-author of the May 20 to celebrate and Elizabeth W. Dixon Professor in Mech- seminal work on the launch of the book “Startup Leadership” anical and Aerospace Engineering, and Robert Socolow climate “stabilization Howard Stone by Derek Lidow (above right). Sergio Verdú, the Eugene Higgins Professor wedges” in 2004. Lidow, a successful entrepreneur of Electrical Engineering, were named to the and business leader, developed the book National Academy of Sciences. Founded by out of his teaching at Princeton, where he has led the creation of three entrepreneurship courses. Congress in 1863, the Academy of Sciences is Photo by Zach Donnell 24 RECENT FACULTY AWARDS 25 FACULTY CHEMICAL AND BIOLOGICAL ENGINEERING Jennifer Rexford BSE ’91 MECHANICAL AND AEROSPACE ENGINEERING Warren Powell BSE ’77 FACULTY NEWS NEWS Clifford Brangwynne Named to “Ten Cloud Emily Carter (MAE and Andlinger Center) Honorary doctorate, University of Québec Sloan Fellow Trailblazers for 2013” Sigillo D’Oro, Societa Chimica Italiana at Montréal by GigaOM Remsen Award, ACS Maryland Section Pablo Debenedetti Ramon van Handel Wole Soboyejo Presidential Early Career Award for Scientists Benjamin Garver Lamme Award, American Olga Troyanskaya U.N. Scientific Advisory Board and Engineers Society for Engineering Education (COS and Genomics) Christodoulos Floudas Ira Herskowitz Award, Robert Vanderbei Genetics Society of OPERATIONS RESEARCH AND Fellow, American Mathematical Society Honorary doctorate, Abo Akademi University FINANCIAL ENGINEERING America National Award and Gold Medal, Olga Troyanskaya Jianqing Fan Hellenic Operational Research Society ELECTRICAL ENGINEERING Guy Medal in Silver, Royal Statistical Society AIChE Fellow Mung Chiang Emily Carter Guggenheim Fellow Athanassios Panagiotopoulos SATISFYING ‘LONGING TO LEARN,’ FACULTY HONORED FOR TEACHING Fellow, American Institute of Stephen Chou Three members of the engineering school Wagner, who joined the engineering faculty Chemical Engineers IEEE Pioneer Award in faculty were recognized this year for out- in 1980, specializes in flexible large-area Nanotechnology Rodney Priestley standing accomplishments in teaching and electronics. His research focuses on devices Fellow, National Acad- Camille Dreyfus Teacher-Scholar mentoring students. such as thin solar cells, medical sensor arrays, emy of Inventors Sloan Fellow Claire Gmachl, the Eugene Higgins Profes- and textiles that incorporate electronics. He Rodney Priestley Presidential Early Career Award for Scientists Paul Cuff sor of Electrical Engineering, received the is also working on methods to include flexible and Engineers Career Award, President’s Award for Distinguished Teaching. electronics into other systems. One gradu- Mung Chiang National Science Sankaran Sundaresan She was one of four faculty members who ate student said that “Professor Wagner has Foundation Fellow, American Association for the received the award during Commencement been an impeccable guru in my graduate life Advancement of Science Claire Gmachl and Gerard Wysocki ceremonies June 3. at Princeton.” Another noted that Wagner was Top-cited Paper Award, Chemical Physics Letters Gmachl is a leader in the development of “always willing to chat, whether at 9 a.m. on CIVIL AND ENVIRONMENTAL ENGINEERING quantum laser cascades for environmental Sunday or 9 p.m. on weekdays.” Claire Gmachl Michael Celia Ph.D. ’83 H. Vincent Poor Ph.D. ’77 and medical applications. Since joining the Celeste Nelson, an associate professor of Honorary Membership Award, International Foreign Member, Royal Society of London Princeton faculty in 2003, she has created chemical and biological engineering, received Society for Porous Media Member, Academia Europaea several courses, including the school’s the School of Engineering and Applied Science Honorary Doctorate of Science in Technology, graduate-level research ethics class, and has Distinguished Teaching Award. Branko Gliši Aalto University, Finland (Oct. 2014) served as vice dean of the engineering school. Nelson, who joined the Princeton faculty in Highly Commended Award, Chartered Institute Booker Gold Medal, URSI (Int’l Scientific A colleague said that Gmachl has gone beyond 2007, specializes in developmental biology. of Building (with Naveen Verma) Radio Union) her specialty to create courses for non-science Her research includes studies of morphogen- Eric Wood Elected to National Academy of Engineering majors such as “New Eyes for the World,” esis and tissue engineering, and she has de- Alfred Wegener Medal, Governing Council which shows how optics can be used for envi- veloped two highly successful elective courses European Geosciences Barry Rand (ELE and Andlinger Center) ronmental and medical applications. A former in biomedical engineering. One course was Union 3M Nontenured Faculty Award graduate student now beginning a career as a originally capped at 60 students but demand professor praised Gmachl’s ability “to motivate was so high that enrollment had to be raised COMPUTER SCIENCE Sergio Verdú each student to grow as a scientist.” to 80 students. Nelson is also known for Corresponding Member, Royal Academy Mark Braverman Sigurd Wagner, a professor of electrical teaching students from many different fields of Engineering of Spain Packard Fellowship engineering, received the Graduate Mentor- of study beyond chemical and biological engi- Sigurd Wagner Thomas Funkhouser Naveen Verma ing Award from the McGraw Center for Teach- neering. One student said, “Professor Nelson Highly Commended Award, Chartered Institute ing and Learning. He was one of five faculty Computer Graphics Branko Gliši introduced me to the material I had been Achievement Award, of Building (with Branko Gliši ) members who received the award during the longing to learn since the beginning of my SIGGRAPH Young Investigator Program Award, AFOSR Graduate School’s Hooding Ceremony June 2. engineering education.” David Wentzlaff Young Investigator Program Award, AFOSR 26 http://bit.ly/LidowClass. tackled: “wicked problem”they in theclassdescribe Hear Lidowandstudents creative problem-solving. of physical spacestospur which involved flexibleuse Innovation andDesign,” “Creativity,ated thecourse Derek Lidow(center)cre- NEWS UNDERGRAD 26
Photo by Danielle Alio TACKLING ‘WICKEDPROBLEM,’ KELLERCLASSSTOKESCREATIVITY for Lidow’s class. Ithasthecapabilitytobe boards, theclassroomwas createdspecifically said. “That’s whatthisclassis reallygoodat.” ofpossiblesolutions,”up withallsorts Lidow chance topracticedivergent thinking, coming the bestanswer, andsostudentsdon’t geta on convergent thinking, howtocomeupwith and theKeller Center. specialist andlecturerinelectricalengineering taught by DerekLidowBSE’73, aprofessional wasuates acrossalldepartments, thecourse problems.Opentoundergrad- about real-world and encouragedadifferentway ofthinking just awarm-up forwhatwas tocome. If theopeninganticswere unusual, they were class offeredby theKeller CenteratPrinceton. “Creativity, Innovation andDesign,” anew games onwhiteboardsanddrinkingcoffee. jumping upanddown, stretching, playing mind have passedaclassroomwith14students Engineering Quadranglethispastspringmay Anyone walking throughtheHwingof With flexibleseatingandrolling white tendstofocusstudents “The University The classfocusedonfosteringcreativity forERG392,The scenewas start anormal your feedback.” develop empathy ortoacton foryourusers and alsothespecifictechniques youuseto ing aboutapplyingcreativity to differentplaces away isbeingreallycreativelyconscious, think- engineering major. “A lotofwhatI’mtaking a memberoftheClass2015andelectrical topracticeit,”opportunities saidYolanda Yeh, unique inthatitgivesyouthetoolsand think youcanlearn, andsothisclassis for possibleimplementationacrosscampus. the studentstocontinueperfectingideas watched thefinalpresentationsencouraged officialswho experiences. ApanelofUniversity education throughonlinesharingofpersonal it contains, andanew way toprovide alcohol cup thataccuratelyshowshowmuchalcohol up withawiderangeofdesignsincluding on Princeton’s campus.Studentteamscame tomitigate high-riskdrinking uct orservice has defiedsolutionsforages:Designaprod- what Lidowcalleda“wicked problem”that flow ofideas. reconfigured atany momenttoencouragea “Creativity usuallyisn’t somethingyou For afinalprojectthestudentstackled –Danielle Alio
Photos by Frank Wojciechowski Engineering Mechanical and Aerospace Kyle O’Neil Engineering Civil andEnvironmental Eliza Learner AwardJ. RichSteers following awards. Applied Sciencegave the School ofEngineeringand Day ceremoniesJune2, the computer science.AtClass 22 whoreceivedanA.B.in -- 223BSEdegreesand from theengineeringschool included 245students The PrincetonClassof2014 STUDENTS CELEBRATED FORRESEARCHANDSERVICE Engineering Civil andEnvironmental EllenTungShue-Ting Tau BetaPiPrize Electrical Engineering Callie Woods Photonics Award in Prism-Newport Engineering Mechanical andAerospace Alexander Creely in EngineeringPhysics Jeffrey ’80Prize O. Kephart Electrical Engineering Abigail Ward Senior Thesis/ProjectAward Calvin DoddMacCracken Engineering Civil andEnvironmental Kevin Ross Engineering Civil andEnvironmental Katherine Flanigan George J.MuellerAward Engineering Mechanical andAerospace Buse Aktas Joseph CliftonElginPrize and hersisterSara. Flanigan; AnnaKornfeld Simpson Shue-Ting EllenTung andKatherine with hisadviseesElizaLearner, sistant ProfessorBranko Gliši Aktas; KatherinePogrebniak; As- June 2.Below, fromleft:Buse the school’s ClassDay ceremony stand withrecipientsofawards at PoorVincent Ph.D. ’77(farright) Teaching Award, andDeanH. Applied ScienceDistinguished of theSchoolEngineeringand Celeste Nelson(farleft), winner Computer Science Katherine Pogrebniak Prize InEngineering James Hayes-Edgar Palmer Engineering Mechanical andAerospace Karen Wang Computer Science Anna Kornfeld Simpson Memorial Prize Lore Von Jaskowsky NEWS UNDERGRAD 27
27 28 29 GRADUATE GRADUATE NEWS GRADUATE STUDENTS PUSH RESEARCH FRONTIERS NEWS Studying resistance of bacteria and cancers to attack by chemicals, analyzing how food trade redistributes water resources around the world, finding hidden patterns in data – these are a few of the projects graduate students at Princeton Engineering have advanced JONATHAN ROBINSON CHEMICAL AND BIOLOGICAL ENGINEERING in the past year. At the intersection of teaching and research, graduate students are Hometown: Fort Collins, Colorado model, he has discovered novel features of the preparing to become the next generation of leaders in their fields. Previous institution: Colorado State network, including the previously unknown role University of an E. coli enzyme in protecting the bacteria Robinson is investigating how nitric oxide, an against nitric oxide. His model serves as a CAROLE DALIN CIVIL AND ENVIRONMENTAL ENGINEERING important antimicrobial chemical generated by valuable predictive tool for the study of nitric our immune system, exerts its antibacterial oxide stress in E. coli. It also demonstrates Hometown: Le Havre, France of global water resources, with relatively more effect, and how bacteria respond and adapt an approach that can be translated to other Previous institution: École Centrale Paris water-efficient countries exporting to less to this stress. He has constructed a computa- organisms and conditions and ultimately aid Dalin’s research focuses on the use of water efficient ones. More recently, she has inves- tional model of the biochemical network that in the rational design of therapeutics. His resources for food production, and on the tigated the policy aspects of her research, interacts with nitric oxide in E. coli. Using the work was recently published in PLoS Compu- way these water resources are “virtually” analyzing virtual water trade between Chinese tational Biology. exchanged between countries as they trade provinces. Dalin currently is combining hydro- agricultural products. In a study published in logical and integrated crop-economic models the Proceedings of the National Academy of to evaluate future food trade and associated JESSICA SHANG MECHANICAL AND AEROSPACE ENGINEERING Sciences, Dalin found that international food water uses under different climate and policy Hometown: Silver Spring, Maryland air, have shown promise but are not robust trade has led to an increasingly efficient use scenarios in China. Previous institution: Harvard University in many practical applications, such as high Shang is investigating the potential of highly speeds. Seeking an alternative, Shang is ZACHARY FEINSTEIN OPERATIONS RESEARCH AND FINANCIAL ENGINEERING water-repelling surfaces (superhydrophobic) studying a liquid-infused superhydrophobic to reduce drag in smooth and turbulent flows. surface, inspired by pitcher plants, which is Hometown: Hastings-on-Hudson, New York financial system is imperiled. Studying Shipping and aerospace industries consume hoped to retain drag-reducing properties under Previous institution: Washington University systemic risk measures, Feinstein is billions of barrels of oil annually, a large frac- adverse conditions. Shang ultimately aims to Feinstein has been studying systemic risk, mathematically defining a set of capital tion of which is needed to overcome drag. discover governing properties of the surface such as the risk of contagion between banks, requirements for each financial institution so Even a small decrease in drag would lead to treatment to improve drag reduction across a which is of increased importance since the that the risk of the entire financial system is global energy savings. Conventional super- wide range of flow configurations. financial crisis of 2008. Due to the intercon- controlled. His approach includes using hydrophobic surfaces, which use entrapped nected nature of banks, bankruptcy of one multiple currencies to hedge risks so capital institution affects the balance sheet of others. requirements in times of uncertainty can be When the negative impacts are enough to met in multiple ways. AMY WU ELECTRICAL ENGINEERING cause other banks to default on debts, the Hometown: Hsin-Chu City, Taiwan; an environment. She then performed RNA Previous institution: National Taiwan sequencing of the resistant cells and dis- PREM GOPALAN COMPUTER SCIENCE University covered how new mutations and never- Wu is studying how cancer becomes resistant mutated genomic regions contribute to the Hometown: Bronx, New York articles that a scientist will want to read next. to chemotherapy based on variations in genet- drug resistance. Wu also models the inter- Previous institution: Purdue University Gopalan’s algorithms emerge from Bayesian ics and the microenvironment surrounding the action between cancer and non-cancer Gopalan is developing scalable algorithms for inference, a common statistical technique that cancer cells. She has created microscopic cells using evolutionary game theory. Her uncovering hidden patterns in massive data he is augmenting with other techniques to structures to mimic the tumor microenviron- proposal for exploring how cancer cells may sets. His algorithms have discovered hidden make scalable to large data sets. Using this ment with a non-uniform drug distribution, and accept DNA from neighboring cells to construct structures such as overlapping communities in approach, he is developing algorithms to learn discovered that chemotherapy resistance of a more heterogeneous genome received the social networks, patterns of user preferences population structure from genotype data and multiple myeloma rapidly emerged in such Young Investigator Award from the National in consumer data, and genomic structure of working with colleagues at Microsoft Research Cancer Institute. populations. These patterns can be used in to create recommendation systems. making predictions -- for example, a list of 30 31 ALUMNI ALUMNI NEWS CHEMICAL ENGINEERS TAKE ON ALUMNI TAKE ON NEWS COLLEGE PRESIDENCIES LEADERSHIP POSITIONS Two Princeton Engineering alumnae have Gregory Adams was U.S. Senate, has been the board’s acting Jerald Murphy was recently been appointed presidents of appointed COO of the state chair. Hart earned BSE and MSE degrees in appointed CEO of ACBB- colleges, in both cases the first women to of Tennessee to oversee mechanical and aerospace engineering at BITS LLC, a subsidiary of lead those institutions. the operating efficiency of Princeton in 1969 and 1971. Atlantic Community Bankers Rebecca Weiss Bergman assumed the state departments. Prior to TransCentra, a provider of billing and pay- Bank. Previously, he was at presidency of Gustavus Adolphus College, in his new role, Adams was at ment software services for consumer and Cognizant Technology Solu- St. Peter, Minnesota, on July 1. IBM for 37 years, serving in business-to-business markets, announced tions Corporation. Murphy Previously, she had a 26-year career at the management positions. Michael McCloskey joined the company as earned an MSE in electrical medical device company Medtronic, where she Adams received an undergraduate degree from CFO. He moves from CFO at Parkmobile USA engineering from Princeton was vice president of research, technology Princeton in 1976 in basic engineering. Inc. McCloskey graduated from Princeton in in 1993. and therapy delivery systems for the Udit Batra was promoted to CEO and 1992 with a BSE in civil engineering and company’s Cardiac Rhythm president at Merck Milli- operations research. Disease Management business. pore, the life science She had served on the Adolphus division of Merck. He board of trustees since 2007. is also the chair of the ALUMNI SERVE AS TRUSTEES AND BOARD MEMBERS Bergman received her food supplements Harvey Bernstein, vice president of McGraw Lisa Jackson, who earned a master’s bachelor’s degree in chemical committee of the Asso- Hill Construction, Industry & Alliances, who degree in chemical engineering from Princeton engineering from Princeton in ciation of the European received an MSE in civil engineering from in 1986 and is currently vice president of 1978 and went on to earn a Self-Medication Industry Princeton in 1968, joined the corporate environmental initiatives at Apple, joined the Ph.D. at the University of Min- and a member of the World Self-Medication advisory board of the World Green Building boards of trustees at Princeton and Tulane nesota. She was elected to Industry. Batra earned a Ph.D. in chemical Council. universities. the National Academy of engineering from Princeton in 1996. James Famiglietti, a professor of earth Former Vudu CEO Mark Jung, Class of Engineering in 2010. Laura Bowles moved from Citibank to system science and civil engineering at Uni- 1982 with a BSE in electrical engineering, was Alice Gast has been named president become CFO of Movement Mortgage, a rapidly versity of California-Irvine, who earned a Ph.D. named executive chair of OnLive. of Imperial College London as of September. growing purchase-mortgage bank founded in civil engineering and operations research John McDonnell, former chair of McDonnell She has been in 2008. Bowles received a BSE in civil engi- from Princeton in 1992, was appointed to Douglas Corporation and Princeton graduate president of Lehigh neering from Princeton in 1997. the Santa Ana Regional Water Quality Control with a BSE in 1960 and MSE in 1962 in aero- University since 2006, George Chesakov was Board by California Governor Jerry Brown. nautical engineering, was elected chair of the and previously was vice named the new chairman- Jonathan Huberman, president and CEO of Donald Danforth Plant Science Center. president for research CEO of OAO OTP Bank, a Tiburon Inc. and Princeton alumnus with an Kimberly Ritrievi, president of the Ritrievi and associate provost financial institution with a A.B. in electrical engineering and computer Group LLC and 1980 undergraduate alumna at the Massachusetts strong presence in Russia science in 1988, was named to the Interna- from chemical engineering, became a member Institute of Technology. and its parent bank in tional Association of Chiefs of Police Founda- of the Tetra Tech board of directors. Gast earned her Hungary. Chesakov received tion board of directors. Eric Schmidt, executive chairman of Google Ph.D. in chemical an M.A. in computer science CEO of BusinessExcelleration and partner and recipient of a BSE in electrical engineering engineering from Princeton in 1984. She has from Princeton University in 1999. at Tandem Capital Beatriz Infante, who has a from Princeeton in 1976, was elected to the been a member of the National Academy of President Barak BSE in electrical engineering from Princeton Mayo Clinic board of trustees. Engineering since 2001. Obama appointed in 1976, was elected to the Liquidity Services Carl Sparks, former president and CEO of Christopher Hart as chair board of directors. Travelocity and recipient of a BSE in mechani- of the National Trans- cal and aerospace engineering from Princeton portation Safety Board. in 1989, was named to Dunkin’ Brands board Hart, whose appointment of directors. requires approval by the 30 31 IDEAS ILLUSTRATED
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