Climate Dynamics

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.

Supercomputers at the Frontline of Climate-Resilient Forests

When he was introduced to forest genetics as a 23-year-old researcher in India, Dr. Om Rajora became obsessed and devoted to forest genetics research. “Sometimes, even at the cost of my health,” he says, laughing.

Decades later and half a world away, he is still going at it, and busier than ever. He heads the forest genetics and genomics lab and is a professor of Forest Genetics and Genomics at the University of New Brunswick, where he joined as the Tier 1 Canada Research Chair in Forest and Conservation Genomics and Biotechnology. He also coordinates the Population, Ecological and Conservation Genetics research unit at the International Union of Forest Research Organizations, and he developed and published a pioneering book series called Population Genomics.

Through his work, Rajora seeks to reveal the secrets hidden within the genes of our woodlands, offering unprecedented insights into resilience, adaptability, and the preservation of biodiversity (genetic diversity) in the face of a rapidly changing world. His research has encompassed a wide range of forest genetic and genomics topics and fields, which besides contributing to basic science, can be used for conservation of genetic resources and sustainable forest management.

One of those areas involves analyzing the genes, gene expression, and metabolic pathways of trees under ambient and changing climate conditions. This in turn gives hints to how forests respond to environmental changes. By sequencing and analyzing the genes expressed under different scenarios, Rajora aims to identify the genes, biological processes and molecular functions affected by climate change, including those related to photosynthesis and stress response. “For example,” he explains, “this could provide us information about what traits could be affected with elevated levels of CO₂.”

Rajora’s research obsession and a strong work ethic have their limits, however, and today’s rapid gene sequencing techniques have created the need for advanced methods of data analysis and storage.

In a recent project, Rajora and his post-doctoral fellow, Dr. Rajni Parmar, needed to undertake extensive genetic analysis of the red spruce transcriptome and chloroplast genome, and identification and characterization of genes and pathways expressed differentially in response to climate change conditions. This required significant computational resources. In the past, they relied on personal computers for certain analyses, but the advent of next-generation sequencing—rapid DNA/RNA sequencing techniques—and the accumulation of massive amounts of data necessitated the use of supercomputers or computer clusters. ACENET and the Digital Research Alliance of Canada have been instrumental in providing these capabilities.

Dr. Serguei Vassiliev, a research consultant with ACENET, played a pivotal role in the study. He delved into the project, learning the fundamentals of computational bioinformatics, installing software, and creating parallelization schemes to process large problems simultaneously. He also trained the group in essential computational techniques, including genome assembly and annotation, transcriptome construction, statistical analysis of gene expression, and protein interaction network identification.

The outcomes were remarkable: computation time was slashed from weeks to hours, the group acquired advanced computational skills, and they published an article in the International Journal of Molecular Science, with another in progress. Vassiliev’s significant contribution earned him co-authorship on the publication.

“The knowledge provided by this research is beneficial to the global plant genomics community,” explains Rajora. The variations found in gene expression clue scientists into what genes may allow forests to survive adverse conditions. Through international collaboration, scientists can pool their resources, data, and insights to develop innovative solutions that can be applied globally in the face of climate change.

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.

Predicting the Future of Fisheries

Ian Bradbury uses DNA technology to understand what aquatic species — whether Atlantic salmon, cod, crab or lobster to name just a few — Eastern Canada has and how they might respond to stressors such as climate change.

“We look at how things are adapted to the environment using genetic and genomic tools and then we use machine learning and climate models to look at how they might respond in the future,” explains Bradbury, a research scientist with the Department of Fisheries and Oceans and an adjunct professor at Dalhousie and Memorial Universities. (Genetics is the study of how genes work while genomics is the study and mapping of genomes, or the full set of genetic instructions for an organism.)

The goal is to be able to make projections in terms of the rate of change happening with a specific species, as well as how it will respond to climate change and how that might impact fisheries and other stakeholders using those resources in the future.

The classic example, he says, is Arctic char in Labrador, which is culturally important for Indigenous groups along the coast, ecologically important because it’s the dominant freshwater coastal fish species there and notable because it’s at the southern portion of its range in Labrador.

“So it would not be surprising that climate change might be pushing it northward,” Bradbury says. “And we’ve done a lot of work over the last couple of years, some of it using ACENET, to understand how Arctic char in Labrador and north of that, are adapted to their climate and then how climate change might affect that.”

Bradbury is building a baseline or map of genetic variation in Arctic char. His projections suggest that the Arctic char’s range will start moving north, meaning the southern portion of Labrador will no longer be suitable for char, which will have implications for the people living in the area and for the ecosystems that remain there.

Bradbury and his team need ACENET because genetic tools generate massive datasets — multiple terabytes in fact — and since data management and data analysis are most of what they do, they couldn’t do their work without ACENET.

“We don’t have access to the computational power that my students would need to do these sorts of analysis,” Bradbury says.

The students he supervises are sequencing the entire genomes of aquatic species and then analyzing them for differences among individuals and populations.

“We’re making associations with climate on a set, and we’re doing projections for future impacts,” Bradbury says.

While there are other options out there, he says, ACENET is particularly useful because it’s accessible to students. His research team includes students at all levels and postdocs at both Atlantic campuses.

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.”

The Mathematics of a Bumpy Ride

Everyone who flies has experienced turbulence – that uncomfortable sensation of dropping and shaking that happens as an airplane flies through a mass of unstable air. It’s always unpleasant, and can even be dangerous in some cases. Scientists have struggled for a long time to understand and predict turbulence and its effect on aircraft, automobiles, buildings and other common objects, but its causes have largely remained a mystery. Now St. John’s-based scientist Jahrul Alam is making inroads in the study of turbulence and he’s using a lot of computational muscle to conduct his research. Alam is an associate professor of mathematics at Memorial University of Newfoundland and an expert in the field of atmospheric turbulence. “I try to characterize atmospheric turbulence mathematically,” he says. To do that he’s harnessing the computing power of ACENET, using a mathematical simulation model called adaptive wavelet large eddy simulation. Turbulence is a complex process involving millions of tiny variables. To try and understand how it works Alam cuts his data down into atmospheric samples that measure 500 cubic meters in volume. “The smaller the sample the more accurately we can study the process, but turbulence has such huge degrees of freedom that we have to filter the data into manageable portions,” he says. “We could never measure it if we broke it down into something like cubic centimetres, for example. The calculations would be too large.” One of the great enigmas about turbulence is the fact that there is so much of it in places like Atlantic Canada where the ground is often cold. It’s one of the questions that Alam seeks to answer with his calculations. “We know that turbulence is created by heat rising from warm ground, but we don’t really understand why it would be so intense in places where the ground is cold,” he says. “Or at night.” In regions with a cool ground, episodes of wind gusting often manifest as short turbulence bursts, making it even more complicated to measure and predict. Varying ground conditions also add complexity to the study, says Alam. “When wind hits mountains, trees or buildings, turbulence is sometimes enhanced by the interaction.” Alam’s research will ultimately have huge practical applications in fields such as airline safety, structural design and environmental science. With climate change, incidences of serious turbulence will increase, he says – particularly the headline-grabbing incidents that involve injured passengers, aircraft damage and emergency landings. “If we can understand turbulence, maybe we can learn to predict it more accurately so that aircraft can avoid it,” says Alam. Alam says his study using wavelets and the ACENET computer network is unique and is producing some significant results. “These are techniques that very few people in the world are using,” he says. Climate change is also making Alam’s work more pressing. “If we continue global warming, the incidences of atmospheric turbulence will increase,” he says. At the same time, humans are constantly changing the surface of the planet by cutting down forests, building tall buildings and reengineering the ground. All of it has an impact on turbulence. “We need to understand it so that we can predict it and design better structures, and better aircraft and automobiles to deal with it.”

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.”

Understanding Greenhouse Gases

Karine Le Bris is an associate professor of physics at St. Francis Xavier University. Her research centres around the development of new optical detection techniques and characterization of greenhouse gases in the atmosphere. Part of her research involves the identification of the spectral signatures of greenhouse gases and the calculation of their global warming potential, a measure of the amount of heat a particular greenhouse gas traps in the atmosphere. The knowledge of the spectral signatures allows the detection of atmospheric gases using optical ground-based techniques or Earth-orbiting satellites, while the global warming potentials identify which gases should be mitigated in priority. The spectral signatures of most greenhouse gases are usually found experimentally using a device called a Fourier transform spectrometer, says Dr. Le Bris. However, the instrument does not always allow scientists access to the full spectral range of the gas. Sometimes, the isomeric composition of the gas is also not known. “Using a method called density functional theory, the spectral signature of a molecule – how much light a gas absorbs at a particular wavelength – can be estimated,” she says. “By comparing the theoretical data to the experimental ones, we can simulate the spectrum outside of the experimental range and sometimes have access to the isomeric distribution.” Dr. Le Bris enjoys spending time in the lab and conducts much of her research there, but she also relies on ACENET. “I’m mostly an experimentalist,” she says. “But I can’t do everything experimentally.” She uses the ACENET advanced computer systems to optimize the geometry of each isomer and find their vibrational frequencies – complex calculations that often take hours to run. “They are not the types of calculations I could do in a timely manner with a regular computer,” she says. While she admits to being motivated by a love of pure scientific research, Dr. Le Bris says that her work offers other researchers and scientists valuable data that they can use to understand and predict changes in the atmosphere – information that can help scientists, environmentalists and civic planners respond to the effects of climate change. “If we understand climate change in advance it helps us be prepared to deal with it.”