By Center For Information And Systems Engineering
The Center for Information and Systems Engineering (CISE) at Boston University invites nominations and expressions of interest for the position of CISE Resident Scholar.
The purpose of the CISE Resident Scholarship is to host emerging or eminent scientists in the Boston University campus on a short-term basis (from a few weeks up to one year) for collaborative research interactions with CISE affiliated faculty.
Faculty members or scientists in any institution worldwide are eligible to be considered for this position. CISE Resident Scholars are required to be in residence in CISE during the term of the appointment. They will be provided with an office and the Center will reimburse them for local living expenses and travel between Boston University and their home institution for an amount that does not exceed $20,000 per semester. They will have no teaching duties, although they are encouraged to deliver seminars, lead discussion groups, and engage with CISE faculty and students. Interested individuals can contact the CISE Director, Yannis Paschalidis,
About CISE: CISE is an inter-disciplinary research center bringing together faculty and students across Boston University with research interests in information and systems engineering methodologies and their relevance to a diverse set of application domains encompassing the design, analysis, control, and management of complex systems. The Center has 39 affiliated faculty, more than 100 affiliated graduate students and on the order of $6.6 million of annual research expenditures from sponsored research directed by CISE faculty. CISE faculty affiliated members have homes in a number of academic units at Boston University including Engineering (Electrical & Computer, Mechanical, Biomedical, and Systems), Math and Statistics, Computer Science, and the School of Management.
Ioannis Ch. Paschalidis
Professor and Distinguished Faculty Fellow
Department of Electrical and Computer Engineering
Division of Systems Engineering
and Department of Biomedical Engineering
Director, Center for Information and Systems Engineering (CISE)
8 St. Mary’s Street
Boston, MA 02215
Massachusetts awards $3 million to BU-led project
By Rich Barlow
With the governor of Massachusetts pledging $3 million in state support, BU leaders Friday announced plans for development of a pathbreaking computing cloud that could spur economic growth and technology innovation.
Azer Bestavros (CS, SE), director of BU’s Rafik B. Hariri Institute for Computing and Computational Science & Engineering, says the University will spend the next three years developing software for the Massachusetts Open Cloud (MOC) in collaboration with the commonwealth, technology companies, and BU’s university partners at the Massachusetts Green High Performance Computing Center(MGHPCC) in Holyoke, where the announcement was made.
In cloud computing, users rent access to massive off-site computational power. Companies such as Amazon and Google offer clouds; like those, the MOC would be public, meaning anyone could purchase computing power. But unlike those closed clouds (each operated by a single provider), the MOC would be open to multiple vendors of software, hardware, and computer services, all of whom would have access to operational data about the MOC: what programs were running on it, as well as any performance or problem reports.
No such public, open cloud currently exists. “The MOC will be the first realization of this model,” says Orran Krieger, director of the Cloud Computing Initiative at the Hariri Institute, who will lead the MOC development. “If it’s successful, we expect other clouds to follow our model, fundamentally changing the nature of cloud computing.” Krieger is also a College of Arts & Sciences research professor of computer science.
The plan calls for hosting the MOC at the MGHPCC data center, where it would tap the computational power of BU and its MOC partners, who have jointly contributed $16 million to MGHPCC, leveraging the $3 million matching grant from the state. Besides the participating universities, MOC partners are tech firms Red Hat, Cisco, EMC, Juniper Networks, SGI, Mellanox, Plexxi, Riverbed, Enterprise DB, Cambridge Computer Services, and DataDirect Networks.
“Investing in innovative sectors that are becoming a prominent part of our economy is critical to meeting the demands of the 21st century,” says Greg Bialecki, Massachusetts housing and economic development secretary.
Bestavros, who is also a CAS computer science professor, compares the MOC to a shopping mall, whose physical mall would be the MGHPCC, eliminating the expense of building a separate data center. And with the MGHPCC’s university partners doing research that could use the MOC, the Holyoke center is “a little petri dish in which the MOC could develop,” says center executive director John Goodhue.
The MOC’s corporate partners would be the equivalent of mall stores, selling their products and services at the Holyoke center. Banding together in a mall-like organization would permit them collectively to draw enough traffic, leveraging economies of scale, Bestavros says. The vendors’ customers would range from academic researchers to corporations and others. For example, Harvard is one of the MGHPCC partners helping to develop the MOC; its Research Computing [https://rc.fas.harvard.edu/] arm, the conduit to computing services for the Faculty of Arts and Sciences, is planning on using the MOC as “one part of our strategy to provide lasting computer resources to our faculty and researchers,” says James Cuff, Harvard’s assistant dean for research computing.
The MOC concept of a cloud marketplace grew out of BU research in 2009. In a recent paper, Bestavros and Krieger argue that closed clouds usually have a single provider, who “alone has access to the operational data.” For this and other reasons, they write, “in the long run, if only a handful of major providers continue to dominate the public cloud marketplace, then any innovation can only be realized through one of them.”
With a cloud designed like the MOC, their paper says, “many stakeholders, rather than just a single provider, participate in implementing and operating the cloud. This creates a multisided marketplace in which participants freely cooperate and compete with each other, and customers can choose among numerous competing services and solutions.”
Another advantage: an open cloud would be more secure than a closed one, Bestavros and Krieger say. It is “the best way to make sure that software is clean,” according to Bestavros, especially as American tech companies complain that federal computer snooping might scare off billions of dollars’ worth of cloud computing customers. With a public, open cloud like the MOC, “the National Security Agency cannot put backdoors in an open-source code, because you can see what the software is doing,” he says.
The state money is a matching grant from the Massachusetts Technology Collaborative, and it will pay for developing software and equipment for the MOC. “The commonwealth’s participation allows BU to create a neutral ground that allows the industry and university partners to collaborate in an area where they also compete,” the MGHPCC’s Goodhue says. That is, the money will pay for development of software that all the MOC investors can use, so that “no partner will be advantaged more than any other.”
Patrick Larkin, director of the Innovation Institute at the Massachusetts Technology Collaborative, the source of the state grant, says the MOC will be “a virtual sandbox that will empower the commonwealth’s researchers, start-ups, industry, and the public sector to explore, develop, and release big data and cloud computing innovations.” Those innovations could spur discoveries spanning the state’s economy, he says, “such as transportation, health care, energy, finance, life sciences, and manufacturing.”
For the past 16 years, Christina worked for the American College of Greece where she established and developed the Department of Communication, the first of its kind in Greece. There, she served as Department Head and Professor and her responsibilities included developing research seminars, advising students, organizing symposiums, etc. Christina earned her B.S. in Business Administration from the BU School of Management and her M.S. in International Communication from the BU College of Communication.
Christina’s phone number at CISE is 617-358-1295. Her email address is cpolyzos at bu.edu. She will be at the CISE Awards and Pizza party this Wednesday at 3:00 in the lobby of 15 Saint Mary’s St.
Please stop by to honor all CISE students who presented posters at BU Scholars day and take the opportunity to meet Christina.
The new IEEE journal Transactions on Control of Network Systems has released its inaugural issue. This publication is available on the IEEE Xplore site. View the table of contents and list of authors.
Congratulations to Ioannis Paschalidis (SE, ECE), Editor-in-chief, and Magnus Egerstedt, Deputy Editor-in-Chief!
Included in this inaugural issue is a paper by Christos G. Cassandras (SE, ECE), Tao (Reno) Wang (SE PhD, 2013), and Sepideh Pourazarm (SE PhD graduate student), Optimal Routing and Energy Allocation for Lifetime Maximization of Wireless Sensor Networks with Non-ideal Batteries. Congratulations to all!
Finding Could Open Up New Drug Discovery Opportunities
By Mark Dwortzan
Over the past six years, an interdisciplinary team of College of Engineering faculty members—Professor Sandor Vajda (BME, SE), Research Assistant Professor Dima Kozakov (BME), Professor Yannis Paschalidis (ECE, SE) and Associate Professor Pirooz Vakili (ME, SE)—have been developing a set of powerful optimization algorithms for predicting the structures of complexes that form when two proteins bind together—structures that, in some cases, generate erroneous cell signaling pathways that can trigger cancer and other inflammatory diseases.
Incorporated into Vajda’s and Kozakov’s protein-protein docking server ClusPro—a website to which any user can submit the three-dimensional coordinates of two proteins and receive a supercomputer-calculated prediction of the structure of the complex formed by those proteins—these algorithms have enabled more than 3,000 research groups across the globe to better understand the inner-workings of the cell and explore potential drug targets without having to run expensive, time-consuming lab experiments.
Now the research team behind these algorithms has, through lab experiments and computational analysis, obtained a sharper understanding of how two proteins come together to form a complex, and plans to apply that knowledge to boost the speed and accuracy of ClusPro’s predictions. They and collaborators from the Hebrew University of Jerusalem and the National Institutes of Health (NIH) report on this new development in a new article in eLife, an open source journal for outstanding biomedical research.
A joint effort of Boston University’s Center for Information and Systems Engineering and Biomolecular Engineering Research Center supported by a five-year, $1.6 million grant from the NIH, the project combines Paschalidis’ and Vakili’s expertise in optimization and systems theory with Vajda and Kozakov’s knowledge of biophysics and bioinformatics.
“The research was a beautiful combination of physics with mathematics,” said Paschalidis. “We leveraged techniques popular in control systems developed to describe movement of complex 3-D objects, such as a robot arm, as well as machine learning methods used to analyze large data sets.”
“Preventing proteins from binding to the wrong partners is an increasingly prominent concept in drug design,” said Janna Wehrle, PhD, of the NIH National Institute of General Medical Sciences, which partially funded the research. “These new computational methods developed by the Boston University team will help researchers quickly discover both healthy protein pairs and disease-causing pairs that we might want to break up.”
Until now, scientists were unable to characterize how protein-protein complexes form from two individual proteins—each analogous to a distinctly-shaped Lego block—because their interactions from the moment they come in contact to the moment they “snap into place” were too fast to detect. But an emerging nuclear magnetic resonance (NMR) technique has made it possible to track their rapidly changing configurations from rendezvous to docking using radio waves.
Applying this technique, the College of Engineering team determined that its protein-protein docking algorithms were already generating these exact transitional states, but labelling them as “false positives” alongside the correctly identified final protein-protein complex.
“What we have so far been calling false positives are ‘transient encounter complexes,’ temporary structures the proteins form as they ‘search’ for the one orientation that will enable them to bind successfully,” said Paschalidis.
All protein-protein encounter complexes are characterized by low energy, with the lowest energy expected to occur at the final, stable complex. By systematically analyzing the energy values corresponding to the transient complexes, the researchers found that with each successive interaction, the intersecting proteins have fewer and fewer ways to twist and turn, thereby accelerating their path to binding. This explains how two proteins can dock very quickly despite the many nooks and crannies that must line up to seal the deal.
The College of Engineering team next aims to exploit its findings to make its docking algorithms faster and more accurate. The researchers also plan to examine the implications of their work for protein-DNA and protein-small molecule interactions that are important in genetic regulation and drug discovery, respectively.
See movie of transient protein-protein encounter complexes.
Nathan Phillips on what we must do to fix decrepit gas lines
By Rich Barlow
A gas leak that left at least seven dead and dozens injured or missing in Harlem earlier this month has given Nathan Phillips’ research a tragically prophetic hue. For years, the College of Arts & Sciences professor of earth and environment has crisscrossed the road grids of major American cities, documenting thousands of leaks in the country’s aging gas lines (3,300 in Boston alone).
Nathan Phillips (SE, ECE, Earth & Environment) has warned that the worst of these gas geysers pose explosion risks. In the case of the Harlem leak, residents had smelled gas for weeks. The blast leveled two buildings and reverberated more than a mile away. New York utility company Con Edison said it had repaired the only reported leak on the block last May and found no leaks during a survey in February. US Senator Edward Markey (Hon.’04) (D-Mass.) has proposed legislation to fast-track repairs to leaking gas lines.
Gas leaks also contribute to climate change, cost ratepayers millions, and kill or damage countless trees in urban areas, Phillips says. Utilities scramble to fix the worst leaks, but must prioritize repairs, given the Swiss-cheese holes in pipes, says Phillips, who discussed the situation—including the potential danger in our nation’s capital, where he looked for leaks last year—with BU Today.
BU Today: Have you ever hunted for gas leaks in New York City?
Phillips: I have not personally, but my research collaborator, Bob Ackley, has, using our BU sniffer. There are definitely leaks there, associated with old cast iron and bare steel pipes. The pipe that exploded in Harlem was eight-inch cast iron from 1887, according to news reports.
Does the Harlem explosion and the resulting deaths make the need to repair leaking lines even more critical than you thought?
Yes. This was the kind of tragic failure that unfortunately often is the kind of event it takes to spur concerted action and awareness of gas safety.
Do you think the Harlem blast will in fact spur action on fixing lines? Or as with similar previous tragedies, will this fade from the headlines and public awareness?
I am hopeful that we are moving in the direction of solving the issue of gas leaks and all their ramifications, rather than just slipping back into complacency. And I feel that there are factors that will make progress stick. These include the mapping technology that we have used to make this issue known to the public at large, a technology that is only increasing in its use across cities and towns and over time. The cat is out of the bag with sensing and mapping gas leaks, and this will put increasing pressure on us to address the problem.
More broadly, I am hopeful that as our cities become “smarter,” we will develop coordination in our attention to our critically interdependent infrastructures, what we call our “infrastructure ecology.” Information technology increasingly allows us to monitor, coordinate, and harmonize how we manage and repair our systems of water, sewer, gas, electricity, and roadwork. We have the ability to surgically and at the same time, holistically, address our city infrastructure, like the amazing strides medicine has made in treating the human body. The barriers are largely ones of political ecology, not technology. Agencies and institutions—utilities, public works departments—need to connect and cooperate to harmonize how infrastructure works.
Does this tragedy suggest that utility companies can’t be counted on to solve this problem without public subsidies and/or mandates to fix the infrastructure?
The utilities are surely a major player, but it is too easy to point the finger solely at this one entity. We live in aging cities, and that is no one’s fault; it’s just a fact. The pipelines that run under our streets and sidewalks are an issue that the public needs to confront and address, and put some level of skin in the game, including, potentially, financial. Right now the incentives need to be better aligned to promote the utilities to also put more skin in the game. The costs associated with lost and unaccounted-for gas have been passed along to consumers. If utilities don’t bear any costs for leaks, they have no real incentive to fix them. In part resulting from our work in Boston, state and federal legislation has been proposed to align these incentives.
You probed for leaks last year in Washington, D.C. How many did you find and how severe were they?
In D.C., we found the situation is the same, if not more severe, than Boston. The number of leaks was almost 6,000, which is about the same as Boston’s 3,300-odd leaks, when considering the road miles are about the same in leaks per mile. If anything, D.C. had higher values of air concentration of natural gas.
By Mark Dwortzan
Cassandras Delivers Distinguished Scholar Lecture
For 30 years, Professor Christos Cassandras(ECE, SE) has solved countless complex problems by translating them into simpler terms and then applying optimization, computer simulation and other tools of the systems engineering trade. A pioneer in the field of discrete event dynamic systems analysis, used extensively in the development and operation of manufacturing, transportation, communications and other complex systems, he has laid the mathematical groundwork for everything from swarms of surveillance robots to hassle-free Smart Cities.
On March 19, Cassandras shared some of the most powerful techniques in his problem-solving toolkit in the 2014 College of Engineering Distinguished Scholar Lecture, “Complexity Made Simple* (*at a Small Price).” Speaking from the podium at the Boston University Photonics Center Auditorium, he addressed students, faculty and researchers from throughout the BU academic community and beyond.
Complexity Made Simple
Focusing his remarks on the optimal design, control and management of complex dynamic systems, Cassandras highlighted methods he’s developed to solve difficult problems by exploiting their specific structure and asking the “right” questions. He demonstrated how these methods outshine conventional engineering approaches, resulting in time and cost savings, enhanced security and other benefits.
Cassandras first challenged the effectiveness of “brute force” trial-and-error techniques, which are often used to systematically learn and predict the behavior of a complex system, but are invariably slow, inefficient and intrusive. He showed how this learning could be achieved far more quickly through simple “thought experiments” constructed at a “small price.” For example, rather than expend hundreds of years of manpower manually testing different alternative configurations of a manufacturing transfer line to improve its efficiency, he explained, one could model the system’s performance with algorithms that evaluate multiple scenarios in less than an hour in a single, low-cost run.
Cassandras next explored two methods to reduce the complexity of a system to make it easier to model: decomposition, or breaking down a complex system into simpler components, and abstraction, or zooming out to a far less detailed representation of the system. Decomposition can provide fast, accurate solutions to difficult problems; abstraction can dramatically simplify such problems at the “small price” of some loss of accuracy.
“Can the abstraction model be used to predict the real system’s behavior? Bad question,” said Cassandras. “Can the abstraction model be used to control or optimize the real system’s behavior? Good question.”
Finally, he challenged conventional time-driven methods for sampling, control and communication in wireless, networked systems. Noting how communication actions dictated solely by clock time drain precious battery power, exacerbate security risks and are often unnecessary, he argued that these actions could instead be triggered by specific events at the “small price” of identifying suitable action-triggering events. To illustrate the point, he showed how communication among a team of cooperating robots patrolling a defined space could be minimized to achieve a specified goal while saving energy and enhancing security.
Cassandras concluded the lecture by highlighting his ongoing efforts to design Smart Cities that collect data, process information, make decisions and control and optimize actions aimed at making urban life easier, safer and more efficient. He also announced a new endeavor to model the progression of cancer as a discrete event system.
“My hope is to turn this into a new direction of research where discrete event systems analysis can be applied to see how treatment and therapies can be used by simulating how cancer progresses with real data, and play what-if games with drugs,” he said.
Three Decades of Taking on Complexity
A member of the BU faculty since 1996, head of the College’s Division of Systems Engineering and cofounder of BU’s Center for Information and Systems Engineering (CISE), Cassandras has published five books and more than 300 refereed papers. He was editor-in-chief of the IEEE Transactions on Automatic Control from 1998 through 2009, and the 2012 president of the IEEE Control Systems Society (CSS). He has chaired several technical conferences and served as plenary speaker at various international conferences, including the American Control Conference in 2001 and the IEEE Conference on Decision and Control in 2002, and Distinguished Lecturer for the CSS.
Cassandras’s numerous awards include a 2012 Kern Fellowship, a 2011 prize for the IBM/IEEE Smarter Planet Challenge competition, the 2011 IEEE Control Systems Technology Award, the Distinguished Member Award of the IEEE Control Systems Society (2006), the 1999 Harold Chestnut Prize (International Federation of Automatic Control (IFAC) Best Control Engineering Textbook) for Discrete Event Systems: Modeling and Performance Analysis, and a 1991 Lilly Fellowship. He is also a Fellow of the IEEE and IFAC.
Initiated in 2008, the annual Distinguished Scholar Lecture Series honors a senior faculty member engaged in outstanding, high-impact research at the College of Engineering. The previous five recipients are Professors Thomas Bifano (ME, MSE), H. Steven Colburn (BME), Theodore Moustakas (ECE, MSE), Irving Bigio (BME) and John Baillieul (ME, SE), and Professor Emeritus Malvin Teich (ECE, BME).
By Mark Dwortzan
Assistant professors James C. Bird (ME, MSE), Ahmad (“Mo”) Khalil (BME) and Mac Schwager(ME, 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 more than $1.5 million over the next five years to pursue high-impact projects that combine research and educational objectives.
Bird intends to apply his CAREER award to explore how submicron aerosol droplets are formed from small bursting bubbles. Using direct, high-speed observations, numerical simulations and experimental models, he will seek out the primary mechanism behind this phenomenon. Because these droplets can persist in the atmosphere for weeks, pinpointing this mechanism is important in engineering applications ranging from turbine corrosion to the dispersion of respiratory diseases.
Bird’s research may also improve models used to predict the progression of global climate change.
“On a global scale, a better understanding of aerosol production is necessary to reduce uncertainty in global climate models,” said Bird, “and will allow policy makers to better assess the risks and rewards of geoengineering mitigation strategies, such as deliberately injecting large amounts of sulfur particulates into the atmosphere in hopes of countering the warming effects of greenhouse gases.”
Khalil will use his CAREER award to better understand the mechanisms underlying how organisms adapt to changing environments, a classic problem in evolutionary biology. The goal of his project will be to test a theory that prions—proteins that can switch between multiple conformational states or shapes—equip microbes with an enhanced capability to survive under fluctuating environmental conditions. Khalil will develop microfluidic systems to study prion behavior and synthetic biology methods to optimize their adaptive properties.
“This work will have broad implications for our basic understanding of evolution, development and cellular systems,” said Khalil. “The project will also shed light on the diverse roles of prions, unique elements that are emerging to be common in the microbial world, and have a transformative impact on synthetic biology, enabling new schemes for rationally engineering a wide array of cellular functions.”
Khalil also aims to inspire and train students to explore how engineering approaches can be applied to better understand how life works, through a “systems & synthetic biology boot camp” for high school students, related high school design challenges to be facilitated by College of Engineering Inspiration Ambassadors, undergraduate research opportunities through the International Genetically Engineered Machine (IGEM) synthetic biology competition, a new integrated course on quantitative systems biology, and other educational activities.
Schwager’s CAREER award will support his efforts to develop algorithms enabling groups of robots to control harmful ecological phenomena such as forest fires, oil spills and agricultural pest infestations. Schwager’s research aims to use a group of robots not only to sense an environment (a passive operation typical of most of today’s research on multi-robot coordination), but also to control the evolution of processes in the environment. He plans to demonstrate the viability of his control strategies through laboratory and outdoor experiments with a network of quadrotor aerial robots.
“Ultimately, the project seeks to alleviate the economic, societal and ecological damage caused by destructive environmental phenomena by laying the foundations of a new robotic technology,” said Schwager.
He also plans to bring quadrotor robots into the classroom to illustrate the principles of feedback control by partnering with the Technology Innovation Scholars Program (TISP). The goal is to engage students from diverse backgrounds at all grade levels and to stimulate their interest in robotic solutions to environmental stewardship.
To date, 37 College of Engineering faculty members have received NSF CAREER awards during their service to the College.
Lucy Hutyra and Robert Kennedy selected to serve on Science Steering Group of the North American Carbon Program
Department of Earth & Environment Assistant Professor Lucy Hutyra and Assistant Professor Robert Kennedy have been selected to serve on the Science Steering Group of the North American Carbon Program (NACP).
As part of their service, Hutyra and Kennedy will be in Washington DC today and tomorrow, February 18th and 19th, to meet meet with fellow members of the Science Steering Group to discuss issues related to the North American Carbon Cycle.
Working with representatives of the federal agencies that fund and support carbon cycle science, the Science Steering Group meets roughly twice a year to discuss and advance the science and understanding of the North American Carbon Cycle.
Tao (Reno) Wang (SE, PhD, 2013) was selected as one of the New Faces of Engineering 2014. New Faces of Engineering recognizes the outstanding abilities young engineers (age 30 or younger) have shown on projects that significantly impact public welfare or further professional development and growth.
The award is based on the evaluation of the candidates’ background and their contribution to the community. Wang’s achievements during his PhD study at Boston University with adviser Professor Christos G. Cassandras (SE, ECE), played a vital role in the nomination.
Wang, 30, is a senior operations research developer, developing Sabre AirCenter products for crew management systems including pairing optimizer and crew control/manager, serving 20+ airlines. His work focuses on adding novel features to the products and improving the efficiency of scheduling algorithms. Wang holds a BS from Shanghai Jiaotong University (China), a master’s from Georgia Institute of Technology, and a PhD from Boston University.