Environmental Sciences

Preparing for Climate Change’s Effects with Geophysics

As climate change causes ever increasing fears of flooding, Dr. Peter Lelievre’s work in geophysical imaging becomes ever more important in the province of New Brunswick and beyond.

An assistant professor in Mount Allison University’s department of mathematics and computer science, Dr. Lelievre is an applied geophysicist who images what’s underground. Earlier in his career, that pursuit was tied to mineral exploration or “trying to help people find the materials such as metals that our society uses for basic building materials.” More recently, he’s become interested in imaging and understanding what happens with flood infrastructure.

“With climate change and rising sea levels, we need to understand more about how water moves through these flood barriers,” Lelievre explains. “Geophysical imaging can help us better understand these things, and also to try and find any erosional issues that could cause a breach.”

Lelievre walks on the fields and marshes near Sackville, N.B. — which are the same places his research now takes place. Being at Mount Allison means he’s surrounded by the dike land and he, his wife, and his dog walk on it frequently.

“It’s far more at the forefront of my mind in my daily life,” he says. “It’s been really nice to be able to shift and connect my research to that part of the local community and my daily life.”

Lelievre uses tools that measure electrical and electromagnetic fields and then he uses heavy mathematical methods and computational power to process the data.

“We run the data through these algorithms that we develop and this creates an image of what’s underground,” he says of his use of the Digital Research Alliance of Canada’s high-performance computing tools. “That’s where the heavy computational part fits in. These are tremendously large computational problems.”

For his heavier research, an imaging task could require 600 central processing units (CPUs), consume roughly two terabytes of random access memory (RAM) and take over four-days to finish. He and his research team use the modern Fortran programming language and create their own software to process their electrical and electromagnetic data and generate images of the Earth.

With the help of his students, postdocs and colleagues, he develops data processing methods that could be used in the field, and he collects field data to help test those methods.

“Eventually we’d like to be able to create data processing methods we can use in the field on a laptop, and so you’d just have a small, everyday laptop, where you get a result in effectively real time,” he says, and adds that the history of computing tells us that could well happen in the near future.

Getting to Net-Zero

Andrew MacDougall studies nature-based solutions to climate change.

“I’m leading a project with Environment and Climate Change Canada (ECCC) and three other universities,” says MacDougall, associate professor at the department of Earth and Environmental Sciences at St. Francis Xavier University. “We’re trying to represent nature-based solutions within climate models to identify any unexpected side effects.”

The nature-based solutions he’s studying are ways to modify either agricultural or natural ecosystems to absorb more carbon.

“The easiest example is growing more trees,” MacDougall says. “It’s the solution governments love the most, even though it’s not terribly effective at cooling the Earth.”

One of the things his group is examining is a local warming effect.

“In the high and mid latitudes such as Canada, forests tend to warm the local environment, even if the overall net effect is cooling globally,” he says. “That’s because coniferous trees absorb heat and hold it. Large scale afforestation — which is ineffective at global cooling — has positive side-effects on climate change, including a surprisingly big effect on sea ice extent – the total area of ocean surface covered by sea ice.”

For that project, the team has been developing models and then using ACENET to run them.

“One of the climate models we’ve been using is the University of Victoria Earth system climate model,” MacDougall says. “We’re also using the Canadian Earth system model, which was developed by Environment and Climate Change Canada (ECCC). Our collaborators at SFU have worked to turn that model into a community model so other researchers will be able to use ACENET infrastructure instead of the computing infrastructure that ECCC maintains.”

MacDougall’s mission with these models is to represent the various climate change solutions within the models to determine how many tons of carbon a given solution will take out of the air.

He also does a lot of work on zero-emissions commitments, which involves trying to figure out whether warming will stop if we do get to net zero. For example, he led a consortium to examine zero-emissions commitments with different climate models.

“It was called the Zero Emissions Commitment Model Intercomparison Project,” he says. “I did the simulations for the Universit of Victoria part of it on ACENET infrastructure. We do most model development on local computers and use ACENET resources for model spin-up and simulations of the future. We often run hundreds of slightly different versions of the model, in what are known as perturbed parameter experiments, to assess uncertainty. The model also needs to be spun-up for 5,000 to 10,000 years, which is 10 to 20 days of computer time. Completing such simulations on local machines is impractical.”

The conclusion from this project was that if we stop emitting carbon dioxide, 50 years later, the amount of warming should stabilize.

MacDougall says doing his work without ACENET’s technology would be very difficult.

Saving the Planet Through Marine Propeller Excellence

Wei Qiu’s research centres around marine hydrodynamics, in the hopes of decreasing noise made by ship propellers, increasing their efficiency as they move through the water, and curbing the negative effects the noise has on marine mammals such as whales. “When ships travel through water, they make noise,” says the department head of ocean and naval architectural engineering in Memorial University’s faculty of engineering and applied science. “As a result of water pressure on the propeller becoming lower than the vapour pressure, propeller cavitation occurs — a phenomenon in which rapid changes of pressure in liquid leads to the formation of small vapour-filled cavities. These vapour-filled cavities, or bubbles, collapse and cause loud popping noises and vibrations, making propeller cavitation the most significant source of noise from a ship. The noise levels jump substantially when propeller cavitation begins. My work is in ship and propeller design, and performance evaluation. I look at how to improve propulsion efficiency – the amount of fuel a vessel consumes — and reduce ship noise by assessing the design and then working to improve it.” The noise issue has traditionally been more critical for navy and research vessels, rather than commercial ones, but in recent years, scientists have discovered the negative effect the noise has on marine mammals, so Qiu’s work also has environmental benefits. “Design is related to the geometry of the ship and how it works with the propeller. If both are designed well, it can help reduce fuel consumption and noise.” Qiu also looks at how ships maneuver in waves, so they don’t capsize, for example. “I want to ensure a ship is designed to operate safely in waves,” he says. In all of his research, the professor often collaborates with industrial partners and government agencies. “I’m working with a propeller manufacturer in Ottawa called Dominis Engineering,” he says. “We’re looking at the effect of manufacturing defects on propeller performance. We started looking into it two years ago and we can see very small defects due to manufacturing can have a pretty big impact on propeller cavitation and therefore noise performance. This partnership helps Dominis manufacture propellers with greater precision.” In his research, Qiu conducts experiments and numerical simulations with computational fluid dynamics (CFD) methods, which he uses to analyze and solve problems involving fluid flows. For his CFD simulations, Qiu relies on Compute Canada and ACENET resources. “We use CFD to simulate the performance of a ship’s propeller,” he says. “This requires pretty extensive computer resources. Without them, I really cannot accomplish my work.” In his own lab, he has a relatively small computer cluster with 700 cores, but through ACENET’s resources, he and his team can access tens of thousands of cores. “For one job, we may need to use hundreds of computer cores for a few days or a few weeks depending on the problem,” he says. “It’s pretty high demand on computer resources. For example, for a ship in waves, we’re dealing with a large area surrounding the ship. That could be 10 times as long as the ship. It implies millions and millions of grids are needed to approximate the domain.”

A Crusade to Protect Crustaceans Against Climate Change

Fraser Clark is a man on a mollusc mission — or you could call it a crustacean crusade. The Dalhousie University animal science and aquaculture professor studies the immunology of crustaceans with a goal of understanding their health and what pathogens threaten them, particularly as East Coast waters warm, and the pH drops, as a result of climate change. He concentrates his research on the wild lobster, crab and shrimp fisheries, with a secondary focus on commercial shellfish, including scallops, oysters and mussels. “My work is on the health, disease and stress in these species,” Clark says. “I look at their immune response, their stress response and how they interact with pathogens.” His research aims to contribute to the health of the Atlantic Canadian fishery industry, helping fishers to have access to hardier and faster-growing products. “With the oysters, mussels and scallops, we find markers for disease and stress resilience, especially as it concerns the ocean’s response to climate change,” he says. When it comes to major wild fisheries, he says, only crustaceans remain. Lobster is the biggest, then crab and shrimp. “We’re finding some interesting differences between crustaceans in the same area, but I can’t say much about pathogens yet,” he says, stressing that none of the pathogens affects humans. “Some are new pathogens, some haven’t been studied before. We’re cataloguing what’s normal and what could come up the Eastern seaboard of the U.S. as waters warm. We know what’s down there, we know what’s up here and we’re able now to monitor it because we have baseline studies.” The differences in immune systems of crustaceans in the same habitat can be used as health-markers, something that currently doesn’t exist for crustaceans. Practically speaking, it’s useful to understand the immune systems of lobsters, for example, as they’re more valuable when alive. When they’re killed, cooked and processed, they are worth less on the market, but live ones that die before they’re sold aren’t worth anything at all, he notes. Surprisingly, he came to this work after doing a master’s in cancer research. “I didn’t feel I was having much of an impact in my local area,” says the Kensington, P.E.I.-born researcher. “So, I got involved in work at the Lobster Science Centre. Now there’s a local impact as I interact with fishers, industry, aquaculture associations and local governments. I can make a difference to their industry.” To do his work, Clark uses resources provided by Compute Canada. He uses its high-powered computing resources to sequence transcriptomes, which are similar to genomes. He then compares different immune genes in different species. He compares the different sequences and constructs models to see how closely related they are. “We’re really interested in how closely related the immune systems are of crab, lobster and shrimp all living in the same area,” he says. “They seem to get sick from different things even though they’ve all been growing in the same area for the last 150 million years.” To that end, the GenAp Galaxy web portal application hosted by Compute Canada has been helpful. “It allows biologists to use high-end computing resources without needing to do high-end coding,” he says. “As long as we understand the assumptions and limitations of the tests, we can get user-friendly data. My undergraduates and graduate students can learn to use these computing resources within days. It’s exceptionally helpful for biologists.”

Exploring the World of Nanoparticles

The world that Martin Mkandawire studies is very, very small, but his work could have a massive impact on human health and the treatment of diseases, including cancer. He’s also playing a significant role in helping to clean up the environment, particularly around mining and industrial sites. Mkandawire is a chemistry professor and scientist at Cape Breton University (CBU) who uses spectroscopy and photochemistry to study the properties of nanoparticles – microscopic objects less than 100 nanometres in diameter. He studies organometallic compounds and interactions between molecules and nanoparticles that have at least one bond between an atom of an organic compound and a metal. He’s also working to develop devices using natural biological processes as the model, including developing and improving efficiency of organic solar cells based on cyanobacterial photosynthesis. As Industrial Research Chair for Mine Water Management at the Verschuren Centre for Sustainability in Energy and the Environment at CBU, Mkandawire devotes much of his research to mine water remediation and management, developing cost-effective cleanup and treatment strategies, mostly based on principles of nanotechnology. One of those strategies involves using sensors that contain protein bound to nanoparticles that change colour, or fluoresce, when they come in contact with certain pollutants – acting as chemical canaries in coal mines. “We’re using nanoparticles for biosensor development,” he says. Mkandawire and his team are also using nanotechnology to make cancer radiation treatments safer and more effective. Amanda Cameron is an undergraduate chemistry student at CBU and the recipient of a 2015 ACENET Research Fellowship. She is also one of the authors of a landmark paper on gold nanoparticle absorption rates published in the Royal Chemical Society journal Nanoscale. Under Mkandawire’s direction she is studying the interaction of nanoparticles with certain cancer drugs. “Right now there are a lot of negative side effects associated with some cancer drugs,” says Cameron. “If we attach those drugs to a nanoparticle that targets the cancer cells we can better target the tumour without affecting the healthy cells around it.” By injecting metallic nanoparticles directly inside cancer cells, small doses of radiation can be highly targeted to kill cancer cells without harming the healthy cells around it. “With this technique, a small amount of radiation has a strong effect,” says Mkandawire. His team also worked on targeting nanoparticles at the mitochondria in cancer cells – a study they published in the Royal Chemical Society journal, Nanoscale. Nanotechnology research may also lead to major improvements in one of the world’s oldest medical treatments: wound dressings. Mkandawire is testing smart wound dressings that contain magnetic nanoparticles incorporated in wound dressing fibres capable of detecting bacteria and increasing conditions during wound healing such as temperature or pH – conditions that can kill the bacteria without the need for antibiotics or other drugs. “Right now you have to keep undressing the wound and checking for infections,” says Mkandawire. “Smart dressings would allow you to keep the dressing on without disturbing the wound and still be well protected from the possibility of infection.” To carry out his studies Mkandawire uses the ACENET computer network to run complex algorithms before he puts his theories to laboratory testing. “We can enter in parameters like thermodynamic properties, reaction rates, the energy of interaction, type of interaction, and strength of the molecular bonding. It allows us to analyze what will occur over time. They are extremely complex calculations and they take a long time to run on the computer. ACENET speeds up the process and allows us to do a lot more in the limited time we have. It’s a great resource.”

Taking the Earth’s Temperature

The greenhouse effect is nothing new. In fact the phenomenon has been influencing the temperature of the Earth for billions of years. The existence of carbon dioxide molecules in the atmosphere acts as a blanket, trapping heat and allowing the Earth’s temperature to remain warmer than it would be otherwise. But in the last 200 years, human activity has been adding greenhouse gases into the atmosphere at rates exceeding any natural process, making the carbon dioxide blanket thicker and warming the Earth even more. As the planet warms up, most of the additional energy from the enhanced greenhouse effect is stored in the ocean – about 93% in total. The rest is distributed among the continents, in the frozen ices known as the cryosphere, and in the atmosphere. Dr. Hugo Beltrami is a professor at the Climate & Atmospheric Sciences Institute, the Environmental Sciences Program at St. Francis Xavier University and a new Canada Research Chair in Climate Dynamics. He and his graduate students conduct research in the area of global-scale climate change. They are using geothermal data obtained from mining exploration boreholes, reaching deep into the ground to study the changes of the temperature at the continental surface during the last millennium. It’s a complicated process. “We have to go down about 500 metres just to measure the remnants of past ground surface temperature changes that occurred in the last millennium,” he says. “If we want to estimate changes further in the past, we have to go much deeper.” Beltrami’s research is attempting to measure how much energy is stored in the ground and also how energy is distributed between the ground and the atmosphere. It’s critical information for environmentalists, policy makers, planners and scientists. As the ground becomes warmer, more carbon dioxide is released from soils, increasing the atmospheric concentration of greenhouse gases. Another aspect of Beltrami’s work relates to regional climate modelling. For example, he and his graduate students have conducted extensive research to project the potential effects of climate change on the propagation of the tick that carries Lyme disease in Nova Scotia and Ontario. He is also developing a climate services centre that will translate global climate model predictions into information that is useful at a local level. The information would allow individual municipalities to access local climate projections, increasing awareness of the potential consequences of climate change on things like infrastructure and public health. The service may also help to support the development of policies to build resilience and mitigate the societal impacts of a changing regional climate. Every part of Beltrami’s research requires his team to use intensive numerical modelling. The numbers are huge and the calculations would be impossible to run on a regular computer. He’s been a user of ACENET since the program started. “ACENET is an essential resource for us,” he says.

St. F.X. Scientist Uses ACENET Network to Study Greenhouse Gas Emissions

Dave Risk spends as much time outdoors as he does in his laboratory at St. Francis Xavier University. He likes it that way. The earth scientist and assistant professor studies gas emissions – CO2, hydrogen sulphide, methane and others – gases that emanate naturally from soils into the Earth’s atmosphere; a passion that takes him to remote places around the world. “We’ve recently set up research sites in Wisconsin, in Cape Breton, in Alaska, in Antarctica,” he says. “We’ve been pretty much in every part of the world from the Arctic Circle to Antarctica.” While much of Risk’s work falls into the realm of theoretical science, it all has a very practical application as well. CO2 and other greenhouse gases are widely accepted to be the culprits of climate change; understanding how they flow in and out of soils is vital for combatting the problem. Risk spends much of his time working in the field or in his Antigonish lab, but he has also enlisted the help of another valuable tool – the ACENET computer system. “I was fortunate to have a graduate student named Nick Nickerson who was very mathematically minded,” says Risk. “He connected with the ACENET Computational Research Consultant, Shah Razul and we talked about our research with him.” Razul looked at a study that Risk was working on from Oregon, measuring the rates of CO2 diffusion over a period of time and then building models to describe the process. “He looked at the study and said: ‘That’s exactly what a supercomputer does,’” says Risk. Razul explained to Risk how he could take the models and recreate them on the ACENET network. It was a eureka moment for the St. F.X. scientist. Today Risk requires all his graduate students to learn computational science skills. He’s also used the ACEnet supercomputer to test real-world instruments that he has developed through another part of his research. In 2011 two of Risk’s graduate students, including Nickerson, started a private company in Halifax called Forerunner Research that provides the techniques developed at St. F.X. to commercial companies in fields such as landfill operation, brownfield remediation, meteorology, mining and oil and gas. The company has received assistance from the Atlantic Innovation Fund and Innovacorp. Today Risk is using ACENET to conduct simulations of soil microbial communities that are producing greenhouse gases. “We’re looking specifically at how they react to higher temperatures – and whether they’ll produce a lot more of the greenhouse gases as a feedback. We have been working on the algorithms for some time, and there are tons of datasets that we now have the ability to digest. We are working with researchers around the world to get these datasets in one place, so that we can run the scripts on ACENET.” He also has plans to use the computer system for some upcoming projects, including new research into human performance. “We have been doing some computer work in this area, which I hope will scale up this coming year.” Risk’s current research could ultimately have a huge impact on the fight to combat greenhouse gas emissions. He says the ACENET computer network could speed up his work considerably. “The ACENET system allows us to see patterns in the field that might be hard to see otherwise. It’s rare to see a field researcher using computer modelling but the two disciplines work together really well.”

Advanced Computing Helps Scientists Track Air Pollution

The health hazards and environmental impacts of emissions from industry, vehicles and other sources are well established: cardiovascular disease, asthma and premature deaths, as well as crop damage and disease outbreaks in certain tree species. Yet little is known about how particulate matter – tiny invisible specks of mineral dust, carbon and other chemicals – moves through the atmosphere and its effects on the health of local populations around the world. That’s changing thanks to the work of Dr. Randall Martin, an atmospheric scientist who uses remote sensing satellites, computer modeling and advanced research computing to identify the trends and magnitude of human exposure to these pollutants. Martin was among six Canadian researchers who met with MPs and Senators on Parliament Hill December 2nd to showcase how government investments in advanced research computing are having an impact internationally, nationally and locally. Organized by Compute Canada and co-hosted by the House of Commons speaker Andrew Scheer, the event attracted several Parliamentarians, including Senator Kelvin Ogilvie, and Minister of State (Science and Technology) Ed Holder who spoke about the importance of advanced computing to many of Canada’s biggest science projects. “Researchers in Canada generate data of unprecedented size and complexity, and our government is committed to ensuring that Canada stays at the cutting edge of this technology,” said Holder. For example, global modeling and the analysis of satellite data require intense calculations and vast data storage – expensive, state-of-the-art technologies that Martin and his team are able to access via ACENET and Compute Canada. “We wouldn’t be able to answer these scientific questions without this level of computational power,” said Martin. “These tools allow us to collaborate with Health Canada and Environment Canada to contribute to science-based decision making to protect the health and well-being of Canadians.” The Atmospheric Composition Analysis Group at Dalhousie is the only research group in the world that has applied satellite remote sensing to infer long-term concentrations of global, ground-level fine particulate matter. Traditional ground-based instruments for monitoring air pollution are located primarily in urban areas, leaving rural and remote communities with no data on the quality of the air they breathe. Martin’s group is able to paint a more comprehensive and accurate picture of air pollution for geographic regions as small as 10 kilometres, using publicly available satellite data generated over the past decade from space agencies around the world, including NASA. “NASA has invested billions of dollars in the preparation and launch of these satellites and in the data collection, and for relatively modest investments here in terms of computing and people, we can leverage that substantial investment,” he said. The biggest surprises from the research have been in areas of south and east Asia, north Africa and the Middle East where coal-fired generating plants and wind-blown mineral dust have contributed to significant air pollution. Other pollution “hot spots” were identified over eastern North America and northern Europe. This research is helping scientists and policymakers understand how chemicals in the atmosphere affect climate change and air quality. The Canadian government used Martin’s data to develop more stringent and comprehensive air quality standards for fine particulate matter, a major component of smog. His team’s work has also contributed to several high-profile global assessments conducted by the Organisation for Economic Co-operation and Development (OECD), the World Health Organization (WHO) and other international agencies. Martin’s group has also had a leading role in the development of an open-source, global, three-dimensional model of atmospheric composition called GEOS–Chem, which is used by more than 70 institutions worldwide. It allows assessment of sources and processes that affect air quality. “One possible benefit from our research is increased life expectancy for people around the world due to improved policies that clean the air that we breathe,” said Martin. “It could also contribute to a better understanding of the effects of human activities on climate change and lead to more informed decisions about how we might best deal with this complex issue.”