Densmore Among High Tech Grant Winners
Our 2013 High Tech Awardees were Assaf Kfoury, Douglas Densmore, and Ramesh Jasti, for developing commercial applications in Information Technology, Healthcare IT, and chemistry, respectively.
Assistant Professor Douglas Densmore (ECE, BME)
Douglas Densmore, Assistant Professor in the Electrical and Computer Engineering Department, works on a high throughput, combinatorial, constraint-based DNA cloning software platform called Clotho. One approach in synthetic biology is a combinatorial exploration of biological “Part” composition directed by the satisfaction of constraints on performance and composition. Creating these designs in parallel with automated liquid handling robotics and introducing them into living systems automatically can be called “High Throughput Cloning” (HTC). The Clotho design software has been created for this process and has been demonstrated successfully as a proof-of-concept. This proposal will transition this proof-of-concept software into commercial grade software for multiple, unique, awaiting customers to launch a large-scale commercial enterprise.
Ramesh Jasti, Assistant Professor in the Chemistry Department, has 
developed a novel method to synthesize cycloparaphenylenes (CPPs), which are nanostructures made of carbon. Porous carbon nanotubes have shown great promise as energy storage materials for high performance batteries and as ultracapacitors. In his research, Dr. Jasti has developed the synthesis of the smallest possible slice of a carbon nanotube – termed “carbon nanohoops.” These structures can be prepared with specific diameters and uniformity in high yield and low cost. Interesting, the 6-CPPs self-assemble in the solid-state into nanotubular materials. This renders them ideal candidates for carbon-based energy storage materials. Carbon nanohoops have wide ranging applications, including hydrogen storage, CO2 sequestration, light emitting diodes, and nanofiltration. In this proposal, the investigators will develop a “flow” system for the continuous chemical synthesis of cycloparaphenylenes nanohoops. In addition, they propose to explore the effects that hoop diameter and crystallinity have on charge capacitance, discharge rate, and energy storage.
Assaf Kfoury, Professor in the Computer Science Department, recently 
supervised the creation of PhD student Mark Reynold’s Software Inspection and Certification Service (SICS). The invention was part of Mark’s doctoral dissertation and he is currently a post-doctoral fellow in the Department of Computer Science. SICS is an entirely novel method for discovering malware in software applications and web pages. Malicious software on the Internet continues to be a pervasive and vexing problem. Among the most serious type of threats are the so-called “zero-day” exploits, so named because they have never been seen before. Antivirus (AV) and Intrusion Preventions Systems (IPS) do a very good job at recognizing known threats, but they do significantly worse when confronted with malware based on a zero-day. Zero-day exploits can hide for months or even years before they are detected, and account for billions of dollars in damage each year. The SICS method is a completely new approach to address the threat of zero-day exploits. SICS has been demonstrated to do extremely well at detecting zero-days, to have a zero positive rate, and a false negative rate that can be tuned to be as small as desired. Funding from this grant will be used to extend the existing SICS implement (Java and Flash) to the Android platform, as well as building out the necessary infrastructure to support the service.
The winners brought in a range of fantastic high tech innovations in healthcare IT, chemistry, and information technology. The funding granted this year will help these innovators reach their goals, and we eagerly await their success.
-Zara Mahmood
This article first appeared on the Boston University Technology Development website.
Three ENG Students Receive NSF Graduate Research Fellowships
Patrick Gregg (ECE)
College of Engineering PhD students Patrick Gregg (ECE), Daniel Reynolds (BME) and Benjamin Weinberg (BME) have received National Science Foundation Graduate Research Fellowships. The prestigious award provides a $30,000 annual stipend and $12,000 cost-of-education allowance for up to three years to outstanding full-time U.S. graduate students deemed likely to contribute significantly to the advancement of science and engineering in the U.S.
The nation’s oldest fellowship program directly supporting graduate students in science, technology, engineering and mathematics fields, the NSF Graduate Research Fellowship Program (GRFP) is highly competitive: this year only 2,000 fellowships were awarded out of more than 13,000 applicants. Since the GRFP’s inception 60 years ago, it has funded several graduate students who went on to become Nobel Prize winners and industry and government leaders.
Daniel Reynolds (BME)
“The success of our graduate students in the NSF Fellowship competition is further evidence of the quality of our doctoral programs and the recognition our research efforts are receiving,” said Professor M. Selim Ünlü (ECE, BME, MSE), associate dean for Research and Graduate Programs. “I congratulate our students for capturing these prestigious and highly competitive grants.”
Gregg, a second-year graduate student, is working with Associate Professor Siddharth Ramachandran (ECE, MSE) on a new method to modify current optical communications systems to provide increased bandwidth, so more information can be transmitted over the same volume of optical fiber.
“One of the current problems with optical communications systems today is the so-called ‘capacity crunch,’ which is dictated by the projected increasing demand for bandwidth and the limitations of current technology,” said Gregg, who with Ramachandran is advancing a potential solution in which light beams that twist forward like a spiral are simultaneously transmitted through an optical fiber.
Benjamin Weinberg (BME)
Reynolds, a first-year graduate student focused on biomaterials research, is considering a project to grow cancer cells on biomaterial scaffolds as a way to simulate the tumor environment in the laboratory setting.
“These engineered tumor constructs provide an advantageous platform on which to investigate basic cancer biology as well as to test anticancer drug efficacy,” explained Reynolds, who is also interested in using biomaterials to improve the delivery of such drugs to tumor cells.
Weinberg, a first-year graduate student, aims to answer major scientific questions and create new therapeutic strategies through genetic reprogramming of mammalian organisms using synthetic biology tools.
“With the fellowship, I plan to engineer novel synthetic genetic circuits in mammalian brains for precise optical control of neural activity,” he said. “This method can be utilized to systematically analyze the causal role of each cell type in neural circuit computation, cognition and pathology, and develop gene therapy-based treatments for neurological and psychiatric disorders.”
-Mark Dwortzan
Opening Movements
Your next security ID may be a defining gesture
In the video above, two College of Engineering professors explain, and demonstrate, the computer software they are developing to recognize a gesture, from your torso, your hand, or perhaps just your fingers. They hope this could be the future security portal to your smartphone, tablet, laptop, or the locked door to authorized personnel-only spaces.
To the casual passerby, Janusz Konrad seems a bit fanatical about tai chi: standing in his office, waving one arm to and fro, then spreading both arms and bringing them together. Duck inside, however, and you’ll notice he’s not stretching for his health; he’s stretching for a camera, and images on a computer monitor are responding to each gesture – zooming in and out of photos or leapfrogging through a photo series.
Konrad, a College of Engineering professor of electrical and computer engineering, and Prakash Ishwar, an associate professor, designed the computer’s software to recognize specific body motions. They’re not making video games. This, they hope, is the future security portal to your smartphone, tablet, laptop, or the locked door: software programmed to recognize a gesture, from your torso, your hand, or perhaps just your fingers.
Armed with an $800,000 grant from the National Science Foundation and collaborating with colleagues at the Polytechnic Institute of New York University, the BU duo is developing algorithms for ever-smarter motion sensors. In doing so, they have to thread a tricky technological needle. “On the one hand,” says Ishwar, “you want security and privacy; nobody else should be able to authenticate on your behalf” by aping your gesture. On the other hand, if the system demands a perfectly precise gesture, you may have to flail your arms or other parts 10 times to get into your own account. “That’s annoying,” says Ishwar. (And people may think you’re either crazy or infested with lice.)
A workable system must be able to screen out distractions, like the motion of someone moving behind you or of the backpack you’re wearing, or changes in ambient lighting.
Yet using gestures as keys to cyber-locks would have some great advantages. A gesture, like a lateral swipe of your hand, has “subtle differences in the way people do it,” Ishwar says – and people vary in arm length, musculature, and other traits that might help a detector distinguish between you and Arnold Schwarzenegger or Elle Macpherson. True, gestures aren’t as unique as fingerprints or as irises or faces, for which there are authentication scanners. But unlike those traits, which theoretically are vulnerable if someone hacks the database storing them, an authenticating gesture that’s been compromised by an impostor can be replaced immediately, whereas getting a new fingerprint – well, “you wouldn’t like it,” says Ishwar.
Security passwords pose another problem: the most effective ones tend to be inconveniently complex. Konrad surveyed one of his classes and found that no one used a smartphone passcode longer than four digits. An effective motion sensor could “simplify, make more secure and more pleasant the process of logging in,” he says. He and Ishwar are working to develop gesture-based authentication software to be test-run on Microsoft’s motion-sensing Kinect camera, used with the Xbox video game and the Windows computer operating system. “It can track your body,” says Ishwar, “get some skeleton approximation for your body, and then that information is provided to you in some real-time format.”
They also hope to use start-up company Leap Motion’s smaller motion-sensing device for notepads and laptops. The company claims that its device, the size of an iPod, will be able to read “micro-motions of your fingers,” says Konrad. In the next three to four years, “we want to develop something that’s extremely simple, inexpensive, and can be imbedded into other products and could be used daily by millions of people.”
One thing that is clear is that certain body parts, like hands, lend themselves to identity authentication better than others. “The degree of freedom that you have with your hands is significantly higher,” Ishwar says. “Maybe if I’m a yoga master, I can move my right leg and put it across my left shoulder, but most people can’t do that.” They’d like to experiment also with the torso, says Konrad, since people’s posture can vary. Then there’s Leap Motion and its potential finger recognition.
“We plan to involve more and more body parts” as the research progresses, Konrad says. If that sounds vaguely Frankenstein-ish, consider that today’s security technology already involves fingerprints, iris scans, and face recognition. “Wouldn’t it be nice,” muses Ishwar, “if we could do that using our everyday body language or gestures?”
-Rich Barlow
Video by Alan Wong
This article originally appeared in BU Today.
Three ENG Faculty Win NSF CAREER Awards
Douglas Densmore (ECE, BME)
Assistant professors Douglas Densmore (ECE, BME), Ramesh Jasti (Chemistry, MSE) and Bobak Nazer (ECE, SE) have each received the National Science Foundation’s prestigious Faculty Early Career Development (CAREER) award in recognition of their outstanding research and teaching capabilities. Collectively, they will receive nearly $2 million over the next five years to pursue high-impact projects that combine research and educational objectives.
Densmore’s CAREER award will advance a synthetic biology platform designed to dramatically reduce the time, costs and complexities associated with assembling DNA to create novel living systems. Such systems could be used to address renewable energy, medical, environmental remediation and other critical societal challenges. The platform Densmore envisions will assemble DNA with automated, optimized and efficient open-source software and liquid handling operations suitable for a wide range of applications.
Ramesh Jasti (Chemistry, MSE)
“This award will allow my research group to push the boundaries of what is possible with DNA assembly automation,” he said. “Our research will not only advance the science and engineering required to perform this work but also introduce a paradigm shift where researchers no longer focus on the tedium of laboratory work but rather on the intellectual exercise of designing new biological systems.”
The award will also help Densmore to continue introducing synthetic biology and DNA assembly techniques to underrepresented students and other researchers ranging from elementary school students to postdoctoral fellows, including College of Engineering students who participate in the annual International Genetically Engineered Machine (iGEM) software division competition.
Supported by his CAREER award, Jasti aims to develop new ways to synthesize well-defined, uniform structures from which carbon nanotubes – extremely thin, hollow cylinders composed of carbon atoms – could be constructed. Because of their unique properties, carbon nanotubes may ultimately be used to enable diverse applications including new solar energy materials, components for faster electronics and single-molecule biosensors.
“Carbon nanotubes have enormous potential for applications in electronics, energy and biotechnology,” said Jasti. “In order to harness the power of these nanomaterials, we need to be able to find a way to synthesize them in a homogeneous manner. My research group is inventing new methods to do just that.”
Bobak Nazer (ECE, SE)
Jasti’s work may lead to new classes of nanotechnologies that could spawn novel devices and systems. He’ll use the NSF funding not only to further his research, but also to introduce high school students to the interdisciplinary nature of nanoscience through a series of workshops.
Nazer plans to use his CAREER award to explore a novel approach to wireless communication that could lead to substantially higher data rates. The conventional wisdom is that interference between users is a source of noise to be avoided at all costs. For instance, modern wireless systems operate by assigning users to dedicated time or frequency slots. However, interfering signals are not simply noise: they encode data sent by other users and often have considerable structure. Nazer has discovered a technique that can harness the inherent algebraic structure of interference; properly applied, it may eventually enable many users to simultaneously occupy the same channel while operating at extremely high data rates.
“Although wireless connectivity is now available almost everywhere, we still only employ wireless communication for the last hop in a network, owing in large part to the interference bottleneck,” said Nazer. “By designing protocols that can harness the structure of interference, we hope to create networks that can effortlessly scale to handle more users while maintaining high throughputs.”
Nazer’s project also incorporates interactive presentations on cellular communication for high school students, tutorials, workshops and other outreach efforts.
To date, 34 College of Engineering faculty members have received NSF CAREER awards during their service to the College.
-Mark Dwortzan
Meeting Tomorrow’s Sustainability Demands Today
A feedback control mechanism monitors the performance of the consolidated applications and makes resource allocation decisions to improve the energy efficiency while meeting the user-defined performance constraints.
When it comes to high-powered computers, increased energy consumption and lack of reliability continue to be problems researchers are trying to overcome. Unfortunately, some of the best current methods for achieving these goals have their flaws.
One example is seen in server consolidation, during which resources are shared across multiple applications and virtual CPUs. Without careful optimization, consolidation may result in sub-optimal energy efficiency or in high temperatures that increase cooling costs.
Over the last year, Assistant Professor Ayse Coskun (ECE) researched how server consolidation could be improved, in part thanks to an award from VMware, a leading provider in virtualization software.
Coskun and her team’s initial work focused on designing server consolidation techniques that run on virtualized servers, targeting high-performance computing applications. They now have a working system that is able to improve energy efficiency on a real-life server.
“Working with VMware has proven to be a rewarding partnership because they’re always offering valuable feedback,” said Coskun. “They work with customers so they’re aware of problems we might not be able to observe in the lab setting.”
Since 2011, she and her team have published several research papers on their progress in improving energy efficiency through server consolidation.
“We have met the early milestones that we set with VMware,” said Coskun. “Now, we’re looking at more broad, realistic data center scenarios and exploring the reliability aspects in addition to improving the energy efficiency.”
Assistant Professor Ayse Coskun (ECE)
Pleased with their initial results, VMware recently renewed Coskun’s funding, providing $75,000 for another year of research.
“Based upon promising early results, we are excited to extend our collaboration with Professor Coskun to investigate techniques for energy-efficient use of multi-core processors with virtualized workloads,” said Steve Muir, director of the VMware Academic Program (VMAP).
Part of Coskun and her team’s continued research will include testing their techniques on multiple server nodes that are connected over the network as a representative data center scenario.
“Professor Coskun plans to build on this base by exploring clustered environments and extending experiments to include general enterprise workloads is particularly interesting; we look forward to our continued relationship over the next year,” said Muir.
The renewed funding will allow Coskun to hire additional PhD students or postdoctoral researchers later this summer. She will also continue supporting student researchers, Can Hankendi (PhD ’15) and Samuel Howes (ECE ’14). Hankendi played a major role in developing a technique for automated resource management while Howes, newer to the project, focuses on setting up the virtualized experimental infrastructure for data center benchmarks.
“Can has single-handedly done most of the implementations and has put together great work so far,” said Coskun, “and Sam is rapidly learning about virtualization, which is a hot research topic right now.”
Truly a team effort, students not only help with the research; they attend company meetings and symposiums with VMware as well.
“VMware is very research focused so we have a lot of exposure to their own researchers and engineers,” said Coskun. “It’s been a beneficial collaboration on both sides, so we hope to keep this partnership going in the future.”
-Rachel Harrington (rachelah@bu.edu)
Related link:
May 19, 2011 -”VMware Funds Coskun’s Server Consolidation Research“
Exploring the Next Wave of Optical Communications
Associate Professor Luca Dal Negro (ECE)
Improving how computer chips communicate with each other could potentially result in smaller, faster and more power efficient devices.
To reach that point, some researchers are studying on-chip optical communications, which rely on the ability to transmit light at high frequencies using light emitters and lasers. Unfortunately, the primary materials used in on-chip lasers tend to be expensive and difficult to integrate with silicon-based microelectronics circuitry.
Many electrical engineers believe that if light were more efficiently generated using a silicon-compatible material, costs of bandwidth could decline and optoelectronic devices could be massively produced at low cost. The problem, however, is that standard silicon materials do not efficiently generate light.
Boston University Associate Professor Luca Dal Negro (ECE), who has conducted much of his research on optical physics and semiconductor nanostructures, recently received a grant that could make silicon-based light sources a real possibility.
“What we’re hoping to do is create novel light sources that leverage distinctive optical resonances, known as gap plasmons,” said Dal Negro. “This would strongly confine electromagnetic fields at the nanoscale on a less expensive silicon platform.”
The Air Force Office of Scientific Research recently awarded Dal Negro $379,989 for his project, “Nanoscale Optical Emitters for High Density Information Processing Using Photonic-Plasmonic Coupling in Coaxial Nanopillars.”
According to his proposal, Dal Negro plans to design and engineer nanoscale-size optical cavities using silicon-compatible electronic materials to demonstrate “dramatically enhanced radiation rates, drastically reduced [size], and room temperature efficient light emitting arrays and laser structures.”
Dal Negro will receive the funding over a two-year period that began in early January.
-Rachel Harrington (rachelah@bu.edu)
Securing our Future Privacy
A growing amount of confidential or private information is shared using computers or phones that aren’t always secure, despite researchers’ best efforts.
Professor Alexander Sergienko (ECE)
Part of the reason for this, Professor Alexander Sergienko (ECE) said, is because current telecommunication security relies on complex coding schemes.
“It’s a very difficult and time-consuming task, but all of these codes could potentially be cracked using sufficient computer power,” said Sergienko. “Many previously secure messages have been accessed recently thanks to the development of more efficient and powerful computers.”
Sergienko and his research team at Boston University think quantum mechanics – and more specifically quantum cryptography – may be the solution.
When using quantum mechanics, the security of legitimate users is protected by not allowing a rogue party to make copies or clones of passwords or messages as they travel in the telecommunication fiber or free space.
“Quantum cryptography has the potential to code messages in a way that is unbreakable and secure forever,” said Sergienko.
Associate Professor Gregg Jaeger (CGS)
To support this research, the Defense Advanced Research Projects Agency (DARPA) has awarded Boston University $1.3 million through the new program, “Quiness: Macroscopic Quantum Communication.” The funding is part of a larger $4 million grant that will be shared with researchers at the University of Maryland, Baltimore, and University of Rochester, who will work with BU to develop secure quantum cryptographic communication technology.
Sergienko will work closely with researchers such as Gregg Jaeger (CGS), an associate professor of natural sciences and mathematics, and University of Maryland’s James Franson, a professor of physics. Jaeger is the author of several related books including Quantum Information and Philosophy of Quantum Information and Entanglement. He also teaches quantum information and quantum theory at BU.
“Quantum cryptography has its roots in and is intertwined with the study of the foundations of quantum theory and quantum entanglement,” said Jaeger, who added that entanglement typically occurs when elementary particles interact then separate. “Entanglement is a property characteristic of the quantum world and is of tremendous interest to physicists and philosophers, as well as engineers working with quantum information.”
At this time, one of the drawbacks of quantum cryptography, which is sometimes known as quantum key distribution, is that it runs at a significantly slower speed than that of a regular telecommunication signal and cannot travel as far.
“The main task of the DARPA Quiness program is to develop new engineering solutions that would bridge this gap and allow quantum cryptography to run at faster speeds over longer distances,” said Sergienko.
Improving secure data exchanges has been a main focus of government and private agencies over the last decade, including the United States Department of Defense.
Sergienko, who has studied quantum optics for more than 20 years, has played an active role in searching for telecommunication security solutions. Working with BBN Technology, Inc. and Harvard University in 2004-06, he helped establish an operational Boston DARPA quantum network, a culmination of previous work.
He and his research team will continue to make advances in the field with this latest project.
-Rachel Harrington (rachelah@bu.edu)
Open for Computing
Holyoke center does environmentally friendly computing
BU is a partner in the just-opened Massachusetts Green High Performance Computing Center (MGHPCC) in Holyoke, Mass. Photos by Cydney Scott
So many machines, so few people.
Ultimately, 20,000 computers will fill an almost acre-sized floor of the Massachusetts Green High Performance Computing Center (MGHPCC). Yet just 10 or so workers have day jobs at the center, which opened earlier this month after BU, four other Bay State research universities, state taxpayers, and business partners poured almost $95 million and two years into its construction.
The hardware-to-human ratio highlights the nature of business at the 90,300-square-foot building approximately two hours west of Boston, in Holyoke, Mass., one of the largest supercomputing data centers east of the Mississippi River. Its computers will be accessed remotely for the most part by researchers at BU and its partners, working from their campuses. But unlike The Terminator’s vision of a dystopia where machines control mankind, the center exists to harness machines to human ends—specifically, to accommodate the five universities’ mushrooming computing needs.
Executive director John Goodhue explains the MGHPCC cooling systems during a recent media tour of the facility.
“Some equipment will be general-purpose clusters available to all researchers at BU,” says Azer Bestavros, a College of Arts & Sciences computer science professor, director of the Rafik B. Hariri Institute for Computing and Computational Science & Engineering, and cochairman of the MGHPCC education and outreach committee. “Other equipment will be more special-purpose, and thus dedicated to specific research.” For example, he and seven BU colleagues have received a National Science Foundation grant to purchase, in tandem with several other universities, a computing cluster to be housed at Holyoke and linked to each member school. Research like this propelled BU’s admission this month to membership in the Association of American Universities, only the fourth school since 2000 invited into the elite research consortium.
In the next few months, the first computers will be installed, making the trip from the center’s loading dock up its six-ton-capacity freight elevator and into that sprawling computing room. Some will be relocated from the five campuses, freeing up space on each. (At BU, that will include space at 881 Commonwealth Ave., 111 Cummington Mall, the Physics Research Building at 3 Cummington Mall, and various schools’ data centers.) Others will be replaced altogether.
Center executive director John Goodhue guided a recent media tour around the austere corridors and cavernous rooms with their factory-like floors, explaining things as adroitly as a seasoned professor, although he’s actually a refugee from Cisco and various computer companies. The electric room has “the equivalent of the fuse box in the basement of your house,” he said, except that the fuses weigh 300 pounds each. The center will make 10 megawatts of energy a day available for computing, which is enough to run up to 10,000 homes.
Ultimately, 20,000 computers will fill these and other cabinets on the one-acre computing floor of the MGHPCC.
The MGHPCC was designed as an environmentally benign computing colossus. Outside, most of the building is a huge rectangle, fronted by towering windows, in a neighborhood of old brick factories. A canal off the Connecticut River meanders by the property, hinting at one of its green aspects: more than 70 percent of the local electricity supply comes from renewable hydroelectric power. The building also meets green building standards, courtesy of its efficient power system and conservation measures.
For example, the electric room’s equipment can function under high temperatures, obviating the need for power-gulping air conditioning. The building’s electric system was installed directly under the computing floor, with shorter wires that minimize wasteful loss of electricity. The average data center requires nine megawatts of power for cooling, Goodhue said; MGHPCC will require less than three, partly by tapping the outside air in winter to cool the computers.
Half the computing floor is lined with black phone booth–sized cabinets, each built to hold about 30 computers. The other half is wide open for expansion and more computers, as is the entire nine-acre property, which has space for additional buildings as needed.
The center devotes an entire corridor to telecommunications equipment—“Computing doesn’t really make any difference unless you can tell people the answer,” noted Goodhue—including a dedicated link to every university in the consortium and thousands of sensors monitoring things from energy efficiency to smoke in the building. Dubbing this corridor “the building’s mouth and ears,” Goodhue said that the “goal is to make all the users of the machines feel like this building is just another building on their campus. The way we do that is by making sure we have very fast, very reliable communication to all of the users.”
BU’s academic partners in the center are Harvard, MIT, Northeastern, and the University of Massachusetts. The state contributed $25 million to the construction, reflecting “what is possible when government, academia, and business work together,” Governor Deval Patrick said. The center “will serve as an economic development model for the state and the nation for generations to come.” Additional funding came from EMC Corporation and Cisco Systems.
-Rich Barlow
This article first appeared on November 27, 2012, in BU Today.
Agilent Renews Funding for Densmore’s Synthetic Biology Research
Using a library of genetic parts like those from DNA sequences and a set of rules (i.e. constraints about the composition), Eugene generates user-defined composite DNA sequences automatically.
Synthetic biology is still a relatively new research field, but we already know that in the future, it might be used to complete tasks too risky for the average human such as explosives detection or oil cleanup.
To make these plans a reality, synthetic biologists typically introduce specific DNA into living organisms like bacteria in order to instruct them to carry out certain jobs. Often, doing so can be a trial-and-error process.
To help create a more systematic approach, Assistant Professor Douglas Densmore (ECE) and his research group designed Eugene, a human and machine readable specification language that can be used to formalize and improve the efficiency.
“Imagine knowing English but not knowing how to put the words together,” said Densmore. “We’re essentially creating rules to make the sentences only instead, we’re working with DNA.”
Eugene is integrated into an eco-system of software tools that help automate the physical construction of the composite DNA sequences (for example, by using liquid handling robotics). Observing the DNA's behavior using technology like flow cytometry will lead to the discovery of novel constraints in composing parts of DNA sequences.
In 2011, Agilent Technologies awarded Densmore over $50,000 for this research. In addition to funding, Agilent also connected Densmore to a mentor in their company, Allan Kuchinsky, a principal project scientist in the Molecular Tools group. To continue their partnership, Agilent recently awarded Densmore another $40,000 to further his work.
Much of this funding has and will help support Ernst Oberortner, a postdoctoral associate in the Department of Electrical & Computer Engineering who has assisted Densmore in his research over the last year.
“When Ernst came, Eugene existed, but he took it back to the basics in order to get better results,” said Densmore.
As a Ph.D. student at the Vienna University of Technology, Ernst Oberortner had already completed a lot of work on domain-specific languages (DSL) and programming languages used in software development.
“During my first year on the project, I was learning synthetic biology and extending Eugene’s functionalities,” said Oberortner. “Now I’d like to augment the Eugene language to move it to the next level.”
Densmore chose to work with Oberortner because of his extensive skills in computer science.
“He’s a good example of how computer science and biology can come together,” said Densmore. “Ernst didn’t have a background in synthetic biology but he was able to apply his experience and move our research forward.”
New funding will be awarded at the start of 2013.
-Rachel Harrington (rachelah@bu.edu)
Related links:
June 7, 2011 – “Agilent Funds Synthetic Biology Research by Densmore”
Uncovering Answers in the Rainforest
Kangping Hu (ECE ’13)
Speaking up about research interests during freshman year might make students a little nervous, but doing so could also take them deep into a Puerto Rican rainforest and provide additional opportunities throughout their undergraduate career.
This was and is the case for Kangping Hu (ECE ’13), who presented his Undergraduate Research Opportunities Program (UROP) poster paper, “Mode Conversion of NAU Launched Whistler Wave Over Arecibo, Puerto Rico,” in October at the George Sherman Union (GSU). His research took first place out of 219 participants at the 15th Annual Undergraduate Research Symposium.
Hu’s work explores the effects of wave-particle interactions in the ionosphere. The ionosphere has become increasingly important as the use of wireless communications rises, because certain ionospheres’ density irregularities can result in signal distortion.
By studying this, Hu says he hopes to “investigate the spectral broadening effects in the ionosphere for communications and remote sensing purposes.”
Hu took advantage of having Professor Min-Chang Lee (ECE) as his advisor soon after he came to BU. Grants Lee received even funded some of Hu’s research with him over the last three summers.
“I have been tutoring Kangping in his research over the past three years, beginning his freshman year in 2009, with my other undergraduate and graduate students,” said Lee. “He is both intelligent and a hard worker.”
Over his last winter and summer breaks, Hu flew to Puerto Rico to conduct research in the rainforest at the Arecibo Observatory, home of the world’s largest radio telescope.
“We did the research in the observatory using a dish that was in the heart of the jungle,” said Hu. “We spent a week there setting up experiments in the middle of the night from 8 p.m. ’til 5 a.m. in order to remove the sun as a variable.”
His work didn’t end after the information was collected. Last summer, Hu analyzed the data during the UROP summer research session. “With this analysis, we made more developments for the presentation,” he explained.
He is currently applying his accumulated research to write his Senior Honors thesis. After graduation, Hu plans to continue his academic career and get a graduate degree in electrical engineering.
-Sneha Dasgupta (COM ’13)
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