Materials Science

A Prize-Winning User

Erin Johnson wouldn’t have won the prestigious Steacie Prize, awarded to early-career scientists, in 2021, without the Digital Research Alliance of Canada’s high-performance computing and the services of ACENET.

“That’s a completely fair statement,” says Johnson, who was an early adopter of high-performance computing, dating back to her student days at Carleton University, Queen’s University and Dalhousie University, as well as her post-doctoral work at Duke University. She’s now a professor and Herzberg-Becke chair in theoretical chemistry at Dalhousie University.

Asked how she would explain her job to a guest at a cocktail party, Johnson says she studies intermolecular interactions within the materials all around us.

“These are the weaker interactions between molecules as opposed to the stronger bonds within a molecule,” Johnson explains. “So, we would, for example, at a cocktail party look at the interactions in beer or wine in a glass — those types of interactions within a liquid or a gas or within a molecular crystal.”

She does this to predict such properties as reactivity, hardness, and conductivity, among others.

“Any chemical observable is something that we can predict through this type of modelling,” she says.

Johnson’s lab, however, might surprise those who envision her working in a chemistry lab full of beakers and bunsen burners. Rather, it’s a computer lab from which she’s developed methods for modeling that are some of the most accurate and efficient available. It was those methods that won her the Steacie Prize.

“We then take those methods and apply them to problems in chemistry,” she explains. “One of the particular problems we’re focusing on is the problem of molecular crystal structure prediction or how molecules would come together to form a 3D solid.”

She likened the ways molecules come together to the ways in which Lego bricks do.

“There are many ways you could conceive of molecules coming and packing together, but not all of those are going to be stable,” she says. “So the challenge is trying to predict how they will actually pack in a solid.”

Once you solve that puzzle, there are applications across several industries, one of the most recognizable being pharmaceuticals.

“If you are producing a drug and you want it in pill form, you want a solid but soluble state,” Johnson says. “When you try to formulate new drugs, you want to screen for all the possible polymorphs (transformations to another form) and find out which ones are the most stable. What you don’t want is for it to easily form a particular polymorph that’s not a very stable one and then change over time so that it’s no longer soluble.”

These methods also have applications for electronics, but instead of looking at solubility, the property of interest would be conductivity.

“Like the solubility, the ability of charge to flow through a material is also dependent on the particular polymorph” Johnson explains. “You can think of many applications where the different solid state properties between polymorphs would affect whether a material was promising or not.”

Johnson says her work would be “completely impossible” without ACENET’s services.

Capturing Excess Heat as a New Energy Source

Jesse Maassen wants to understand how electrons and heat flow through materials so he can capture excess energy from heat sources and use it to generate electrical power. “My research group’s overarching theme is the study of electro-thermal transport in materials and devices — such as semi-conductors and metals — using theory and simulation,” says Maassen, a professor in the physics and atmospheric science department at Dalhousie University. “We focus on understanding what controls the movement of electrons and heat in materials, so we can design new materials with enhanced properties.” One of the materials he studies is called thermoelectrics. When thermoelectrics are placed in contact with heat sources, they can convert the thermal energy into useful electrical energy, that can be used for everything from charging our phones to powering our homes. For example, using heat from combustion in a car, you can power some of the car’s battery. “Thermoelectrics could have a big impact,” he says. “Roughly 60 per cent of the energy we produce is lost as waste heat — it just evaporates into the environment. On a global scale, this adds up to a huge amount of energy we’re throwing away. Thermoelectrics could harness this waste heat.” Maassen’s goal is to improve the efficiency of the energy conversion from thermal to electrical, so this technology can become more widespread. But that requires optimizing how the electrons and heat flow through these materials. “Heat corresponds to the vibrations of the atoms that make up the material — just like waves, the collective motion of the atoms carries thermal energy from one location to another,” Maassen says. “Since we need to resolve things on the atomic scale, our electron and thermal calculations are based on quantum mechanics simulations. This cutting-edge modeling also helps us identify or design materials with exceptional properties even if they don’t yet exist. This can guide experimental researchers towards new discoveries.” In addition to helping reduce global energy consumption, he’d like to improve the speed of computer processors. “The circuits driving our phones and computers are made from billions of tiny electronic devices,” he says. “They’ve been getting smaller, and are now below 10 nanometers. When an electrical current flows through these tiny devices, it generates heat, however heat doesn’t dissipate efficiently in such small structures because the physics are different. This results in higher temperatures that can prematurely burn out the circuit.” It’s a major challenge for the semiconductor industry and the main reason the speed of processors stopped increasing over a decade ago. “Understanding and controlling thermal generation and flow on the nanoscale could have an impact on information technology,” he says. “These insights can help us design new electronics with reduced heating that would run faster and more efficiently.” He uses simulations to gain insights into what controls electron and heat flow in existing and new materials. He does these calculations using ACENET’s super-computers. “Without good computing resources, we wouldn’t be able to make these calculations, and these insights that we’re getting would evaporate,” he says. Even with access to high-powered computing resources, the calculations take a long time. ACENET’s resources played a role in his return to Canada from the U.S. “I knew life would be easier having ACENET available to me,” he says. “The very tough calculations we do can take weeks, but without all these resources, we just wouldn’t do them.”

Outsmarting Superbugs

The evolution of antibiotic-resistant superbugs is one of the biggest threats facing medicine today. Modern antibiotics – long the key to fighting deadly infections – have little effect on the new resistant strains of bacteria that commonly infect hospital patients who are in a weakened state. Now a Cape Breton University scientist is working with a Halifax-based drug company to develop one possible solution to this looming problem. Matthias Bierenstiel is an associate professor of inorganic chemistry and chair of the chemistry department at Cape Breton University. Much of his research involves studying and synthesizing new transition metal complexes – complex molecules that contain two metal centres. Some of the complexes he studies have been found to possess antimicrobial properties that are capable of switching off a bacterium’s resistance to antibiotics. Bierenstiel is helping to develop a way of synthesizing polymer molecules that can be used to fight drug resistant bacteria. “My area of expertise is in the binding of the iron to the polymer,” he says. There are two fundamental questions he’s trying to answer. The first is how these polymers can be manufactured to use as pharmaceuticals. The other is how exactly does the process work. “One of the questions we’re trying to answer is how the polymer wraps around iron molecules. The ACENET network gives us the computer power to model it to examine ways that it binds together. We can also use ACENET to make the next generation of compounds better.” Bierenstiel is working with Chelation Partners, a Halifax-based development stage company. that is using his research in the quest to develop a new platform of chemically synthesized chelating compounds that withhold iron from pathogens. “ACENET allows us to model the reactions without the need to go into the lab. Some runs take several weeks. Even with a supercomputer it takes a considerable amount of time.” Bierenstiel first used the ACENET system six years ago. He turned to it again last year when he began working with Chelation Partners. “My interest is in making a compound and putting it in someone else’s hands to develop and distribute,” says Bierenstiel. Bierenstiel’s research has attracted more than $2 million in equipment and operating funds over the past six years, including from the Canada Foundation for Innovation (CFI), Natural Sciences & Engineering Research Council of Canada (NSERC), Springboard Atlantic, Mitacs, Innovacorp and the National Research Council Canada (NRC).

Designing New Molecules

Jason Masuda has something in common with the alchemists of old. But instead of trying to turn lead into gold, he’s building substances that have never been seen on Earth before. Masuda is a chemistry professor at Saint Mary’s University who is building new molecules from atoms. He says the idea is to use new combinations of atoms to make an actual physical compound with unique chemical properties. “In organic chemistry there are a number of functional groups – specific groups of atoms within molecules that have very characteristic properties, such as aldehydes, ketones, and alcohols – but what we’re doing is making functional groups that have not been made before. Organic chemists understand how the normal functional groups react. We make a new arrangement of atoms and then we study them and how they react with other molecules. That gives us insights into their reactivity. That’s what chemistry is about. Reactions.” The majority of Masuda’s work is done in the lab using glove boxes in an inert environment because many of the molecules he creates are reactive to water and air. “The compounds that we make are not transient things,” he says. “They are actually something you can physically store in a lab.” Once a new molecule has been created, Masuda studies it and catalogs its properties in a library of molecules. “We purify these molecules, we crystallize them and then we analyze them using a variety of techniques. One of the key methods is by using an Xray defractometer on single crystals. That lets us see the places of the atoms in three dimensions.” Masuda also uses ACENET to conduct electronic structure calculations using software called Gaussian09 – a program that places groups of atoms into a structure that is the most stable configuration.“We use that alongside our experimental work to predict the reactivity of these molecules,” he says. Masuda will often use Gaussian to see ahead of time if a molecule will be stable enough to exist in nature. “Gaussian09 is a great tool to save us from wasting time. Because we’re pushing the boundaries of what nature allows, quite often I will generate a molecule and get it to optimize on ACENET and then, if it looks promising, we’ll make it in the lab. There’s a saying that two hours in the library saves you two months in the lab. It’s the same with ACENET. Sometimes a couple of hours with Gaussian09 will save you weeks or months in the lab.” While Masuda creates molecules in the name of pure science, he says giving scientists such as cancer researchers a palette of molecules to work with will ultimately have many practical applications as well. “Basic science leads to new discoveries,” he says. “Often we have no idea what those discoveries will be ahead of time.”

Developing New Products at the Molecular Level

Erika Merschrod is a professor of chemistry at Memorial University and an expert in the field of materials science. She designs, optimizes and tests new materials that respond to the environment in particular ways. Merschrod and her colleagues design, manufacture and study large molecules that have complex structures contained within them, particularly materials that form films. They look for unique properties that can be used to develop useful products, such as colour changes that happen when the films come in contact with other substances. The group then uses those properties to design coatings that can be used in applications like antifouling coatings, sensors and medical tissue development. Modelling the properties of a film, as opposed to an individual molecule, is a complicated process. “Once molecules touch each other, they behave differently than they would if they were just single molecules,” says Merschrod. While Merschrod ultimately tests the materials she develops in a wet lab, she says computer modelling is also essential to the process. “Modelling is crucial. It might take us 10 or 12 steps to develop a material. That can take a lot of time in a lab. If you can use computer modelling to predict ahead of time the kinds of materials you’re going to produce, that can save a lot of time.” “We focus on sensing capabilities, things like colour changes that the molecules help to amplify. One of the questions we try to answer is how do you transform a chemical event into something a human can see. If we can answer that question we can develop materials that detect trace elements that a layperson can use.” “We also develop hierarchical materials computationally. Constructing a multi-scale system is not trivial because of the computational cost, but this forces us to consider and test what the important features of a given system are.” Merschrod says that the ACENET system is useful even to scientists who don’t have a background in computing. “ACENET has a real service oriented approach. That’s one reason it works so well. It’s designed to help real high performance users but it also has a core group of users who are not theorists. It works because the focus is on ease of use; because of the excellent support staff. That support means that my students don’t have to be experts to use it.”

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.”

Making Molecules Dance

It’s a revolutionary idea – a technique that could change the design of nuclear power plants. Mount Allison University scientist Khashayar Ghandi is experimenting with the possibility of converting nuclear radiation directly into electricity using gold nanoparticles that act as a sponge to soak up electrons. Currently nuclear reactors create electricity by heating steam to drive large dynamos. The conversion process Ghandi envisions would eliminate the steps required to convert the energy to thermal and then mechanical energy – increasing efficiency and decreasing costs. Ghandi is an associate professor in chemistry & biochemistry and an associate of the physics department at Mount Allison. His research focuses on sustainable and environmentally friendly energy production methods, and chemical processes for industry. He is working with Atomic Energy of Canada Limited to study radiation produced in nuclear reactors, and with the Atomic Energy of France (a country that produces 75% of its electricity from nuclear power) to understand more about the safe storage of nuclear waste. Ghandi and his team are also working on other green energy solutions, including the development of a process to use sunlight to create hydrogen – a potential storage system for solar energy that would make solar a practical main energy source even when the sun isn’t shining. Other projects include the development of nuclear shields that could lead to more effective radiation treatments for cancer. Ghandi is also experimenting with using specialized clay materials to compress atoms and molecules from three dimensions down to two – a process that has the potential of changing the properties of substances at a molecular level. “If you think about carbon atoms, a diamond is made of carbon atoms spread out into three dimensions,” he says. “Graphite has the same atom in two dimensions.” Because of the complexity of his work, Ghandi and his team often travel to facilities such as TRIUMF national laboratory in Vancouver, ISIS at the Rutherford Appleton Laboratory in the UK and JPARC in Japan to use particle accelerators, pulsed muon sources and other advanced technology. But much of his experimental work is conducted at Mount Allison, often requiring elaborate computer simulations, scientific mechanical design that also need computer design and simulations, spectroscopic and quantum mechanical simulations. Ghandi was one of the first users of the ACENET computer network, joining the ACENET program shortly after it began. “ACENET is a very important resource for us and provides my research students with great opportunities,” he says. The computational power of the ACENET system allows Ghandi to construct elaborate chemical reaction models and test them mathematically before subjecting his ideas to real world testing in the lab. “We’re dealing with lots of data and we have to do some heavy data crunching,” he says. “By doing it this way it helps us to understand the chemistry that’s at work and allows us to make predictions of how reactions are going to behave. That way we can design new materials to perform certain functions before we go to the lab. I always like to have some intuition and a mathematical model before I start.” Ghandi says his work is motivated by the need to develop cost-effective green energy systems, but another passion drives him as well. “The other works we do don’t have a practical application at all,” he says. “We do it for pure imagination. To increase our fundamental understanding of the way atoms and molecules behave. To watch them dance and to understand how this dance led to new physics and chemistry.”

Pushing the Envelope (or Molecule) with Quantum Chemistry

Dr. Jason Pearson’s research team of seven at the University of Prince Edward Island strives to understand the properties of molecules at the electronic level; why they behave the way they do, why some interactions are strong while others are not, and ultimately predict how molecules will behave when interacting with other molecules. It’s a broad scope. They do this by developing and applying computational algorithms. For example, an experimental researcher might have samples from which they are searching for new compounds. Along the way, they might find something with interesting properties, but need to identify the chemical substance. This is where Dr. Pearson’s group can take the experimental data, build every possibility into models and then run simulations with the data that ultimately allows them to understand the molecule. Researchers then can examine the molecule through a new lens so to speak. But it doesn’t stop there. Along the way, Pearson is developing new computational tools and new simulation techniques useful for other researchers. Already a resource to colleagues at the University, Pearson’s long-term focus is to utilize and develop computational technology for the purpose of designing new molecules and materials. His group employs a two-pronged approach whereby state-of-the-art simulation techniques are applied to probe the molecular level of detail in chemical systems, allowing for accurate quantifications of structure, interactions, and mechanisms of action. Simultaneously, they design the next generation of computational algorithms and methodologies for the investigation of electronic structure, specifically focused on the concept of the electron pair. The methods developed in Pearson’s lab can be applied to almost all matter, and therefore can be used in many fields, such as designing new materials, new industrially relevant catalysts and nanotechnologies to name a few. Pearson hopes to further push the bounds of what’s possible in computational chemistry by gathering large data sets in the chemical sciences, creating a database for others to access and utilizing the data to develop new simulation techniques that are faster and more accurate. For example, this approach could enable very accurate simulations on large systems like biomolecules and other polymers. His goal is to develop algorithms that behave like a robot, travelling through the data sets, collecting data and solving problems. The chemistry research that is enabled by Dr. Pearson’s group is addressing a broad scope of the world’s most important technological and societal challenges, such as climate change, energy, security, food supply and health.

Why Materials Do the Things They Do

Dr. Geoffrey Lee-Dadswell is a theoretical physicist at Cape Breton University, who for the past 15 years has been studying why materials do the things they do. Specifically, he studies heat and momentum transport on a very small scale. For an example of large scale heat transport, take a frying pan on a stove. We know that the stove element heats the bottom of a pan to the point that food cooks. However, the handle of the pan doesn’t get as hot. Why? The answer lies in understanding the transport of heat, which obeys Fourier’s Law of Heat Conduction. This law has been known for almost 200 years, but surprisingly, is not well understood. One of the mysteries about Fourier’s Law is that it doesn’t seem to work for some objects on the nanometre-scale. A nanometre is one billionth of a metre. If you were to lay atoms across a nanometre, you might fit only about 10! Computers for example have become faster largely because the parts of their chips have been made smaller over the years. As this process continues, more and more parts of an ordinary desktop computer or smart phone are nano-electronics. Lee-Dadswell studies nano-systems that are one-dimensional, which is to say that for theoretical purposes, they have only length. Now because we live in a three-dimensional world, everything has a width and a depth. However, in some nano-systems, these are so small that they can be ignored. Examples of one-dimensional systems are carbon nano-tubes (think of these like a sheet of graphite that’s been rolled up into a tube) and polymer chains such as the polyethylene chains that pop bottles are made of. Carbon nano-tubes are often a few micrometres long, but can be only five to ten nanometres wide. Physicists once believed that everything obeyed Fourier’s Law of Heat Conduction, but researchers have found that these one-dimensional systems behave differently from other systems –disobeying Fourier’s Law. Moreover, they don’t know why, which also means that they don’t have a solid understanding of why everything else does obey Fourier’s Law. Physical laws are preferably derived from the more fundamental mechanics, but nobody knows how to derive Fourier’s Law from mechanics. If they can’t derive it, then they really don’t understand the law. This drives physicists nuts! It means that we don’t understand things like heat flow as well as we thought. This puzzle began to surface in the early 1900s, but didn’t come to the forefront until the 1970s. It’s challenging to make progress on such a long-standing mystery, and tackling it is therefore rather scary. Lee-Dadswell is one of only a few researchers in the world doing so. Lee-Dadswell generally has one or two undergraduate students working with him. He develops models, and the students then run dozens of simulations in parallel on ACENET systems, each running for possibly weeks and involving tens or hundreds of thousands of atoms interacting with each other. By understanding the fundamental laws of transport, solving problems such as removing heat from nano-electronics and improving refrigeration technology become possible.

Edible Oils

Have you ever wondered why foods contain trans fats, or why dough needs so much salt, or why cheese tastes so good? Dr. David Pink at St. Francis Xavier University is a theoretical physicist working on edible oils, with the intent of making them healthier for people to eat. Food companies will have to replace certain trans fats in their products and the big question is “by what can they be replaced?” The problem arises from the fact that (solid) trans fats help create liquid oil-binding structures in products such as shortenings. Without their “Oil Binding Capacity”, shortenings and similar products just won’t work. But, industrially-manufactured trans fats created via hydrogenation have been shown to damage human health and the US Food & Drug Administration (USFDA) will require producers to cease using them. Accordingly, to replace them, we need alternatives that are inexpensive, edible and behave the same way as trans fats so that consumers won’t be able to tell the difference. Working in collaboration with Dr. Alejandro Marangoni, Professor of Food Science at the University of Guelph, the process begins with trying to understand what solid fats structures arise in edible oils and why they trap the oil so as to exhibit the desired Oil Binding Capacity. Without understanding those fundamental things, researchers can only make, at best, educated guesses as to what ingredient can be used to successfully replace them – an inefficient way to try to solve a multimillion dollar problem. Instead, Pink began by modelling crystalline nanoplatelets, the most stable small solid fats in the oils, then simulated their interactions to study them. Because of the models’ complexity – edible oils involve many components – he had to make use of computer simulations, working with his Research Associate, Bonnie Quinn, and using ACENET. The goal was to predict what structures develop in edible oils. Pink says, “If it wasn’t for ACENET, I wouldn’t even be able to begin.”. Pink predicted the experimental structures which arise in systems using ultra-small angle X-ray scattering (USAXS). He also predicted the existence of stacks of crystalline nanoplatelets, called TAGwoods. His predictions were all confirmed by his PhD student. He then made predictions about solid fats which become coated with semi-liquid oil components. He, Dr. Shajahan Razul of ACENET and Pink’s undergraduate student carried out atomic scale molecular dynamics simulations and showed that Pink’s assumptions about coated solid fats were justified and that they will indeed bind oil. Subsequent projects will address how larger structures get formed, so that he can begin searching for replacements for trans fats. One such project will probe the dynamics of edible oils using dissipative particle dynamics, a simulation technique that can study larger scale systems over longer timescales. In recent months, Pink has branched out. With Dr. Marangoni’s leadership and an industry collaboration, he is modelling cheeses to discover the essential aspects of their structures. Pink is also modelling dough. Bread makers will be required to reduce the amount of salt and this can make the dough sticky. Working with Dr. Erzsebet Papp-Szabo, who provides input about the chemistry of dough, he has just finished developing models and has some preliminary results. Now in his 70s, by most people’s standards, David Pink should be retired. “But,” he said, “I’m simply having too much fun working with Alejandro, with my other colleagues and with my students.” And he is pleased that his work has been recognized by the 2015 Distinguished Service/Outstanding Achievement Award from the Edible Applications Technology division of the American Oil Chemists’ Society.