By Mark Dwortzan
Research Assistant Professor Swapnil Bhatia (ECE) was awarded the first annual Allan Kuchinksy International Workshop on Bio-Design Automation (IWBDA) Scholarship by the Bio Design Automation Consortium, which promotes education, research, training and advancement of state-of-the-art technology in synthetic biology and bio-design automation.
Kuchinsky made seminal contributions to synthetic biology and design automation that have led to the creation of foundational, state-of-the-art technologies and tools. The scholarship recognizes his efforts by highlighting a student or young researcher who shares his vision for the field.
Bhatia, who is also a co-founder of Lattice Automation, has made significant contributions to bio-design automation in the areas of liquid handling automation, design space specification/generation, and end-to-end toolchain integration. He collaborated with Kuchinsky on several occasions and was an active participant in many of his interactions with Boston University.
By Gabriella McNevin
One hundred and fifty-one teams from 6 continents were admitted into the preliminary round of the ASC 15 (ASC15) Student Supercomputer Challenge, which was held in Taiyuan City, China. Sixteen teams were accepted into the final round, only one of which was from a university in the United States.
A group of five Boston University students specializing in supercomputing, entered the competition as The Boston Green Team. The students- Winston Chen (CE ’16), Nicolas Hinderling (CS ‘17), Huy Le (CS ’16 ), Quentin Li (CE ‘15), and Scott Woods (CS ‘16)- met through a student organization, BUILDS, which serves as the Association of Computer Machinery local university chapter. Boston University Professor Martin Herbordt (ECE) and MIT Professor Kurt Keville advise the team.
The preliminary round of the competition, involving a remote cluster located in Japan, consisted of a three-tier challenge. To advance, the teams were measured by performance metrics like LINPACK testing, NAMD, and their input on the Square Kilometre Array project.
On April 10 the Boston Green Team was notified that they were invited to the ASC15 Finals, held at Taiyuan University of Technology. The teams were given four days to solve six supercomputing application challenges. Ultimately, the top prize went to the Tsinghua University team, and Nanyang Technological University from Singapore broke the world record for their performance on LINPACK.
The ASC Student Supercomputer Challenge is organized by Asia Supercomputer Community, Inspur Group, and the Taiyuan University of Technology. The competition began four years ago, and has since become the world’s largest supercomputer contest.
The ASC Student Supercomputer Challenge is organized by Asia Supercomputer Community, Inspur Group and the Taiyuan University of Technology. Initiated four years ago, the competition has since become the world’s largest supercomputer contest.
“ASC15 has encouraged more and more college students to learn, understand and love the cutting-edge technology of supercomputers,” said Lv Ming, president of Taiyuan University of Technology. “[It] will significantly boost interdisciplinary academic study and talent cultivation in universities, sparking creativity and innovation in students.”
The next student cluster competitions will take place on November 15-20 in Austin, Texas. Students interested in BUILDS are encouraged to subscribe to the mailing list and follow the group on Facebook.
$4.5M NSF CPS Frontier Award to Fund BU-Led Project
By Mark Dwortzan
Researchers have long sought to enable collections of living cells to perform desired tasks that range from decontaminating waterways to growing tissue in the lab, but their efforts have largely relied on trial and error. Now a team of scientists and engineers led by Boston University is developing a more systematic approach through a deft combination of synthetic biology and micro-robotics. Supported by a National Science Foundation (NSF) five-year, $4.5 million Cyber-Physical Systems Program (CPS) Frontier grant, the researchers aim to engineer bacterial or mammalian cells to exhibit specified behaviors, and direct a fleet of micro-robots to corral the engineered cells into working together to perform desired tasks.
Drawing on experts in control theory, computer science, synthetic biology, robotics and design automation, the team includes Professor Calin Belta (ME, ECE, SE), the lead principal investigator, and Associate Professor Douglas Densmore (ECE, BME, Bioinformatics) from the BU College of Engineering; University of Pennsylvania Professor Vijay Kumar; and MIT Professor Ron Weiss, who directs the Institute’s Synthetic Biology Center; and members of SRI International.
“We came up with the idea of bringing robotics in to control in a smart way the emergence of desired behavior patterns among collections of engineered cells,” said Belta, who will develop algorithms to catalyze such behavior. “Our ultimate goal is to automate the entire process from engineering individual cells to controlling their global behavior, so that any user could submit requests from the desktop.”
If successful, the research could yield new insights in developmental biology, lead to greater standardization and automation in synthetic biology, and enable a diverse set of applications. These range from nanoscale robots that can manipulate objects at the micron (one-millionth of a meter) level to chip-scale technologies that transform stem cells into tissues and organs for human transplantation or drug design.
The team’s first main challenge is to advance a synthetic biology platform—what it calls a Bio-Design Automation (BDA) workflow system—that can predictably engineer cells to sense their environment, make decisions, and communicate with neighboring cells. To produce such “smart cells,” Densmore will use and enhance software he’s developed to specify, design and assemble gene networks (also known as gene circuits) with desired functions, and insert them in living cells.
The complex behaviors we wish to engineer are too difficult to manually specify and analyze,” said Densmore. “Design software makes this project manageable as well as formally captures the process so that it can be used in the future to enable new discoveries.”
The second challenge is to design micron-scale, mobile robots that can affect cells’ interactions so that they ultimately bring about a specified global behavior. Composed of organic and inorganic material and controlled by magnetic fields and light, each micro-robot interacts and communicates with individual cells at specified locations and times, implementing control strategies needed to achieve the desired global behavior. For example, the micro-robots could be controlled to optimize tissue formation from stem cells by triggering desired chemical reactions within the cells.
Finally, the researchers will test how well the micro-robots are able to direct the emergent, global behavior of collections of engineered bacterial cells and mammalian cells. They’ll attempt to form Turing patterns—dots and patches of varying sizes—in E. coli and hamster ovarian cells, and liver tissue from human stem cells. In the process, they will employ a magnetic manipulation system developed by SRI to control multiple robots with sub-millimeter precision.
Project leaders also plan to develop associated educational activities for high school students; lab tours and competitions for high school and undergraduate students; workshops, seminars and courses for graduate students; and specific initiatives for underrepresented groups. At BU, the Technology Innovation Scholars Program will develop hands-on design challenges and disseminate them in Boston schools.
Designed to address grand challenge research areas in science and engineering and limited to one or two multi-university teams per year, NSF CPS Frontier Awards support large-scale engineered systems built from, and dependent on, the seamless integration of computational algorithms and physical components.
Finding better ways to produce clean energy, fight infection, attack cancer
By Sara Rimer, BU Research
Imagine the state-of-the-art 21st-century life sciences and engineering lab. It would bring together forward-thinking researchers from the hottest fields in bioengineering. These scientists would combine genomic technologies like DNA sequencing and synthesis, 3-D printers, and robots to make new molecules, tissues, and entire organisms. They would tinker in pursuit of cutting-edge questions like these: How do you guide cells to regenerate and build new tissue? How do you reprogram bacteria to fight infection—or reengineer the body’s immune system to attack tumors so they disappear? How do you organize the circuitry inside a cell so it sends all the right signals for optimal health?
This is the lab that Christopher Chen, a College of Engineering Distinguished Professor and one of the world’s leading experts in tissue engineering and regenerative medicine, began dreaming up last summer with three ENG faculty who are young stars in synthetic biology—Ahmad (Mo) Khalil, Douglas Densmore, and Wilson W. Wong.
Now this dream is on its way to becoming a reality. The University is launching the new Biological Design Center (BioDesign Center), with Chen as the director and Khalil, an ENG biomedical engineering assistant professor and an Innovation Career Development Professor, as associate director. The other two core faculty members at the outset will be Densmore, an ENG electrical and computer engineering assistant professor and a Junior Faculty Fellow with the Hariri Institute for Computing and Computational Science & Engineering, and Wong, an ENG biomedical engineering assistant professor and a recipient of a National Institutes of Health Director’s New Innovator Award.
Through advances in genomics and stem cell research, many of the molecular and cellular building blocks of life have been cataloged. A central challenge is to understand, control, and reengineer how these component parts fit together to bring about functional biological systems that define life and solve important societal problems, ranging from producing clean energy to fighting infection and attacking cancer. That is the fundamental quest that brought Chen, Khalil, Densmore, and Wong together and that will drive the new center.
“Unlocking the underlying design logic of biological systems will revolutionize our approach to medicine, energy, and the environment,” Chen says, describing their shared vision. “Spanning synthetic biology, cell and tissue assembly, and systems biology, the Biological Design Center is positioned to lead this revolution.”
Up until now, he says, fields such as synthetic biology and tissue engineering have arisen as separate disciplines. Synthetic biology involves designing and synthesizing genes, genetic and signaling networks, and genomes to predictably control cellular behavior. Tissue engineering involves trying to manipulate and combine cells and extracellular materials to induce the assembly of tissues.
“But we realized that even though these two fields may involve slightly different tools,” Chen says, “they belong under one roof.”
Kenneth R. Lutchen, dean of ENG, was immediately excited about the possibilities when Chen broached the group’s idea.
“This is a unique approach to using engineering principles to understand and exploit biology,” Lutchen says. “Very few people are using bioengineering techniques and methods to help discover fundamental principles that govern how biological systems work, especially on multiple levels, from the gene level up to multiple organs.”
Chen, who earned an MD at Harvard Medical School and a PhD at the Harvard-MIT Division of Health Sciences and Technology, arrived at BU in 2013 from the University of Pennsylvania, where he was the founding director of the Center for Engineering Cells and Regeneration. Khalil, Densmore, and Wong had all been recruited to the University a few years earlier and were already collaborating.
“Chris is a very dynamic, visionary engineering scientist who is highly respected throughout the biomedical engineering community,” Lutchen says. “He brings a very deep sense of how to connect visionary research to medical and clinical questions. He has the depth and breadth of understanding the engineering challenges, the biological challenges, and the medical challenges as well as a sense of how things are connected between the gene level and the synthetic and systems biology level up to the level of multiple organ systems.”
Creating a community with no walls
Chen and his core faculty members will begin working together out of their existing labs in nearby buildings along Cummington Mall until they can move the BioDesign Center into laboratory space on several floors at what will be the Center for Integrated Life Sciences and Engineering (CILSE) building. Construction on the 610 Commonwealth Avenue building will begin late this spring and is expected to be completed within two years. Four to six new researchers—all exceptional innovators, says Chen—will be added to the center’s faculty over the next several years.
Housing the group at the CILSE, says Gloria Waters, University vice president and associate provost for research, “is a prime example of the goals of the new building—bringing together great scientists from different fields and breaking down the barriers to collaboration.”
Chen’s work spans tissue engineering and mechanobiology, which combines engineering and biology to study how physical forces and changes in cell or tissue mechanics affect development, physiology, and disease. He is a pioneer in the use of 3-D printing to help create organs using a patient’s own cells.
“One of the areas I’m interested in is regeneration,” Chen says. “How do you get cells not to go down the path of inflammation or dying or pathologic response? How do you guide them to go into a regenerative response where they might heal tissue?”
Khalil’s research involves using synthetic biology to understand and engineer genetic circuits that govern important cellular decisions and behaviors. Densmore, who is a Kern Faculty Fellow and the director of the Cross-Disciplinary Integration of Design Automation Research group, automates the specification, design, assembly, and verification of synthetic biological systems using techniques from computer design and manufacturing. Wong’s research focuses on ways to reprogram the body’s immune system to target and kill tumors.
The idea for the center was born when Chen, Khalil, Densmore, and Wong got together over a working lunch early last summer. The chemistry among the group flowed.
“We were talking about what kind of science we each want to do,” Chen says. “We realized how much commonality we shared in terms of the general concept of trying to understand how biological systems operate through the process of trying to control them. We just developed different kinds of tools to manipulate these systems. At that point we realized we should be working in one space rather than doing things separately.”
“It was clear to me, within a few minutes of speaking to Chris,” says Khalil, “that he fundamentally shares the synthetic biology philosophy, which is a desire to understand the rules of building complex and functional biological systems, regardless of whether one uses molecular parts, cellular components, or other raw biological materials.”
To achieve their vision, the BioDesign Center will mix and match researchers from multiple academic fields, undergraduates, graduate students, and innovators from industry. Their lab will have no walls. They will create a community, sharing tools, resources, and ideas with scientists across the University and beyond. They will invent, discover, experiment.
“The idea of tinkering is key,” Khalil says.
They want the center to be a leader in reinventing biological education, engaging students by framing concepts around understanding the logic of how things work. And they want students to learn through hands-on work—by making things and doing things in the lab.
“Classically, biology in high schools and colleges is often taught as a facts-based field,” says Chen. “We think that being able to actively tinker with a biological system—for example, making cells do things they weren’t intended to do—is how one learns more deeply about how these systems work. And the process of being able to do an experiment to see if an idea makes sense is part of the learning cycle for us as scientists, but also for students. The center will be a place where that cycle will be fostered amongst students as well as researchers.”
Khalil says he views the BioDesign Center as an experiment and an opportunity to shape the future of synthetic biology. For all its excitement and vast potential, he says, “if this discipline looks largely the same in five years, then it will have been a failure.”
It is his opinion, he says, that “we will have succeeded when this engineering approach to biology is adopted by all life science researchers—both to understand living systems and to exploit biology as a new technology for addressing societal problems.”
A version of this article originally appeared on the BU Research website.
White House pledge to address major global challenges of the 21st century
By Jan Smith
College of Engineering Dean Kenneth Lutchen is one of 122 deans presenting a letter of commitment to President Barack Obama this week to educate a new generation of engineers expressly equipped to tackle some of the most pressing issues facing society in the 21st century.
These “Grand Challenges,” identified through initiatives such as the White House Strategy for American Innovation, the National Academy of Engineering (NAE) Grand Challenges for Engineering, and the United Nations Millennium Development Goals, include complex yet critical goals such as engineering better medicines, making solar energy cost-competitive with coal, securing cyberspace, and advancing personalized learning tools to deliver better education to more individuals.
In his commitment letter Dean Lutchen explained how the College of Engineering’s long-standing focus on creating Societal Engineers addresses the Grand Challenges.
“Societal Engineers have the passion and attributes to integrate people from all disciplines and lead organizations to address society’s challenges and improve lives,” he wrote. “In addition to their discipline strength, Societal Engineers’ attributes include broad communication skills, systems thinking, global awareness, and a passion and understanding of the entrepreneurial process, the role public policy plays in technology innovation, and strong social consciousness. These attributes, which echo those of the National Academy of Engineering’s Engineer of 2020, are developed with the specific courses and programs that will translate into creating Grand Challenge Scholars.”
The Grand Challenge, organized by the National Academy of Engineering, is supported by 122 signing schools, each of which has pledged to graduate a minimum of 20 students per year who are specially prepared to lead the way in solving such large-scale problems. The Grand Challenge goal is to train more than 20,000 formally recognized “Grand Challenge Engineers” over the next decade.
Grand Challenge Engineers will be trained through special programs at each institution that integrate five educational elements: a hands-on research or design project connected to the Grand Challenges; real-world, interdisciplinary experiential learning with clients and mentors; entrepreneurship and innovation experience; global and cross-cultural perspectives; and service-learning.
“The NAE’s Grand Challenges for Engineering are already inspiring more and more of our brightest young people to pursue careers that will have direct impacts on improving the quality of life for people across the globe,” said NAE President C.D. Mote, Jr. “Imagine the impact of tens of thousands of additional creative minds focused on tackling society’s most vexing challenges. ‘Changing the world’ is not hyperbole in this case. With the right encouragement, they will do it and inspire others as well.”
By Gabriella McNevin and Donald Rock (COM ’17)
A man in a wheelchair is home alone when he accidentally maneuvers too close to a staircase. One wheel passes over the edge of the top stair, and the wheelchair teeter-totters on the brink. Instinctively, the man jerks his arms upwards to regain balance, but he can’t. He and the heavy wheelchair tumble down the steps.
The wheelchair and the man are suited for this situation. The man and his chair are connected to devices that transmit information through the Internet to the man’s health care provider. The caretaker is alarmed to see the chair’s abnormal degree of orientation, the acceleration, and the man’s rapid heartbeat. The health care provider jumps into action and rushes to the man’s aid.
Although the story above is fictitious, the technology is not. Anish Shah, a Boston University electrical and computer engineering graduate student, developed the novel technology with a team of Intel interns. For twelve weeks Shah was focused on creating a practical gateway device to improve the wheelchair experience and benefit health care monitoring.
The team linked the wheelchair to the “Internet of Things” by developing technology that attaches to the chair and to the user to collect and send information. The technology monitors fluctuating data and transmits it to a second party by route of an Internet application. The story above illustrates how the technology can be used to help caretakers respond in emergency situations.
Shah and his team started the design thinking process with a 3-4 week research period. The team discovered a huge variation in the needs of wheelchair users due to varying mobility and health restraints of each individual. To answer the range in needs, the team created technology that measured and sent information to Internet applications. The applications were designed for different health and wellbeing needs.
The technology integrated a bio-harness able to track bio data of the wheelchair user. It was programmed to track a range of body measurements like heart rate, skin temperature, and the orientation of whoever sits in the wheelchair. The harness was a tool with a number of applications when it was connected to the Internet. The technology can connect to Internet applications specifically designed to allow health care providers to respond to emergency situations. The technology can also be connected to applications designed to improve how long-term internal vitals were monitored.
Another feature of the gateway device was mechanical data monitoring. Here, the orientation of the chair, rather than the orientation of the user was observed. This capability can be applied to identify mechanical usage patterns and anomalies.
The wheelchair’s battery was also connected to the internet-of-things to answer questions like, “Will the chair battery die tomorrow?” and “is the chair consuming an irregular amount of energy?”
Lastly, a geo-location monitor was enabled to benefit user navigation of urban areas. With this technology, wheelchair users could find wheelchair accessible venues and thus improve their future transportation preparations.
Shah and his team tested the technology during a two-week trial period. They collected data and feedback and found highly positive results.
Stephen Hawking, world-renowned theoretical physicist and user of wheelchairs, publicly lauded the technological advancement. In a video response, Hawking applauded the design for it’s potential to change lives. “Medicine can’t cure me so I rely on technology,” noted Hawking. “It lets me interface with the world. It propels me. It is how I’m speaking to you now. It is necessary for me to live.”
Shah started the Intel internship one year into the Master of Engineering program at Boston University. He arrived at the Department of Electrical and Computer Engineering with an interest in embedded systems in 2013, and successfully applied the knowledge to create a device that received press coverage around the world. Now, he is working under Professor Thomas Little in the NSF Smart Lighting Engineering Research Center at Boston University.
By Gabriella McNevin
As a Senior Member, Densmore has the ability to hold executive IEEE positions and serve as a reference for other applicants for senior membership. To be eligible one must have shown significant performance in at least ten years in professional practice. Additionally, three references must be submitted on behalf of the applicant.
Densmore’s research is focused on bio-design automation. He elaborated, “my work uses principles from computer engineering like abstraction, modularity, and standardization to design living systems. Computer software is going to be vital to not only store large amounts of biological material but also to implement algorithms for its specification, design, and assembly.”
Densmore is pleased to receive IEEE validation for interdisciplinary research. “It is great that IEEE is realizing that those working in interdisciplinary fields have an important role to play in the organization and serve as ambassadors for IEEE.”
Douglas Densmore is an Affiliated Investigator in the Synthetic Biology Engineering Research Center (SynBERC), an Affiliate Faculty Member of the Department of Biomedical Engineering, and Bioinformatics faculty member. Densmore participated in the 2013 National Academy of Engineering (NAE) U.S. Frontiers of Engineering Symposium and received a National Science Foundation CAREER award.
In regards to recognition received from Boston University’s internal programs, Densmore received a 2013 Ignition Award, 2013 College of Engineer Early Career Excellence Award, and was named 2012-2014 Hariri Institute Junior Faculty Fellow. A list of Densmore’s awards, research interest, and selected publications are available on the Department of Electrical and Computer Engineering website.
“When I told my wife I was coming here to speak as a Distinguished Lecturer, she laughed and replied, ‘that just means you are growing more gray hair.’”
Professor David Lilja opened his lecture on “When Close is Good Enough: Exploiting Randomness for Highly Reliable Approximate Computing” with humor before diving into the details of his research findings. Professor Lilja is the Louis John Schnell Professor of Electrical and Computer Engineering at the University of Minnesota in Minneapolis, where he also serves as the ECE departmenthead,a member of he graduate faculties in Computer Science and Scientific Computation, and a fellow of the Minnesota Supercomputer Institute. Lilja visited Boston University as part of the Department of Electrical and Computer Engineering Distinguished Lecture Series.
In his lecture Professor Lilja related the technological movement towards miniaturized systems and the resulting need to improve energy efficiency and reliability. He proposed to use stochastic techniques for improving the cost-performance of computing operations while ensuring that the resulting solution is within acceptable limits i.e. the approximate result is close enough to the true result. In addition, Professor Lilja also addressed the issue of greater variability, defects and noise in today’s circuits due to the aggressive scaling of device technologies. He demonstrated that the proposed stochastic approach makes the circuits more tolerant to noise. In particular, any bit flips that may occur in the logic circuits do not result in large errors.
Lilja showed that a variety of functions can be implemented using the stochastic approach. He focused on four common image processing applications – edge detection, median filter noise reduction, contrast enhancement and segmentation based on kernel density estimation, and pointed out that energy-efficient approximate image processing solutions using stochastic methods would be highly suitable for cameras, for instance.
Lilja was the second speaker to be featured in the three-part Fall 2014 Distinguished Lecture Series. Next, Philippe Fauchet, Professor of Electrical Engineering, College of Engineering of Vanderbilt University will take part in the series. He will speak on the topic, “Nanoscale Silicon as an Optical Material.” His lecture will be held October 29, 2014 at 4 pm in PHO 210.
By Gabriella McNevin
By Donald Rock (COM’17)
A reader picking up Nature Methods would not expect to see an article about computer engineering. ECE Assistant Professor Douglas Densmore and BU researcher Evan Appleton have just changed that notion by publishing a paper on automated DNA assembly, which offers a computer engineering approach to synthetic biology.
The researchers’ novel methodology may profoundly affect the field of synthetic biology. If utilized, this software can help biologists build genetic constructs at greater efficiency and scale so that organisms can be more efficiently altered to act as biosensors to detect harmful chemicals in the environment or act as biotherapeuthics to produce low cost drugs for patients, or as biomaterials, such as specialized silks.
The paper entitled “Interactive Assembly Algorithms for Molecular Cloning“ describes how software can provide optimized assembly plans for genetic constructs made from numerous DNA segments. Once assembled, these DNA segments can be introduced to living organisms to alter their behavior. The software not only provides optimized plans to build these constructs, but in the event of an assembly failure, it also offers alternative plans that reuse much of the original plan. Additionally, the software allows for assembly “standards” to be followed which democratize the process across the field.
Professor Densmore is not a newcomer to interdisciplinary research. He serves as the director of BU’s Cross-disciplinary Integration of Design Automation Research (CIDAR) group. His CIDAR team works to develop computational and experimental tools for synthetic biology.
Professor Bellotti Receives Two New Grants to Develop Vertical Power Electronic Devices and Heterogeneous Computer Architectures
The Computational Electronics Group led by Professor Enrico Bellotti (ECE, MSE) has been awarded funding for two new programs to study novel power electronic devices based on III-Nitride semiconductors and to develop and evaluate heterogeneous computer architectures to simulate advanced materials and devices.
The new grant from the National Science Foundation will provide Prof. Bellotti with $336,000 over a period of three years to establish the theoretical foundation of vertical power switches based on III-Nitride semiconductors. If successfully developed, the power switches proposed in this program may lead to a number of breakthroughs in the areas of energy conversion that may profoundly change how and to what extent energy is consumed by society. First of all, these devices will aid in the implementation of the smart grid concept, delivering an unprecedented quality of service to the utilities’ customers while reducing transmission losses and increasing the capacity of these systems for wind and solar sources. In the area of transportation systems, they will enable the cost and size effective design of electric drives, not only for cars, but also for large vehicles, such as trucks or buses with immediate environmental benefits. They will reduce the development cost of electric trains, reducing the size of the motor control systems, leading to a further expansion and upgrade of local and regional railway systems.
The Army Research Office (ARO), through a DURIP Award, will provide the Computational Electronics Group with the resources totaling $150,000 to develop a heterogeneous computational hardware platform composed of distributed and shared memory systems integrated with GPUs to evaluate novel simulation methodologies for the design of electronic and optoelectronic materials and devices. Exploiting heterogeneous computing platform may significantly increase the ability of material scientists to predict novel material properties and possibly design new ones with specific properties.
For further information contact Prof. E. Bellotti at firstname.lastname@example.org