MARINA RUSTOW, historian of the medieval Middle East, wins MacArthur Fellowship

Marina Rustow

Marina Rustow (Photo courtesy of John D. & Catherine T. MacArthur Foundation

Marina Rustow, the Khedouri A. Zilkha Professor of Jewish Civilization in the Near East and professor of Near Eastern studies and history, has been awarded a 2015 MacArthur Fellowship.

Rustow is among 24 scientists, artists, scholars and activists who will each receive $625,000 no-strings-attached grants over a five-year period from the John D. and Catherine T. MacArthur Foundation. The MacArthur Fellows Program awards unrestricted fellowships to talented individuals who have shown originality and dedication in their creative pursuits and a capacity for self-direction.

Rustow’s area of specialization is the medieval Middle East, particularly texts from the Cairo Geniza, a cache of more than 300,000 folio pages of legal documents, letters and literary materials that span more than a millennium and were preserved in an Egyptian synagogue. In its announcement, the MacArthur Foundation cited Rustow for research on the Geniza texts “that shed new light on Jewish life and on the broader society of the medieval Middle East. Rustow’s approach to this archive goes beyond decoding documents, in itself a formidable task, to questioning the relationship between subjects and medieval states and asking what that relationship tells us about power and the negotiation of religious boundaries.”

Listening in on bacterial communications

Leah Bushin and Mohammad Syedsayamdost

While an undergraduate, Leah Bushin (left) co-authored an article on the structure of a signaling molecule involved in bacterial communication with co-first author Kelsey Schramma and adviser Mohammad Seyedsayamdost (right), assistant professor of chemistry, PHOTO BY C. TODD REICHART

BACTERIA SPEAK TO ONE ANOTHER using a soundless language known as quorum sensing. In a step toward translating bacterial communications, researchers have revealed the structure and biosynthesis of streptide, a signaling molecule involved in the quorum sensing system common to many diseasecausing streptococci bacteria.

The research team included undergraduate Leah Bushin, who was the co-first author on an article published on April 20, 2015, in Nature Chemistry. Bushin helped determine the structure of streptide as part of her undergraduate senior thesis project.

To explore how bacteria communicate, first she had to grow them, a challenging process in which oxygen had to be rigorously excluded. Next, she isolated the streptide and analyzed it using two-dimensional nuclear magnetic resonance (NMR) spectroscopy, a technique that allows scientists to deduce the connections between atoms.

The experiments revealed that streptide contains an unprecedented crosslink between two unactivated carbons on the amino acids lysine and tryptophan. To figure out how this novel bond was being formed, the researchers took a closer look at the gene cluster that produces streptide. Within the gene cluster, they suspected that a radical S-adenosyl methionine (SAM) enzyme, which they dubbed StrB, could be responsible for this unusual modification.

“Radical SAM enzymes catalyze absolutely amazing chemistries,” said Kelsey Schramma, a graduate student and the other co-first author on the article. The team showed that one of the iron-sulfur clusters reductively activated one molecule of SAM, kicking off a chain of one-electron (radical) reactions that gave rise to the novel carbon-carbon bond.

Kelsey Schramma is a graduate student in chemistry working on a project to study bacterial communication. Disrupting communication could lead to novel strategies to fight infections. PHOTO CREDIT: C. TODD REICHART

Kelsey Schramma is a graduate student in chemistry working on a project to study bacterial communication. Disrupting communication could lead to novel strategies to fight infections. PHOTO CREDIT: C. TODD REICHART

“The synergy between Leah and Kelsey was great,” said Mohammad Seyedsayamdost, an assistant professor of chemistry who led the research, which was supported by the National Institutes of Health. “They expressed interest in complementary aspects of the project, and the whole ended up being greater than the sum of its parts,” he said.

Future work will target streptide’s biological function — its meaning in the bacterial language — as well as confirming its production by other streptococcal bacteria strains.

–By Tien Nguyen

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COMPUTER SCIENCE: Tools for the artist in all of us

Art

FROM TRANSLATING FOREIGN LANGUAGES to finding information in minutes, computers have extended our productivity and capability. But can they make us better artists?

Researchers in the Department of Computer Science are working on ways to make it easier to express artistic creativity without the painstaking hours spent learning new techniques. “Computers are making it faster and easier for beginners to do a lot of things that are time-consuming,” said Jingwan (Cynthia) Lu, who earned her Ph.D. at Princeton in spring 2014. “I’m interested in using computers to handle some of the more tedious tasks involved in the creation of art so that humans can focus their talents on the creative process.”

The techniques that Lu is creating are far more versatile than the simple drawing and painting tools that come pre-installed on most computers, yet they are much easier to use than the software marketed to artists and designers. “Lu has created tools that enable artistic expression by leveraging the use of computation,” said Professor of Computer Science Adam Finkelstein, Lu’s dissertation adviser.

Last year, Lu introduced RealBrush, a project that permits people to paint on a computer using a variety of media, ranging from traditional paints to unconventional materials such as glittered lip gloss. The software contained a library of photographs of real paint strokes. As the artist painted on a tablet or touch screen, the software pieced together the stored paint strokes.

This year, Lu has introduced two new techniques that further her goal of making it easy to create art digitally:

decoBrush

decoBrush allows the user to create floral designs and other patterns such as those found as borders on invitations and greeting cards. Many design programs offer such borders but they come in set shapes and are not easy to customize, requiring a designer to painstakingly manipulate individual curves and shapes.

With decoBrush, users can create highly structured patterns simply by choosing a style from a gallery and then sketching curves to form the intended design or layout. The decoBrush software transforms the sketched paths into structured patterns in the style chosen. For example, a user might select a floral pattern and then sketch a heart, creating a heart with a floral border.

The challenge for Lu and her codevelopers was to guide the computer to learn existing decorative structured patterns and then apply automatic algorithms to replace the tedious process of manipulating the individual curves and shapes.

“Given a target path such as a sketch that the pattern should follow, the computer copies, alters and merges segments of existing pre-designed patterns, which we call ‘exemplars,’ to compose a new pattern,”  Lu said. “It does this by searching for candidate segments that have similar curviness to the target sketch that the user drew. The candidate segments are then copied and merged using a specialized texture synthesis algorithm that transforms the curves to align with each other seamlessly at the segment boundaries.”

Lu constructed decoBrush with assistance from Connelly Barnes, who earned his doctorate degree from Princeton in 2011 and is now at the University of Virginia; undergraduate Connie Wan, Class of 2014; and Finkelstein. She also collaborated with Paul Asente and Radomir Mech of Adobe Research, where Lu interned for three summers and now works as a researcher. Lu presented decoBrush at the Association of Computer Machinery Siggraph Conference in August 2014.

RealPigment

A second project enables artists and novices to explore mixing of colors in digital painting, with the goal of making the digital results more faithful to the physical behaviors of paints.

Software programs for painting are not adept at combining colors, especially when they are simulating complex media such as oil paints or watercolors. One of the most common techniques for combining colors, alpha blending, estimates that yellow and blue make gray rather than green. Lu and her colleagues came up with a different method for figuring out how colors will blend using techniques borrowed from real-world (non-digital) painting.

The researchers use color charts that artists make to find out what color arises when overlaying or mixing two colors of paint. Making these color charts involves painting rows of one color, and then overlaying them with columns each containing a different color. The resulting grid reveals how all pairs of color will look when layered. Similar charts can be made for mixed rather than layered colors.

Lu’s approach is to feed these color charts into the computer to teach it how to combine colors in a specific medium, such as oil paints or watercolors. “The goal is to learn from existing charts to predict the result of compositing new colors,” Lu said. “We apply simplifying assumptions and prior knowledge about pigment properties to reduce the number of learning parameters, which allows us to perform accurate predictions with limited training data.”

Lu’s research was supported by a Siebel Fellowship and funding from Google. The project included Willa Chen, Class of 2013; Stephen DiVerdi of Google; Barnes and Finkelstein. The work was presented at the June 2014 International Symposium on Non-Photorealistic Animation and Rendering.

Site-specific shades offer sun protection

Sun shade

Civil and environmental engineering graduate student Matthew Horner sits with Assistant Professor Sigrid Adriaenssens beneath a prototype of a pavilion designed to block harmful UV radiation by accounting for the sun’s path within its specific geographic location. (Photo by Denise Applewhite)

Children exposed to a lot of sunlight have a higher chance of developing skin cancer as adults, according to the Centers for Disease Control and Prevention. With this in mind, structural designer and assistant professor in the Department of Civil and Environmental Engineering Sigrid Adriaenssens is creating a sun shade designed to account for the sun’s path within a specific geographic location. This would allow the shade to work anywhere, protecting against the sun’s power and helping reduce skin cancer — the most common form of cancer in the United States.

Adriaenssens’ approach is to produce a dome shaped grid for the sun shade that works with surrounding climatic conditions and uses the least amount of building material possible. To do this, her team uses data from the National Oceanic and Atmospheric Administration and NASA coupled with their sun path algorithms to identify specific sunlight angles in the sun shade’s location and ensure that the grid shades for only those angles. This allows the structure to block damaging UV radiation, but lets through light that doesn’t affect the target shade area.

The inspiration for the shade’s design came in part from existing commercial sun shades, which are typically “one design fits all” and thus ineffective at actually shading their target areas. Individuals sitting under a patio set with a sun shade, for example, can find that the perimeter of the table around which they are sitting is not shaded at all, Adriaenssens explained.

Adriaenssens uses a “dialectic” strategy in her work, which is a reference to the dialectic form of discourse that looks for a solution to a problem by using various arguments, or design drivers in this case. For Adriaenssens, the drivers include engineering considerations such as structure and material as well as questions of environmental performance.

“I think sometimes you can design, in a very economic way, very elegant systems,” she said, noting that she encourages the dialectic approach among her students. Adriaenssens’ colleagues, including Assistant Professor of Civil and Environmental Engineering Mark Zondlo, Postdoctoral Research Associate Landolf Rhode- Barbarigos, and graduate students Matthew Horner and Dan Reynolds, recently erected a prototype sun shade near the Princeton University Stadium.

Other sun-related projects that adapt to different environmental conditions are on Adriaenssens’ radar. One of her models takes its cue from plants such as the waterwheel plant (Aldrovanda vesiculosa), which uses two lobes that rapidly snap shut to catch prey. The mechanics of this motion serve as the basis for shading structures that open and close based on the amount of sunlight present at a given time, ensuring lower manufacturing costs and energy consumption.

Adriaenssens hopes that the high efficiency of her creations will ensure a low-resource path to useful designs, especially in cities. With 70 percent of the world population predicted to live in urban environments by 2050, carbon emissions from existing and additional buildings — and the construction materials for creating them — required to support their needs will only increase, she explained.

“We must find more efficient ways to provide people with a good quality of life using fewer resources,” she said. “My research is all about how we can develop an engineering design framework for a future-oriented urban environment.”

–By Tara Thean

About the Cover

Discovery 2012Tree, by Zhen James Xiang 2012 Ph.D. in electrical engineering

Second-place winner in Princeton’s 2011 Art of Science competition

The algorithm used here recursively cuts an image into smaller rectangular pieces. For each cut, a larger rectangle is divided either horizontally or vertically into two equal smaller rectangles. This results in a division of the input image into many rectangular pieces, similar to those shown, organized into a data structure called a dyadic tree.