Category: Grants
Security at our Fingertips
ECE student Jonathan Wu (PhD '15), who is working with Professors Ishwar and Konrad on this research, performs an arm swing to test new gesture-based authentication algorithms he has been working on.
In today’s world, it’s easier to find a college student carrying a laptop, smartphone, or iPod than to spot one without.
As people become increasingly dependent on electronic devices, more personal information, including credit card and bank account passwords, go on these handheld machines as well.
Security is now of great concern since many of these digital pieces require only a four digit passcode to sign in – but what if these tablets could recognize the swipe of your finger?
That’s the idea behind research by Boston University’s Professor Janusz Konrad (ECE) and Associate Professor Prakash Ishwar (ECE), who are collaborating with Professor Nasir Memon and Associate Professor Katherine Isbister, both from the Polytechnic Institute of New York.
“We hope the swipes can be unique enough, by linking several of them to form a word for example, to verify user identity,” said Konrad.
To support the project, the National Science Foundation recently awarded the teams nearly $800,000, with $400,000 of that going to Konrad and Ishwar.
Konrad, Ishwar, and their research team will focus their side of the project on examining how hand and body gestures can be used for authentication.
“For example, hand or body movements could be used to open a door instead of a card swipe if the camera recognized an individual’s gestures,” said Konrad.
Ishwar added that swipes and hand gestures are revocable, meaning that you can update the gesture you use to authenticate yourself. This is different from fingerprints and iris scans which, if compromised, cannot be replaced.
“There are endless choices for personalizing gestures that are easy to remember and reproduce, reliable, and pleasant to work with,” said Ishwar.
Though Ishwar and Konrad have long been exploring the possibility of using cameras in action recognition, they didn’t think their results would be good enough for authentication until they met Memon when he visited BU as an Institute of Electrical and Electronics Engineers (IEEE) Distinguished Lecturer.
“He had already worked on the swipes idea, but when he saw our gesture results, it all clicked together,” said Konrad.
Initial tests using a Microsoft Kinect camera have shown promise, Konrad added, and he and Ishwar are already looking toward other places where their technology might be used.
“One of the challenges will be extending this to regular surveillance cameras often deployed at entrances to buildings,” said Konrad.
If successful, the project has the chance not only to reduce breach-related costs but also increase our sense of security.
-Rachel Harrington (rachelah@bu.edu)
Spinning with Light’s Possibilities
Pictured above is the spiral phase structure of an optical vortex, extracted by interfering it with a conventional light beam.
When we think about light, what often comes to mind are the beams that keep the world from being a dark and dreary place or the electricity and bulbs that keep our homes bright.
In all these cases, light’s energy is coming from the center of its beams, but sometimes light can possess orbital angular momentum. When this is the case, those beams, called optical vortices, allow no energy in the center and essentially look like donuts. The energy, rather than moving in a straight line along the beam path, spins around the donut.
In May 2011, a team headed by Associate Professor Siddharth Ramachandran (ECE) that includes Dr. Steve Golowich of MIT Lincoln Laboratory and Dr. Poul Kristensen of OFS-Fitel received a grant from the Defense Advanced Research Project Agency (DARPA) to study optical vortices and whether optical fibers can be used to generate and transmit them.
Associate Professor Siddharth Ramachandran (ECE)
Previously it was thought that optical vortices, while exotic and interesting, have little use because of their instability in fibers, but recent work by Ramachandran and Kristensen suggests that novel optical fiber structures can help transmit these beams, which opens up the prospect of using them for telecommunications.
Pleased with their initial results, DARPA has awarded a Phase II grant worth approximately $800K to Ramachandran, Golowich, and Kristensen to continue this project.
“We are delighted to have received this highly competitive award, for it provides the necessary resources to investigate much more complex optical fiber structures which we expect to use to generate very high order orbital angular momentum states,” said Ramachandran. “This has never been done, but if the investigations are successful, we expect the results to help increase the data carrying capacity of optical fibers significantly.”
Added Ramachandran, learning more about optical vortices could lead to advances in fields outside telecommunications, such as DNA sorting, high-resolution imaging, and nonlinear and quantum optics.
Already, Ramachandran and his team have published several reports showing the use of these beams to perform quantum encryption for secure networks and for studying spin-orbit interactions in quantum systems.
At the European Conference on Optical Communication in September, the team demonstrated a significant breakthrough that led to a four-fold data capacity enhancement over a single wavelength channel with fibers that use these exotic beams. With their new funding, the researchers hope to continue making progress on this work.
If you’d like to hear more about Ramachandran’s work on optical vortices, he will be giving a talk on the subject at the Future of Light Symposium on November 29. Learn more.
-Rachel Harrington (rachelah@bu.edu)
Related links:
“DARPA Funds Optical Vortices Research by Prof. Ramachandran and MIT Lincoln Lab”
Better Data Management, Lower Healthcare Costs
Professor Ioannis Paschalidis (ECE/SE)
Today, people with chronic conditions like diabetes are benefitting from real-time monitoring devices like miniaturized implants, home monitoring equipment, and smartphone applications. Unfortunately, even though tracking a person’s symptoms and vitals has improved, hospitals and their medical teams are not ready to benefit from possessing so much personalized health data.
Boston University’s Professor Ioannis Paschalidis (ECE/SE) and Dr. William Adams (BMC) have teamed up with MIT’s Professor Dimitris Bertsimas to develop algorithms that can systematically process all patient data in hospital electronic medical records and personalized health records. These algorithms will be designed to classify patients based on the risk of developing an acute condition that would require hospitalization. Such information can then be used to drive preventive actions.
Dr. William Adams (BMC)
“What motivated us to start this particular project is the recognition that the US health care system is extremely inefficient as it is geared toward treating acute conditions,” said Paschalidis. “There are, we believe, tremendous opportunities for preventing the occurrence of these conditions and the expensive hospitalizations they cause.”
To support their work, the National Science Foundation (NSF) has awarded Paschalidis (PI), Adams (Co-PI), and Bertsimas (Co-PI) a five-year, nearly $2 million grant for the project.
By focusing on disease prevention and keeping patients out of the hospital, their work has the potential to improve a healthcare system that is often considered to be very expensive and highly inefficient.
“To that end, the meaningful use of electronic health records is seen as a key to improving efficiency,” the team wrote in their proposal.
The research will utilize Paschalidis’s expertise in data models, optimization and decision theory, but it is truly a collaborative project. Adams, for example, will work with physicians to get feedback on the outcome of the algorithms.
“The main challenge is going to be the adoption of the techniques we develop by physicians in particular and the healthcare system in general,” Paschalidis said. “Dr. Adams will serve as our ambassador to that community.”
Adams said that the Boston Medical Center has spent more than ten years “developing a robust and rich clinical informatics infrastructure for clinical care and research” and welcomes this new partnership.
“Translational science involves collaborative efforts between traditionally independent scientists,” Adams said. “This project is innovative and important in that it brings together mathematicians, engineers, clinicians, and informaticians to better understand and improve healthcare.”
As healthcare costs increase, their research may prove not only to be timely but also life-changing and cost-effective.
-Rachel Harrington (rachelah@bu.edu)
CIDAR: Where Biology Meets Engineering
New life forms reporting to robots reporting to humans may seem like something out of a science fiction movie, but this may be closer to reality than you think.
With recent Office of Naval Research, DARPA, Agilent, and NSF funding, researchers from Boston University, alongside those from Harvard, MIT, UC Berkeley, Northeastern, and the University of Pennsylvania, are working on projects that combine humans, robots, and genetic engineering. The work has the potential to alert humans of harmful bacteria, create “assembly lines” of genetic parts, and create specialized cells to fight a host of diseases.
Boston University’s laboratory, the Cross-disciplinary Integration of Design Automation Research (CIDAR) group, plays a central role in these projects. As members of the lab work on software and experimental “design drivers” to help synthetic biologists work more efficiently, they focus on the following research areas: specification, design, assembly, and community outreach.
Synthetic biology merges technology and biology to solve emerging problems pertaining to areas such as energy, health, food, and the environment. The CIDAR group aims to use computation techniques, largely derived from electrical engineering and computer science, and apply those to experimentally verified synthetic biological systems.
With students in electrical and computer science; bioinformatics; biomedical engineering; and molecular cell biology and biochemistry, CIDAR researchers yield nontraditional results thanks to the cross-disciplinary nature of the group. The work is particularly useful to students interested in electronic design automation, synthetic biology, or professional software development and engineering.
The CIDAR laboratory also brings computationalists and experimentalists together. Computationalists often focus on theoretically interesting problems, which alone does not directly make the engineering of today’s biological systems a reality. Experimentalists, on the other hand, spend time designing ad-hoc, piecewise software that computationalists can develop better by taking a holistic approach. By bringing the two types of research styles together, Assistant Professor Douglas Densmore (ECE), who leads the CIDAR lab, hopes to come up with new solutions to apply toward synthetic biology.
CIDAR supports on-campus projects such as Clotho, Eugene, and Puppeteer.
Learn more about CIDAR in this video overview with Densmore.
If you’re interested in joining CIDAR, see open available positions.
-Sneha Dasgupta (COM ’13)
Related links:
“Life is Suite”
Life is Suite
A group of software apps helps synthetic biologists work faster and better
Douglas Densmore is the Richard and Minda Reidy Family Career Development Assistant Professor. A $1.1 million grant from the National Science Foundation will help Densmore take Clotho from proof of concept to viable commercial software. Photo by Jessica Scranton
As biologists continue the decades-long race to map the genomes of living things, a group of forward-thinking BU engineers is asking the kind of questions that engineers can’t help but ask: what if we built a different genome?
Known as synthetic biologists, they believe that with some skillful genomic tweaks, living organisms, such as cells and microbes, can be put to work doing things that are too dangerous or not even possible for higher life-forms like ourselves.
“There are so many possibilities,” says Douglas Densmore, the Richard and Minda Reidy Family Career Development Assistant Professor in the College of Engineering electrical and computer engineering department. “Some are biotherapeutic. For example, we use chemotherapy to kill cancer cells, which is horribly damaging to the body. We may be able to noninvasively use bacteria that are already in your body to kill cancer cells. Or we can use bacteria to make clean energy.”
In the last few years, as computing power has multiplied and the cost of decoding and synthesizing DNA has nose-dived, synthetic biological possibilities have started to look more like probabilities. Oil spill cleanup is also high on the things-to-do list for customized microbes. So is weapons detection, which may explain why the Office of Naval Research is funding a $7.5 million project called Utilizing Synthetic Biology to Create Programmable Micro-Bio-Robots. The project, which involves Densmore and two other BU engineers as well as researchers from Harvard, MIT, Northeastern, and the University of Pennsylvania, intends to create a dynamic trio of humans, robots, and genetically engineered bacteria, all of which will work together to detect whatever the bacteria are programmed to detect. That could be explosives or toxins or heat or light. The customized bacteria will talk to one another, and they will report to miniature “chaperone robots,” a mere 10 to 100 centimeters long, that will each control thousands of microbes. Finally, the chaperone robots will wirelessly report back to humans.
BU's synthetic biology dream team (from left): Ahmad "Mo" Khalil, James Collins, Douglas Densmore, and Wilson Wong. ENG's James Collins says synthetic biology is "genetic engineering on steroids." Photos by Kalman Zabarsky
While all of that sounds fantastical—new life-forms reporting to robots reporting to humans—it seems perfectly doable to the BU engineers who are working on the project. They include James Collins, a William Fairfield Warren Distinguished Professor and an ENG professor of biomedical engineering, who is regarded as one of the founders of the field of synthetic biology. Collins will determine the DNA modifications required for the project. Calin Belta, an ENG associate professor of mechanical engineering, systems engineering, and bioinformatics, will help design and assemble both the microbiotic robots and the chaperone robots. Densmore will find the best way to assemble and verify the DNA used to enable the microbes to sense specific environmental signals.
“The idea,” says Densmore, “is to engineer living organisms—in this case bacteria—that respond to external stimuli in the environment. They will generate a fluorescent or chemical signal that can be measured by the chaperone robots, which can produce signals as well that the bacteria can detect. So you have a two-way communication system. And finally, we will create chaperone robots that can also communicate with human users.”
Traditionally, as much as anything can be traditional in a field that is just a few years old, finding the correct DNA sequences would be a painstakingly slow and error-prone process, but Densmore has some help in the form of a software tool suite called Clotho. He describes Clotho, named for the youngest of the Three Fates in Greek mythology and the one who spins the thread of life, as an app environment, similar to the iPhone software platform, where a variety of tools can perform specific yet interconnected tasks. In this case, however, the tools connect to repositories of biological “parts” organized in such a way that they can be used to transform descriptions readable by humans into gene networks, designing DNA assembly commands for liquid-handling robots or archiving designs to share with other labs. Densmore admits that he’s a big fan of Clotho—and he should be. He built it.
The idea came to him in 2007, when he was finishing a PhD in electrical engineering at the University of California, Berkeley. He had heard about a talk given by biological engineering expert Chris Voigt, then at UC San Francisco and now at MIT, and it struck him that the genetic circuits Voigt was describing looked very much like the digital circuitry of his own studies in electrical engineering.
Densmore teamed up with friend and colleague J. Christopher Anderson, now an assistant professor at UC Berkeley, and the two of them came up with a schema of how to organize biological information. “It works like this,” says Densmore. “Let’s say there’s this small molecule X floating around in the environment. You want to design a bacterium so that if it sees X, it glows green, and if it doesn’t see X, it glows yellow. We have programming languages that let me literally write, ‘If X, glow green, if no X, glow yellow.’ Then we also have our database of parts connected to Clotho. Clotho apps take these programming instructions and compile them.”
Finally, he says, the information goes to another Clotho app, called Puppetshow, which has “a whole bunch of instructions about what has to happen biologically to make this work. Then it sends code to a liquid-handling robot, and the robot effectively says, ‘You need to go to your fridge and get sample A and put it together with sample B.’
“Basically,” says Densmore, “it’s fancy domain-specific data management and work-flow management, but it’s one of the things that this field desperately needs.”
In November 2011, Clotho apps helped a team of undergraduates from BU and Wellesley edge out teams from the United States, Europe, and Asia to win in the Best Software Tool category at the International Genetically Engineered Machine (iGEM) World Jamboree at MIT. The team had earlier won a gold medal for its overall performance at the iGEM Americas Regional Jamboree in Indianapolis.
The undergrad team designed five software apps that could speed the assembly of DNA sequences that modeled gene interactions of the bacterium that causes tuberculosis—information that could lead to more effective diagnostics and drugs for TB.
In February, Clotho and Densmore got a big vote of confidence from the National Science Foundation in the form of a three-year grant of $1.1 million. The grant, he says, paves the way for Clotho to go “from proof of concept to viable commercial software.” The project includes collaborations with other researchers at BU, as well as at UC Berkeley and the University of Washington.
Three months later, the Office of Naval Research gave Densmore more than $400,000 to buy machinery that will give him a better understanding of the behavior of DNA and proteins in biological systems. And while Clotho has yet to be widely adopted by synthetic biologists, Densmore says it has at least 10 power users and several groups that use it collaboratively. Collins, who also is codirector of the BU Center for Biodynamics and a core founding faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard, says Clotho “is a novel computer-aided design platform for the field, one that will help fast-track efforts to reprogram organisms.”
Avi Robinson-Mosher, a Wyss Institute researcher who is reengineering caffeine production in E. coli, agrees. Clotho reduces the likelihood of errors, he says, and allows him to work much faster. “I heard that Doug was developing this,” he says, “and I contacted him. He said, ‘Come on over.’” Densmore’s graciousness is typical in the field of synthetic biology. “In general,” he says, “we like to share.”
Which doesn’t mean that synthetic biologists are welcome everywhere. “There is a group of biologists out there who say, ‘Biology is way too complicated to engineer,’” Densmore says. “Biology is complicated, but that doesn’t mean you shouldn’t try to push the boundaries. We are saying, ‘Let’s not wait. We are going to learn things and we are going to predict things and we are going to build things.’”
BU is poised to become a synthetic biology powerhouse
The age of synthetic biology was turned on, literally, with a switch built by two BU researchers 13 years ago. James Collins, now a William Fairfield Warren Distinguished Professor and a College of Engineering professor of biomedical engineering, and his graduate student Timothy Gardner (ENG ’00) altered the genes of E. coli bacteria so that they could be made to produce proteins or not produce proteins, essentially creating a two-gene on/off switch for a biological circuit.
The researchers described the achievement in a paper published in Nature in January 2000, an issue that also described a three-gene oscillating circuit built with the same genetic components by two Princeton physicists. Exactly 10 years later, Nature described the work done at BU and Princeton as the “defining pair of experiments” that mark the start of synthetic biology.
In those days, says Collins, who is also a Howard Hughes Medical Institute investigator, the Human Genome Project had captured the attention of cutting-edge biologists, as well as of the press. It would be years before the appellation “synthetic biology” entered the vernacular, and more important, before the science was distinguished from genetic engineering. Today, he says, the difference between the two fields is almost as clear as on and off.
“What genetic engineers were doing was cutting and pasting,” says Collins. “They were introducing genes to enable organisms to be production organisms—they were essentially swapping a red lightbulb for a green lightbulb.” By contrast, he says, synthetic biologists design and build the circuits that power the bulb. “Introducing the lightbulb is not engineering. That’s home design. Designing the circuit is engineering. Synthetic biology is genetic engineering on steroids.”
Collins’ standard definition of the field goes like this: “Synthetic engineering is a new field that is bringing together engineers and biologists who design and construct biomolecular components and synthetic gene networks to reprogram cells, endowing them with novel functions.”
The novel functions he refers to include the production of new fuels and medical treatments. Collins was recently awarded a Bill & Melinda Gates Foundation grant to engineer a yogurt bacterium that will respond to, and kill, cholera bacteria in the human intestine.
Synthetic biology has intrigued scientists at dozens of research institutions, but the field’s alpha schools are generally considered to be the University of California, Berkeley, and the University of California, San Francisco, on the West Coast, and Harvard and MIT on the East. Recently, however, with encouragement from President Robert A. Brown, as well as Jean Morrison, University provost and chief academic officer, and Kenneth Lutchen, ENG dean, Collins has been strengthening the ranks of synthetic biology expertise at BU.
Douglas Densmore, the Richard and Minda Reidy Family Career Development Assistant Professor in the ENG electrical and computer engineering department, came to BU two years ago from UC Berkeley. Ahmad “Mo” Khalil, an ENG assistant professor of biomedical engineering and a former postdoctoral fellow under Collins, joined BU last fall. Also last fall, Collins helped to recruit Wilson W. Wong, an ENG assistant professor of biomedical engineering and previously a postdoctoral scholar in cellular and molecular pharmacology at UC San Francisco. The recruits, who like Collins work in a large, new state-of-the-art lab at 36 Cummington Mall, belong to a happily incestuous community: Khalil earned a PhD at MIT, which is a member of SynBERC, the Synthetic Biology Engineering Research Center, where Densmore was a postdoc. Collins is also affiliated with Harvard through that university’s Wyss Institute for Biologically Inspired Engineering.
“You could build it around the four of us,” Collins says. “And I don’t think there’s much doubt that BU is a major player in this exciting new field.”
To learn more, click here for VIDEO: Synthetic biology, a field born 13 years ago from work done at BU and Princeton, is building a home here, following the recruitment of top-flight researchers. Video by Devin Hahn
-Art Jahnke, Bostonia
BU-Led Team Wins $1M NSF Grant for Smart City Research
The closed-loop system defining a Smart City entails not only collecting data from sensors, but also implementing control actions through devices based on intelligent decision making.
Imagine driving in a city where you never have to search for a parking spot, traffic tie-ups are rare, and information on nearby accidents is displayed on your dashboard almost instantaneously. If a research team led by Professor Christos Cassandras (ECE, SE) achieves its goals, such “smart cities” could become commonplace across the U.S. in the coming decade.
The team—which includes Professors Yannis Paschalidis (ECE, SE), Azer Bestavros (CS) and Assaf Kfoury (CS, SE) from Boston University; University of Massachusetts-Amherst Professor Weibo Gong (ECE); and University of Connecticut Professor Robert Gao (ME)—has received a $1 million grant from the National Science Foundation to create the technological infrastructure for a wide range of Smart City applications aimed at reducing the congestion, pollution, fossil fuel consumption, accidents, cost, and sheer inconvenience associated with operating motor vehicles in urban environments.
Professor Christos Cassandras (ECE, SE) and systems engineering graduate student Yanfeng Geng (PhD '13) developed a preliminary version of a Smart Parking system that enables a driver to enter a desired destination and price range into a mobile device and reserve a vacant, appropriately priced parking space that's closest to the destination.
“Our Smart City focus has the potential of revolutionizing the way we view the city in the future: from a passive living and working environment to a highly dynamic one with new ways to deal with transportation, energy and safety,” said Cassandras.
These new ways include a Smart Parking system that assigns and reserves parking spaces based on a driver’s requested destination and price range, a traffic regulation system that dynamically controls traffic lights based on real-time road conditions to improve the flow of vehicles throughout a city, and electric vehicle charging stations where drivers can pay to download electric power to their vehicle from a smart grid—or get paid to upload excess electric power from their vehicle to the grid.
To create an infrastructure for these and other Smart City applications, the team plans to design a mobile sensor network of motor vehicles, each equipped to collect data from its onboard sensor and quickly transmit it across the network from one vehicle to the next. Using the network, a driver who comes across an accident scene could, for instance, punch a dashboard menu button and transmit the accident location to every other motor vehicle in the network.
The mobile sensor network that the researchers envision will collect and exchange data such as accident locations or hazardous road conditions; dynamically allocate resources such as available parking spaces or electric vehicle charging stations; ensure secure and reliable data exchange across the network; and make real-time decisions, such as coordinating sets of traffic lights, without compromising the safety of drivers, bikers or pedestrians. To achieve those objectives, they will advance new sensing, data acquisition, decision-making and dynamic resource allocation capabilities.
The team will test these capabilities via the Sustainable Neighborhood Lab (SNL), a BU-organized living laboratory for sustainable urban development in Boston’s Back Bay in cooperation with the Neighborhood Association of Back Bay, local commercial groups, the City of Boston and the local electricity distribution utility. At BU, a garage is already partially instrumented and will be fully equipped to implement the Smart Parking system, which will also be tested with on-street parking in collaboration with the SNL and the City of Boston.
“The whole concept of a Smart City is beginning to gain prominence in the U.S. and abroad,” said Cassandras. “Our approach is unique in its focus on sensor network infrastructure, its use of optimization techniques for dynamic resource allocation, and its development of a new software framework for real-time, Smart City applications.”
-Mark Dwortzan
Doctors, Engineers Team Up to Fight Cancer
Catherine Klapperich, an ENG associate professor of biomedical engineering and of mechanical engineering and FTCC director, will lead BU's effort to fight cancer by teaming doctors with engineers. Photo by Kalman Zabarsky
Imagine a world where a simple mouth swab could predict lung cancer, a blood test could warn of a recurrence of melanoma, and a rectal scan could tell if you would benefit from a colonoscopy.
That world is the vision of the Center for Future Technologies in Cancer Care (FTCC), founded here in July with help from a five-year, $9 million grant from the National Institute of Biomedical Imaging and Bioengineering (NIBIB) at the National Institutes of Health. The center will foster collaboration among doctors, engineers, and public health and business professionals at BU and elsewhere who hope to develop technology to diagnose, screen, and treat a variety of cancers faster, cheaper, and better than is done now.
BU is one of three recipients, with Harvard and Johns Hopkins University, of a U54 award, given by NIBIB’s Point-of-Care Technologies Research Network (POCTRN).
Catherine Klapperich, a College of Engineering associate professor of biomedical engineering and of mechanical engineering and the FTCC director, says this isn’t the first time that BU engineers and clinicians have collaborated to tackle major health problems. The FTCC effort is unique, however, in its focus on cancer care. The new center will draw expertise from programs like the W. H. Coulter Translational Partnership Program and the Boston University Fraunhofer Alliance for Medical Devices, Instrumentation and Diagnostics and will try to develop and commercialize promising prototypes.
“Cathie understands that cancer is not a high- or middle-income country problem; it’s a global problem,” says Jonathon Simon, director of the Center for Global Health & Development and the School of Public Health Robert A. Knox Professor. “With the increasing longevity of populations in low- and middle-income countries and our ability to manage the infectious disease and maternal mortality burdens, there’s just a lot more cancer that comes about because of the age structure of populations, but also because the competing risks on what else is getting people have been diminished.”
The center’s first five seed projects focus on lung, colon, skin, and liver cancers. Avrum Spira (ENG’02), a School of Medicine professor of medicine, pathology, and bioinformatics and a pulmonologist at Boston Medical Center (BMC), has found a way to detect lung cancer at an earlier and therefore far more treatable stage than it is usually found, by studying changes in cells in the windpipes of smokers. With help from the FTCC, he hopes to develop a blood test or mouth or nose swab that could reveal a high risk of lung cancer.
Irving Bigio, an ENG professor of biomedical engineering and electrical and computer engineering, demonstrates how a fiber-optic probe can read tissue samples. Photo by Chitose Suzuki
Irving Bigio, an ENG professor of biomedical engineering and of electrical and computer engineering, and Satish Singh, a MED assistant professor of medicine and a BMC gastroenterologist, have teamed up to develop a prescreening tool for colon cancer, the second leading cause of death by cancer in the United States.
Doctors recommend that everyone age 50 and over have a colonoscopy at least once every 10 years, yet compliance is low, Bigio and Singh say, because people dislike the invasive nature of the procedure. Singh notes that only half of those people who undergo a colonoscopy actually have intestinal polyps, and half of those have precancerous polyps. With this in mind, Bigio developed a fiber-optic probe that uses light and a spectrometer to detect potentially cancerous polyps, and thus signal a real need for a colonoscopy. FTCC funding will advance their research, and if it’s successful, help develop a prototype that is disposable and affordable.
Klapperich herself is working with San Francisco–based Wave 80 Biosciences to develop a blood test to detect liver cancer. The researchers are designing a cartridge that would separate the nucleic acid RNA from blood or plasma samples and use isolated nucleic acid to flag liver cancer, which kills more than 20,500 yearly in the United States, according to the American Cancer Society.
Rhoda Alani, MED’s Herbert Mescon Professor and Chair of dermatology, chief of BMC’s department of dermatology, and one of four NIBIB co–principal investigators, hopes to develop a similar technology with colleagues from the University of Texas at Austin that will analyze RNA within patients’ blood samples to determine the likelihood of a recurrence of melanoma, an aggressive form of skin cancer discovered yearly in more than 76,000 people in the United States, according to American Cancer Society figures.
Rhoda Alani, MED's Herbert Mescon Professor and Chair of dermatology and chief of BMC's dermatology department, hopes blood samples are the key to early detection of a melanoma recurrence. Photo by Vernon Doucette
The center’s fifth seed project, a collaboration between MIT and Michigan State University called My LifeCloud, is a cell phone–based system aimed at empowering patients at risk for colorectal cancer—particularly the African American population, which the American Cancer Society says has the highest incidence of, and mortality rate from, colorectal cancer of all racial groups in the United States.
Over the five-year NIBIB grant period, Klapperich says the center will encourage several new proposals, weed out a few, and provide funding for an annual summer innovation fellowship to transition lab research to a working prototype.
The grant will also allow another NIBIB co–principal investigator, Bennett Goldberg, a CAS professor of physics, an ENG professor of biomedical engineering, and director of the Center for Nanoscience and Nanobiotechnology, to lead training workshops and informal meetings at BU and around the country for students, clinicians, and faculty interested in an interdisciplinary approach to tackling cancer.
The other two NIBIB co–principal investigators are David Seldin, a MED professor of medicine and microbiology and BMC’s chief of hematology-oncology, and Arthur Rosenthal, an ENG professor of biomedical engineering and director of the Coulter Translational Partnership Program.
Franklin Huang, a fellow in the department of medical oncology at the Dana-Farber Cancer Institute, will guide the public health side of the center’s pursuits, determining population needs and assessing which advances might have the greatest impact. “One criterion for screening technology,” says the CGHD’s Simon, “is that the movement forward of science should to the greatest extent possible benefit the largest numbers of people.”
Klapperich echoes Simon’s objective to do the greatest good. As engineers, she says, she and her colleagues could sit around and “impress each other with the stuff that we made,” or they could apply their expertise in ways that will do the greatest good.
-Leslie Friday, BU Today
SE/ECE/CS Team Wins $1M NSF Grant with UMass and UConn for “Smart City” Research
A team of faculty led by Christos Cassandras (SE-ECE, Head of SE Division) with Yannis Paschalidis (SE-ECE, Co-Director of CISE), Azer Bestavros (CS) and Assaf Kfoury (SE-CS) has won a major new NSF grant to support their research project: A Cyber-Physical Infrastructure for the Smart City.
The project aims at making cities “smarter” by engineering processes such as traffic control, efficient parking services, and new urban activities such as recharging electric vehicles. To that end, the research will study the components needed to establish a Cyber-Physical Infrastructure for urban environments and address fundamental problems that involve data collection, resource allocation, real-time decision making, safety, and security. Accordingly, the research is organized along two main directions: (i) sensing and data acquisition using a new mobile sensor network paradigm designed for urban environments; and (ii) decision support for the “Smart City” relying on formal verification and certification methods coupled with innovative dynamic optimization techniques used for decision making and resource allocation. The work will bring together and build upon methodological advances in optimization under uncertainty, computer simulation, discrete event and hybrid systems, control and games, system security, and formal verification and safety.
Target applications include: a “Smart Parking” system where parking spaces are optimally assigned and reserved, and vehicular traffic regulation. The research has the potential of revolutionizing the way cities are viewed: from a passive living and working environment to a highly dynamic one with new ways to deal with transportation, energy, and safety. Teaming up with stakeholders in the Boston Back Bay neighborhood, the City of Boston, and private industry, the research team expects to establish new collaborative models between universities and urban groups for cutting-edge research embedded in the deployment of an exciting technological, economic, and sociological development.
This is a collaborative research project with UMass and UConn. The investigators outside BU include: Weibo Gong (UMass Amherst) and Robert Gao (UConn). The award totals $1M ($700K to BU + $150K to UMass + $150K to UConn). Congratulations to the whole team!
-News courtesy of the Boston University Division of Systems Engineering
Densmore Shares DARPA Grant to Design New Synthetic Biology Assembly Line
Assistant Professor Douglas Densmore (ECE)
Today’s synthetic biologists tend to work in silos, developing novel, biologically engineered materials and devices on dedicated platforms through sophisticated, trial-and-error experiments. As a result, new biologically manufactured products often require more than seven years to build and tens to hundreds of millions of dollars to finance. But a new, more universal synthetic biology platform is emerging that promises to dramatically accelerate the process, enabling on-demand production of new materials and devices, from biofuels to wound sealants, at a much lower cost.
In pursuit of this vision, the Defense Advanced Research Projects Agency (DARPA) has awarded a $3.6 million, 30-month grant to Assistant Professor Douglas Densmore (ECE) and collaborators at MIT, University of California-San Francisco and Pivot Bio (a biotech startup) to help establish a “living foundry” where researchers can access, design, assemble and test synthetic genetic systems composed of hundreds of DNA parts. The new project is administered by DARPA’s Living Foundries Program, which seeks to create an engineering framework for biology that speeds production and reduces its costs by a factor of ten while radically expanding the complexity of systems that can be engineered.
Informed by databases of DNA sequence information and equipped with an extensive library of DNA parts, the MIT team will build gene clusters with the potential to produce corrosion-resistant chemicals called siderophores and test the resulting siderophores to see how well they work. Densmore will then analyze the DNA used to create the siderophores to determine rules that distinguish gene clusters that work well from those that don't, and use those rules to hypothesize how to take known gene clusters and produce better ones.
The research team’s proposed method consists of three sequential tasks. The first is to create a library of more than 10,000 modular DNA parts, derived from bacteria, that would serve as biological building blocks.
The team’s second challenge is to develop an automated process to systematically assemble and use these parts to perform specific biological functions, from processing nitrogen to producing antimalarial drugs.
Densmore will be deeply involved in the third task, which is to apply this process to the production of siderophores, chemicals that bind to metal surfaces and form a protective layer to prevent corrosion, a widespread and costly (an estimated $23 billion per year) problem faced by the Department of Defense, which must operate in some of the most corrosively aggressive environments on the planet. Siderophores could be sprayed on ships, planes and other military vehicles to keep them in operation longer.
“Our goal is to engineer bacteria that can create siderophore compounds in a more tuned, engineered way so that they are better performing, cheaper to manufacture and faster to produce” said Densmore. “To accomplish that goal, I will use the Eugene programming language my group has developed to create new gene clusters with machine learning techniques that use rules to bias new designs away from past failures and toward future successes.”
“Doug’s software and background in electrical engineering is critical in managing the design process and extracting actionable information from the data,” said Christopher Voigt, an associate professor of biological engineering at MIT and the project’s principal investigator.
Once the collaborators identify the gene clusters they believe will perform the best, Densmore will synthesize them using liquid-handling robots at BU.
“We envision an automated process in which people send us materials they want to design, we learn from them and improve them, and then we build new ones,” said Densmore. “If our living foundry is really streamlined, robots will test each new material and teach themselves how to build the next one.”
-Mark Dwortzan
Designing a More Self-Sufficient Solar Panel
An illustration of electrodynamic removal of dust from solar collectors
As companies and homeowners alike look for greener ways to power their homes and businesses, solar panels are becoming an increasingly popular option.
Unfortunately, how much energy a solar panel generates is dependent on how clean the equipment is and it’s not always easy – or cheap – to keep the panels spotless. Both dust and dirt can block sunlight and reduce the amount of energy yielded.
Boston University professors, Malay Mazumder (ECE), Mark Horenstein (ECE), and Nitin Joglekar (SMG), are hoping to solve this problem by designing a more self-sufficient panel that includes a cleaning component that would rely on electrodynamic removal of dust.
Research Professor Malay Mazumder and Professor Mark Horenstein (both ECE)
“Because cleaning solar collectors with water is expensive in desert conditions, solar plants often operate with dusty panels until water is absolutely necessary,” said Mazumder. “Electrodynamic dust removal would not require water and could be operated as frequently as needed at a miniscule cost.”
The BU professors are now one step closer toward achieving their goal after the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy (DOE EERE) and the Massachusetts Clean Energy Center (MassCEC) awarded them grants for their research. The DOE will provide $955,340 for solar mirrors for photothermal energy conversion while MassCEC will give another $40k that will be used toward developing self-cleaning photovoltaic solar panels.
“The solar energy industry is growing at a rate of 33% or better in the U.S., and the renewable energy industry has shown strong growth since 2011,” said Mazumder. “It is very timely that the DOE and Mass CEC would want to invest in this project so that the solar plants can operate at their highest efficiency.”
Professor Nitin Joglekar (SMG)
Mazumder, Horenstein, and Joglekar are engaged in making prototypes that use electric fields to lift and move dust particles across the solar collector and ultimately remove them entirely.
As part of this project, Boston University will partner with Abengoa Solar, who will assist them in developing and testing out the prototype devices in the field. Abengoa is currently installing the world’s largest solar plant in Arizona and is a leader in solar energy technology development. Sandia National Laboratories will also help evaluate the new solar collectors.
Mazumder, the principal investigator on the grant, has been working toward developing an electrodynamic screen for solar panels for nearly 12 years. NASA funded his initial project, which centered around developing self-cleaning panels that could be used in missions to Mars and the moon. He has been working with Abengoa for the last two years and Sandia for one year.
-Rachel Harrington (rachelah@bu.edu)
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