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Unfurling on Command

~ saracody

Douglas Holmes Explores the Science of Swelling

A murmur of thunder and pulses of lightning roll across the night sky, illuminating the formidable outline of a forest of baobab trees, an ancient species found in Africa. The soothing voice of British naturalist David Attenborough narrates as the flowers of the baobab begin to blossom as they fill with water, unfurling the delicate tissue in less than a minute as the water guided its new shape. This clip from BBC’s Planet Earth inspired Assistant Professor Douglas Holmes (ME), who runs the Mechanics of Slender Structures (MOSS) research group, to pursue an experiment that was recently featured on the cover of Soft Matter.

“My research group does a lot of work with soft matter physics, so I was really excited when I saw these baobab flowers,” says Holmes. “I was curious if the dramatic shape change causing the flowers to open was caused by swelling, so I wanted to see if I could recreate that in a laboratory setting. Engineers are constantly looking for new ways to make materials change shape on command, and I thought this phenomenon might provide insight into utilizing the effects of swelling in a controlled way.”

Holmes devised a simple experiment where he took two thin sheets of rubber, hung them from a rod and lowered them into a bath of fluid until their tips were submerged. Initially, the sheets pulled together, but as the liquid permeated the structure, the swelling caused the ends to curl up and peel away from each other in an outward motion, similar to the movement of the baobab blossoms.


During the experiment, as liquid permeated the rubber sheets, elastocapillary swelling caused them to curl. Video provided by Assistant Professor Douglas Holmes (ME)

“It took some trial-and-error to get the materials for the experiment just right, because we needed to find a balance where the wetting, swelling and bending were all on the same playing field and competing with each other,” says Holmes. “Depending on which of these forces we focus on, this sweet spot we found acts as a good baseline. Even a simple experiment like this can lead to a variety of complicated physics.”

By understanding the physics of how and why this phenomenon, known as elastocapillary swelling, happens, Holmes can apply his engineering perspective to figure out a way to develop materials from thin structures that are able to change shape on command, which has a host of potential applications.

“There are a variety of different stimuli you can use to change an object’s shape, like heat, voltage, light, or fluid. In our case, we are using swelling,” says Holmes. “By incorporating fluid in the structure to begin with, we could control the swelling to make the material change shape, like the baobab flower. Imagine a smart needle that can be injected into something, and using this concept, you can tell it to bend back and forth while navigating towards a certain target.”

Holmes also sees potential application in industry, where companies that manufacture soft materials would benefit from the knowledge of how to account for environmental factors like humidity, which could cause swelling that would put stress on the manufactured materials. Holmes has even been contacted by cosmetics companies which are interested in developing hair products that prevent frizzing.

“This study was an interface between things that are soft and things that are thin, so with any small change to the environment, you are bound to see a drastic deformation in the shape,” says Holmes. “Going forward, we’ll continue to explore how to get that object to bend, and how different surroundings and stimuli affect it.”

Boston University College of Engineering

Originally published July 1, 2016

Appears on: BU ENG News site

BU Students Represent U.S. in International Supercomputing Competition

~ saracody

A group of six BU students were the sole team from the U. S. to compete in the world’s largest supercomputing hackathon in Wuhan, China in April.

“Supercomputing uses very powerful hardware to run large and complex programs,” explains Hannah Gibson (ECE’17), a member of the BU Green Team who competed at the Asia Supercomputing Community Student Supercomputer Challenge. “It’s used in CGI for movies and for weather modeling-huge programs that require a lot of power. In the competition, the goal is to get the best performance with consideration for power and speed with the setup and software you designed and built.”

The competition featured 16 teams selected from 146 applicants that hailed from around the globe, from China and Russia to Hungary and Colombia. Each team provided a wish list of hardware to the sponsoring company, Inspur, and had to prepare software in advance to bring with them to the competition. Teams had four days total for the competition, including time for setup and installation.

“It was awesome being in a different country and seeing how our team stacked up to teams from all around the world,” says Wasim Khan (ECE’17), a member of the BU Green Team. “It was interesting to compete against other teams who come from schools that have supercomputing as a major and to see that we, an extracurricular student-run group, gave them a run for their money.”

In computing, performance is often measured by floating-point operations per second, or flops. The higher the number of flops, the better the computer performance and, in competition, the higher the score. Teams were given six applications, where they were tasked with rewriting portions of each program to work better on the target hardware, optimizing it to work on their architecture and complete real-world scientific workloads while obeying the competition constraint of 3,000 watts of power maximum.

Five of the applications were programmed to run on their own hardware setup, or cluster, to measure the number of flops it generated. The other application was run on the Tianhe-2, currently the world’s fastest supercomputer. The score was an algorithm that was based on the number of problem sets, or workloads, that were completed, with consideration for accuracy, timing and flops generated, if applicable. Awards were given to top scorers, “most innovative,” and “best overall.” In order to support the ASC mission to promote supercomputing outreach, teams were encouraged to tweet throughout the competition and the team with the most retweets was awarded the “most popular” designation.

“This is an impressive and highly motivated group of students who had to specify and acquire equipment, optimize the configurations, tune, and in some cases refactor the applications, and ultimately qualify for these competitions entirely of their own volition,” says Professor Martin Herbordt (ECE), who is the faculty advisor for the group. “It goes without saying that students learn a lot in their classes, but this type of professional, real-world experience that is self-guided takes their learning to a whole other level.”

The BU Green Team represented BU’s High Performance Computing (BUHPC) team, led by Winston Chen (CE’17) and Huy Lee (CS’16), is affiliated with BUILDs, the BU hackerspace that provides resources for students to undertake technology projects. Since their return from China, BUHPC is fundraising to attend the ISC Student Cluster Competition in Germany in June. In addition to competing, the event also includes professional development workshops and networking opportunities for students interested in the field of supercomputing.

Boston University College of Engineering

Originally Published May 20, 2016

Appears on: BU ENG News website

Ünlü Delivers DeLisi Distinguished Lecture

~ saracody

On Thursday, April 14, Professor M. Selim Ünlü (ECE, BME, MSE), recipient of the 2016 Charles DeLisi Award and Distinguished Lecture, presented “Optical Interference: From Soap Bubbles to Digital Detection of Viral Pathogens” to a packed room of students, faculty and researchers.

The first named endowed lecture in the history of the College of Engineering, the Charles DeLisi Award and Distinguished Lecture recognizes faculty members with extraordinary records of well-cited scholarship, and outstanding alumni who have invented and mentored transformative technologies that impact our quality of life.

When Ünlü arrived at BU in 1992, he was inspired by the collegial interdisciplinary environment, which led him to apply his background in electrical engineering and electromagnetic waves to developing innovative methods for biological imaging and sensing. His presentation, peppered with video and audio messages from past students and mentors who have contributed to his work, chronicled his career path from graduate school to present day and centered on his current research in optical sensing and developing new bioimaging technologies that address the obstacles that currently plague the field of diagnostics.

“When you are trying to look at pathogens, the most distinguishing thing is to look at its genome, but obstacles like logistics and cost are prohibitive and drive scientists to find more compact and affordable ways that have the same functionality,” said Ünlü. “Single particle detection has been the physicist’s dream of addressing these issues, so that’s what we set out to explore.”

Synergy between Engineering and Medicine

In developing his optical detection technology, he drew inspiration from, of all places, a soap bubble. Specifically, the patterns of colors that develop on the surface when light is being reflected through it. According to Ünlü, the same interference phenomenon that gives rainbow colors to soap bubbles can also provide extremely high sensitivity as illustrated by the recent news on detection of gravity waves by optical interferometry.

“Most people don’t realize that just by calling out a certain color, you are making a measurement in the order of nanometers,” said Ünlü.

Ünlü extended this idea to develop his optical detection technology for single nanoscale particles, where the interference of light reflected from the sensor surface is modified by the presence of nanoparticles, producing a distinct signal that reveals the size of the particle that is otherwise not visible under a conventional microscope. Using this technology, Ünlü and his research team demonstrated label-free identification of some of the most deadly viruses in the world, including hemorrhagic viruses like Ebola, Lassa and Marburg, at a high sensitivity on par with state-of-the-art laboratory technologies. They have even been able to detect particles as small as individual protein and DNA molecules by labeling them with gold nanoparticles to provide sufficient visibility.

“Proteins are too small. We can’t see them directly so we decorate them with gold nanoparticles, which are not much bigger than the proteins themselves,” said Ünlü. “Decorating them with gold nanoparticles increases visibility of the molecules bound on the sensor surface, and we are able to count them in serum or whole blood.”

The resulting technological development in biomarker analysis that Ünlü has spearheaded is digital detection, an approach that counts single molecules, which provides resolution and sensitivity beyond the reach of ensemble measurements. Digital detection for medical diagnostics not only provides very high sensitivity, but also has the potential of making the most advanced molecular diagnostic tools broadly accessible at low cost.


Digital detection captures images of individual viruses in real time

“Optical interference is a very powerful sensing technique,” summed up Ünlü. “With this biological imaging technology, we can detect single particles if they are large enough on the nanoscale, such as viruses, and see them directly. If they are proteins or DNA molecules we have to label them with a small, metallic nanoparticle to see them.”

In terms of next steps, Ünlü and his team will continue to refine the technology for commercialization, including applying some of these findings to produce microarray chips that provide calibration and quality control in industry. His laboratory will continue to work on advancing the technology further and gaining a deeper understanding of the theoretical basis in order to enhance the methodology. In particular, they are looking into applying the technology to such areas as real-time DNA detection, rare mutations, and most recently a project to characterize viruses that target cancer cells.

To conclude his presentation, Ünlü expressed his appreciation of the support he received from the College to foster collaboration, and to his students, mentors and family who helped him along the way.

“I’m very thankful to Boston University for providing an incredibly rich environment for research because there are no barriers between disciplines,” said Ünlü. “Multidisciplinary innovation is the driving force of discovering new things and making society better, and ultimately that is my motivation.”

The DeLisi Lecture continues the College’s annual Distinguished Lecture Series, initiated in 2008, which has honored several senior faculty members. The previous recipients are Professors John Baillieul, (ME,SE), Malvin Teich (ECE) (Emeritus), Irving Bigio (BME), Theodore Moustakas (ECE, MSE), H. Steven Colburn (BME), Thomas Bifano (ME, MSE), Christos Cassandras (ECE, SE) and Mark Grinstaff (BME, MSE, Chemistry, MED).

Boston University College of Engineering

Originally Posted April 22, 2016

Appears on: BU ENG News website

Cancer Treatment Goes Local

~ saracody

In two studies, Grinstaff offers new therapeutic approaches to mesothelioma and esophageal cancer

When it comes to treating cancer, one Boston University researcher is going local. Mark Grinstaff, a BU College of Engineering professor of biomedical engineering and materials science and engineering, published two studies in January 2016 that offer new approaches to the treatment of two intractable cancers—mesothelioma and esophageal cancer—by delivering therapeutic agents directly to the tumor site.

“Local drug delivery allows us to maximize drug dose at the disease site while reducing drug exposure to the rest of the body,” says Grinstaff, who is also a professor of chemistry and of medicine. “This approach affords significantly fewer negative side effects, like hair loss and an overall decrease in the immune system, which are common with conventional intravenous chemotherapy treatments.”

The first study, published in Scientific Reports, describes a highly targeted approach to treating mesothelioma, an aggressive and highly fatal cancer associated with asbestos exposure. Mesothelioma progresses locally, Grinstaff noted, and current chemotherapy treatments—which infuse toxic drugs throughout the body for a relatively brief period—have not been effective in extending survival.

Postdoctoral research associate Aaron Colby (ENG’09, ’14) prepared 100-nanometer particles that were small enough to enter a cancer cell, but expanded to 1,000 nanometers once exposed to the cell’s low pH level. In addition, the nanoparticles were engineered to attract a chemotherapy drug and draw it away from healthy cells through a process similar to that which causes oil to separate from vinegar. With the particles acting as beacons for the chemotherapy and the cancer cells unable to expel them quickly, the drug spent more time on target while avoiding healthy tissue.

“In our strategy, we are sending in a nanoparticle first and the drug second, which we have found to increase the amount of drug delivered to the tumor itself compared to the current treatment method,” says Colby.

The second study, published in Angewandte Chemie International Edition, reports a novel drug delivery technology to treat esophageal cancer. A common problem that arises with esophageal cancer patients is difficulty swallowing, as a result of the tumor narrowing or blocking the esophagus. Doctors insert a wire mesh stent to open the passageway.

Grinstaff and his research team had the idea to integrate drug delivery with this tool as a one-two punch to focus the drug on the problem itself. Graduate student Julia Wang wrapped a drug-infused polymer sheath around the stent so that when it is stretched, it releases drug directly to the disease site.

“By changing the treatment method from a more passive release system to a more active release system, we are able to control when and how much drug is released,” says Wang.

“What is unique about this drug delivery system is that the amount of drug delivered depends on the extent the cloth is stretched. Using this approach a clinician can tune the dose, something they cannot do today,” says Grinstaff. “That control comes from the polymer composition and the engineering aspects of the design.”

Grinstaff and his team continue to refine the technology so it can pass through the regulatory process and get into the clinics. According to Grinstaff, his unique approaches to treating these diseases will not only lead to more effective treatment, but also will reduce the exposure of healthy cells to toxic chemotherapy drugs.

“Above all else, the potential benefit of both studies is the impact on patient care,” says Grinstaff. “By improving upon and streamlining the processes in place to treat aggressive diseases that currently have poor prognoses and no good therapies, not only are you going to treat the disease itself more effectively, but you will also improve the patient’s quality of life.”

Boston University College of Engineering

Originally Posted April 25, 2016

Appears on: BU ENG News Website, BU Research

From Cells to Circuits

~ saracody

Densmore leads BU team that collaborates with MIT in Science engineering biology study

Whether it’s artificial skin that mimics squid camouflage or an artificial leaf that produces solar energy, a common trend in engineering is to take a page out of biology to inspire design and function. However, an interdisciplinary team of Boston University researchers have flipped this idea, instead using computer engineering to inspire biology in a study published in Science in April 2016.

“When you think about it, cells are kind of computers themselves. They have to communicate with other cells and make decisions based on their environment,” says Douglas Densmore, associate professor of electrical and computer engineering and biomedical engineering, who oversaw the BU research team. “By turning them into circuits, we’ve figured out a way to make cells that respond the way we want them to respond. What we are looking at with this study is how to describe those circuits using a programming language and to transform that programming language into DNA that carries out that function.”

Using a programming language commonly used to design computer chips, electrical and computer engineering graduate student Prashant Vaidyanathan created design software that encodes logical operations and bio-sensors right into the DNA of Escherichia coli bacteria. Sensors can detect environmental conditions while logic gates allow the circuits to make decisions based on this information. These engineered cells can then act as mini processing elements, enabling the large-scale production of bio-materials or helping detect hazardous conditions in the environment. Former postdoctoral researcher Bryan Der facilitated the partnership between BU and the Massachusetts Institute of Technology to pursue this research study.

“Here at BU, we used our strength in computer-aided design for biology to actually design the software and MIT produced the DNA and embedded it into the bacterial DNA,” says Densmore. “Our collaboration is a result of sharing the same vision of standardizing synthetic biology to make it more accessible and efficient.”

Historically, building logic circuits in cells was both time-consuming and unreliable, so fast, correct results are a game changer for research scientists, who get new DNA sequences to test as soon as they hit the “run” button. This novel approach of using a common programming language opens up the technology to anyone, giving them the ability to program a sequence and generate a strand of DNA immediately.

“It used to be that only people with knowledge of computers could build a website, but then resources like WordPress came along that gave people a simple interface to build professional-looking websites. The code was hidden in the back end, but it was still there, powering the site,” says Densmore. “That’s exactly what we are doing here with our software. The genetic code is still there, it is just hidden in the back end and what people see is this simplified tool that is easy, effective, and produces immediate results that can be tested.”

According to Densmore, this study is an important first step that lays the foundation for future research on transforming cells into circuits, and the potential for impact is global, with applications in health care, ecology, agriculture, and beyond. Possible applications include bacteria that can be swallowed to aid in digestion of lactose to bacteria that can live on plant roots and produce insecticide if they sense the plant is under attack.

“The possibilities are endless, and I am excited about it because this is the crucial first step to reach that point where we can do those amazing things,” says Densmore. “We aren’t at that level yet, but this is a stake in the ground that shows us we can do this.”

The BU/MIT collaboration will continue underneath the Living Computing Project, which wasawarded a $10 million grant from the National Science Foundation in January 2016. Future studies will look to improve upon the circuits that were tested, add other computer elements like memory to the circuits, and expand into other organisms such as yeast, which will pave the way for implanting the technology into more complex organisms like plant and animal cells.

Boston University College of Engineering

Originally Posted April 13, 2016

Appears on: BU ENG News Website, BU Research