Graduate School

High-performance computer modeling to tackle fisheries future

Timely forecasts of storms and effective management of commercial fishing are essential in the wake of extreme weather events and unprecedented warming in the Gulf of Maine.

Damian Brady, University of Maine assistant professor in the School of Marine Sciences at the Darling Marine Center, is working to advance both of those goals.

The National Science Foundation recently awarded Brady and colleagues a $266,309 grant to advance UMaine high-performance computer modeling tools to do just that.

The project — “Major Research Instrumentation Program Track 1: Acquisition of High Performance Computing to Model Coastal Responses to a Changing Environment” — includes buying a system that nearly triples computing power at the university and acquiring an off-site backup system for project data.

The project is ideal because it joins world-class researchers and experts in cyberinfrastructure to create a platform that advances goals of the research and creates a platform that benefits research and education across all disciplines, says Bruce Segee, the Henry R. and Grace V. Butler Professor of Electrical and Computer Engineering and director of the Advanced Computing Group.

“Computing and storage are the test tubes and microscopes of the 21st century. They support the creation of knowledge, collaboration, communication and economic growth,” he says.

“Maine is fortunate to have a High Performance Computation facility available to its researchers and students, and this grant will help significantly increase the complexity of the questions that can be asked and the number of users it can support. Demand for computing resources is growing at a rapid pace, and this grant provides a great step forward to help meet the demand.”

The tools will help scientists better predict climate changes and extreme weather, as well as understand ensuing ecological and physical consequences, and weigh costs and benefits of adaptation or mitigation.

“The effects of climate change are not likely to be straightforward. There are species and ecosystems that will benefit and those that will not,” says Brady.

“The purpose of running computer models is that they ask the really tough questions like: What will happen to the lobster industry under a 1-, 2-, or 3-degree (temperature) increase? What will the impact of increased rainfall be on shellfish along the coast? Although models will not perfectly predict the consequences of these changes, they can give us a range of potential futures.”

Maine is uniquely positioned physically and economically to be affected by climate change, Brady says. The state is on one of the sharpest latitudinal temperature gradients in the world and has one of the longest coastlines in the United States.”

And the potential impacts of climate change are significant for Maine, where the economy is linked to marine resources and infrastructure. The aquaculture industry (predominantly salmon and shellfish) doubled in value from 2005 to 2013. And Maine’s commercial fisheries were valued at a record $585 million in 2014, says Brady.

Boosting computing capacity at UMaine will allow coastal modelers to inform local decisions and increase undergraduate and graduate student access to high-performance computing, Brady says.

UMaine colleagues Huijie Xue, professor of oceanography; Fei Chai, professor of oceanography; Qingping Zou, assistant professor of coastal engineering, and Sean Birkel, research assistant professor with the Climate Change Institute, are taking part in the three-year project with Brady and Segee.

Gorse evaluates how much aquaculture regions can support

Graduate research assistant Libby Gorse, whose lab is in the basement of Boardman Hall at the University of Maine, is excited about research she’s spearheading for a Sustainable Ecological Aquaculture Network (SEANET) project.

She and Aria Amirbahman, professor of civil and environmental engineering, are studying the effects that aquaculture farms have on sediment below them.

Gorse, a civil engineering Ph.D. student, has been interested in chemistry and has been using chemistry lab equipment since she was a youth. Her father was an analytical chemist and Gorse followed in his footsteps and studied chemistry at Baldwin Wallace University in Berea, Ohio.

Maine EPSCoR at the University of Maine administers the SEANET project. A five-year, $20 million grant from the National Science Foundation is being utilized to learn how different types and scales of aquaculture fit into the state’s multiuse working waterfront.

Researchers will monitor the environment through field investigations, lab analysis and buoy-based sensor technology to learn about trophic dynamics of aquaculture in Maine’s coastal ecosystem.

Specifically, they’ll study how nutrients move from the physical environment into living organisms and are then recycled.

SEANET has split the state into three bioregions to study in-depth and determine how much aquaculture an area can support.

The Maine coast serves as a living laboratory, allowing researchers to explore the special feasibility of aquaculture operations.

Gorse will explore each bioregion to contribute to an understanding of the carrying capacity — what density of aquaculture operations can be maintained, what kind of sites, and how many sites are appropriate — considering local conditions.

“My study will look at the different biodeposits from oysters, mussels, finfish and all the different operations Maine supports,” she says.

“We need to grasp how to balance aquaculture operations to keep everything healthy and know how many sites or types of sites are appropriate.”

By studying the sediment below aquaculture farms, Gorse and Amirbahman seek to learn how best to advise aquaculture farmers regarding growth and placement of farms along the coast.

“It’s important to know the footprint — chemical and biological — of these farms,” Amirbahman says.

“It’s especially important for us to understand the role that these operations have on the overall nutrient budget of these systems. It will help us understand where to site — for instance how far apart from each other these operations should be. What kind of flushing rate you have, for instance — dilution via the tide or the current that can solve a lot of problems.”

Collaboration across departments

To create equipment for her study, Gorse worked with UMaine’s Advanced Manufacturing Center (AMC) to construct flux chambers to hold sediment samples.

A pump system moves water through the chambers and a chiller unit keeps the temperature of the samples at a consistent bottom water level of 45–55 degrees Fahrenheit.

John Belding, AMC director, says facility professionals and researchers collaborate to fabricate products and move research forward.

“For Libby’s project, we worked from drawings and pictures of other systems that were used at other universities,” he says.

“We came up with a design that met their needs based on what they were doing. Libby’s research is specialized, so it needed some special equipment to accomplish it.”

Belding says engineering students employed at the AMC get an opportunity to work on different parts and components of the project, from doing drafting drawings to being hands-on engineers.

“It teaches students a lot about what it means to be a project manager,” he says.

After months of testing and trial and error, Gorse’s system works just as she envisioned it. She plans to have preliminary results from the project in two to three months.

Working with stakeholders

The next phase of the study, likely in summer 2017, will be to gather samples from beneath aquaculture farms and obtain comparison samples from outside the area.

Work like this has never been done in Maine, Amirbahman says, and will be important for the next stage of research.

And, just as it’s important for various UMaine departments to collaborate, it’s key for researchers to work closely with farmers.

“We look forward to being educated and informed on the very practical aspects of this work,” Amirbahman says.

“These are aspects that you don’t read in scientific papers or books. These are people with experience. We need to get a better understanding of the impact of these facilities, especially on the environment and being able to inform them about the carrying capacity of the region.”

This research, say Gorse and Amirbahman, will help grow a viable aquaculture economy in Maine.

Contact: Andrea Littlefield, 207.581.2289

From UMaine News

UMaine researchers’ wireless leak detection system bound for International Space Station

UMaine researchers’ wireless leak detection system bound for International Space Station

A wireless leak detection system created by University of Maine researchers is scheduled to board a SpaceX rocket bound for the International Space Station this summer.

The prototype, which was tested in the university’s inflatable lunar habitat and Wireless Sensing Laboratory (WiSe-Net Lab), could lead to increased safety on the ISS and other space activities.

This is the first hardware from UMaine in recent history that is expected to function in space for a long period of time, according to the researchers.

In advance of the Aug. 1 launch, UMaine researchers are working with NASA to prepare three of the wireless leak detector boxes for flight.

From April 18–20, electrical engineering graduate students Casey Clark and Lonnie Labonte will test the payload, perform an electromagnetic interference (EMI) test, and complete the Phase 2 safety review of the prototype at NASA Johnson Space Center in Houston, Texas.

Wirless sensor from WiSeNet-LabThe project was one of five in the nation to receive funding from NASA–EPSCoR for research and technology development onboard ISS.

Ali Abedi, a UMaine professor of electrical and computer engineering, was awarded the three-year, $100,000 NASA grant through the Maine Space Grant Consortium in 2014. Collaborators on the project include Vince Caccese, a UMaine mechanical engineering professor, and George Nelson, director of the ISS Technology Demonstration Office at the NASA Johnson Space Center.

Leaks causing air and heat loss are a major safety concern for astronauts, according to Abedi. It is important to save the air when it comes to space missions — find the leak and fix it before it’s too late.

The project involves the development of a flight-ready wireless sensor system that can quickly detect and localize leaks based on ultrasonic sensor array signals. The device has six sensors that detect the frequency generated by the air as it escapes into space and triangulates the location of the leak using a series of algorithms. The device then saves the data on SD cards that are sent back to Earth.

The device is fast, accurate and capable of detecting multiple leaks and localizing them with a lightweight and low-cost system, according to Abedi.

“Our goal is to push the boundaries of hardware and software to design a highly accurate, ultra-low-power and lightweight autonomous leak detection and localization system for ISS,” says Abedi, who directs the WiSe-Net Lab.

Similar systems on the market require astronauts to walk around with a device, scanning walls to detect holes, while the team’s prototype offers a “set-it-and-forget-it” solution, says Clark of Old Town, who graduates in May and will begin work this summer as a ground segment engineer at SpaceX in Hawthorne, California.

“This is the first step in a very progressive movement to monitor structural parameters of spacecraft and the ISS,” says Labonte of Rumford.

The lab prototype was developed from scratch by Clark and Labonte, and includes components that were both created with a 3-D printer and bought off the shelf. Their work followed that of UMaine Ph.D. student Joel Castro and postdoctoral fellow Hossein Roufarshbaf, who developed a leak localization algorithm as part of a previous NASA EPSCoR project.

The additional funding allowed the researchers to make the system more rugged and capable for microgravity environment testing at the NASA Johnson Space Center, and eventually onboard the ISS.

While the devices are in space, astronauts who live in the ISS will install each of the three identical boxes and allow them to collect data for two intervals of about 30 hours, for a total of 60 hours each, according to the researchers.

“While the hardware is in space, our team at UMaine will be on standby mode until data collection is completed,” Clark says. “The system is designed to be automated. So we do not interact with the device during on-board operations.”

After each device collects data, NASA will send the information to the researchers for analysis and processing.

Once the hardware returns to Earth on a re-entry vehicle sometime next year, the team will observe how well the devices survived the launch, deployment and return with the intention of proposing a new design for the next generation, the researchers say.

Contact: Elyse Kahl, 207.581.3747


Zachary Wood: “What an early spring means for Maine’s lakes” published in the Bangor Daily News

SPIA student discusses Syrian conflict on WZON Pulse Morning Show

Majd Zeidan, a first-year UMaine graduate student, discussed the ongoing conflict and refugee crisis in his home country of Syria on the WZON AM620 Pulse Morning Show today. Listen to the podcast of the interview (link here).

Zeidan is from Hama, Syria. He entered SPIA’s MA Global Policy program after receiving an MBA from Husson University in May 2015.  During his studies at Husson, Zeidan worked at the Maine International Trade Center in its Future Global Leaders internship program which offers students and young professionals the chance to improve their research and communications skills as they assist local companies with growth in international markets.  Zeidan’s current studies focus on international security and development so that he may someday be able to return to Syria, where his family still lives, and positively impact Syria’s education system and economy.


Samuel Belknap featured in Hakai Magazine article titled “A Warming Threat to Maine’s Lobsters”


Jesica Waller wins People’s Choice Award in the Vizzies for her photograph of 3-week-old American Lobster

Climate Change | Marine Sciences | Signature and Emerging Areas

And the People’s Choice winner is … Jesica Waller

For some, a picture is worth a thousand words. For Jesica Waller, it’s worth $500, the opportunity to introduce people to her research through beautiful art and to be published in “Popular Science” magazine. Her photograph of a 3-week-old American lobster won the People’s Choice Award and its accompanying cash prize in the Vizzies, a… read more And the People’s Choice winner is … Jesica Waller

For Heller, ancient trash heaps hold clues to healthy future fisheries

Climate Change | Marine Sciences | Research | Signature and Emerging Areas

For Heller, ancient trash heaps hold clues to healthy future fisheries

At age 7, Sky Heller was captivated digging through a buried trash heap protruding from an eroding bank at her family’s farm in the foothills of Pennsylvania. “When I found out I could do it for a career, I’ve never looked back,” says Heller, now a Ph.D. candidate in anthropology and environmental policy at the… read more For Heller, ancient trash heaps hold clues to healthy future fisheries


Jesse Kaye-Schiess: KPE master’s student works with outdoor program for middle school boys

Outreach | Student and Alumni Stories

Jesse Kaye-Schiess: KPE master’s student works with outdoor program for middle school boys

A chance meeting in the dairy aisle at the grocery store in summer 2013 led Jesse Kaye-Schiess to enroll in the master’s program in kinesiology and physical education at the University of Maine. He had finished his undergraduate degree in KPE at UMaine in 2012 and taught for a year in Lincoln, Maine. But like… read more Jesse Kaye-Schiess: KPE master’s student works with outdoor program for middle school boys

UMaine Ph.D. student receives prestigious Switzer Environmental Fellowship

Marine Sciences | Signature and Emerging Areas

UMaine Ph.D. student receives prestigious Switzer Environmental Fellowship

Joshua Stoll, University of Maine Ph.D. candidate in the School of Marine Sciences, has been selected as a Switzer Environmental Fellow by the Robert and Patricia Switzer Foundation. This year, the Switzer Foundation awarded 22 fellowships of $15,000 each for emerging environmental leaders who are pursuing graduate degrees and are dedicated to positive environmental change.… read more UMaine Ph.D. student receives prestigious Switzer Environmental Fellowship


Noah Oppenheim: Lobster presentation best at ecosystem symposium

Marine Sciences | Research | Signature and Emerging Areas | Student and Alumni Stories

Noah Oppenheim: Lobster presentation best at ecosystem symposium

In November, Noah Oppenheim won the best student oral presentation award at the American Lobster in a Changing Ecosystem symposium in Charlottetown, Prince Edward Island. “Forecasting the future of the American lobster in the Gulf of Maine and Southern New England: trouble on the horizon?” was the title of his talk. In it, the University… read more Noah Oppenheim: Lobster presentation best at ecosystem symposium