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Brookhaven National Laboratory

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From left, Deyu Lu (sitting), Anatoly Frenkel (standing), Yuwei Lin and Janis Timoshenko. Photo from BNL

By Daniel Dunaief

What changes and how it changes from moment to moment can be the focus of curiosity — or survival. A zebra in Africa needs to detect subtle shifts in the environment, forcing it to focus on the possibility of a nearby predator like a lion.

Similarly, scientists are eager to understand, on an incredibly small scale, the way important participants in chemical processes change as they create products, remove pollutants from the air or engines or participate in reactions that make electronic equipment better or more efficient.

Throughout a process, a catalyst can alter its shape, sometimes leading to a desired product and other times resulting in an unwanted dead end. Understanding the structural forks in the road during these interactions can enable researchers to create conditions that favor specific structural configurations that facilitate particular products.

First, however, scientists need to see how catalysts involved in these reactions change.

That’s where Anatoly Frenkel, a professor at Stony Brook University’s Department of Materials Science and Chemical Engineering with a joint appointment in Brookhaven National Laboratory’s Chemistry Division, and Janis Timosheko, a postdoctoral researcher in Frenkel’s lab, come in.

Working with Deyu Lu at the Center for Functional Nanomaterials and Yuwei Lin and Shinjae Yoo, both from BNL”s Computational Science Initiative, Timoshenko leads a novel effort to use machine learning to observe subtle structural clues about catalysts.

“It will be possible in the future to monitor in real time the evolution of the catalyst in reaction conditions,” Frenkel said. “We hope to implement this concept of reaction on demand.”

According to Frenkel, beamline scientist Klaus Attenkofer at BNL and Lu are planning a project to monitor the evolution of catalysts in reaction conditions using this method.

By recognizing the specific structural changes that favor desirable reactions, Frenkel said researchers could direct the evolution of a process on demand.

“I am particularly intrigued by a new opportunity to control the selectivity (or stability) of the existing catalyst by tuning its structure or shape up to enhance formation of a desired product,” he explained in an email.

The neural network the team has created links the structure and the spectrum that characterizes the structure. On their own, researchers couldn’t find a structure through the spectrum without the help of highly trained computers.

Through machine learning, X-rays with relatively lower energies can provide information about the structure of nanoparticles under greater heat and pressure, which would typically cause distortions for X-rays that use higher energy, Timoshenko said.

The contribution and experience of Lin, Yoo and Lu was “crucial” for the development of the overall idea of the method and fine tuning its details, Timoshenko said. The teaching part was a collective effort that involved Timoshenko and Frenkel.

Frenkel credits Timoshenko for uniting the diverse fields of machine learning and nanomaterials science to make this tool a reality. For several months, when the groups got together for bi-weekly meetings, they “couldn’t find common ground.” At some point, however, Frenkel said Timoshenko “got it, implemented it and it worked.”

The scientists used hundreds of structure models. For these, they calculated hundreds of thousands of X-ray absorption spectra, as each atom had its own spectrum, which could combine in different ways, Timoshenko suggested.

They back-checked this approach by testing nanoparticles where the structure was already known through conventional analysis of X-ray absorption spectra and from electron microscopy studies, Timoshenko said.

The ultimate goal, he said, is to understand the relationship between the structure of a material and its useful properties. The new method, combined with other approaches, can provide an understanding of the structure.

Timoshenko said additional data, including information about the catalytic activity of particles with different structures and the results of theoretical modeling of chemical processes, would be necessary to take the next steps. “It is quite possible that some other machine learning methods can help us to make sense of these new pieces of information as well,” he said.

According to Frenkel, Timoshenko, who transferred from Yeshiva University to Stony Brook University in 2016 with Frenkel, has had a remarkably productive three years as a postdoctoral researcher. His time at SBU will end by the summer, when he seeks another position.

A native of Latvia, Timoshenko is married to Edite Paule, who works in a child care center. The scientist is exploring various options after his time at Stony Brook concludes, which could include a move to Europe.

A resident of Rocky Point during his postdoctoral research, Timoshenko described Long Island as “extremely beautiful” with a green landscape and the nearby ocean. He also appreciated the opportunity to travel to New York City to see Broadway shows. His favorite, which he saw last year, is “Miss Saigon.”

Timoshenko has dedicated his career to using data analysis approaches to understanding real life problems. Machine learning is “yet another approach” and he would like to see if this work “will be useful” for someone conducting additional experiments, he said.

At some point, Timoshenko would also like to delve into developing novel materials that might have an application in industry. The paper he published with Frenkel and others focused only on the studies of relatively simple monometallic particles. He is working on the development of that method to analyze more complex systems.

This work, he suggested, is one of the first applications of machine learning methods for the interpretation of experimental data, not just in the field of X-ray absorption spectroscopy. “Machine learning, data science and artificial intelligence are very hot and rapidly developing fields, whose potential in experimental research we have just started to explore.”

 

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From left, BNL Staff Scientist Lihua Zhang, former postdoctoral researcher Vitor Manfrinato and BNL Senior Scientist Aaron Stein. Photo courtesy of BNL

By Daniel Dunaief

It took a village to build this particular village or, more precisely, a pattern so small it could fit thousands of times over on the head of a pin.

Working at Brookhaven National Laboratory’s Center for Functional Nanomaterials, a team of researchers wanted to exceed the boundaries of creating small patterns with finely honed features. The group included Aaron Stein, a senior scientist at CFN, Charles Black, the head of CFN, Vitor Manfrinato, a former postdoctoral researcher at BNL and several other key members of the BNL team. The team added a pattern generator that allowed them to control a microscope to create a pattern that set a record for drawing at the 1-nanometer scale.

Just for reference, the width of a human hair is about 80,000 to 100,000 nanometers. The size of the pattern is a breakthrough as standard tools and processes generally produce patterns on a scale of 10 nanometers. “We were able to push that by a factor of five or 10 below,” Stein said. “When you get to those small size scales, that’s pretty significant.”

In this case, the novelty that enabled this resolution originated with the idea of employing the scanning transmission electron microscope, which isn’t typically used for patterning to create these images. The scanning transmission electron microscope has an extraordinarily high resolution, while the pattern generator allowed them to control the patterns they drew and other aspects of the exposure.

Researchers at CFN are focusing on this spectacularly small world to manipulate properties such as chemical reactivity, electrical conductivity and light interactions. “This new development is exciting because it will allow other researchers to create nanomaterials at previously impossible size scales,” Kevin Yager, a group leader at CFN explained in an email. “There are numerous predictions about how materials should behave differently at a size scale at 1 to 3 nanometers. With this patterning capability, we can finally test some of those hypotheses,” he said.

Stein and the research team were able to create this pattern on a simple polymer, polymethyl methacrylate, or PMMA for short. “It’s surprising to us that you don’t need fancy materials to create these kinds of features,” said Stein. “PMMA is a common polymer. It’s Plexiglas. It’s kind of exciting to do something that is beyond what people have done” up until now.

One of the many possible next steps, now that the researchers have developed this proof of principle, is to apply this technique to a substance that might have commercial use. Taking the same approach with silicon, for example, could lead to innovations in electronics. “We can make them with a high clarity of patterns and sharp corners, which we can’t do with other techniques,” Stein said.

The BNL research team would “like to apply this to real world research,” which could include electronics and transistors, as well as photonics and plasmonics, he added. This project arose out of a doctoral thesis that Manfrinato was conducting. He is one of the many scientists who came to BNL, which isa Department of Energy funded user facility that provides tools to conduct research for scientists from around the world.

Manfrinato was a doctoral student in Professor Karl Berggren’s group at the Massachusetts Institute of Technology. In an email, Manfrinato explained that he was interested in pushing the resolution limits of e-beam lithography. “BNL has state of the art facilities and expert staff, so our collaboration was a great fit, starting in 2011,” he explained.

Other scientists thought it was worthwhile to continue to pursue this effort, encouraging him to “come here and work on this. It’s a home grown project,” Stein said. Manfrinato worked on his doctorate from 2011 to 2015, at which point he became a postdoctoral researcher at BNL. His efforts involved several groups, all within the Center for Functional Nanomaterials at BNL. Stein, Manfrinato and Black worked on the lithography part of the project, while Lihua Zhang and Eric Stach developed the microscopy. Yager helped the team to understand the processes by which they could pattern PMMA at such small scale lengths.

“No one or two of us could have made this happen,” Stein said. “That’s really the joy of working in a place like this: There are [so many] permutations for collaborating.” Indeed, the other scientists involved in this study were Yager; Zhang, a staff scientist in electron microscopy; Stach, the electron microscopy group leader at CFN; and Chang-Yong Nam, who assisted with the pattern transfer.

Manfrinato, who is now a research and development engineer at a startup company in the San Francisco Bay area, explained that this lithographic technique has numerous possible applications. Other researchers could create prototypes of their devices at a level below the 10-nanometer scale at CFN. Manfrinato interacts with the BNL team a few times a month and he has “exciting results to be further analyzed, explored and published,” he wrote in an email.

Stein said BNL would like to offer this patterning device for other users who come to BNL. Ultimately, researchers use materials at this scale to find properties that may vary when the materials are larger. Sometimes, the properties such as color, chemical reactivity, electrical conductivity and light interactions change enough to create opportunities for new products, innovations or more efficient designs.

A resident of Huntington, Stein and his wife Sasha Abraham, who works in the planning department for the Town of Huntington, have a 15-year-old daughter Lily and a 13-year-old son Henry.

As for his work, Stein said he’s interested in continuing to push the limits of understanding various properties of nanomaterials. “My career has been using the e-beam lithography to make all sorts of structures,” he said. “We’re in a regime where people have not been there before. Finding the bottom is very interesting. Figuring out the limits of this technique is, in and of itself” an incredible opportunity.

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From left, Lisa Miller with her research team Andrew McGregor, Alvin Acerbo, Tiffany Victor, Randy Smith, Ruth Pietri, Ryan Tappero, Nadia Hameed, Tunisia Solomon, Paul Panica and Adam Lowery. Photo by Roger Stoutenburgh, BNL

By Daniel Dunaief

Most of the people at the building that cost near a billion dollars are pulled in different directions, often, seemingly, at the same time. They help others who, like them, have numerous questions about the world far smaller than the eye can see. They also have their own questions, partnering up with other researchers to divide the work.

Lisa Miller, a senior biophysical chemist at Brookhaven National Laboratory, lives just such a multidirectional and multidimensional life. The manager for user services, communications, education and outreach at the National Synchrotron Light Source II, Miller recently joined forces with other scientists to explore the potential impact of copper on a neurodegenerative disease called cerebral amyloid angiopathy (CAA).

Miller is collaborating with Steve Smith, the director of structural biology in the Department of Biochemistry and Cell Biology at Stony Brook University and William Van Nostrand, a professor in the Department of Neurosurgery at SBU who will be moving to the University of Rhode Island. The trio is in the second year of a five-year grant from the National Institutes of Health.

Miller’s role is to image the content, distribution and oxidation state of copper in the mouse brain and vessels. Van Nostrand, whom Smith described as the “glue” that holds the group together, does the cognitive studies and Smith explores the amyloid structure.

In an email, Smith explained that Van Nostrand’s primary area of research is in CAA, while he and Miller were originally focused elsewhere.

Potentially toxic on its own, copper is transported in the body attached to a protein. When copper is in a particular ionic state — when it has two extra protons and is looking for electrons with which to reduce its positive charge — it reacts with water and oxygen, producing hydrogen peroxide, which is toxic.

Miller and her colleagues are working on a technique that will enable them to freeze the tissue and image it. Seeing the oxidation state of the metal requires that it be hydrated, or wet. The X-rays, however, react with water, causing radiation damage to the tissue.

To minimize this damage, the researchers freeze the tissue. At NSLS-II, a team of scientists are working to develop X-ray-compatible cryostages that will allow them to freeze and image the tissue.

Miller is trying to figure out where and why the copper is binding to an amyloid beta protein. This is the same protein that’s involved in plaques prevalent in the brains of people with Alzheimer’s disease.

In Alzheimer’s patients, the plaques are found in the parenchyma, or the extracellular space around the brain cells. In CAA, the deposits are attached to the surface of the blood vessels on the brain side.

Lisa Miller and her dog Dora on a recent 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina Photo from Lisa Miller

The current hypothesis about how copper becomes reactive in the brain originates from work Van Nostrand and Smith published recently. They suggested that the amyloid fibrils in CAA adopt an anti-parallel orientation and the fibrils in the plaques in Alzheimer’s are in a parallel orientation. The anti-parallel structure predicts that there is a binding site for copper that, if occupied, would stabilize the structure.

“We are currently working to establish if this idea is correct,” Smith explained in an email, suggesting that the NSLS-II provides a “unique resource for addressing the role of copper in CAA. The data [Miller] is collecting are essential, key components of the puzzle.”

The NSLS-II will provide the kind of spatial resolution that allows Miller to measure how much copper is in the deposits. Ideally, she’d like to see the oxidation state of the copper to see if a reaction that’s producing hydrogen peroxide is occurring.

A challenge with peroxide is that it’s hard to find in a living tissue. It is highly reactive, which means it does its damage and then reverts to water and oxygen.

As someone with considerable responsibilities outside her own scientific pursuits, Miller said she spends about a quarter of her time on her own research. One of Miller’s jobs during the summer is to host the open house for NSLS-II, which allows members of the community to visit the facility. This year, at the end of July, she “was thrilled” to host about 1,600 members of the community.

“Most of them wanted to go on the floor and meet the scientists and walk” around the three quarters of a mile circle, she said. While they are interested in the research, the surprising mode of transportation strikes their fancy when they trek around the site.

“The thing that fascinates them when they walk in the door is the tricycles,” she said. The NSLS-II can’t take credit for being the first facility to use these adult-sized tricycles, which number over 100 at the facility. “It’s a synchrotron thing.”

The previous NSLS at BNL was too compact and had too many turns, which made the three-wheeled vehicles, which, like a truck, need a wider turning radius to maneuver on a road, impractical.

Miller, who is a part of the trike-share program, is an avid hiker. This summer, she completed a 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina. This section was located in the area of totality for the solar eclipse and Miller was able to witness the astronomical phenomenon at Siler Bald in North Carolina.

A resident of Wading River, Miller, who grew up in the similarly flat terrain of Cleveland, spends considerable time walking and running with her rescue mutt Dora, who accompanied her on her recent hike.

While Miller finds the research she does with copper rewarding, she said she also appreciates the opportunities NSLS-II affords her. “Every day is different and we never know what project will show up next,” she said.

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Alex Orlov on the campus of the University of Cambridge. Photo by Nathan Pitt, University of Cambridge

By Daniel Dunaief

The Ukranian-born Alex Orlov, who is an associate professor of materials science and chemical engineering at Stony Brook University, helps officials in a delicate balancing act.

Orlov, who is a member of the US-EU working group on Risk Assessment of Nanomaterials, helps measure, monitor and understand the hazards associated with nanoparticles, which regulatory bodies then compare to the benefit these particles have in consumer products.

“My research, which is highlighted by the European Union Commission, demonstrated that under certain conditions, [specific] nanoparticles might not be safe,” Orlov said via Skype from Cambridge, England, where he has been a visiting professor for the past four summers. For carbon nanotubes, which are used in products ranging from sports equipment to vehicles and batteries, those conditions include exposure to humidity and sunlight.

“Instead of banning and restricting their production” they can be reformulated to make them safer, he said.

Orlov described how chemical companies are conducting research to enhance the safety of their products. Globally, nanotechnology has become a growing industry, as electronics and drug companies search for ways to benefit from different physical properties that exist on a small scale. Long Island has become a focal point for research in this arena, particularly at the Center for Functional Nanomaterials and the National Synchrotron Light Source II at Brookhaven National Laboratory.

Alex Orlov on the campus of the University of Cambridge. Photo by Nathan Pitt, University of Cambridge

Indeed, Orlov is working at the University of Cambridge to facilitate partnerships between researchers in the chemistry departments of the two universities, while benefiting from the facilities at BNL. “We exchange some new materials between Cambridge and Stony Brook,” he said. “We use BNL to test those materials.”

BNL is an “essential facility,” Orlov said, and is where the postdoctoral student in his lab and the five graduate students spend 30 to 60 percent of their time. The data he and his team collect can help reduce risks related to the release of nanomaterials and create safer products, he suggested.

“Most hazardous materials on Earth can be handled in a safe way,” Orlov said. “Most scientific progress and environmental protection can be merged together. Understanding the environmental impact of new technologies and reducing their risks to the environment should be at the core of scientific and technological progress.”

According to Orlov, the European Union spends more money on technological safety than the United States. European regulations, however, affect American companies, especially those that export products to companies in the European Union.

Orlov has studied how quickly toxic materials might be released in the environment under different conditions.

“What we do in our lab is put numbers” on the amount of a substance released, he said, which informs a more quantitative understanding of the risks posed by a product. Regulators seek a balance between scientific progress and industrial development in the face of uncertainty related to new technologies.

As policy makers consider the economics of regulations, they weigh the estimated cost against that value. For example, if the cost of implementing a water treatment measure is $3 million and the cost of a human life is $7 million, it’s more economical to create a water treatment plan.

Orlov teaches a course in environmental engineering. “These are the types of things I discuss with students,” he said. “For them, it’s eye opening. They are engineers. They don’t deal with economics.”

In his own research, Orlov recently published an article in which he analyzed the potential use of concrete to remove pollutants like sulfur dioxide from the air. While concrete is the biggest material people produce by weight and volume, most of it is wasted when a building gets demolished. “What we discovered,” said Orlov, who published his work in the Journal of Chemical Engineering, “is that if you take this concrete and expose new surfaces, it takes in pollutants again.”

Fotis Sotiropoulos, the dean of the College of Engineering and Applied Sciences at SBU, said Orlov has added to the understanding of the potential benefits of using concrete to remove pollutants.

Other researchers have worked only with carbon dioxide, and there is “incomplete and/or even nonexistent data for other pollutants,” Sotiropoulos explained in an email. Orlov’s research could be helpful for city planners especially for end-of-life building demolition, Sotiropoulous continued. Manufacturers could take concrete from an old, crushed building and pass waste through this concrete in smokestacks.

To be sure, the production of concrete itself is energy intensive and generates pollutants like carbon dioxide and nitrogen dioxide. “It’s not the case that concrete would take as much [pollutants] out of the air as was emitted during production,” Orlov said. On balance, however, recycled concrete could prove useful not only in reducing waste but also in removing pollutants from the air.

Orlov urged an increase in the recycling of concrete, which varies in the amount that’s recycled. He has collaborated on other projects, such as using small amounts of gold to separate water, producing hydrogen that could be used in fuel cells.

“The research showed a promising way to produce clean hydrogen from water,” Sotiropoulos said.

As for his work at Cambridge, Orlov appreciates the value the scientists in the United Kingdom place on their collaboration with their Long Island partners.

“Cambridge faculty from disciplines ranging from archeology to chemistry are aware of the SBU/BNL faculty members and their research,” Orlov said. A resident of Smithtown, Orlov has been on Long Island for eight years. In his spare time, he enjoys hiking and exploring new areas. As for his work, Orlov hopes his work helps regulators make informed decisions that protect consumers while making scientific and technological advances possible.

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From left, scientist Lin Yang at the LiX beamline demonstrates how the beam hits the sample to high school teachers James Ripka, Mary Kroll, Fred Feraco, Janet Kaczmarek and Jocelyn Handley-Pendleton. Photo from BNL

By Daniel Dunaief

He helped build it and now a range of researchers are coming.

Lin Yang helped create the LiX beamline at the National Synchrotron Light Source II at Brookhaven National Laboratory, which is attracting researchers eager to study the fine structure and function of everything from proteins to steel.

The lead scientist for the LiX beamline at the NSLS-II at BNL, Yang was the control account manager for the construction of the beamline and was the spokesperson for a team that wrote the original beamline development proposal.

“In our case, the scattering from the sample is sensitive to the underlying structure” of materials, Yang said. “That’s why people want to use scattering to study their samples.”

Like the other beamlines at the NSLS-II, the LiX enables scientists to use sophisticated equipment to search for links between structures and function. Each beamline has a three-letter acronym. In the case of LiX, the “Li” stands for life sciences, while the “X” represents X-ray scattering.

When they designed the beamline, LiX researchers were seeking optics that were capable of producing a beam to conform to the specifications required for different types of measurements. They then designed an experimental station that is suitable for handling biological samples. Specifically, that involved developing an automated sample handler for measurements on protein molecules in solution.

“With atomic resolution structures and functional assays, we do get new insights [about] important ions such as calcium,” which are involved in signaling and physiology, Qun Liu, a principal investigator in the Biology Department at BNL, described in an email. “LiX will be essential to allow us [to see] the transport process in real time and space.” Liu wrote that Yang is an “outstanding X-ray beamline scientist” who is also well known for his pioneering work on membrane diffraction.

The ability to perform measurements using a beam of a few microns is “pretty unique right now,” which also attracted researchers working with steel samples, Yang said. “When we designed the instrument, our focus [was] on the biological structure” but the beamline is “versatile enough” that it has found other uses, Yang said.

Researchers working with steel realized that the same diffraction-based approach to finding underlying structures in living tissue could also shed light on the structures of their samples.

In everyday life, diffraction is visible from the wavelengths of light that form the hologram on a credit card. Scientists working with steel have been applying for time on the LiX beamline, too, creating a competitive environment for researchers working in both fields.

Lynne Ecker, the deputy department chair in the Nuclear Science and Technology Department at Brookhaven National Laboratory, has used the beamline to study the effect of neutrons and ions on steel.

“Ions will only damage steel so far,” Ecker said. The LiX is “perfect” to study the degree of the damage. Ecker said she’s tried this kind of analysis in other places, but the LiX provides better spatial resolution. The LiX scientists are working on improving the degree of automation for sample handling and data processing.

“We are about to install a six-axis robot, which is typically seen in industrial automation, to help realize unattended overnight measurements on protein solution samples,” Yang said. The robot is already at the facility and Yang and his team will be installing the support structure to mount the robot in the experimental station this month. “The more challenging task is to put the software in place so that the beamline can control the robot,” he explained in an email.

The LiX beamline uses lenses made from beryllium, which are transparent to X-rays. For X-rays at the wavelength of about one angstrom, about 93 percent can pass through about a millimeter of beryllium. That compares favorably to aluminum, which allows about 2 percent to pass through at the same thickness.

The LiX beamline can run at 500 frames per second, which produces a wealth of data. In practice, it may take up to a second for the detector to accumulate enough signal from the sample. Still, the beamline can generate enough data that the experimenter may not be able to examine it frame by frame, which makes automated data processing more important.

Scientists have used the beamline to explore the structure of plants. These researchers mainly want to understand how materials like cellulose are organized within different parts of the plant and in different plants.

In bones, researchers can differentiate between organic matter like collagen and inorganic matter. Not only can they determine where they are, but they can also explore their orientation in a sample. Bones are easy samples since collagen and minerals in bone have distinctive scattering and diffraction patterns, Yang said. Researchers “like to look at how biological molecules change their shape as they interact with their functional partners,” Yang said.

A resident of East Setauket, Yang lives with his wife Mian Wang, who is an architect in Farmingdale, and their two daughters. A fan of tennis, Yang plays as often as he can during the summer at the Three Village Tennis Club.

Yang grew up in Yunnan province in the southwest of China. Trained as a physicist, Yang picked up knowledge of molecular biology from his years of working with other scientists. In his work, he gets to combine his talents in engineering, programming and molecular biology.

“We learn new things when we interact with our users/guest researchers since we first need to learn about their problems before we can help solve them,” he described in an email. Yang hopes the research he and the team at the LiX support will result in high-impact publications. “As more researchers know about us and our capabilities, I expect more people will want to perform experiments at our beamline,” he said.

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Standing near one of the X-ray scattering instruments, Kevin Yager holds a collection of samples, including a self-assembling polymer film. Photo courtesy of BNL

By Daniel Dunaief

Throw a batch of LEGOs in a closed container and shake it up. When the lid is opened, the LEGOs will likely be spread out randomly across the container, with pieces facing different directions. Chances are few, if any, of the pieces will stick together. Attaching strong magnets to those pieces could change the result, with some of the LEGOs binding together. On a much smaller scale and with pieces made from other parts, this is what researchers who study the world of self-assembled materials do.

Scientists at the Center for Functional Nanomaterials and at the National Synchrotron Light Source II at Brookhaven National Laboratory experiment with small parts that will come together in particular ways based on their energy landscapes through a process called self-assembly.

Every so often, however, a combination of steps will alter the pathway through the energy landscape, causing molecules to end up in a different final configuration. For many scientists, these so-called nonequilibrium states are a nuisance.

Above, Kevin Yager listens to sonified data. When data is sonified, it is translated into sound. Photo by Margaret Schedel

For Kevin Yager, they are an opportunity. A group leader at the CFN who works closely with the NSLS-II, the McGill University-educated Yager wants to understand how the order of these steps can change the final self-assembled product. “In the energy landscape, you have these peaks and valleys and you can take advantage of that to move into a particular state you want,” Yager said. “The high level goal is that, if we understand the fundamentals well enough, we can have a set of design rules for any structure we can dream up.”

At the CFN, Yager manages a nanofabrication facility that uses electron-beam lithography and other techniques to make nanostructures. He would like to fabricate model batteries to show the power of nanomaterials. He is also determined to understand the rules of the road in the self-assembly process, creating the equivalent of an instruction manual for miniature parts.

In future years, this awareness of nonequilibrium self-assembly may lead to revolutionary innovations, enabling the manufacture of parts for electronics, drugs to treat disease and deliver medicine to specific locations in a cell and monitors for the detection of traces of radioactivity or toxins in the environment, among many other possibilities.

Yager’s colleagues saw considerable opportunities for advancement from his work. Nonequilibrium self-assembly has “significant potential for a broad range of nanodevices and materials due to its ability to create complex structures with ease,” Oleg Gang, a group leader in Soft and Bio Nanomaterials at the CFN, explained in an email. Yager is an “excellent scientist” who produces “outstanding results.”

One of the things Yager hopes his research can develop is a way to “trick self-assembly into making structures they don’t natively want to make” by using the order of steps to control the final result.

As an example, Yager said he developed a sequence of steps in which nanoscale cylinders pack hexagonal lattices into a plane. These lattices tend to point in random directions as the cylinders form. By following several steps, including sheer aligning a plane and then thermal processing, the cylinders flip from horizontal to vertical as they inherit the alignment of the sheered surface. Flipping these cylinders, in turn, causes the hexagons all to point in the same direction. When Yager conducted these steps in a different order, he produced a different structure.

Broadly speaking, Yager is working on stacking self-assembling layers. In his case, however, the layers aren’t like turkey and swiss cheese on a sandwich, in which the order is irrelevant to the desired final product. Each layer has a hand in directing the way the subsequent layers stack themselves. Choosing the sequence in which he stacks the materials controls their structure.

Yager is working with Esther Takeuchi and Amy Marschilok at Stony Brook University to develop an understanding of the nanostructure of batteries. Gang suggested that Yager’s expertise is “invaluable for many scientists who are coming to the CFN to characterize nanomaterials using synchtrotron methods. In many cases, it would probably be impossible to achieve such quantitative understanding without [Yager’s] input.”

Yager and his wife Margaret Schedel, an associate professor in the Department of Music at Stony Brook University who is a cellist and a composer, live in East Setauket. The couple combined their talents when they sought ways to turn the data produced by the CFN, the NSLS and the NSLS-II into sound.

Scientists typically convert their information into visual images, but there’s “no reason we can’t do that with sound,” Yager said. “When you listen to data, you sometimes pick up features you wouldn’t have seen.”

One of the benefits of turning the data into sound is that researchers can work on something else and listen to the collection of data in the background, he said. If anything unexpected happens, or there is a problem with a sample or piece of equipment, they might hear it and take measures more rapidly to correct the process. “This started as a fun collaboration,” Yager said, “but it is useful.”

Schedel is working on sonifying penguin data as well. She also sonified wave data on Long Island. “By listening to the tides quickly, larger patterns emerge,” she said, adding that Yager thought the idea was theoretically interesting until he listened to misaligned data and then he recognized its benefit.

Schedel’s goal is to see this sonification effort spread from one beamline to all of them and then to the Fermilab near Chicago and elsewhere. She wants sonification to become “an ear worm in the science community.”

While Schedel introduced Yager to the world of sound in his research, he introduced her to sailing, an activity he enjoyed while growing up in the suburbs of Montreal. When she sails with him, they are “half in and half out of the boat,” Schedel said. It’s like two people “flying a kite, but you are the kite. You have to learn how to counterbalance” the boat. They hike out so they can take turns faster without tipping over, she said.

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HXN team members, from left, Evgeny Nazaretski, Ken Lauer, Sebastian Kalbfleisch, Xiaojing Huang, Yong Chu, Nathalie Bouet and Hanfei Yan. Photo courtesy of BNL

By Daniel Dunaief

There’s precision in measurements and then there’s the world of Yong Chu. The head of a beamline that’s housed off to the side in a separate, concrete structure from similar efforts at Brookhaven National Laboratory, Chu led the design, construction and commissioning of a sophisticated beamline with a resolution of as low as 3 nanometers, which he hopes will get down to 1 nanometer within a year.

Just as a measure of contrast, a human hair is about 80,000 nanometers wide. Why so fine a resolution? For starters, seeing objects or processes at that high level can offer insights into how they function, how to improve their manufacture or how to counteract the effects of harmful processes.

With a battery, for example, the Hard X-ray Nanoprobe, or HXN beamline, could help reveal structural weaknesses in the nanostructure that could cause safety issues. In biology, numerous functions involve sub-cellular organelles that respond to proteins. Proteins are typically smaller than the HXN beamline can image, although researchers can tag the proteins with metals, which allows Chu, his colleagues and visiting scientists to see an aggregate of these proteins.

The HXN beamline can also help explore environmental problems, such as how plants transport harmful nanoparticles to their fruits or how artificial compounds absorb nuclear waste. Imaging beamlines that use micro-focused beams typically offer spatial resolution of 10 microns, 1 micron or even 100 nanometers, according to Ryan Tappero, the head scientist at the X-ray Fluorescence Microprobe at BNL, who has used the HXN for his research. Using the NSLS II source properties and a new x-ray optics development routinely offers resolution of 10 nanometers, which pushes the spatial resolution down by another factor of 10, which makes the HXN, according to Tappero, a “game changer.”

Tappero described Chu as a “rock star” and suggested he was an “exceptional beamline scientist” who is “very knowledgeable about X-ray optics.”

BNL houses 19 beamlines at the National Synchrotron Light Source II, a state-of-the-art facility large enough that scientists ride adult tricycles inside it to travel from one beamline to another and to transport supplies around the facility. BNL is building another nine beamlines that it hopes to have operational within the next 18 months. Each of these beamlines offers a different way to explore the world of matter. Some beamlines do not use a focused beam, while others produce beams with high angular or high energy resolution. Imaging beamlines such as the HXN produce a small beam size.

The HXN beamline has the highest spatial resolution of any beamline at the NSLS-II. Scientists building the HXN grew a nanofocusing lens with a dedicated deposition system that was constructed at the NSLS-II Research and Development lab. The system grew a nanofocusing lens a layer at a time, alternating materials and controlling the thickness at better than 1 nanometer, Chu explained.

The beamline where Chu works has padded walls, a door separating it from the rest of the light source and a monitor that records the temperature to the thousandths of a degree. “We are constantly monitoring the temperature around the X-ray microscope and inside of the X-ray microscope chamber,” he said. Around the microscope, he can keep the temperature stable within 0.03 degree Celsius. In the chamber, the scientists maintain the temperature at better than 0.003 degree Celsius.

So, now that Chu and his colleagues built their beamline, have the scientists come? Indeed, the interest in using the HXN has been well above the available time slots. For the three cycles each year, BNL receives about four requests for each available time. This reflects the unique qualities of the instrument, Chu said, adding that he doesn’t expect the rate to drop considerably, even as the HXN continues to operate, because of the ongoing demand.

Researchers have to go through a peer review process, where their ideas are graded for the likelihood of success and for the opportunity to learn from the experiments. All beam time proposals are reviewed by external expert panels, which examine the scientific merit, appropriateness of use of the facility, capability of proposers and quality of prior performance and the research plan and technical feasibility.

Chu fields about 10 calls per month from scientists who want to speak with him about the feasibility of their ideas. He may suggest another station at the NSLS-II or at the Advanced Photon Source at Argonne National Laboratory in Chicago, where he was a beamline scientist starting in 1999.

“I know many of the beamlines” at the Advanced Photon Source, he said. “I recommend some of the potential users to perform experiments at the APS first before coming to the HXN.” By the time scientists arrive at his beamline, Chu said he’s gotten to know them through numerous discussions. He considers them “as a guest” at the HXN hotel. “We try to make sure the experimental needs for the users are met as much as possible,” he said.

The HXN beamline has three staff scientists and two postdoctoral fellows who remain in contact with scientists who use the facility. “For most of the users, at least one of us is working throughout the weekends and late evenings,” said Chu.

Not just a staff scientist, Chu is also a user of the HXN, with currently one active general user proposal through a peer review process in which he is collaborating with Stony Brook University and BNL scientist Esther Takeuchi to explore the nanostructure of metal atoms during phase separation in batteries.

Chu and his wife Youngkyu Park, who works at Cold Spring Harbor Laboratory as a research investigator in basic and preclinical cancer research, live in Northport. The couple’s 22-year-old son Luke is attending Nassau Community College and is planning to transfer to Stony Brook this fall to study engineering. Their daughter Joyce is 18 and is enrolled in the Parsons School of Design in New York.

Chu grew up in Seoul, South Korea, and came to the United States when he was 18. He attended Caltech. While Chu’s parents wanted him to become a doctor, he was more inspired by a cartoon called Astro Boy, in which a scientist, Dr. Tenma, is a hero solving problems. As for the work of the scientists who visit his beamline, Chu said the “success of individual users is the success of the beamline.”

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Percy Zahl. Photo courtesy of BNL

By Daniel Dunaief

When he was in high school in Negenborn, Germany, Percy Zahl built his own computer, with some help from one of his father’s friends. Nowadays, Zahl spends considerable time improving the computer capability of an open-source community drive software project that helps researchers see structures and interactions at a subatomic level.

Recently, Zahl, who is an associate scientist in the Proximal Probe Microscopy facility at the Center for Functional Nanomaterials at Brookhaven National Laboratory, completed an extensive upgrade to software called Gnome X Scanning Microscopy, or GXSM, that adds a whole suite of new features. Zahl re-coded about half of the original 300,000 lines of code during this project.

The software, which is used to operate any kind of scanning probe microscopy system which includes atomic force microscopy and scanning tunneling microscopy, has a wide range of applications, from understanding catalysts that facilitate chemical reactions, to capturing gases, to biomedical sensors.

Oliver Monti, a professor of chemistry and biochemistry and a professor of physics at the University of Arizona, has been working with Zahl for over four years and has been using this system to explore atomic and molecular-scale processes that determine efficiency in plastic solar cells and other next-generation low-energy-use technologies. He said he uses the GXSM for data analysis.

Zahl “often introduces modifications and upgrades as instantaneous response to some scientific need,” which has “helped us solve specific problems efficiently,” Monti explained in an email. A former student of Monti’s needed to analyze molecule-to-molecule interactions. The two came up with an algorithm to study that and, unprompted, Zahl “introduced a version of this algorithm to his software.”

Percy Zahl (front of line) during a Tour of Somerville race in 2011. Photo by Anthony Skorochod.

Monti said he is “very much aware of the most recent release,” which he considers a “major upgrade” and he is in the process of installing it. The new software allows the export of images in formats such as PDF and SVG, which are editable and resolution independent, Zahl explained. A PDF output of a graph has publication quality, while the images with high-resolution displays are enhanced and sharper than the previous bitmap PNG files.

The upgrade also includes making a remote control process for automating scanning and manipulation tasks “easy to use,” which is a “big plus for less experienced users,” Zahl explained. It can help automate complex or tedious repetitive jobs. As an example, Zahl said the need to scan an image that takes 10 minutes each for 20 different settings creates a laborious task. “I can either sit there and enter manually a new number every 10 minutes” or he can program a script that he made to use a list of bias voltages and hit execute in the new remote console, he explained, leaving him time to work on other projects for the next two hours and 20 minutes.

Recently, Zahl ran a spectra covering the area of a molecule, which is a task he can do reliably without worrying about user typos or errors. An additional noncontact atomic force microscopy simulation plug-in module provides researchers with a more efficient way to generate data. The new approach measures the force between atoms and molecules of the surface of a sample and a probe smaller than the diameter of an atom. Zahl has calculated and simulated forces between atoms, taking into account all atoms of a molecule and the probe atom and finds the equilibrium position of his probe. Using that three-dimensional force field, he can extract an image that he compares to the model.

Zahl spends about three quarters of his time working with users like Monti, while he dedicates the remaining time to his own projects. He appreciates the opportunity to work with many different systems and with people in a wide range of scientific disciplines.

“It’s really as diverse as it can get in this particular field of fundamental surface science — a specialty of solid state physics,” Zahl explained in an email. He has the experience to work with many different sample types while still continuing to learn “all the tricks on how to get the best images possible.”

Monti appreciates Zahl’s dedication to his work. “Data processing and analysis can be challenging,” he explained. His students often compare a trip to BNL to drinking from a firehose.

Zahl has been “essential in helping us figure out how to sift through the data and quickly focus on the most important observations,” Monti added. That appreciation extends well beyond Monti’s lab. “Whenever I meet colleagues across the world who had the pleasure to interact with [Zahl], they lavish praise on his scientific and technical expertise,” Monti said.

Bruce Koel, a professor in the Department of Chemical and Biological Engineering at Princeton University, appreciated Zahl’s contribution to his research on chemical reactions at surfaces. Zahl has “enabled us to do very high impact research,” Koel explained in an email. This work would “not have been possible without [Zahl’s] technical support and guidance about what experiments could be done.”

A resident of Rocky Point, Zahl rides the 20 miles to work as often as he can on one of several of his bicycles. An avid cyclist, Zahl has a high-end racing bike, a commuter bike and a mountain bike from those “beloved times” riding mountain trails in Switzerland.

In Chile, he reached a top speed of around 56 miles per hour descending the Osorno Volcano. In a YouTube video of his ride, he can be seen passing a car in a clearing along the windy road.

As for his work, Zahl remains committed to continuing to improve the software scientists use to enhance their visual understanding of the small surfaces of the substances they study. “I am pretty much always working on some new details or fixing this and that tiny issue,” he said. “No software is ever done. It’s evolving.”

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Jun Wang in her laboratory with a transmission x-ray microscope. Photo from BNL

By Daniel Dunaief

The first time is most definitely not the charm. That’s what Jun Wang and her colleagues at Brookhaven National Laboratory discovered about sodium ion batteries.

Wang, a physicist and lead scientist at the facility, looked deep into the inner workings of a sodium ion battery to determine what causes structural defects as the battery functions. As it turns out, the first time a sodium ion battery charges and discharges, it develops changes in the microstructure and chemical composition of iron sulfide. These changes, which degrade the performance of the battery, are irreversible during the first charging cycle.

“We found that the cracks happened during the first cycle, then, after that, the structure kind of reached equilibrium,” said Wang, who published her research in the journal Advanced Energy Materials. “All these changes happen during the first cycle.”

Collaborators from Brookhaven’s Photon Sciences and Sustainable Energy Technologies groups stand behind the new transmission x-ray microscope (TXM) at BNL’s National Synchrotron Light Source. From left: Yu-chen Karen Chen-Wiegart, Can Erdonmez, Jun Wang (team leader), and Christopher Eng. Photo from BNL

Sodium ion batteries are considered an alternative to lithium ion batteries, which are typically found in most consumer electronics. Like lithium, sodium is an alkali metal, which means that it is in the same group in the periodic table. Sodium, however, is more abundant and, as a result, considerably less expensive than lithium.

Using a synchrotron-based hard X-ray full-field microscope, Wang was able to see what happened when sodium ions moved into and out of an iron sulfide electrode through 10 cycles. “We can see this microstructure evolution,” she said.

Wang monitored the evolution as a function of time while the battery is charging and discharging. The results are the first time anyone has studied a sodium-metal sulfide battery with these tools, which provides information that isn’t available through other methods. “It is challenging to prepare a working sodium ion battery for the in operandi/in situ TXM study to correlate the microstructural evolution with its electrochemical performance,” she said.

Other researchers suggested that Wang has developed a following in the scientific community for her ground-breaking research. “She has a very good reputation in the area of X-ray nanotomography, applied to a wide range of different materials,” Scott Barnett, a professor of materials science and engineering at Northwestern University, explained in an email. “I am most familiar with her work on fuel cell and battery electrodes — I think it is fair to say that this work has been some of the best pioneering research in this area,” he said.

Barnett, who started collaborating with Wang in 2010 on measuring fuel cell and battery electrodes with X-ray tomography, suggested that Wang’s work on capacity loss “could certainly lead to new breakthroughs in improved batteries.”

In her most recent work with sodium ion batteries, Wang found that the defects start at the surface of the iron sulfide particles and move inward toward the core, Wang said. The microstructure changes during the first cycle and is more severe during sodiation. The particles don’t return to their original volume and shape. After the first cycle, the particles reach a structural equilibrium with no further significant morphological changes, she said.

In other cycles, the material does not show further significant morphological changes, reach a structural equilibrium and electrochemical reversibility. Wang and her colleagues confirmed these observations with X-ray nanotomography, which creates a three-dimensional image of the battery material while recording the change in volume.

Wang suggested that a way to reduce these structural defects could be to reduce the size of the iron sulfide particles to create a one-phase reaction. She will work with other collaborators on modeling and simulations that will enhance the design of future battery materials.

In addition to conducting research on batteries, Wang is an industrial program coordinator in the Photon Science Directorate at BNL. She works with industrial researchers and beamline staff to find and explore new opportunities in industrial applications using synchrotron radiation. She leads the industrial research program, interacting with user groups through consultation, collaboration and outreach.

To manage her research, which includes a lab of three other researchers, and to accomplish her mission as manager of an industrial research program, Wang jokes that she “spends 100 percent of her time” with each responsibility. “I try to do my best for the different things” she needs to do with her time, she said.

Jun Wang with her husband Qun Shen and their 11-year old son Sam in Waikiki last year. Photo from Jun Wang

A native of Wuhu, China, Wang earned her bachelor’s degree in physics from Anhui University in China and her doctorate in physics from the Chinese Academy of Sciences in Beijing. She worked at the Beijing Synchrotron Radiation Facility, which was the first synchrotron light source in China. During her doctoral training, she studied multilayer films using X-ray diffraction and scattering.

A resident of Poquott, Wang is married to Qun Shen, who is the deputy director for science at the NSLS-II. The couple has an 11-year-old son, Sam, who is a sixth-grade student at Setauket Elementary School. Shen and Wang met at an international X-ray crystallography conference in the early 1990s.

Shen trained in the United States after he graduated from Beijing University in 1980, when he went to Purdue University for his doctorate through the China-US Physica Examination and Application Program. The couple have worked together a few times over the years, including publishing a paper in Nature Communications. Wang is hoping that her work with battery research will lead to improvements in the manufacture and design of sodium ion batteries.

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Line Pouchard at the Great Smoky Mountains National Park in 2013. Photo by Allan Miller

By Daniel Dunaief

They produce so much information that they can’t keep up with it. They use the latest technology to gather data. Somewhere, hidden inside the numbers, might be the answer to current questions as well as the clues that lead to future questions researchers don’t know how to ask yet.

Scientists in almost every facility, including at Brookhaven National Laboratory, Cold Spring Harbor Laboratory and Stony Brook University, are producing information at an unprecedented rate. The Center for Data-Driven Discovery at Brookhaven National Laboratory can help interpret and make sense of all that information.

Senior researcher Line Pouchard joined BNL’s data team early this year, after a career that included 15 years at Oak Ridge National Laboratory (another Department of Energy facility) and more than two-and-a-half years at Purdue University. “The collaborations at the [DOE] lab are highly effective,” she said. “They have a common purpose and a common structure for the scientist.” Pouchard’s efforts will involve working with metadata, which adds annotations to provide context and a history of a file, and machine learning, which explores large blocks of information for patterns. “As science grows and the facility grows, we are creating more data,” she said.

Scientists can share large quantities of information, passing files through various computer systems. “You may want to know how this data has been created, what the computer applications or codes are that have been used, who developed it and who the authors are,” she said.

Knowing where the information originated can help the researchers determine whether to trust the content and the way it came together, although there are other requirements to ensure that scientists can trust the data. If the metadata and documentation are done properly “this can tell you how you can use it and what kind of applications and programs you can use to continue working with it,” Pouchard said. Working in the Computational Science Initiative, Pouchard will divide her time between responding to requests for assistance and conducting her own research.

“At Purdue, [Pouchard] was quite adept at educating others in understanding metadata, and the growing interest and emphasis on big data in particular,” explained Jean-Pierre Herubel, a professor of library science at Purdue, in an email. Herubel and Pouchard were on the research council committee, and worked together with other members to shepherd their research agendas for the Purdue University library faculty.

Pouchard “has a capacity to participate well with colleagues; regarding national and international venues, she will be a strong participating member,” Herubel continued. “She does well working and integrating with others.”

Pouchard recently joined a team that submitted a proposal in the area of earth science and data preservation. She has also worked on something called the Semantic Web. The idea, which was proposed by Tim Berners-Lee, who invented the World Wide Web, is to allow the use of data items and natural language concepts in machine readable and machine actionable forms. As an example, this could include generating rules for computers that direct the machines to handle the multiple meanings of a word.

One use of the Semantic Web is through searches, which allows people to look for information and data and, once they’re collected, gives them a chance to sort through them. Combined with other technologies, the Semantic Web can allow machines to do the equivalent of searching through enormous troves of haystacks.

“When I first started talking about the Semantic Web, I was at Oak Ridge in the early days,” Pouchard said. Since then, there has been considerable progress, and the work and effort have received more support from scientists.

Pouchard was recently asked to “work with ontologies [a Semantic Web technology] in a proposal,” she said, which suggests they are getting more traction. She is looking forward to collaborating with several scientists at BNL, including Kerstin Kleese van Dam, the director of the Computational Sciences Initiative and the interim director of the Center for Data-Driven Discovery.

Kleese van Dam has “an incredible vision of what is needed in science in order to improve computational science,” said Pouchard, who met the director about a decade ago when van Dam was working in England. Pouchard has an interest in data repositories, which she explored when she worked at Purdue University.

Living temporarily in Wading River, Pouchard bought a home in Rocky Point and hopes to move in soon. Her partner Allan Miller, from Knoxville, Tennessee, owned and managed the Disc Exchange in Knoxville for 26 years. He is starting to help small business owners and non-profit organizations with advertising needs. Pouchard experienced Long Island when she was conducting her Ph.D. research at the City University of New York and took time out to visit a friend who lived in Port Jefferson.

When she’s not working on the computer, Pouchard, who is originally from Normandy, France, enjoys scuba diving, which she has done in the Caribbean, in Hawaii, in Mexico and a host of other places.

When Pouchard was young, she visited with her grandparents during the summer at the beach in Normandy, in the town of Barneville-Carteret. Her parents, and others in the area, lectured their children never to go near or touch metal objects they found in the dunes because unexploded World War II devices were still occasionally found in remote areas. The environment on Long Island, with the marshes, reminds her of her visits years ago.

Pouchard has an M.S. in information science from the University of Tennessee and a Ph.D. in comparative literature from the City University of New York.

As for her work, Pouchard said she is “really interested in the Computational Science Initiative at BNL, which enables researchers to collaborate. Computational science is an integral part of the facilities,” at her new research home.

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