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Brookhaven National Laboratory

Electrons, shown as red dots above, collide with an ion. Such a collision will reveal the internal structure of the quarks and gluons that are the building blocks of the proton and neutron. Image from BNL

National labs, including Brookhaven National Laboratory, received considerable additional funds as a part of the federal Inflation Reduction Act.

BNL, which will get an additional $224 million over a five-year period, will collect the additional funding from the Department of Energy’s Office of Science to support several projects designed

In a statement, Secretary of Energy Jennifer Granholm called the additional funds for energy-related research and support, which total $1.5 billion, “one of the largest ever investments in national laboratory infrastructure” and suggested that the effort would “develop advanced energy and manufacturing technologies we need to advance the frontiers of science and tackle tomorrow’s challenges.”

At BNL, the Electron-Ion Collider, an enormous project that will start construction in 2024 and should start running experiments in the early part of the next decade, will receive $105 million.

BNL is building the EIC in partnership with the Thomas Jefferson National Accelerator Facility in Virginia, which will also receive $33 million for work towards the new facility.

As its name suggests, the EIC will collide electrons and protons or heavier atomic nuclei and hopes to make numerous discoveries, including providing an understanding of how the energy from quarks and gluons provides the mass of a proton.

Additionally, the EIC will provide advances in health and medicine, national security, nuclear energy, radioisotope production and industrial uses in particle beams. Research on the technologies that will become a part of the EIC will advance the development of magnets and other particle accelerator parts. These advances could lead to energy efficient accelerators, shrinking the size and costs of future accelerators, which could attack cancer cells, design solar cells and batteries and develop drugs and medical treatments.

While the additional funds will help advance the development of the EIC, the total cost is considerably higher, at an estimated $1.7 billion to $2.8 billion.


Additionally, the Office of Science will provide $18.5 million to speed the creation of three new beamlines at the National Synchrotron Light Source II.

The NSLS II already has a host of beamlines that enable researchers from around the world to study the structure of batteries as they are operating, catalysts that help tap into energy sources, and biologically active molecules that could play a role in understanding basic biochemistry or that could lead to the development of drugs.

The new beamlines, which, like others at the NSLS II, have three-letter abbreviations. The ARI will provide a complete picture of the electronic structure of a sample, particularly in connection with temperature, chemical, structural and atomic variation.

ARI will help understand and control the electronic structure of next generation quantum materials.

CDI, meanwhile, will explore the condensed matter macroscopic and microscopic physical properties of matter, including the solid and liquid phases that arise from electromagnetic forces between atoms. CDI is in its final stages of its design.

The SXN will provide element access from carbon to sulfur. The beamline will offer measurements of different signals, such as X-ray fluorescence and total electron yield absorption, which is important in catalysis, condensed matter physics and environmental science.

The DOE is also providing $20 million for five Nanoscale Science Research Centers. The Center for Functional Nanomaterials is leading the effort to revitalize the nanoscience infrastructure.

The funds will accelerate the acquisition, development and installation of five instruments, which will advance research in fuel cells, solar cells and other materials that are part of the country’s efforts to develop cleaner forms of energy.

A/C and Heating

BNL will receive $33 million to support an upgrade to the ATLAS detector at the Large Hadron Collider in Europe’s CERN laboratory. The upgrades will enable a high-energy particle detector to make use of increased particle collision rates.

The lab, which focuses on energy research, will also receive $14.5 million towards infrastructure improvements that will increase the efficiency in distributing electricity and heating and air conditioning in labs throughout the facility.

Finally, the lab will receive $1 million to develop instrumentation for a nuclear physics experiment that seeks to find neutrinoless double beta decay, which is led by the Lawrence Livermore National Laboratory.

BNL Lab Director Doon Gibbs described the funding as an investment in the nation’s innovation-based economy.

The funding will support “research with direct impact on the development of clean energy technologies as well as ground-breaking basic research in nuclear and high-energy physics — fields that could lay the foundation for future advances,” Gibbs said in a statement.

Commemorating the start of construction for the Science and User Support Center from the U.S. Department of Energy and Brookhaven Lab are (from left) Joe Diehl, Caroline Polanish, Robert Gordon, Geri Richmond, Doon Gibbs, Chris Ogeka, Tom Daniels, Peggy Caradonna, Andrea Clemente, and Gary Olson. Photo from BNL

Construction is underway for the newest facility at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory. The Science and User Support Center (SUSC) is the first building for the planned Discovery Park, a development the Laboratory is pursuing near its entrance along William Floyd Parkway.

The three-story, 75,000-square-foot facility will serve as a welcome center for the 75-year-old Brookhaven Lab, which is home to seven Nobel Prize-winning discoveries and hosts thousands of guests annually. The SUSC will also offer conference and collaboration areas for scientists as well as office space for the Lab‘s support staff.

Officials from DOE and Brookhaven Lab commemorated the start of construction during a groundbreaking ceremony Wednesday, Oct. 26.

DOE’s Under Secretary of Science and Innovation Geri Richmond said, “This strategy—of welcoming the community to be part to our nationallaboratories and focusing on creative, innovative ways for public-private partnerships to strengthen the economy—is so important. This is a centerpiece, a catalyst for the campus and for the future.”

Manager of DOE’s local Brookhaven Site Office, Robert Gordon, said, “This is transformative for Brookhaven National Laboratory. We should be accessible. We’ve done that with our words and our actions. Now we’re doing it with concrete.”

Brookhaven Lab Director Doon Gibbs said, “This construction is a milestone in the Laboratory‘s long-term strategy to revitalize its physical plant. We look forward to welcoming visitors, users, students, and members of the community to connect with Brookhaven, the DOE, our science, and the impact it has.”

Plainview-based E.W. Howell is leading construction as the project’s general contractor. The Laboratory announced in February that it awarded E.W. Howell a $61.8 million contract to build the SUSC. DOE approved a total cost of $86.2 million for the project. E.W. Howell and BrookhavenLab are targeting 2024 for construction to be completed.

The SUSC is the first building planned for Discovery Park, a new vision for Brookhaven Lab‘s gateway with approximately 60 acres of previously used, publicly accessible land. The Laboratory is working with DOE on a process for developers, collaborators, and entrepreneurs to propose, build, and operate new facilities that could complement DOE and Brookhaven Lab‘s missions and leverage opportunities from close proximity to the Laboratory.

Empire State Development is supporting Brookhaven Lab‘s efforts for Discovery Park with a $1.8 million capital grant, recommended by the Long Island Regional Economic Development Council.

The future Science and User Support Center. Rendering courtesy of BNL

Increasing Efficiency for Discoveries, New Technology

Brookhaven Lab attracts scientists from across the country and around the world by offering expertise and access to large user facilities with unique capabilities.

Brookhaven hosted more than 4,400 in-person and virtual scientists from universities, private industry, and government agencies in fiscal year 2021. In the years before the COVID-19 pandemic, more than 5,000 guests and facility users visited each year. The Laboratory expects the number of guests researchers to increase in the coming years, particularly as capabilities expand at the National Synchrotron Light Source II—a DOE Office of Science User Facility—and with the design and construction of the future Electron-Ion Collider.

The SUSC, when complete, is where those guests will arrive. The SUSC will also help improve the guests’ experiences of visiting Brookhavenbecause the Laboratory will consolidate a number of guest services into a central, modern building close to the site entrance.

The SUSC will also feature reconfigurable conference space, designed in response to requests from facility user communities to create opportunities for scientists to collaborate.

In addition, the SUSC will help the Laboratory increase efficiencies by reducing its building footprint atop the 5,322-acre site. The Laboratory plans to relocate approximately 225 staff at the SUSC. They are currently spread across the Lab site, which contains 314 buildings—some that date back to the World War II era, when the Laboratory was the site of the Army’s former Camp Upton.

The SUSC project is funded by the DOE Office of Science.

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.

Mercy Baez. Photo by Joseph Rubino/ BNL

By Daniel Dunaief

She is a greeter, a corporate concierge, a facilitator, a point of contact for people traveling thousands of miles, a Spanish translator, an important contact in case of emergencies, and whatever else visitors need.

While Mercy Baez, who was promoted to User Program Coordinator for the National Synchrotron Lightsource II and the Laboratory for BioMolecular Structure at Brookhaven National Laboratory early in October, wears many hats, one of the only ones she doesn’t wear is scientist, although that doesn’t keep her from appreciating and taking pride in the research conducted at the Department of Energy facility.

“We’re helping them and they are helping the world,” Baez said.

BNL has a steady stream of users who apply for time at the various research facilities at the national laboratories. 

Baez is specifically responsible for providing a wide range of support and services to the NSLS II and the LBMS. Users, which is how BNL describes potential visiting scientists who conduct research at the lab’s facilities, submit proposals to her office, which then distributes them to a proposal review panel.

When visiting scientists learn that their work, which includes monitoring batteries as they function and searching for fine structural sites in the molecular battle against pathogens, has earned a high enough score to receive coveted time on the lab’s instruments, they prepare for their visit by interacting with Baez and her current team of four by getting registered and approved for access.

Baez offers soup to nuts guidance that often also includes helping users literally find soup, nuts and numerous other items. Baez ensures that users take any necessary training courses, provides guidance regarding registering for on site access to BNL, provides information on the steps or items necessary when they arrive, helps find nearby hotels, coordinate travel to and from the lab and, if necessary, secures places to stay if they miss their planes, get snowed in or have other unforeseen changes in their schedules.

As of October 1st, visitors also have to have some type of active shooter training to access the lab’s facilities. Currently, users are required to take five training courses. Last week, the lab decided to incorporate active shooter training into one of these other training courses.

The lab has always had routine emergency training courses and drills for lab employees. With the changing times and current events, the lab is looking to equip users for such emergencies. The lab hopes never to have to use this training, but if such an event occurs, staff and users will know how to handle such a situation.

In addition to training to help users prepare to visit the facility, Baez provides visitors with a host of on site facilities, including adaptors in case they are using European electronics that don’t connect with the outlets, laptops in case the computer a scientist brought isn’t working, conference rooms for impromptu meetings, and dorm rooms for a respite while running time-intensive experiments.

BNL hosts employee resource groups including the African American Advancement Group, the Asian Pacific American Association, the Brookhaven Veterans Association, Brookhaven Women in Science, the Early Career Resource Group, the Pride Alliance and the Hispanic Heritage Group. Baez said the lab tries to involve users and visitors in as many cultural and social events as possible, which include outings to dinners, plays and cultural virtual cooking classes.

In September, Baez participated in the Port Jefferson Dragon Boat Race Festival which the Asian Pacific  American Association sponsored. 

Baez, whose mother is from Puerto Rico and whose father is from Ecuador, is a member of the Hispanic Heritage Group.

A people person

A member of the user offices since 2003, Baez had recently been responsible for coordinating conferences, workshops, and training courses, including financial and logistical aspects of the events for NSLS-II and the LBMS. She had been functioning as the user program coordinator since January, when Gretchen Cisco retired. Baez feels fortunate to have worked with Cisco since she joined NSLS in 2005.

A self-described “people person,” Baez said she loves the opportunity to interact with scientists from all over the world. She particularly appreciates the chance to get to know about other cultures and has added destinations to her travel itinerary from speaking with visitors. She is hoping to travel to Morocco and Peru next year and is hoping to travel to Japan and a few other countries in the near future.

Coming from a Latina family that tends to be loud and outspoken and whose family gatherings often includes more than 30 people, she has learned to speak in a softer voice, particularly with people from other cultures or backgrounds.

She also has a tendency to speak quickly and has learned to slow the pace down so visitors who haven’t interacted with her can understand what she’s saying.

A resident of Medford, which is a ten-minute drive from the lab, Baez has a son Xzavier and a granddaughter Francesca. She is excited for the upcoming arrival of her second granddaughter in November.

When she’s not at the lab, she uses her leisure time to go hiking, fishing and camping.

With her then teenage son in tow, she went to the jungle of Belize for a survival course, where they learned how to catch their own food, build shelters, and harpoon fish. She also learned which plants are safe to eat and which are poisonous.

While her work responsibilities can be hair-raising, particularly in emergencies, she “loves the feeling that I was able to help a scientist, whether to get him or her on site or in an emergency,” she said. Knowing that she’s a part of making all this science happen makes her day and job rewarding, she said.

Baez has had some requests from scientists who have wanted cultural foods, such as Turkish or vegan dishes, that might be harder to find, particularly during off hours.

Around Thanksgiving each year, some visitors have asked if they can hunt wild turkeys at BNL, which is located within the Pine Barrens and has turkeys and deer wandering on site. She has told those users that the lab does not allow hunting.

Hunting aside, Baez said she is “here to help [users] do what they need to do.”

Duckweed. Photo from BNL
Scientists drive oil accumulation in rapidly growing aquatic plants

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and collaborators at Cold Spring Harbor Laboratory (CSHL) have engineered duckweed to produce high yields of oil. The team added genes to one of nature’s fastest growing aquatic plants to “push” the synthesis of fatty acids, “pull” those fatty acids into oils, and “protect” the oil from degradation. As the scientists explain in a paper published in Plant Biotechnology Journal, such oil-rich duckweed could be easily harvested to produce biofuels or other bioproducts.

John Shanklin. Photo from BNL

The paper describes how the scientists engineered a strain of duckweed, Lemna japonica, to accumulate oil at close to 10 percent of its dry weight biomass. That’s a dramatic, 100-fold increase over such plants growing in the wild—with yields more than seven times higher than soybeans, today’s largest source of biodiesel.

“Duckweed grows fast,” said Brookhaven Lab biochemist John Shanklin [https://www.bnl.gov/staff/shanklin], who led the team. “It has only tiny stems and roots—so most of its biomass is in leaf-like fronds that grow on the surface of ponds worldwide. Our engineering creates high oil content in all that biomass.

“Growing and harvesting this engineered duckweed in batches and extracting its oil could be an efficient pathway to renewable and sustainable oil production,” he said.

Two added benefits: As an aquatic plant, oil-producing duckweed wouldn’t compete with food crops for prime agricultural land. It can even grow on runoff from pig and poultry farms.

“That means this engineered plant could potentially clean up agricultural waste streams as it produces oil,” Shanklin said.

Leveraging two Long Island research institutions

The current project has roots in Brookhaven Lab research on duckweeds from the 1970s, led by William S. Hillman in the Biology Department. Later, other members of the Biology Department worked with the Martienssen group at Cold Spring Harbor to develop a highly efficient method for expressing genes from other species in duckweeds, along with approaches to suppress expression of duckweeds’ own genes, as desired.

As Brookhaven researchers led by Shanklin and Jorg Schwender [https://www.bnl.gov/staff/schwend] over the past two decades identified the key biochemical factors that drive oil production and accumulation in plants, one goal was to leverage that knowledge and the genetic tools to try to modify plant oil production. The latest research, reported here, tested this approach by engineering duckweed with the genes that control these oil-production factors to study their combined effects.

“The current project brings together Brookhaven Lab’s expertise in the biochemistry and regulation of plant oil biosynthesis with Cold Spring Harbor’s cutting-edge genomics and genetics capabilities,” Shanklin said.

One of the oil-production genes identified by the Brookhaven researchers pushes the production of the basic building blocks of oil, known as fatty acids. Another pulls, or assembles, those fatty acids into molecules called triacylglycerols (TAG)—combinations of three fatty acids that link up to form the hydrocarbons we call oils. The third gene produces a protein that coats oil droplets in plant tissues, protecting them from degradation.

From preliminary work, the scientists found that increased fatty acid levels triggered by the “push” gene can have detrimental effects on plant growth. To avoid those effects, Brookhaven Lab postdoctoral researcher Yuanxue Liang paired that gene with a promoter that can be turned on by the addition of a tiny amount of a specific chemical inducer.

“Adding this promoter keeps the push gene turned off until we add the inducer, which allows the plants to grow normally before we turn on fatty acid/oil production,” Shanklin said.

Liang then created a series of gene combinations to express the improved push, pull, and protect factors singly, in pairs, and all together. In the paper these are abbreviated as W, D, and O for their biochemical/genetic names, where W=push, D=pull, and O=protect.

The key findings

Overexpression of each gene modification alone did not significantly increase fatty acid levels in Lemna japonica fronds. But plants engineered with all three modifications accumulated up to 16 percent of their dry weight as fatty acids and 8.7 percent as oil when results were averaged across several different transgenic lines. The best plants accumulated up to 10 percent TAG—more than 100 times the level of oil that accumulates in unmodified wild type plants.

Some combinations of two modifications (WD and DO) increased fatty acid content and TAG accumulation dramatically relative to their individual effects. These results are called synergistic, where the combined effect of two genes increased production more than the sum of the two separate modifications.

These results were also revealed in images of lipid droplets in the plants’ fronds, produced using a confocal microscope at the Center for Functional Nanomaterials [https://www.bnl.gov/cfn/] (CFN), a DOE Office of Science user facility at Brookhaven Lab. When the duckweed fronds were stained with a chemical that binds to oil, the images showed that plants with each two-gene combination (OD, OW, WD) had enhanced accumulation of lipid droplets relative to plants where these genes were expressed singly—and also when compared to control plants with no genetic modification. Plants from the OD and OWD lines both had large oil droplets, but the OWD line had more of them, producing the strongest signals.

“Future work will focus on testing push, pull, and protect factors from a variety of different sources, optimizing the levels of expression of the three oil-inducing genes, and refining the timing of their expression,” Shanklin said. “Beyond that we are working on how to scale up production from laboratory to industrial levels.”

That scale-up work has several main thrusts: 1) designing the types of large-scale culture vessels for growing the modified plants, 2) optimizing large-scale growth conditions, and 3) developing methods to efficiently extract oil at high levels.

This work was funded by the DOE Office of Science (BER). CFN is also supported by the Office of Science (BES).

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/]

Dr. John Clarke. Photo from BNL

By Daniel Dunaief

Live from Upton, New York, it’s … Dr. John Clarke.

While the arrival of the new Occupational Medicine Director and Chief Medical Officer at Brookhaven National Laboratory doesn’t involve late-night comedy, or a live studio audience, it does bring a medical doctor with a passion for bringing his rap and musical skills to a health care audience.

Dr. John Clarke. Photo from BN

Formerly the director of occupational medicine at Cornell University, Dr. Clarke joined the Department of Energy lab as Occupational Medicine Director and Chief Medical Officer for BNL in June..

“My role is to help maintain safety and wellness among the workers,” said Dr. Clarke. “If we have employees who start coming in for some sort of complaint and we see a pattern, that may help us identify who could be at risk of something we didn’t know about that we are detecting.”

A doctor who served as chief resident at New York Medical College in family residency and Harvard University in occupational & environmental medicine, Dr. Clarke said he plans to support a range of preventive efforts.

“I’m excited about the potential to engage in what’s considered primary prevention,” said Clarke, which he defined as preventing a disease from occurring in the first place.

Through primary prevention, he hopes to help the staff avoid developing chronic illnesses such as cancer, while also ensuring the health and responsiveness of their immune systems.

Through physical fitness, a plant-based diet including fruits and vegetables, adequate sleep and hydration with water, people can use lifestyle choices and habits to reduce their need for various medications and enable them to harness the ability of their immune systems to mount an effective response against any threat.

“Modifying your lifestyle is the therapy,” he said. “If you engage [in those activities] in the right way, that is the treatment.”

Dr. Clarke added that the severity and stage of a disease may impact the effectiveness of such efforts. For any vaccine and for the body’s natural immunity to work, people need a healthy immune system.

When Dr. Clarke practiced family medicine, he saw how patients lost weight through a diet that reduced the need for medication for diabetes and high blood pressure.

“Losing weight and staying active does provide a therapeutic impact, where you could be medication free,” he said.

To be sure, living a healthier lifestyle requires ongoing effort to maintain. After reaching a desired weight or cholesterol level, people can backslide into an unhealthier state or condition, triggering the occurrence or recurrence of a disease.

In the vast majority of cases, Clarke said, “you have to make a permanent lifestyle change” to avoid the need for pharmaceutical remedies that reduce the worst effects of disease.

BNL has an exercise physiologist on staff who “we hope to engage in consultations with employees,” said Clarke. He would like the exercise physiologist to go to the gym with staff to show them how to use equipment properly to get the maximum benefit.

BNL already has some classes and various initiatives that promote wellness. “One of the things we’d like to do is coordinate and try to publicize it enough where employees are aware” of the options available at the lab to live a healthier and balanced life, he added.

BNL also has a dietician on staff. Dr. Clarke has not worked with the dietician yet, but hopes it will be part of an upcoming initiative. As he and his staff respond to the demand, they will consider bringing on other consultants and experts to develop programs. 

Covid concerns

Like others in his position in other large employers around Long Island, Dr. Clarke is focused on protecting workers from any ongoing threat from Covid-19.

“We’re still learning more as [SARS-CoV2, the virus that caused the pandemic] evolves,” he said. BNL does a “great job about monitoring the prevalence and the numbers of cases in Suffolk County and among workers.”

Dr. Clarke said he and others at BNL are following the Department of Energy, New York State and Centers for Disease Control and Prevention guidance on these issues.

If the numbers of infections and hospitalizations increase in the coming months, as people move to more indoor activities, BNL may consider deploying a strategy where the lab provides more opportunities for staff to work remotely.

Prior to his arrival at BNL, Dr. Clarke worked as a consultant for a company that was looking to create numerous permanent jobs that were remote.

He suggested that workers need to remain aware of their remote surroundings and shouldn’t work near a furnace or any heater that might release dangerous gases like carbon monoxide. 

Additionally, people should avoid working in areas that aren’t habitable, such as in an attic. Dr. Clarke urges people to notify and consult their employer if they have concerns about working safely at home or on site.

Music vs. medicine

A native of Queens who spent three years of his childhood in Barbados, Dr. Clarke attended Columbia University, where he majored in sociology and music while he was on a pre-med track.

While he was an undergraduate, Dr. Clarke wrote, produced and performed original music. An independent label was going to help secure a major label deal.

He chose to attend medical school at Icahn School of Medicine at Mount Sinai.

Dr. Clarke has championed a program he calls “health hop,” in which he has used rap to reach various audiences with medical care messages. In 2009, he won a flu prevention video contest sponsored by the Department of Health and Human Services for an “H1N1 rap.”

Train commuters may also recognize him from his work for the Long Island Railroad, for which he created a “gap rap.” The public service announcement was designed to protect children from falling into or tripping over the gap between the train and the platform.

Dr. Clarke has produced music for numerous genres, including for a children’s album and a Christian album.

As for life outside BNL, Dr. Clarke is married to Elizabeth Clarke, who is a nurse practitioner and is in the doctorate of nursing practice and clinical leadership program at Duke University.

When he’s not spending time with his wife or their children, he enjoys home projects like flooring and tiling.

Dr. Clarke is pleased to be working at the national Department of Energy lab.“BNL is a great place, because the science and the work they do has an impact,” he said.

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.”

Aleida Perez during BNL's virtual teaching sessions this summer

By Daniel Dunaief

For well over two years, herd immunity, vaccination status, social distancing, masking and airborne particles became regular topics of conversation. 

People have a range of understanding of these terms and how to apply them to understanding the fluid conditions that are an evolving part of the pandemic.

Aleida Perez

This summer, with funding from the National Science Foundation, a group of scientists and doctors from Brookhaven National Laboratory, Stony Brook University, New York University and MoMath, the National Museum of Mathematics, worked together with middle school and high school teachers around Long Island to prepare lesson plans on how to use and understand the application of statistics to the pandemic.

“It was a wildly successful summer,” said Dr. Sharon Nachman, Chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital. “We spent hours and hours of time” working with teachers who developed lessons that addressed a host of issues related to COVID-19.

It was “an amazing experience” and the teachers “were the best part,” said Dr. Nachman.

Allen Mincer, Professor of Physics at New York University, has been working on and off with BNL for over two decades on various educational programs. He has been more actively engaged in the last four years.

As he and his collaborators were discussing possible educational outreach topics, they focused on the disruptive disease that changed the world over the last few years.

“This year, we were talking about it and, instead of doing random applications of statistics, we figured, why not do something that’s very practical in everyone’s mind,” Mincer said.

The projects and discussions, which were all conducted virtually, centered on numerous misconceptions people have about the pandemic. Teachers focused on questions including: what is the “efficiency” of a vaccine and how is it determined, what does a positive virus test result mean, if I am vaccinated, why do I care if others are, why take a vaccine when there are side effects, and I have to go to school and mix with people, so why shouldn’t I also let down my guard in other ways, among others.

“The challenges that this virus brings concerning topics like herd immunity was very interesting,” said Scott Bronson, manager of outreach to K-12 teachers and student for BNL’s Office of Educational Programs.

Scott Bronson during the BNL virtual teaching sessions this summer.

For teachers and their students, the realities of the pandemic were the backdrop against which these teachers were seeking to provide guidance. “It was happening live,” said Bronson. “What is herd immunity? That’s where the work of [Dr. Nachman and Mincer] came together beautifully.”

Bronson added that students will have a chance to explore the kinds of questions pharmaceutical companies are addressing, such as “What would you want the next vaccine to do” and “What would you do to make the vaccine better at preventing infection.”

The organizers put together teams of three to four high school and middle school teachers who created statistics lessons plans for the group.

“The way we worked it out, we put teachers in groups,” said Aleida Perez, supervisor of student research and citizen science programs for Brookhaven National Laboratory’s Office of Educational Programs. “We wanted to have different teachers with different courses and different perspectives on how to do things.”

One of the overarching goals was to help students understand such lessons as what it means to have a negative result on a virus test or what it meant when scientists and pharmaceutical companies described a vaccine’s efficacy.

The teachers explored the probability of side effects like myocarditis and whether the “benefit outweighs the risk of taking the vaccine,” Perez said.

For many of the teachers, the discussion expanded beyond COVID to an analysis of any infectious agent. Indeed, one of the groups of teachers described a zombie apocalypse.

The teachers provided a “nice overview to look at the education of public students,” said Perez.

The group hopes to make these lessons available for other teachers, although they haven’t determined where or how to post them.

The scientific team also hasn’t determined yet how to measure the long term impact or effectiveness of these lessons.

ATLAS project

As a part of the team involved in the ATLAS physics program at the Large Hadron Collider in Geneva, Switzerland, Mincer uses statistics to design, test and implement the tools to pick and choose from numerous reactions and then to study the data collected.

“We actually keep about a billion events out of the 100 trillion or so interactions the LHC produces in a year,” Mincer explained.

In previous years, Mincer has taught about statistics in general and its use in ATLAS. This year, he focused on statistics and its application to pandemic questions.

Several years ago, Mincer taught a freshman seminar called “Great science, fabulous science and voodoo science,” in which he described what students could learn from statistics, how the media covers science, science and government policy and how lawyers use science in the courtroom.

“After explaining statistics [and sharing] why we can only say we have evidence down to this level, I had a student tell me he’s dropping out of science as a major because he wanted certainty and I disillusioned him,” Mincer said.

As for the work with the high school teachers, Mincer said it was “great what they have been able to do” in preparing lessons for their students and sharing information about statistics.

Mincer has received some additional funds from the NSF to support two more such educational outreach programs, one of which will tentatively cover climate change.

“Statistics can be used to quantify the likelihood of events in the absence of climate change,” he explained.

Statistics provide a tool to document subtle but potentially significant changes in climate.

While Bronson wouldn’t commit to a discussion of climate change for the next group of teachers, he said he “wouldn’t be surprised if we look at climate change” and that “there’s a lot of interesting areas to explore in this field.”

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.”

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.

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