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Babak Andi holds a 3-D model of the coronavirus responsible for the COVID-19 pandemic. Photo courtesy of BNL

By Daniel Dunaief

For close to two and a half years, the world has had a microbial enemy. The SARS-CoV2 virus, which causes Covid-19, has resulted in close to 6.5 million deaths, caused lockdowns, restricted travel, closed businesses, and sickened millions. The key to fighting such a dangerous enemy lies in learning more about it and defeating its battle plan.

Working with principal investigator Daniel Keedy, Assistant Professor at the City University of New York and Diamond Light Source in the United Kingdom, Babak Andi, who is a beamline scientist from the structural biology group at Brookhaven National Laboratory, spent over two years studying a key viral enzyme.

Recently, the researchers revealed the structure at five temperatures of an enzyme called Mpro, for main protease. This enzyme, which separates proteins the virus makes, is critical for the maturation of the SARS-CoV-2 virus particles. They published their work in the Journal of the International Union of Crystallography (IUCrJ).

Using the Frontier Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II at BNL, Andi collected data on the structure of the enzyme at temperatures ranging from 100 degrees Kelvin, which is about negative 280 degrees Fahrenheit, all the way up to 310 degrees Kelvin, which is normal body temperature. “Nobody had done that, specifically for this protein,” said Andi.

Keedy, who guided the data collection, processed the information and wrote most of the paper, described the effort as a “great collaboration.” The gradual change in the conformation of the enzyme helped the scientists learn how it may move or shape-shift in general, he explained.

Keedy had worked with BNL in the past and pursued research at the FMX beamline because the scientists at BNL had “been working with Mpro on site, and were very approachable and open to the idea.”

Finding the specific structure of important proteins like Mpro can help researchers, pharmaceutical companies and doctors search for inhibitors or small molecules that could be specific to these proteins and that might interfere with their function.

Andi and other scientists at this beamline worked through the pandemic shutdown because of the potential practical application of what they were doing.

“We almost had all the infrastructures in place to allow other scientists to connect and operate the beamlines remotely, enabling them to collect data on Covid-19 virus proteins,” said Andi. “In my opinion, being able to support all the academic and industrial scientists to collect data for Covid-19 research was our greatest achievement during the worst period of the pandemic.”

While coming into the lab in those early months raised concerns about their own health, Andi and his colleagues, who developed safety protocols, felt an urgency to conduct this research.

“When Covid hit, we had a sense that this is our duty, this is our job to contribute to this field, to make sure that every scientist who works on Covid-19 had easy access to our beamlines, facilities and all the tools [necessary] to make new drugs,” said Andi. 

How they solved the structure

The technology for the beamline enables Andi and other scientists to collect data quickly and even remotely. Speed helps because the longer x-rays hit a protein, the more likely they are to cause the kind of damage that makes determining the structure difficult, particularly at higher temperatures.

The first step in this research was in producing this protein, which Andi’s collaborators at BNL in the biology department provided. The biology department also helped with crystallization.

Andi prepared the beamline and aligned the x-ray beam, which are necessary to collect data.

The scientists rotated and moved the crystal through the x-ray, distributing the beam over the length of the crystal to minimize radiation damage.

The small size of the x-ray beam made it possible to keep the beam focused on the smallest dimension of the structure. The researchers studied the crystal at five different temperatures, starting at cryogenic all the way up to physiological.

Of the 195,000 structures listed in the Protein Data Bank, or PDB, only five had been determined at body temperature. That includes two from the group of collaborators who participated in this study.

Andi collected three or four data sets at each temperature.

“The different conformations we saw may inspire a new twist on antiviral drug development that targets a different place in the protein, but with a similar or better effect,” Keedy explained.

The researchers did not include other factors that might affect the conformation of the protein, such as pH, pressure, the number of ions or salts in the environment, among others. For the Mpro protease to work, it has to bond to another similar protein, forming a dimer.

Andi said the Pfizer treatment Paxlovid binds to the active site of this enzyme, inactivating it.

The drugs he is looking for are similar, although he is also searching for other places on the enzyme besides its active site.

Keedy hopes to try to make a monomeric form of the enzyme through a mutation. He could then find drug-like small molecules that target the exposed interface between the two copies.

BNL origins

After he completed his PhD and post doctoral work at the University of Oklahoma, Andi started his career at BNL 11 years ago as a post doctoral researcher.

During his childhood, Andi was initially interested in astronomy. When he enrolled at a university outside the United States, he took an entrance exam.

“Based on your score, it tells you which discipline of science you can go into,” he said. His score directed him to the field of cell and molecular biology.

“I’m happy this happened,” he said. “I find that I’m actually more interested in molecular biology than in astronomy.”

Outside of work, Andi enjoys do-it-yourself projects. Astronomy also continues to appeal to him, as he is fascinated with astrophotography and reads astronomy articles.

As for the work with a Covid enzyme, Andi hopes he has other opportunities to contribute. 

“I am interested [in continuing] the research in this field,” he explained. “That depends on time, resources and current or future priorities.”

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Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility

By Daniel Dunaief

Clouds and rain often cause people to cancel their plans and seek alternative activities.

The opposite was the case for Katia Lamer this summer. A scientist and Director of Operations of Brookhaven National Laboratory’s Center for Multiscale Applied Sensing, Lamer was in Houston to participate in ESCAPE and TRACER studies to understand the impact of pollution on deep convective cloud formation. 

Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility

With uncharacteristically dry weather and fewer of the clouds she and others intended to study, she had some down time and created a plan to study the distribution of urban heat. “I am always looking for an opportunity to grow the Center for Multiscale Applied Sensing and try to make the best of every situation,” she said.

Indeed, Lamer and her team launched 32 small, helium-filled party balloons. She and Stony Brook University student Zachary Mages each released 16 balloons every 100 meters while walking a one mile transect from the suburbs to downtown Houston. A mobile observatory followed the balloons and gathered data in real time through a radio link. 

While helium-filled party balloons are not the best option, Lamer said the greater good lay in gathering the kind of data that will be helpful in measuring and monitoring climate change and explained that until some better balloon technology was available, this is what they had to use.

“Typically, we launch the giant radiosonde balloons, but you can’t launch them in a city,” she said because of the lack of space for these larger balloons to rise without hitting obstacles. The balloons also might pass through navigable airspace, disturbing flight traffic.

The smaller party balloons carried sensitive equipment that measured temperature and humidity and had a GPS sensor tucked into foam cups.

“If we can demonstrate that there is significant variability in the vertical distribution of temperature and humidity at those scales, then this would suggest that we should push to increase the resolution of our models to improve climate change projections,” she explained.

By following these balloons closely with a mobile observatory, Lamer and her team can avoid interference from other signals and signal blockage by buildings.

The system they used allowed them to select a cut-off height. Once the balloons reached that altitude, the string that connected the sensors to the balloon burns off and the sensors start free-falling while the balloon climbs until it pops.

The sensors collect continuous data on temperature, humidity and horizontal wind during the ascent and descent. Using the GPS, researchers can collect the sensors.

While researchers have studied urban heat using mesoscale models and satellite data, that analysis does not have the spatial resolution to understand community scale variability. Urban winds also remain understudied, particularly the winds above the surface, she explained.

Winds transport pollutants, harmful contaminants, and heat, which may be relieved on some streets and trapped on others.

Michael Jensen, principal investigator for the Tracking Aerosol Convection interaction Experiment, or TRACER and meteorologist at BNL, explained that Lamer is “focused on what’s going on in the urban centers.” Having a truck that can move around and collect data makes the kind of experiment Lamer is conducting possible. Jensen described what Lamer and her colleagues are doing as “unique.”

New York model 

Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility

Lamer had conducted similar experiments in New York to measure winds. The CMAS mobile observatory’s first experiment took place in Manhattan around the One Vanderbilt skyscraper, which is 1,400 feet high and is next to Grand Central Terminal. No balloons were launched as part of that first experiment.She launched the small radiosonde balloons for the first time this summer in Houston around the 990 foot tall Wells Fargo complex. 

Of the 32 balloons she and Mages launched, they collected data from 24. The group lost connection to some of the balloons, while interference and signal blockage disrupted the data flow from others.

Lamer plans to use the information to explore how green spaces such as parks and blue infrastructure including fountains have the potential to provide some comfort to people in the immediate area.

Such observations will provide additional insight beyond numerical models into how large an area a park can cool in the context of the configuration of a neighborhood.

This kind of urban work can have numerous applications.

Lamer suggested it could play a role in urban planning and in national security, as officials need to know the dispersement of pollutants and chemicals. Understanding wind patterns on a fine scale can help inform models that indicate areas that might be affected by an accidental release of chemicals or a deliberate attack against residents.

Bigger picture

Katia Lamer during her experiment in Houston. Photo by Steven Andrade/ BNL

Lamer is gathering data from cities to understand the scale of heterogeneity in properties such as heat and humidity, among others. If conditions are horizontally and vertically homogeneous, only a few permanent stations would be necessary to monitor the city. If conditions are much more varied, more measurement stations would be necessary.

One way to perform this assessment is to use mobile observatories that collect data. The ones Lamer has deployed use low-cost, research-grade instruments for street level and column wide observations.

Over the ensuing decades, Lamer expects that the specific conditions will likely change. Collecting and analyzing data now will enable scientists to develop a baseline awareness of typical urban conditions.

Scientific origins

A native of St.-Dominique, a small farmer’s village in Quebec Canada, Lamer was impressed by storms as she was growing up. She would often watch them outside her window, fascinated by what she was witnessing. After watching the Helen Hunt and Bill Paxton movie Twister, she wanted to invent her own version of the Dorothy instrument and start chasing storms.

When she spoke with her high school guidance counselor about her interest in tornadoes, which do not occur in Quebec, the counselor said she was the first person to express such a professional passion and had no idea how to advise her.

Lamer, who grew up speaking French, attended McGill University in Montreal, where she studied earth system science, aspects of geology and geography and a range of earth-related topics.

Instead of studying or tracking tornadoes, she has worked on cloud physics and cloud dynamics. Hearing about how clouds are the biggest wild card in climate change projections, she decided to embrace the challenge.

During her three years at BNL, Lamer, who lives with her husband and children in Stony Brook, has appreciated the chance to “push the envelope and be creative,” she said. “I really hope to stay in the field of urban meteorology.”

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The temperatures at the poles are heating up more rapidly than those at the equator. Pixabay photo

By Daniel Dunaief

On any given day, heat waves can bring record-breaking temperatures, while winter storms can include below average cold temperatures or snow.

Edmund Chang. Photo from SBU

Weather and climate experts don’t generally make too much of a single day or even a few days amid an otherwise normal trend. But, then, enough of these exceptional days over the course of years can skew models of the climate, which refers to average temperature and atmospheric conditions for a region.

If the climate is steady, “we should see approximately the same number of hot and cold records being broken,” said Edmund Chang, Professor at the School of Marine and Atmospheric Sciences at Stony Brook University. “Over the past few decades, we have seen many more hot records being broken than cold records, indicating the climate is getting hotter.”

Recent heat

Indeed, just last week, before a heatwave hit the northeastern United States, the United Kingdom reported the hottest day on record, with the temperature at Heathrow Airport reaching above 104 degrees.

Erinna Bowman, who grew up in Stony Brook and has lived in London since 2009, said the temperature felt “like a desert,” with hot, dry heat radiating up in the urban setting. Most homes in London don’t have air conditioning, although public spaces like supermarkets and retail stores do.

“I’m accustomed to the summer getting quite hot, so I was able to cope,” said Bowman. Indeed, London is usually considerably cooler during the summer, with average temperatures around 73 degrees.

Michael Jensen. Photo from BNL

News coverage of the two extraordinarily hot days in London “was very much framed in the context of a changing climate,” Bowman said. The discussion of a hotter temperature doesn’t typically use the words “climate change,” but, instead, describes the phenomenon as “global heating.”

For climate researchers in the area, the weather this summer has also presented unusual challenges.

Brookhaven National Laboratory meteorologist Michael Jensen spent four years planning for an extensive study of convective clouds in Houston, in a study called Tracking Aerosol Convection Interactions, or Tracer.

“Our expectation is that we would be overwhelmed” with data from storms produced in the city, he said. “That’s not what we’re experiencing.”

The weather, which has been “extremely hot and extremely dry,” has been more typical of late August or early September. “This makes us wonder what August is going to look like,” he said.

Jensen, however, is optimistic that his extensive preparation and numerous pieces of equipment to gather meteorological data will enable him to collect considerable information.

Warming at the poles

Broadly speaking, heat waves have extended for longer periods of time in part because the temperatures at the poles are heating up more rapidly than those at the equator. The temperature difference between the tropics and the poles causes a background flow from west to east that pushes storms along, Chang explained.

The North Pole, however, has been warming faster than the tropics. A paper by his research group showed that the lower temperature gradient led to a weakening of the storm track.

When summer Atlantic storms pass by, they provide relief from the heat and can induce more clouds that can lead to cooler temperatures. Weakening these storms can lead to fewer clouds and less cooler air to relieve the heat, Chang added.

Rising sea levels

Malcolm Bowman. Photo from SBU

Malcolm Bowman, who is Erinna Bowman’s father and is Distinguished Service Professor at the School of Marine and Atmospheric Sciences at Stony Brook University, believes the recent ice melting in Greenland, which has been about 10 degrees above normal, could lead to a rise in sea levels of about one inch this summer. “It will slowly return to near normal as the fresh water melt spreads slowly over all the world’s oceans,” he added.

Bowman, who has studied sea level rises and is working on mitigation plans for the New York area in the event of a future major storm, is concerned about the rest of the hurricane season after the level of warming in the oceans this summer. 

“Those hurricanes which follow a path over the ocean, especially following the Gulf Stream, will remain strong and may gather additional strength from the heat of the underlying water,” he explained in an email.

Bowman is the principal investigator on a project titled “Long Island South Shore Sea Gates Study.”

He is studying the potential benefit of six possible sea gates that would be located across inlets along Nassau and Suffolk County. He also suggests that south shore sand dunes would need to be built up to a height of 14 feet above normal high tide.

Meanwhile, the Army Corps of Engineers has come up with a tentatively selected plan for New York Harbor that it will release some time in the fall. Bowman anticipates the study will be controversial as the struggle between green and grey infrastructure — using natural processes to manage the water as opposed to sending it somewhere else — heats up.

As for the current heat waves, Bowman believes they are a consistent and validating extension of climate change.

Model simulations

In his lab, Chang has been looking at model simulations and is trying to understand what physical processes are involved. He is comparing these simulations with observations to determine the effectiveness of these projections.

To be sure, one of the many challenges of understanding the weather and climate is that numerous factors can influence specific conditions.

“Chaos in the atmosphere could give rise to large variations in weather” and to occasional extremes, Chang said. 

Before coming to any conclusions about longer term patterns or changes in climate, Chang said he and other climate modelers examine collections of models of the atmosphere to assess how likely specific conditions may occur due to chaos even without climate change.

“We have to rule out” climate variability to understand and appreciate the mechanisms involved in any short term changes in the weather, he added.

Still, Chang said he and other researchers are certain that high levels of summer heat will be a part of future climate patterns. 

“We are confident that the increase in temperature will result in more episodes of heat waves,” he said.

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BEST OF THE BEST The seven students who received top honors are (top row, from left) kindergartener Rebecca Tyler, first grader Violet Radonis, second grader Taran Sathish Kumar, (lower row, from left) third grader Adam Dvorkin, fourth grader Liam Savage, fifth grader Michaela Bruno, and sixth grader Rebecca Bartha. Photos from BNL
Annual contest offers Long Island, NYC students an opportunity to showcase their science projects

Should you sanitize your television remote? How can we keep apple slices looking fresh? Do dogs have a favorite color? Long Island and New York City students tackled questions of all kinds using the scientific method in the 2022 Elementary School Science Fair hosted virtually by the U.S. Department of Energy’s Brookhaven National Laboratory.

The goal of the annual competition organized by the Office of Educational Programs (OEP) at Brookhaven Lab is to generate an interest in and excitement about science and engineering for all ages.

“It’s an honor and inspiration for us to look at all of the posters by students who are joining Brookhaven in a passion for discovery,” said Scott Bronson OEP manager of K-12 programs. “Just like the scientists here at Brookhaven Lab, Science Fair participants study questions of ‘how?’ and ‘why?’ to meet science challenges.”

This year’s competition invited projects by students from Suffolk County, Nassau County and New York City schools in kindergarten through sixth grade.

From left, Northport Middle School, sixth grader Grace Rozell received an Honorable Mention and fifth grader Michaela Bruno captured First Place in her grade at the BNL Science Fair on July 10. The students are pictured with Assistant Principal Dr. Chelsea Brown and Principal Timothy Hoss. Photo from BNL

Participants qualified for the Brookhaven Lab contest by winning science fairs held by their schools. Volunteer judging teams consisting of elementary school teachers and Brookhaven Lab scientific and engineering staff evaluated a total of 189 projects.

“We were so excited to expand the Science Fair and welcome projects from students across all of Long Island and New York City,” said Amanda Horn, a Brookhaven Lab educator who coordinated the virtual science fair. “We loved seeing the projects from other areas and we hope to see even more projects in the future.”

The following students earned first place in their grade level and received medals and ribbons, along with banners to hang at their school to recognize the achievement:

◆ Kindergartener Rebecca Tyler of Miller Avenue Elementary School, Shoreham-Wading River School District, for her project, “How to get Permanent Marker Out of Clothes?” 

◆ First grader Violet Radonis of Pines Avenue Elementary School, Hauppauge School District, for “Bad Hair Days…No More! Let’s Learn about the Land of the Rapunzals”

◆ Second grader Taran Sathish Kumar of Bretton Woods Elementary School, Hauppauge School District, for “Cleaning Up Oil Spills Using Natural Organic Sorbents” 

◆ Third grader Adam Dvorkin of Pulaski Road Elementary School, Northport-East Northport School District, for “Sardine Pop in a Bathtub” 

◆ Fourth grader Liam Savage of Ruth C. Kinney Elementary School, East Islip School District, for “Weight is Tow-Tally Helpful” 

◆ Fifth grader Michaela Bruno of Northport Middle School, Northport-East Northport School District, for “Here Comes The Sun” 

◆ Sixth grader Rebecca Bartha of Raynor Country Day School in Speonk for “Super Sea Shells Save the Seas”

Young scientists share their results

OEP staff announced the winners and honorable mentions during an online awards ceremony on June 10. Students with top-notch projects shared how they conducted their experiments.

First-grader Violet Radonis asked whether rice water can make hair grow faster and stronger. After four weeks of testing a mixture of basmati rice and water—plus orange peels for a nice scent—on eight test subjects, she found: “It does help make it a little bit better than it was before.”

Orange peels also played a part in second grader Taran Sathish Kumar’s experiment. In his search for an environmentally safe sorbent to protect marine life from oil spills, his hypothesis that orange peels would remove the most oil from water was correct. He also tested a corn cob, banana peel, and a pomegranate husk. 

“Around the world when boats go in the water, oil spills from the boat and it’s harmful to the animals,” he said.

Third grader Adam Dvorkin wanted to find out what sort of pop pop (or putt putt) boat design is the fastest. He built and observed three boats, each with a different sized boiler made from a soda can bottom. The biggest boiler was the best, confirming his hypothesis. 

“My favorite part was when me and my dad had to check how fast each pop pop boat was to see which one was the fastest,” he said.

Fourth grader Liam Savage tested whether adding weights to the top of a remote-control truck would increase its towing ability. He found that a specific amount of weight increased the truck’s tower power by giving it extra traction. But with too much weight, the truck would stall. With too little weight, the truck didn’t have enough grip. “My favorite part was driving my car and seeing how much weight it could pull,” he said.

Aspiring astronaut and fifth grader Michaela Bruno searched for the best material to block ultraviolet rays for protection.”I want to be an astronaut when I grow up and I want to know how the UV lights in space affect them,” she said.

By shining a UV flashlight on UV beads covered by different materials she learned that aluminon foil and dark cotton fabric offered the best protection. With those results in mind, Bruno went on to engineer a model space suit and visor.

Honorable mentions

Kindergarten: Kacey Stidd, Riverhead; Lucas Luna, Hampton Bays; John O’Donnell, Kings Park

First Grade: Hudson Costales, East Northport; Jaxon Romano, Middle Island; Marilla Pendelton, Aquebogue 

Second Grade: Jude Roseto, Cutchogue; Ashleigh Bruno,  Northport; Kayleigh Moore, East Northport 

Third Grade: Matthew McHugh, Hauppauge; Riona Mittal, Hauppauge; Maxin Vetoshkin, Hauppauge

Fourth Grade: Evan Pereyra, Westhampton Beach; Agnes Van Winckel, Kings Park; Emma Lochner, Sayville 

Fifth Grade: Mihir Sathish Kumar, Hauppauge; Faith Andria, Remsenburg;  Madeline Croce, Sayville 

Sixth Grade: Grace Rozell, Northport; Elle Redlinger, Montau

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, please visit www.science.energy.gov

 

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In left photo, Zhiyang Zhai, on the right, with John Shanklin and Jantana Keereetaweep; in right photo, Zhiyang Zhai with Hui Liu. Photos courtesy of BNL

By Daniel Dunaief

In a highly competitive national award process, the Department of Energy provides $2.5 million to promising researchers through Early Career Research Funding.

Recently, the DOE announced that Zhiyang Zhai, an associate biologist at Brookhaven National Laboratory, was one of 83 scientists from around the country to receive this funding.

“Supporting talented researchers early in their career is key to fostering scientific creativity and ingenuity within the national research community,” DOE Office of Science Director Asmeret Asefaw Berhe, said in a statement.

Zhai, who has worked at BNL for 11 years, is studying a signaling protein called Target Of Rapamycin (TOR) kinase, which is important in the plant and animal kingdom.

He hopes to develop a basic understanding of the way this kinase reacts to different conditions, such as the presence of carbon, to trigger reactions in a plant, including producing oils through photosynthesis or making seeds.

Zhiyang Zhai. Photo from BNL

“Ancient systems like this evolve in different lineages (like plants and animals) to work differently and [Zhai] wants to find out the details of how it works in plants,” John Shanklin, chair of BNL’s Biology Department, explained in an email. 

Zhai is trying to define which upstream signals interact with TOR and what the effects of those interactions are on TOR to learn how the kinase works.

He is hoping to get a clear idea of how different nodes interact and how signaling through carbon, nutrients and sunlight affects TOR kinase levels and its configuration.

Researchers may eventually use the knowledge of upstream regulators to reprogram responses by introducing enzymes that would cause the synthesis, or degradation, of upstream regulatory metabolites, Shanklin suggested.

This could be a way to “tune” the sensor kinase activity to increase the synthesis of storage compounds like oil and starch.

In the bigger picture, this type of research could have implications and applications in basic science that could enhance the production of renewable resources that are part of a net-zero carbon fuel strategy.

The DOE sponsors “basic science programs to discover how plants and other organisms convert and store carbon that will enable a transition towards a net zero carbon economy to reduce the use of fossil fuels,” Shanklin said.

In applying for the award, Zhai paid “tremendous attention” to what the DOE’s mission is in this area, Shanklin said. Zhai picked out a project that, if successful, will directly contribute to some of the goals of the DOE.

Through an understanding of the way TOR kinase works, Zhai hopes to provide more details about metabolism.

Structure and function

Jen Sheen, Professor in the Department of Genetics at the Harvard Medical School, conducted pioneering work on how TOR kinase regulates cell growth in plants in 2013. Since then, TOR has attracted attention from an increasing number of biologists and has become “a hot and rapidly-developing research direction in plant biology,” Zhai explained.

He hopes to study the structure of TOR using BNL’s Laboratory of Biomolecular Structure at the National Synchrotron Lightsource II.

Zhai, who hopes to purify the plant version of TOR, plans to study how upstream signaling molecules interact with and modify the structure of the enzyme.

He will also use the cryo-electron microscope to get a structure. He is looking at molecular changes in TOR in the presence or absence of molecules or compounds that biochemically bind to it.

Through this funded research, Zhai hopes to explain how signals such as carbon supply, nutrients and sunlight regulates cell growth.

Once he’s conducted his studies on TOR, Zhai plans to make mutants of TOR and test them experimentally to see if a new version, which Zhai described as “TOR 2.0,” has the anticipated effects.

Zhai is building on his experience with another regulatory kinase, called SnRK1, which is involved in energy signaling.

“His expertise in defining SnRK1’s mechanism ideally positions him to perform this work,” Shanklin said.

At this point, Zhai is focused on basic science. Other researchers will apply what he learns to the development of plants for commercial use.

A seminal moment and a call home

Zhai described the award as “very significant” for him. He plans to continue with his passionate research to explore the unknown.

He will use the funds to hire new postdoctoral researchers to build up his research team. He also hopes this award gives him increased visibility and an opportunity to add collaborators at BNL and elsewhere.

The funding will support part of Zhai’s salary as well as that of his staff. He will also purchase some new lab instruments and tap into the award to attend conferences and publish papers.

When he learned he had won the award, Zhai called his mother Ruiming, who lives in his native China. “She is so proud of me and immediately spread the good news to my other relatives in China,” Zhai recalled.

When Shanklin spoke with Zhai after the two had learned of the award, he said he had “never seen Zhai look happier.”Shanklin suggested that this is a “seminal moment” in a career that he expects will have other such milestones in the future.

A resident of Mt. Sinai, Zhai lives with his wife Hui Liu, who is a Research Associate in Shanklin’s group specializing in plant transformation, fatty acids and lipidomics analysis.The couple has two sons, nine-year-old Terence and three-year-old Steven.

As for his work, Zhai hopes it has broader implications.

“The knowledge of TOR signaling will provide us [with] tools to achieve hyperaccumulation of lipids in plant vegetative tissues, which is a promising source for renewable energy,” he said.

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Milinda Abeykoon, lead beamline scientist at Pair Distribution Function Beamline, NSLS-II, aligning a sample holder for high-speed measurements, 2019. Photo courtesy of BNL

By Melissa Arnold

Over the past 75 years, Brookhaven National Lab (BNL) in Upton has become an international hub for innovative research and problem-solving. Their hard work has led to advancements in energy, medicine, physics and more, as well as seven Nobel Prizes.

A scientist at a fast neutron chopper at the Brookhaven Graphite Research Reactor (BGRR), 1953. Photo courtesy of BNL

This year, the Long Island Museum in Stony Brook will celebrate the lab’s myriad achievements and explore their deep roots in the area. The new exhibit, titled Atoms to Cosmos: The Story of Brookhaven National Laboratory, opens April 21.

BNL and the Long Island Museum started working on ideas for a future exhibition back in 2018 with plans to open in April of 2020. But as with other museums, the pandemic led to a halt in operations.

In some ways, the rescheduled timing of the exhibit is better than their initial plans.

“While the exhibition was temporarily shelved, both the lab and the museum wanted very much to still make it happen. We had done so much work in advance and preparation for it in 2020, and so we really wanted to get back to this opportunity,” said Joshua Ruff, Deputy Director and Director of Collections and Interpretation for the Long Island Museum. “We are especially pleased we were able to do it now, as it fits nicely with the lab’s 75th anniversary celebration.”

Brookhaven National Laboratory was founded in 1947 at the former site of the U.S. Army’s Camp Upton, becoming the first large research facility in the Northeast. At the time, they were exploring peaceful ways to utilize atomic energy. 

“The BNL site has been in federal ownership since 1917 when it became the location of Camp Upton. Before that, the site was used for the cordwood industry and there was a small farm near the eastern edge of what is now the lab,” explained Timothy Green, BNL’s Environmental Compliance Section manager. “After World War I, all of the buildings were sold at auction and the site sat empty until around 1934, when it was declared the Upton National Forest and the Civilian Conservation Corps started planting trees. At the end of World War II [and a second period as Camp Upton], the land was transferred to the Atomic Energy Commission and became Brookhaven National Laboratory.”

It took some time for local residents to adjust to having a laboratory in the area, Ruff said.

A Positron Emission Tomography Halo Scanner/Detector.
Photo courtesy of BNL

“The lab has often been misunderstood in its past, in fact from its origins. Many Suffolk County residents were not entirely sure that atomic research was safe, nor did they fully understand the relevance and significance [of that research] to their lives,” he explained. “The lab devoted years of hard work and financial resources to strengthen public dialogue and communication, which the exhibition details.”

Today, the lab employs almost 3,000 people and spans 5,320 acres.

The exhibit is co-curated by Joshua Ruff and Long Island Museum curator Jonathan Olly. They’ve included more than 140 items that showcase the lab’s growth and varied discoveries from the 1950s to the present day. The Smithsonian Museum of American History in Washington is lending four of the objects, including a 1,000-pound, 94-inch square magnet lamina from the Cosmotron, BNL’s first major particle accelerator. 

Another 40 objects are coming directly from the lab. Their contribution includes equipment from their facilities, personal belongings of former director Maurice Goldhaber, and “Atoms for Peace,” a famous painting that came to symbolize the lab’s work in its early years.

“A lot of the scientific research at BNL over the years has involved [developing] and testing cutting edge technologies. When these machines are no longer useful they’re usually recycled. Fortunately we do have two examples in the exhibition of early PET (Positron Emission Tomography) scanners, one from 1961 and another from 1981,” Olly said. “In the case of these early machines, the focus was on the brain — the machines used radiation sensors arranged in a ring to produce a picture of a slice of your brain. Brookhaven scientists have used this PET technology (specifically the PETT VI scanner in the exhibition) in studying drug and alcohol addiction, eating disorders, ADHD, aging, and neurodegenerative disorders. The 1961 version is a prototype that was never used on patients.”

Also on view are an original chalkboard from the Graphite Research Reactor that still has writing on it; a 7-foot window from a bubble chamber that helped track the paths of atomic particles; and a detector that aided BNL chemist Raymond Davis Jr. in his Nobel Prize-winning neutrino research. 

Recently, the lab was a part of the ongoing effort to study and contain COVID-19. The exhibit will include a model of the virus, with the familiar spiky shape that’s become commonplace since the pandemic began.

“Scientists at the lab’s National Synchrotron Light Source II worked on imaging the virus and the proteins … that allowed it to attach to human cells. At the same time, BNL computer scientists began developing algorithms to evaluate existing chemicals and drugs that could potentially prevent infection. One past experiment by [BNL biophysicist] William Studier, the T7 expression system, ended up being critical to the rapid development of two of the vaccines,” Green said.

Both the Long Island Museum and BNL staff hope that visitors to the exhibit come away with a deeper interest in science and an appreciation for the lab’s work.

“There are 17 national laboratories scattered throughout the United States, and Long Islanders can be proud to have one in their backyard. Long Island children have been inspired to pursue careers in science as a result of attending educational programs at the lab during public visitor days dating back to the 1950s. And the lab is invested in addressing our real-world problems, whether the dangers posed by DDT on Long Island in the 1960s or COVID now. This summer BNL should be resuming their “Summer Sundays” visitor program, and I encourage everyone to visit the lab, walk around, talk to staff, and get a glimpse of our scientific present and future,” Olly said.

Atoms to Cosmos: The Story of Brookhaven National Lab is on view now through Oct. 16 in the Long Island Museum’s History Museum and Visitor Center’s Main Gallery, 1200 Rt. 25A, Stony Brook. Regular museum hours are Thursday through Sunday from noon to 5 p.m. Masks are required at this time, though health and safety guidelines are subject to change Admission is $10 for adults, $7 for seniors, and $5 for students 6 to 17 and college students with I.D. Children under six are admitted for free. Tickets are available at the door; pre-registration is not required. For more information visit longislandmuseum.org or call 631-751-0066. 

Learn more about Brookhaven National Lab at www.BNL.gov.

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Members of the research team include: Daniel Mazzone (formerly of Brookhaven Lab, now at the Paul Scherrer Institut in Switzerland), Yao Shen (Brookhaven Lab), Gilberto Fabbris (Argonne National Laboratory), Hidemaro Suwa (University of Tokyo and University of Tennessee), Hu Miao (Oak Ridge National Laboratory—ORNL), Jennifer Sears* (Brookhaven Lab), Jian Liu (U Tennessee), Christian Batista (U Tennessee and ORNL), and Mark Dean (Brookhaven Lab). *Photo Credit: DESY, Marta Mayer
Scientists identify a long-sought magnetic state predicted  60 years ago
Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have discovered a long-predicted magnetic state of matter called an “antiferromagnetic excitonic insulator.”
“Broadly speaking, this is a novel type of magnet,” said Brookhaven Lab physicist Mark Dean, senior author on a paper describing the research just published in Nature Communications. “Since magnetic materials lie at the heart of much of the technology around us, new types of magnets are both fundamentally fascinating and promising for future applications.”
The new magnetic state involves strong magnetic attraction between electrons in a layered material that make the electrons want to arrange their magnetic moments, or “spins,” into a regular up-down “antiferromagnetic” pattern. The idea that such antiferromagnetism could be driven by quirky electron coupling in an insulating material was first predicted in the 1960s as physicists explored the differing properties of metals, semiconductors, and insulators.
“Sixty years ago, physicists were just starting to consider how the rules of quantum mechanics apply to the electronic properties of materials,” said Daniel Mazzone, a former Brookhaven Lab physicist who led the study and is now at the Paul Scherrer Institut in Switzerland. “They were trying to work out what happens as you make the electronic ‘energy gap’ between an insulator and a conductor smaller and smaller. Do you just change a simple insulator into a simple metal where the electrons can move freely, or does something more interesting happen?”
The prediction was that, under certain conditions, you could get something more interesting: namely, the “antiferromagnetic excitonic insulator” just discovered by the Brookhaven team.
Why is this material so exotic and interesting? To understand, let’s dive into those terms and explore how this new state of matter forms.
In an antiferromagnet, the electrons on adjacent atoms have their axes of magnetic polarization (spins) aligned in alternating directions: up, down, up, down and so on. On the scale of the entire material those alternating internal magnetic orientations cancel one another out, resulting in no net magnetism of the overall material. Such materials can be switched quickly between different states. They’re also resistant to information being lost due to interference from external magnetic fields. These properties make antiferromagnetic materials attractive for modern communication technologies.
Next we have excitonic. Excitons arise when certain conditions allow electrons to move around and interact strongly with one another to form bound states. Electrons can also form bound states with “holes,” the vacancies left behind when electrons jump to a different position or energy level in a material. In the case of electron-electron interactions, the binding is driven by magnetic attractions that are strong enough to overcome the repulsive force between the two like-charged particles. In the case of electron-hole interactions, the attraction must be strong enough to overcome the material’s “energy gap,” a characteristic of an insulator.
“An insulator is the opposite of a metal; it’s a material that doesn’t conduct electricity,” said Dean. Electrons in the material generally stay in a low, or “ground,” energy state. “The electrons are all jammed in place, like people in a filled amphitheater; they can’t move around,” he said. To get the electrons to move, you have to give them a boost in energy that’s big enough to overcome a characteristic gap between the ground state and a higher energy level.
An artist’s impression of how the team identified this historic phase of matter. The researchers used x-rays to measure how spins (blue arrows) move when they are disturbed and were able to show that they oscillate in length in the pattern illustrated above. This special behavior occurs because the amount of electrical charge at each site (shown as yellow disks) can also vary and is the fingerprint used to pin down the novel behavior.

In very special circumstances, the energy gain from magnetic electron-hole interactions can outweigh the energy cost of electrons jumping across the energy gap.

Now, thanks to advanced techniques, physicists can explore those special circumstances to learn how the antiferromagnetic excitonic insulator state emerges.
A collaborative team worked with a material called strontium iridium oxide (Sr3Ir2O7), which is only barely insulating at high temperature. Daniel Mazzone, Yao Shen (Brookhaven Lab), Gilberto Fabbris (Argonne National Laboratory), and Jennifer Sears (Brookhaven Lab) used x-rays at the Advanced Photon Source—a DOE Office of Science user facility at Argonne National Laboratory—to measure the magnetic interactions and associated energy cost of moving electrons. Jian Liu and Junyi Yang from the University of Tennessee and Argonne scientists Mary Upton and Diego Casa also made important contributions.
The team started their investigation at high temperature and gradually cooled the material. With cooling, the energy gap gradually narrowed. At 285 Kelvin (about 53 degrees Fahrenheit), electrons started jumping between the magnetic layers of the material but immediately formed bound pairs with the holes they’d left behind, simultaneously triggering the antiferromagnetic alignment of adjacent electron spins. Hidemaro Suwa and Christian Batista of the University of Tennessee performed calculations to develop a model using the concept of the predicted antiferromagnetic excitonic insulator, and showed that this model comprehensively explains the experimental results.
“Using x-rays we observed that the binding triggered by the attraction between electrons and holes actually gives back more energy than when the electron jumped over the band gap,” explained Yao Shen. “Because energy is saved by this process, all the electrons want to do this. Then, after all electrons have accomplished the transition, the material looks different from the high-temperature state in terms of the overall arrangement of electrons and spins. The new configuration involves the electron spins being ordered in an antiferromagnetic pattern while the bound pairs create a ‘locked-in’ insulating state.”
The identification of the antiferromagnetic excitonic insulator completes a long journey exploring the fascinating ways electrons choose to arrange themselves in materials. In the future, understanding the connections between spin and charge in such materials could have potential for realizing new technologies.
Brookhaven Lab’s role in this research was funded by the DOE Office of Science, with collaborators receiving funding from a range of additional sources noted in the paper. The scientists also used computational resources of the Oak Ridge Leadership Computing Facility, a DOE Office of Science user facility at Oak Ridge National Laboratory.
Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov. [https://www.energy.gov/science/]
Related Links
Online version of this news release with related graphics [https://www.bnl.gov/newsroom/news.php?a=119438]
Scientific paper: “Antiferromagnetic Excitonic Insulator State in Sr3Ir2O7” [https://www.nature.com/articles/s41467-022-28207-w]
Media Contacts
Karen McNulty Walsh [mailto:[email protected]], (631) 344-8350, or Peter Genzer [mailto:[email protected]], (631) 344-3174

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Jason Trelewicz Photo from SBU

By Daniel Dunaief

One day, ships in the Navy may not only last longer in the harsh environment of salt water, but some of their more complicated parts may also be easier and quicker to fix.

That’s thanks to the mechanical engineering efforts of researchers at Stony Brook University and Brookhaven National Laboratory, who have been teaming up to understand the microstructural origins of corrosion behavior of parts they produce through laser additive manufacturing into shapes with complex geometries.

The Navy is funding research at the two institutions.

Eric Dooryhee. Photo from BNL

“As you would expect you’d need near any marine environment with salt water, [the Navy] is interested in laser additive manufacturing to enable the production of parts at lower cost that have challenging geometries,” said Jason Trelewicz, Associate Professor of Materials Science and Engineering at Stony Brook University. Additionally, the Navy is hoping that such efforts can enable the production of parts with specific properties such as corrosion resistance on demand.

“If you’re out at sea and something breaks, can you make something there to replace it?” asked Trelewicz. Ideally, the Navy would like to make it possible to produce parts on demand with the same properties as those that come off a manufacturing line.

While companies are currently adopting laser additive manufacturing, which involves creating three-dimensional structures by melting and resolidfying metal powders one layer at a time with the equivalent of a laser printer, numerous challenges remain for developing properties in printed materials that align with those produced through established routes.

Additive materials, however, offer opportunities to structure products in a way that isn’t accessible through traditional techniques that create more complex geometry components, such as complex heat exchangers with internal cooling channels.

In addition to the science remaining for exploration, which is extensive, the process is driving new discoveries in novel materials containing unique microstructure-chemistry relationships and functionally graded microstructures, Trelewicz explained.

“These materials are enabling new engineering components through expanded design envelopes,” he wrote in an email.

With colleagues from BNL including Research Associate Ajith Pattammattell and Program Manager for the Hard X-ray Scattering and Spectroscopy Program Eric Dooryhee, Trelewicz published a paper recently in the journal Additive Manufacturing that explored the link between the structure of the material and its corrosive behavior for 316L stainless steel, which is a corrosion resistant metal already in wide use in the Navy.

The research looked at the atomic and microstructure of the material built in the lab of Professor Guha Manogharan at Penn State University. Working with Associate Professor Gary Halada in the Department of Material Science and Chemical Engineering, Trelewicz studied the corrosive behavior of these materials.

Often, the surface of the material went through a process called pitting, which is common in steels exposed to corrosive environments, which occurs in cars driven for years across roads salted when it snows.

The researchers wanted to understand “the connection between how the materials are laser printed, what their micro structure is and what it means for its properties,” Trelewicz said, with a specific focus on how fast the materials were printed.

While the research provided some structural and atomic clues about optimizing anti corrosive behavior, the scientists expect that further work will be necessary to build more effective material.

In his view, the next major step is understanding how these defects impact the quality of this protective film, because surface chemical processes govern corrosive behavior.

Based on their research, the rate at which the surface corrodes through laser additive manufacturing is comparable to conventional manufacturing.

Printed materials, however, are more susceptible to attack from localized corrosion, or pitting. 

At the hard x-ray nanoprobe, Pattammattel explored the structure of the material at a resolution far below the microscopic level, by looking at nonstructural details.

“It’s the only functional beamline that is below 10 nanometers,” he said. “We can also get an idea about the electronic structures by using x-ray absorption spectroscopy,” which reveals the chemical state.

Pattammattel, who joined BNL in 2018, also uses the beamline to study how lung cells in mice interact with air pollutants. He described “the excitement of contributing to science a little more” as the best part of each day.

Meanwhile, Dooryhee as involved in writing the seed grant proposal. By using the x-rays deflected by the variety of crystalline domains or grains that compose the materials, HE can interpret the material’s atomic structure by observing the diffraction angles. The discrete list of diffraction angles is a unique fingerprint of the material that relates to its long-range atomic ordering or stacking.

In this study, researchers could easily recognize the series of diffraction peaks associated with the 316L stainless steel.

Dooryhee was able to gather insight into the grain size and the grain size distribution, which enabled him to identify defects in the material. He explained that the primary variable they explored was the sweeping rate of the laser beam, which included 550, 650 and 700 millimeters per second. The faster the printing, the lower the deposited energy density.

Ultimately, Dooryhee hopes to conduct so-called in situ studies, in which he examines laser additive manufacturing as it’s occurring.

“The strength of this study was to combine several synchrotron techniques to build a complete picture of the microstructure of the [additively manufactured] material, that can then be related to its corrosion response,” he explained in an email.

Dooryhee grew up in Burgundy France, where his grandfather used to grow wine. He worked in the vineyards during the fall harvest to help pay for his university studies. Dooryhee has worked at BNL for over 12 years and appreciates the opportunity to collaborate with researchers at Stony Brook University.

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Alex Harris. Photo from BNL

The U.S. Department of Energy’s (DOE) Brookhaven National Laboratory has named Alex Harris as Director of the Lab’s Energy Sciences Department, effective May 1, 2021. The announcement was made in a June 21 press release.

In his new position, Harris will manage several divisions of the Laboratory, including the Center for Functional Nanomaterials, the Chemistry Division, and the Condensed Matter Physics and Materials Science Division. Together, these divisions conduct fundamental research on advanced energy technologies and clean energy solutions, spanning from electric vehicle batteries to artificial photosynthesis, as well as research on quantum materials and nanomaterials to advance quantum information science.

“The Energy Sciences Department has leading scientists in chemical, materials, and nanosciences working together on problems that address DOE and national priorities in energy and quantum science,” Harris said. “Those are topics of rising national importance and there are exciting opportunities ahead. I’m honored to lead the Department to continue developing those themes and to strengthen collaborations with other departments, particularly with the National Synchrotron Light Source II, which is a key partner in much of our research.”

Beginning in September 2020, Harris simultaneously handled the role of Interim Energy Sciences Director and his regular role as Chair of the Chemistry Division, which he has held since 2003. As Chemistry Chair, Harris made significant contributions to the Lab’s vision for sustainable energy conversion. He will now continue as Acting Chair of the Chemistry Division while the Lab conducts a search for a new chair.

“The Chemistry Division is at the center of Brookhaven’s fundamental research on clean energy solutions. It has been rewarding to work with the division scientists to develop programs that address important national needs and are producing some great science. Chemistry has a family spirit and I look forward to continue working with people in the division in my new role,” Harris said.

Harris originally came to Brookhaven from Agere Systems, where he was Director of the Guided Wave and Electro-optics Research Department. His early career was at AT&T’s Bell Laboratories, where he became department head of Materials Chemistry Research. Harris earned a Ph.D. in physical chemistry from the University of California at Berkeley and a B.A. in Chemistry from Swarthmore College.

Brookhaven National Laboratory is supported by the U.S. Department of Energy’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://energy.gov/science.

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