Attendees Celebrate New IEEE Journal Edited by ENG’s Paschalidis
By Mark Dwortzan
Microbes are all around us—even inside us—and that’s a good thing. Left alone, these tiny organisms have a huge impact on everything from human health to wastewater treatment. But with a little engineering, they could do even more. In certain environments, their metabolic processes could be exploited to make biofuels, vaccines and other useful products and services. To tap their potential, Associate Professor Daniel Segrè (Biology, BME, Bioinformatics) and collaborators have developed mathematical models to predict the metabolic interactions that occur among different microbial species under varying environmental conditions, and to design new microbial networks with desired properties.
Sponsored by the IEEE Control Systems Society and the Center for Information and Systems Engineering at Boston University, SCONES celebrated the inaugural March 2014 issue of theIEEE Transactions on Control of Network Systems(TCNS), a new IEEE Transactions journal edited by Professor Yannis Paschalidis (ECE, BME, SE) focused on problems related to the control, design, study, engineering, optimization and emerging behavior of network systems.
“We live in a world that is extremely interconnected,” said Paschalidis, the journal’s editor-in-chief. “This is also true of systems, biological or manmade, that support our modern way of life. Networks, which both connect system components and influence how they function as a whole, are increasingly the focus of leading edge research, and this is the impetus forTCNS and SCONES.”
One author of each paper in the inaugural issue presented at the symposium, along with talks and posters from several other researchers in the field.
Representing major research institutions from around the world, SCONES presenters explored the analysis, control and optimization of electric power, computer, communication, transportation, biological, cyber-physical, social and economic networks. As if bringing the TCNS journal to life, the 23 featured speakers illustrated complex concepts with a flurry of equations, algorithms, graphs and diagrams.
“TCNS aspires to become the premiere destination for mathematically rigorous work in network systems,” said Magnus Egerstedt, an ECE Professor at Georgia Tech and the TCNS deputy editor-in-chief—and the SCONES presenters lived up to that promise.
In addition to Segrè, two other Boston University researchers shared highlights of papers they co-authored in the inaugural issue of TCNS on resource allocation and routing, the selection of optimal path by which to transmit information across the nodes of a network.
Professor Lev Levitin (ECE, SE) presented an alternative to wormhole routing, a widely used routing technique that’s prone to deadlock—multiple messages getting blocked by one another in a vicious cycle—under heavy computer network traffic. Levitin described a series of new, high-performance algorithms that he, Professor Mark Karpovsky (ECE) and ECE Visiting Researcher Mehmet Mustafa developed to break such cycles and prevent deadlock formation during routing and thus preserve network connectivity.
Professor Christos Cassandras (ECE, SE) presented an optimal control strategy that he, Tao Wang (SE, PhD’13) and Sepideh Pourazarm (SE, PhD candidate) devised to maximize the lifetime of sensor batteries deployed at each node of a wireless sensor network for surveillance, environmental monitoring or other applications where human intervention may be inconvenient or costly.
“Because every node has limited energy, you have to worry about the battery dying and the network ceasing to function,” said Cassandras, “so you need to focus on battery lifetime.”
Modeling each battery as a dynamic system in which energy does not dissipate in a linear fashion, the strategy uses an algorithm to determine the routing scheme that will minimize that energy loss.
The symposium, which was well-attended and featured many fruitful exchanges between speakers and attendees, signified how well the TCNS journal has been received by the international research community, Paschalidis observed.
“In the first three TCNS issues published in 2014, we have seen papers covering many types of network systems, from networked control and multi-agent systems, to communication, transportation, electric power, biological and social networks,” he noted. “SCONES is playing a key role in coalescing a community of researchers around the journal.”
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.
Alum’s Company Boosts Customer Loyalty Using Indoor Location Technology
By Mark Dwortzan
Imagine you’re strolling through the aisles of a supermarket and just as you approach your favorite pasta sauce, a virtual “buy one, get one free” coupon for the product, redeemable at checkout, appears on your smartphone. Rather than having you page through a weekly compilation of in-store offers—that’s so 20th century—the store has delivered the coupon directly to your phone based on your current location and shopping history.
Making this possible are standard overhead LED lights that not only illuminate the room but also function as an indoor GPS. Enhanced with microchips, the bulbs contain sophisticated software that causes them to flicker fast enough to transmit a distinctive, information-rich signal that a smartphone camera can detect and a retailer’s mobile app can decode.
In just three years, the Boston-based startup that developed the software, ByteLight, has become a market leader in indoor location solutions, a burgeoning industry enabling mobile device users to access discounts, directions, and other highly targeted services at precise locations within buildings. Energized by a recent influx of $3 million from investors, ByteLight is piloting its technology at several global retailers, including 3 of the top 10 big-box stores, as well as at 100 stores in China.
Spearheading this success story is ByteLight’s CEO, Daniel Ryan (ENG’10), who cofounded the company with classmate Aaron Ganick (ENG’10) in 2011 based on concepts they studied and implemented as research assistants in ENG professor of electrical and computer engineering Thomas Little’s NSF Smart Lighting Engineering Research Center. Inspired to pursue careers in electrical engineering by childhood visits to Boston’s Museum of Science, Ryan and Ganick devised ByteLight’s core technology in the lab, developed a prototype and business plan in the technology incubator space at the BU Photonics Center and Highland Capital Partner’s Summer Program, and then raised sufficient capital to launch the company. While Ganick moved on last year to pursue other endeavors, Ryan continues to grow ByteLight to meet a surging demand for its unique indoor location solution.
It’s a demand driven partly by the rapid adoption of LEDs, and partly by the product’s market-leading accuracy, responsiveness, and reliability. LED lights equipped with ByteLight software can pinpoint a mobile device user’s location to within one meter in less than a second—far outpacing the performance of other indoor positioning systems developed by industry giants, including Apple and Google, that triangulate distances between hotpots and handsets on wireless networks.
“Sub-meter accuracy has long been the holy grail for retailers experimenting with indoor location,” says Ryan. “With ByteLight, retailers finally have the opportunity to install a wall-to-wall solution that just works.”
Also lifting ByteLight above its competitors are its low infrastructure cost and compatibility with all mobile devices. Unlike other solutions that require additional hardware such as WiFi hotspots or Bluetooth beacons, ByteLight software exploits an existing and ubiquitous infrastructure: overhead lighting. ByteLight not only uses light waves to transmit useful information to smartphone-toting customers at specific locations, but also to quickly and securely verify their presence for loyalty programs, mobile payments, and more at “tap-and-go” check-in and check-out locations equipped with the company’s Light Field Communication readers. Compatible with all smartphones, the ByteLight readers cost five percent as much as the increasingly popular Near Field Communication (NFC) readers, which use radio signals to process such transactions and work only with a limited set of mobile devices.
Once integrated into a retailer’s app and LED lights, ByteLight software promises to boost customer loyalty and sales by delivering personalized savings from store shelf to checkout. Since ByteLight technology was introduced in 100 stores in China, the stores have seen a 30 percent increase in loyalty reward redemptions.
“Brick-and-mortar retailers are demanding new solutions that can leverage digital assets within physical store locations to engage and retain customers,” says Don Dodge, developer advocate at Google and an industry leader in indoor location technology. “ByteLight’s indoor location solutions assist retailers with delivering hyper-targeted information and content to customers on mobile devices within their stores based on the device’s precise location. More importantly, these solutions fully integrate physical commerce with eCommerce to give retailers an omni-channel offering.”
ByteLight’s primary focus is on the retail industry, but the company’s technology could also be deployed in venues ranging from museums—including Boston’s Museum of Science, where ByteLight is used in one exhibit to display location-sensitive content—to factories to airplanes. To expand the company’s repertoire, ByteLight provides its customers with a software development kit they can use to invent new applications for the software-enhanced lights. In the coming years, as the use of LED lighting and mobile devices continues to grow, Ryan envisions integrating ByteLight technology into stadiums, conference centers, schools, office buildings, hospitals, and other domains.
Little, who is also affiliated with ENG’s division of systems engineering, served as mentor to Ryan during his undergraduate years, and is now an advisor to the company. He is bullish about his former student’s prospects. “Dan is an exceptional individual who epitomizes what engineering school is all about—learning to solve problems. Any problem,” says Little. “And to be adaptable and agile in a continuously changing technological world. He has demonstrated the ability to deliver a product coupled with software integration and analytics that support a complex supply and distribution chain with diverse market stakeholders.”
In his role as ByteLight’s CEO, Ryan draws on engineering, entrepreneurial, and interpersonal skills that he cultivated at ENG, where he helped launch a small satellite while participating in the BU Student Satellite for Applications and Training (BUSAT) program, took an ENG/SMG course in entrepreneurship, and served as the Class of 2010 Commencement speaker. Today, as he steers ByteLight toward a rollout in US stores from a new office in Boston’s Fort Point Channel neighborhood, Ryan finds himself applying these skills to solve a full spectrum of problems.
“Each day brings a new problem, ranging from product development to technology to new competition,” he says. “The key to responding effectively and moving forward through the chaos is your team. It’s that simple. At ByteLight, we’ve been fortunate to build an incredibly talented core of technologists to take our vision and turn it into reality.”
One of Ryan’s valued team members is former classmate, Manny Malandrakis (ENG’10), one of the first ENG alumni to become a ByteLight employee. He focuses on digital signal processing and communications systems, the subject of two courses he took as an undergraduate.
“These classes were the foundation of this company,” says Ryan. “We’re leveraging the core theories and techniques we learned in these courses every day.”
Mark Dwortzan can be reached at firstname.lastname@example.org.
A version of this story was originally published in the spring 2014 edition of Engineer.
Imagine two hiring managers sizing up an applicant. The first gathers all the information she can before forming a first impression. The second collects the bare minimum but does so strategically, arriving at virtually the same impression with far less effort and in far less time.
It turns out that the latter approach can be taken to produce reasonably accurate photos of objects under low lighting conditions using a remote sensing technology such as LIDAR, which bounces pulsed laser light off of a targeted object to form an image. Rather than waiting to collect and compare hundreds of reflected photons to generate each pixel of the image, as is typically done, you can instead count the number of laser pulses it takes to detect the first photon at each pixel. The lower the number, the greater the intensity of the light reflected off the object’s surface — and thus, the brighter the pixel.
Assistant Professor Vivek Goyal (ECE), who joined the College of Engineering faculty in January, and who, along with former colleagues at MIT’s Research Laboratory of Electronics, demonstrated the concept in a recent issue of the journal Science, calls his method “first-photon imaging.”
“The project started out as a thought experiment,” said Goyal, whose research was funded by the Defense Advanced Research Projects Agency’s (DARPA) Information in a Photon Program, and the National Science Foundation. “We wondered what we could infer about a scene from detecting only one photon from each pixel location, and eventually realized that when the intensity of light is very low, the amount of time until you detect the photon gives you information about the intensity of the light at each pixel.”
First-photon imaging may ultimately improve night vision and low-light remote sensing technologies by extending the distance at which images may be taken. The new method may also dramatically increase the speed of biological imaging and the variety of samples — many of which degrade when subjected to higher-intensity lighting — that can be photographed.
To produce a high-quality image from the raw, single-photon-per-pixel data, Goyal’s method applies a computer model of surfaces and edges typically encountered in three-dimensional, real-world objects, correcting the intensity and depth of neighboring pixels as needed to fit the model; and filters out noise coming from ambient light sources.
While many researchers are pursuing new techniques to boost remote sensing and microscopy capabilities, most focus on building more effective detectors. Goyal is working to significantly enhance existing detectors by incorporating accurate physical models in signal processing, and to further explore the potential impact of first-photon imaging on remote sensing and microscopy.
Over the last few weeks, nearly 20 million Americans tried accessing a broken United States health care site that couldn’t handle the traffic, among other problems. And even if you weren’t one of the many applying for health coverage, you’ve probably experienced network congestion at some point.
Typically, network congestion occurs if a link or node is carrying too much data; as a result, the quality of service drops. The most severe form of communication disruption is deadlocks. A deadlock happens when several messages mutually block each other so that their delivery is not just delayed but stopped permanently.
“This is a long-standing problem, which is practically important and theoretically challenging,” said Distinguished Professor Lev Levitin (ECE, SE). “It has been attracting the efforts of many researchers for decades.”
Professors Levitin and Mark Karpovsky (ECE) have been working with their students on this problem for several years, developing new algorithms, specifically turn prohibition algorithms, to help direct data and essentially prevent information from being stuck in a deadlock as it travels through communication networks. This work covered a lot of ground by establishing lower and upper bounds for an optimal solution, outlining their discovery of a new class of algorithms, and developing a few algorithms that could actually solve the initial optimization problem.
The last advance on this project was achieved this year by Levitin and his team – ECE alum, Ye Wu (MEng ’13), and Visiting Scholar, Mehmet Mustafa. They have been working on developing new algorithms, specifically turn prohibition algorithms, to help direct data and essentially prevent information from being stuck in a deadlock as it travels through communication networks.
“Without changing the topology of existing networks, we managed to improve saturation points so that congestion is less likely to happen and latency is reduced which means lower waiting time for users,” said Wu.
The team recently presented their work at OPNETWORK 2013, a conference that focused on advancing the state of application and network performance management. Impressed by their research, “A Study of Modified Turn Prohibition Algorithms for Deadlock Prevention in Networks,” the judges awarded them Best Technical Paper.
“Computer experiments, executed earlier and in the latest work by Ye Wu and other students under the guidance of Dr. Mustafa, clearly showed the superior performance of our algorithms versus different algorithms suggested by other research groups,” said Levitin. He went on to add that the majority of publications in the field are on ad hoc algorithms as opposed to the “tree-free” algorithms he and his team explored.
The work gave Wu a chance to travel to Washington, D.C., and deliver the presentation at the Ronald Reagan Building and International Trade Center.
“I met some really nice students and professors from different countries who were happy to talk about their research,” said Wu. “The audience, I think, was also smart enough to understand the key points of our project and asked really good questions.”
Now a Boston University graduate, Wu looks back at his professor fondly, describing Levitin as open-minded, even when his student was questioning his own theories.
“Professor Levitin is the best professor I’ve ever known,” said Wu. “Even when we had no idea how to begin a project, he’d point us in the right direction.”
-Rachel Harrington (email@example.com)
New Laser Technique Boosts Accuracy of DNA Sequencing Method
Low-cost, ultra-fast DNA sequencing would revolutionize healthcare and biomedical research, sparking major advances in drug development, preventative medicine and personalized medicine. By gaining access to the entire sequence of your genome, a physician could determine the probability that you’ll develop a specific genetic disease or tolerate selected medications. In pursuit of that goal, Associate Professor Amit Meller (BME, MSE) has spent much of the past decade spearheading a method that uses solid state nanopores — two-to-five-nanometer-wide holes in silicon chips that read DNA strands as they pass through — to optically sequence the four nucleotides (A, C, G, T) encoding each DNA molecule.
Now Meller and a team of researchers at Boston University — Professor Theodore Moustakas (ECE, MSE) and research assistants Nicolas Di Fiori (Physics, PhD ’13) and Allison Squires (BME, PhD ’14) — and Technion-Israel Institute of Technology — have discovered a simple way to improve the sensitivity, accuracy and speed of the method, making it an even more viable option for DNA sequencing or characterization of small proteins.
In the November 3 online edition of Nature Nanotechnology, the team demonstrated that focusing a low-power, commercially available green laser on a nanopore increases current near walls of the pore, which is immersed in salt water. As the current increases, it sweeps the salt water along with it in the opposite direction of incoming samples. The onrushing water, in turn, acts as a brake, slowing down the passage of DNA through the pore. As a result, nanoscale sensors in the pore can get a higher-resolution read of each nucleotide as it crosses the pore, and identify small proteins in their native state that could not previously be detected.
“The light-induced phenomenon that we describe in this paper can be used to switch on and off the ‘brakes’ acting on individual biopolymers, such as DNA or proteins sliding through the nanopores, in real time,” Meller explained. “This critically enhances the sensing resolution of solid-state nanopores and can be easily integrated in future nanopore-based DNA sequencing and protein detection technologies.”
Slowing down DNA is essential to DNA or RNA sequencing with nanopores, so that nanoscale sensors, like sports referees, can make the right call on what’s passing through.
“The goal is to hold a base pair of DNA nucleotides in the nanopore’s sensing volume long enough to ‘call the base’ (i.e, determine if it’s an A, C, G or T),” said Squires, who fabricated nanopores and ran experiments in the study. “The signal needs to be sufficiently different for each base for sensors in the nanopore to make the call. If the sample proceeds through the sensing volume too quickly, it’s hard for the sensors to interpret the signal and make the right call.”
Other methods designed to slow down DNA in nanopores change the sensing properties of the pore, making it more difficult to ensure accuracy of detected base pairs. Shining laser light on the nanopore alters only the local surface charge, an effect that’s completely reversible within milliseconds by switching the laser off.
As an added bonus, the researchers found that the sudden increase in surface charge and resulting flow of water reliably unblocks clogged nanopores, which can take a long time to clean, significantly extending their lifetime.
Meller and his team characterized the amount of increase in current under varying illumination in many different-sized nanopores. They next aim to explore in greater detail the mechanism underlying the increase in surface current when the green laser is applied to a nanopore, information that could lead to even more sensitivity and accuracy in DNA sequencing.
The research is funded by a $4.2 million grant from the National Institute of Health’s National Human Genome Research Institute under its “Revolutionary Sequencing Technology Development — $1,000 Genome” program, which seeks to reduce the cost of sequencing a human genome to $1,000.
The monthly magazine that publishes articles pertaining to embedded systems and programming initially reached out to Coskun for a Q&A session in its July 2012 issue. Pleased with the in-depth knowledge of the NSF CAREER Award winner, the editors contacted her again last spring to offer a permanent position.
Editor-in-Chief C. J. Abate said that because the magazine is international, he believed Coskun, who has professional and educational experience in the US, Switzerland and Turkey, would be a good fit.
“I’m always looking for contributions from talented, engaging engineers and academics who are working on cutting-edge technologies, such as green computing, thermal management and many-core systems,” Abate added. The magazine’s needs aligned with Coskun’s main research focus – energy-efficient computing.
Coskun was eager to begin. “This opportunity allows me to communicate research ideas, practical implementation aspects of research problems and solutions to engineering problems we come across in my lab to a general engineering and embedded systems audience,” she said.
So far Coskun has enjoyed the change of pace. As opposed to writing technical articles that involve solving open-ended problems specific to research communities, the columns enable her to connect aspects of her work to real-world problems in order to reach a broader audience. In her first column, Coskun discussed how one can build ‘leakage-power aware’ cooling control strategies to save energy and demonstrated an example implementation on a commercial server.
It was only after Coskun wrote her first column that she discovered she was the first female columnist in a magazine with a 25-year history. Noting that one of the magazine’s main goals is to inspire a wider, more diverse audience, Abate expects Coskun’s work to be an inspiration for young engineers and academics.
To add value to Circuit Cellar, Coskun plans to emphasize practical aspects while discussing solutions to energy efficiency problems. She looks forward to receiving feedback from readers to better understand their expectations and interests.
- Chelsea Hermond (SMG ’15)
When it comes to wireless communications, the school of thought is that interference between users is an obstacle to avoid.
That is to say, when multiple users transmit on the same frequency band, nearby receivers only see the superposition of their signals, which makes it hard to discern the individual packets of data.
Work by Assistant Professor Bobak Nazer (ECE) and Professor Michael Gastpar, who holds positions at the École Polytechnique Fédérale de Lausanne in Switzerland and the University of California, Berkeley, is causing other researchers to rethink that notion.
A paper by them titled, “Compute-and-Forward: Harnessing Interference Through Structured Codes,” explores the possibility of exploiting the algebraic structure of interference to achieve higher data rates.
Specifically, their framework makes it possible for a receiver to recover linear combinations of packets from superimposed signals. Recovering the original packets is simply a matter of collecting enough equations to solve for the unknowns. Ultimately, this technique may enable wireless networks to operate at significantly higher throughputs by allowing several users to simultaneously occupy the same channel.
“Much of the prior work has focused on the statistical aspects of the interference problem,” said Nazer. “One of the main emphases of this paper is that there is a benefit to thinking about algebraic structure as well.”
“I was very happy to hear about the award and really appreciate the recognition from the communications and information theory communities,” said Nazer. “This is a project we’ve been working on for a long time. More than anything it’s nice to see that others are getting as excited about the work as we’ve been.”
In July, Nazer and Gastpar were recognized with a plaque and honorarium at the IEEE International Symposium on Information Theory in Istanbul, Turkey.
-Rachel Harrington (firstname.lastname@example.org)
New “Atom Calligraphy” Technology Could Lead to Mass-Produced Nanodevices
One of the biggest obstacles on the road to mass-producing nanoscale devices ranging from integrated circuits to biosensors is a persistent inability to precisely manipulate nanomaterials to build reliable, functional products at a reasonable cost. The main challenge has been to pattern materials at precise locations in a repeatable manner over relatively large areas. Conventional approaches have proven inconsistent, wasteful and expensive.
To meet this challenge, Professor David Bishop (ECE, Physics, MSE) and collaborators at Boston University and Bell Laboratories have developed a low-cost, microelectromechanical system (MEMS)-based machine that directs atoms onto a surface through different-sized holes – each no more than 50 nanometers across – on silicon plates. These MEMS plates can move with nanometer precision to create exacting patterns over surfaces of more than 400 square microns, roughly the area of a human white blood cell. Shutters positioned a micrometer or so above each MEMS plate enable high-speed control of where and when atoms are deposited.
The researchers have produced lines, bridges, rings, infinity symbols, BU logos and many other nanoscale metal patterns by depositing gold and chromium atoms through the holes while moving the plates. The machine and the concept behind it are described in Nano Letters.
“We’ve figured out a way to directly write with small numbers of atoms, to do calligraphy with atoms,” said Bishop, who compared the new MEMS-based machine to a nano-spray painter. He envisions that the method could lead to a cost-effective, chip-based fabrication process for atomic-scale materials and devices that are initially designed in digital simulations, making possible everything from downsized electronics to more compact biosensors.
To come up with the idea to build a programmable device that could directly write with atoms, Bishop drew upon previous experiences working with MEMS technology and nanostencils, or stencils used to fabricate nanoscale patterns on a surface. The new method effectively uses MEMS technology to move a nanostencil over a silicon surface.
“People have devised a variety of techniques for moving atoms around that are expensive, complicated or not scalable,” said Bishop. “Our system avoids these drawbacks and provides programmability. It is fun technology to play with, we’re having a blast.”
Many of us type passwords into computers and ATMs more times a day than we care to remember. The process isn’t exactly fun but it does help protect our identity and belongings.
In the future, Boston University Electrical & Computer Engineering professors, Janusz Konrad and Prakash Ishwar, believe passwords and ID cards could be replaced by human gestures. In other words, you might find yourself moonwalking into your office in the near future.
In The Boston Globe, Ishwar and Konrad explained how one’s physical features and unique cadence of movements can help identify a person.
“We’re not trying to recognize gestures per se; we’re trying to recognize users making the gestures,” Ishwar told the Globe.
The professors have received funding from the National Science Foundation for this research and are in the early stages of examining the feasibility of the approach.
-Rachel Harrington (email@example.com)