Thursday, January 22nd, 2015

Time	Event
12:00a	Telling stories using computer science For MIT senior Shannon Kao, expert storytelling is essential, even — if not especially — when it comes to coding. The computer science major relies on narrative everywhere from her science fiction writing to her research on educational computer games at the MIT Media Lab — and it all stems from a childhood replete with books. Kao grew up in Michigan and then China, where her mother, who was her school’s librarian, exposed her and her two younger brothers, from an early age, to everything from picture books to hefty novels.  “Instead of hanging out, we would all just grab a book and sit in our living room and read,” Kao says with a laugh. After two semesters of organic chemistry doused her interest in medical school, Kao stumbled on course 6.01 (Introduction to Electrical Engineering and Computer Science) and immediately saw computer science as a way to use her love of math to build something tangible and interactive. The summer after her freshman year, she took on a research position with the Affective Computing Group at the Media Lab, where she worked on a free app called StoryScape. The program, geared toward families with developmentally challenged children, lets users drag and drop animated characters and illustrations, from a gallery Kao helped build, onto a page where users can write original stories, and can then share those stories with others. The animated characters can react to stimuli in users’ environments, such as loud noises, or the shaking of the phone or tablet on which the app is installed. Working on StoryScape’s graphic gallery was Kao’s first experience in a computer science lab — her first research position at MIT was in a biology lab — but even though she had very little expertise in the field at that point, the new research setting immediately felt natural. “It’s important that there’s a strong story underneath something, and the rest will follow,” she says. Modeling for beginners Kao has since expanded her research to MIT’s Scheller Teacher Education Program (STEP), which develops learning technology. For the past 2 1/2 years, she has worked with software developer Daniel Wendel, a research associate in MIT’s Department of Urban Studies and Planning, on a project called StarLogo. It teaches students with no computer science background how to build a program for modeling decentralized systems, like traffic jams. StarLogo’s accessibility to inexperienced coders hinges on a system of blocks-based programming, which works like virtual LEGO bricks: To build a program, rather than writing out lines of code using individual symbols and numbers, users drag and drop ready-made blocks of text that code for 3-D graphics; only certain combinations of text blocks create a functioning program. The process of building a modeling program this way is a lot like building a story — it needs a coherent beginning, middle, and end, or else it won’t function. Kao’s role has been to develop the 3-D graphics that the blocks code for. “[Blocks] make programming more intuitive for people who don’t necessarily have the background,” she says.  Kao has helped run several workshops to make ongoing improvements to StarLogo. STEP invites in parents and children with no programming background to complete a series of challenges; the researchers then ask for feedback on usability. Some of the biggest issues the team has encountered are with interfaces that control zooming and scrolling. After each workshop, it’s back to the lab, where Kao and her colleagues whittle away at a list of tweaks in preparation for the next workshop and set of feedback.  From mindless doodles to an aesthetic sensibility Kao’s interest in telling stories through design and graphics started as mindless doodles in class, but soon grew into full-on illustrations that she later learned to turn into animations, using her computer science skills to bring her art to life. Looking at the illustrations, it’s easy to see that some of her inspiration comes from Japanese animator Hayao Miyazaki, but Kao cites the 2007 Disney film “Ratatouille” as her favorite animated movie.   “I feel like part of my interest in art is that I was just in this constant stream of picture books and young adult books that I would read regardless of what age I was,” she says. “I still really enjoy some picture books.” Kao also works with written narrative: As the literature editor of Rune, MIT’s literary magazine, during her sophomore year, she was responsible for vetting incoming submissions. For the past two years, she has focused more on her own writing, winning MIT’s Ilona Karmel Prize for Science Fiction in 2013 and 2014.  Despite her passions in art and literature, Kao’s occupational focus remains with computer science, but always with her hobbies and upbringing as her guideposts. “Computer graphics is that in-between space,” she says. “You need to have some kind of aesthetic sensibility, since the whole point is still to tell a story, but you’re using computer science and math to do that.”  (Comment on this)
5:00a	New analysis explains collagen’s force Research combining experimental work and detailed molecular simulations has revealed, for the first time, the complex role that water plays in collagen — a protein that is a component of tendons, bone, skin and other structural tissues in the body. The new analysis reveals an important mechanism that had never been observed before: Adding even small amounts of water to, or removing water from, collagen in tendons can generate surprisingly strong forces, as much as 300 times stronger than the forces generated by muscles. The findings are reported this week in the journal Nature Communications by researchers at MIT and the Max Planck Institute for Colloids and Interfaces in Germany. “We don’t really know the physiological role of water” in the human body’s collagen-based tissues, explains Professor Markus Buehler, head of MIT’s Department of Civil and Environmental Engineering and a co-author of the paper. “Here we show that it can develop significant forces, especially in tendons, which are thought of as a passive material.” One of the challenges in previous studies has been that natural biological samples are all different, Buehler says — so trying to determine the underlying causes of variability is tricky. In the new work, the team was able to study the same samples under a variety of conditions, enabling them to probe the causes of variations. Then, these same materials were analyzed using an atom-by-atom computer model that can simulate the structure down to the level of individual molecules, providing a detailed view of the underlying mechanisms. The molecular simulations, carried out at MIT by Buehler and postdoc Shu-Wei Chang, matched and complemented the experimental results observed by the team members in Germany, led by Professor Peter Fratzl. The real and the virtual “We can look at the same scale, the same phenomena, in both experiments and simulations,” Buehler says. “We’re very excited by the results,” he adds, because the simulations make it possible to view “mechanisms that you cannot easily measure” in physical experiments. Chang explains that based solely on the experimental data, there are two possible explanations for the behavior of the tendon material — but the simulations reveal that one of these explanations is infeasible. The researchers showed that within the complex structure of the protein chains that make up tendon collagen, the addition of water causes some parts of the molecule extend, and others to shrink. The balance between the two mechanisms determines whether there is an overall shrinkage or extension of collagen molecules, Chang says — but overall, when water is removed from the molecular structure, it shrinks. Powerful forces The pull of that contraction is startlingly large: The force the drying process exerts “is almost three orders of magnitude greater than the forces generated by muscles,” Chang says. It remains to be understood what, if any, role those forces play in normal biological functioning. Whatever the function of this process in the body, it could potentially be harnessed through tissue engineering and used for other purposes, Buehler says: “We could use water as a driver, as one of the variables to control the material.” Previously, he adds, “We would not worry about the amount of water in the material.” But now it’s possible to envision, for example, “a self-assembling system where water is regulating the process.” Scientists might also be able to get the contrary characteristics of different biological materials to work in concert. For example, combining a material like spider silk — which actually shrinks with the addition of moisture — with a material like tendon collagen could yield a hybrid structure that doesn’t expand or shrink as humidity varies, Buehler suggests, providing a very stable structure. In addition, the methods used in this analysis, combining detailed molecular modeling with direct experimental observation, could also be applied to many other biological materials, Chang says. Sandra Shefelbine, an associate professor of mechanical and industrial engineering at Northeastern University who was not connected with this research, says the MIT team’s analysis “is an excellent example of how computational molecular models can be used in coordination with experiments to discover mechanisms at the atomic level.” David Mooney, a professor of bioengineering at Harvard University, adds that “this is a very striking finding, as it reveals new aspects of the structure and function of collagen, and is likely to lead to many new studies.” The work was supported by the Alexander von Humboldt Foundation, the Max Planck Society, the German Research Foundation, the U.S. Office of Naval Research, and the National Institutes of Health. (Comment on this)

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