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Stony Brook University

SBU Journalism Newsroom

Stony Brook University recently announced that the School of Journalism will be renamed to the School of Communication and Journalism. The School is the first, and only, in the 64-campus SUNY system that is accredited by the Accrediting Council on Education in Journalism and Mass Communications (ACEJMC).

The new name aligns more closely with the School’s expanding undergraduate and graduate degree programs, and with the increased demand for professionals with backgrounds and experience in different communication-related disciplines.

“Communication goes beyond journalism, and Stony Brook’s School of Communication and Journalism will offer new opportunities for our students to explore important fields in science communication, health communication and mass communication, in addition to journalism,” Fotis Sotiropoulos, interim university provost and dean of the College of Engineering and Applied Sciences said.

In the past year, the School has begun to offer graduate programs in science communication, in collaboration with the Alan Alda Center for Communicating Science, and in public health, in collaboration with the Stony Brook Program in Public Health. Additional programs are in development.

“Faculty at the School and the Alda Center work closely on communication research, particularly in the field of science communication, and by renaming the School, we will be able to foster additional communication research,” said Laura Lindenfeld, dean of the School, executive director of the Alda Center, and vice provost for academic strategy and planning at Stony Brook. “Effective communication builds trust among people, enhances mutual understanding, and creates opportunities for collaboration. Now more than ever, we need effective communicators, and Stony Brook is eager to help fill that need.”

The School of Journalism was founded in 2006 and enrolls approximately 250 students. Its faculty include Pulitzer Prize winners, award-winning international and foreign correspondents, and experts in digital innovation. Graduates have gone on to work as reporters and media professionals at organizations around the country, including the New York Times, Buzzfeed, Moth Radio Hour, Council of Foreign Relations, Major League Baseball, and Nieman Lab.

The School is home to the Alda Center, the Marie Colvin Center for International Reporting and the Center for News Literacy. It also offers the Robert W. Greene Summer Institute for High School Journalists, a one-week intensive program designed to introduce students from across Long Island and New York City to the possibilities of journalism as a career.

Learn more about the School of Communication and Journalism at www.stonybrook.edu/commcms/journalism/

#33 India Pagan. Photo courtesy of SBU Athletics

DURHAM, N.H. — India Pagan achieved a milestone and the Stony Brook women’s basketball team headed home on a high note.

Pagan tallied her 1,000th career point as the Seawolves defeated New Hampshire, 64-41, on Sunday afternoon at Lundholm Gynasium. Stony Brook split its two-game weekend trip to New Hampshire and now stands at 6-4 overall and 4-2 in America East. 

“Today we played four quarters of Stony Brook basketball,” head coach Caroline McCombs said. “I’m proud of our balanced attack, focus and response in the quick turnaround.”

The Seawolves never trailed on Sunday.

Pagan’s historic point came on free throw with 2:43 remaining in the game. She became the 18th player in program history to amass that total with the Seawolves, and the fourth player during McCombs’ seven seasons as a head coach.

“I can’t believe it’s been four years and it’s finally setting in that I have 1,000 points,” Pagan said. “I’m blessed to have been able to reach that milestone in high school and now in college as well. I’m thankful to be part of an elite and special group. Without them, the coaches and my family and friends, this wouldn’t have been possible. We’re not done yet!”

Brittany Snow tallied 1,314 points from 2012-13 through ‘15-16, Sabre Proctor amassed 1,205 from 2012-13 through ‘14-15, and Korie Bayne-Walker had 1,045 from 2013-14 through ‘16-17.

Kaela Hilaire reached 1,000 points last season with Stony Brook after playing the bulk of her career at Seton Hall.

On Sunday, Anastasia Warren led the Seawolves in scoring for a second straight day, this time with 13 points. She had tallied 19 points in Saturday’s narrow 52-49 loss.

Nairimar Vargas-Reyes (10 points) also reached double-figures in scoring in Sunday’s victory.

The team returns to action next weekend with a pair of games against conference newcomer NJIT at Island Federal Arena.

Mouhamadou Gueye drives during the first half of Sunday’s game against UNH. Photo by Andrew Theodorakis

Coach Geno Ford gathered the Stony Brook men’s basketball team by the home bench after last Sunday’s loss and told his players that he was proud of their effort and toughness. “The results are not what we signed up for,” Ford added to his team. “And we have to stick together.”

Unfortunately, Stony Brook suffered a heartbreaker Sunday afternoon. The Seawolves were edged by New Hampshire, 67-64, at Island Federal Arena. UNH swept the back-to-back games after Stony Brook returned from a 20-day COVID pause. The Seawolves had entered that pause on a five-game winning streak.

With the team’s deadlocked at 62, Nick Johnson’s layup for UNH with 93 seconds remaining provided a two-point lead for the Wildcats. Tykei Greene and Mouhamadou Gueye then were whistled for offensive fouls the next two trips down the floor for Stony Brook (6-6, 4-2 AE). Still, after a shot-clock violation by the Wildcats, spurred in part by a block from Gueye, the Seawolves had another opportunity in a one-possession game.

Juan Felix Rodriguez then was fouled while driving with 14.2 seconds remaining and the Seawolves trailing 64-62.

Rodriguez missed both free throws. And New Hampshire converted a pair of free throws at the other end for a four-point lead. A potential game-tying three-pointer shortly before the buzzer from Rodriguez also came up short.

“It’s a frustrating loss,” Ford said. “I thought the guys really battled. I thought we physically tried hard. We missed a bunch of free throws in the last six or seven minutes that we had been making most of the game. And I think losing some possessions in there really hurt. And give them credit. They hit a couple of real timely threes.”

Frankie Policelli’s driving layup with 3:18 remaining had staked Stony Brook to a 61-59 lead. However, Qon Murphy answered with a three-pointer for UNH shortly thereafter to give the Wildcats a one-point advantage. Greene then sank one of two free throws with 1:53 remaining to even the score at 62.

Four Seawolves scored in double-figures: Greene (14 points), Policelli (13), Gueye (10) and Jaden Sayles (10).

Gueye also had five blocks, giving him 101 for his career. He became the second-fastest in program history to the 100-block plateau at 45 games. Only Jeff Otchere was quicker (44). “I don’t set out to get those accolades,” Gueye said. “It kind of just happens. I know shot blocking is a big part of my game.” 

Sayles returned to action after missing Saturday’s game, but was limited to 13 minutes as he eased back into play. Omar Habwe, however, missed Sunday’s contest after being deemed unavailable shortly before tip-off. The Seawolves return to action next weekend with a pair of games at conference newcomer NJIT.

Stony Brook University. File photo

Stony Brook University has been at the center of the COVID-19 pandemic, as hospital staff has treated and comforted residents stricken with the virus and researchers have worked tirelessly on a range of projects, including manufacturing personal protective equipment. Amid a host of challenges, administrators at Stony Brook have had to do more with less under budgetary pressure. In a two-part series, Interim Provost Fotis Sotiropoulos and President Maurie McInnis share their approaches and solutions, while offering their appreciation for their staff.

Part I: Like many other administrators at universities across the country and world, Fotis Sotiropoulos, Dean of the College of Engineering and Applied Sciences and Interim Provost of Stony Brook University, has been juggling numerous challenges.

Named interim provost in September, Sotiropoulos, who is also a SUNY Distinguished Professor of Civil Engineering, has focused on ways to help President Maurie McInnis keep the campus community safe, keep the university running amid financial stress and strain, and think creatively about ways to enhance the university’s educational programs.

In January, Stony Brook University which is one of two State University of New York programs to earn an Association of American Universities distinction, plans to announce new degree programs aimed at combining expertise across at least two colleges.

“We have charged all the deans to work together to come up with this future-of-work initiative,” Sotiropoulos said. “It has to satisfy a number of criteria,” which include involving at least two colleges or schools and it has to be unique. Such programs will “allow us to market the value of a Stony Brook education.”

Sotiropoulos said Stony Brook hoped to announce at least two or three degree ideas by the middle of January.

Fotis Sotiropoulos. File photo from SBU

Under financial pressure caused by the pandemic, the university has “undertaken this unprecedented initiative to think of the university as one,” Sotiropoulos said. Looking at the East and West campus together, the university plans to reduce costs and improve efficiency in an organization that is “complex with multiple silos,” he said. At times, Stony Brook has paid double or triple for the same product or service. The university is taking a step back to understand and optimize its expenses, he added.

On the other side of the ledger, Stony Brook is seeking ways to increase its revenue, by creating these new degrees and attracting more students, particularly from outside the state.

Out-of-state students pay more in tuition, which provides financial support for the school and for in-state students as well.

“We have some room to increase out-of-state students,” Sotiropoulos said. “There is some flexibility” as the university attempts to balance between the lower tuition in-state students pay, which benefits socioeconomically challenged students, and the higher tuition from out-of-state students.

While the university has been eager to bring in talented international students as well in what Sotiropoulos described as a “globally-connected world,” the interim provost recognized that this effort has been “extremely challenging right now,” in part because of political tension with China and in part because Chinese universities are also growing.

Stony Brook “recognizes that it needs to diversify right now. The university is considering strategies for trying to really expand in other countries. We need to do a lot more to engage students from African countries,” he said.

Sotiropoulos described Africa as an important part of the future, in part because of the projected quadrupling of the population in coming decades. “We are trying to preserve our Asian base of students,” he said, but, at the same time, “we are thinking of other opportunities to be prepared for the future.”

While the administration at the university continues to focus on cutting costs, generating revenue and attracting students to new programs, officials recognize the need to evaluate the effectiveness of these efforts for students. “Assessment is an integral part,” Sotiropoulos said. The school will explore the jobs students are able to find. “It’s all about the success of our students,” he added. The school plans to assess constantly, while making adjustments to its efforts.

Pandemic Response

Stony Brook University has been at the forefront of reacting to the pandemic on a number of fronts. The hospital treated patients during the heavy first wave of illnesses last spring, while the engineering school developed ways to produce personal protective equipment, hand sanitizer, and even MacGyver-style ventilators. The university has also participated in multi-site studies about the SARS-CoV-2 virus that causes COVID-19.

Stony Brook has been involved in more than 200 dedicated research projects across all disciplines, which span 45 academic departments and eight colleges and schools within the university.

Sotiropoulos, whose expertise is in computational fluid mechanics, joined a group of researchers at SBU to conduct experiments on the effectiveness of masks in stopping the way aerosolized viral particles remain in the air, long after patients cough, sneeze, and even leave the room.

“Some of these droplets could stay suspended for many minutes and could take up to half an hour” to dissipate in a room, especially if there’s no ventilation, Sotiropoulos said, and added he was pleased and proud of the scientific community for working together to understand the problem and to find solutions.

“The commitment of scientists at Stony Brook and other universities was quite inspirational,” he said.

According to Sotiropoulos, the biggest danger to combatting the virus comes from the “mistrust” of science, He hopes the effectiveness of the vaccine in turning around the number of people infected and stricken with a variety of difficult and painful symptoms can convince people of the value of the research.

Sotiropoulos said the rules the National Institutes of Health have put in place have also ensured that the vaccine is safe and effective. People who question the validity of the research “don’t understand how strict this process is and how many hurdles you have to go through.” 

Part 2 will appear in next week’s issue.

Illustration depicting Falcatakely amid nonavian dinosaurs and other creatures during the Late Cretaceous in Madagascar. (Credit: Mark Witton)

By Daniel Dunaief

Dromomeron and Falcatakely lived nowhere near each other. They also lived millions of years apart, offering the kind of evolutionary pieces to different puzzles that thrill paleontologists.

Left, Alan Turner holds a model of the maxilla of Falcatakely, with a CT reconstruction on his computer screen.

These two creatures, the first a three-foot long dinosaur precursor discovered in Ghost Ranch, New Mexico, and the second a crow-sized bird fossil discovered in Madagascar, have taken center stage in recent scientific circles.

What they have in common is Alan Turner, Associate Professor in the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook University.

The discoveries, which were made over a decade ago, were recently parts of publications in consecutive issues of the prestigious journal Nature. “It’s really exciting,” Turner said. “I definitely feel fortunate” to contribute to these two publications.

Turner, who is not the lead author in either study, emphasized that these papers were only possible through teamwork. “These large, collaborative efforts are one of the ways these really significant discoveries can happen,” he said.

The work that includes Dromomeron, in particular, is one that “any one of our groups couldn’t have done [alone]. It hinged on a series of discoveries across multiple continents.”

Each paper helps fill out different parts of the evolutionary story. The Dromomeron discovery helps offer an understanding of a major evolutionary transition from the Triassic Period, while the Falcatakely find offers a look at the diversification of birds during the Cretaceous Period.

Dromomeron

Starting with the paper in which Dromomeron appears, researchers used a collection of dinosaur precursor fossils to study a smaller group of animals called lagerpetids, whose name means “rabbit lizard” or “rabbit reptile.”

These creatures lived during the age of the earliest relatives of lizards, turtles and crocodylians.

Above, a reconstruction of a pterosaur, a lagerpetid from the Triassic Period/Rodolfo Nogueria

Pterosaurs, which have a characteristic elongated fourth finger that forms a large portion of their wing, lived 160 million years ago, which means that the earlier, flightless lagerpetids roamed the Earth about 50 million years before pterosaurs.

Turner discovered Dromomeron in Ghost Ranch, New Mexico 14 years ago. Since then, other scientists have unearthed new bones from this prehistoric rabbit lizard group in North America, Brazil, Argentina and Madagascar.

Scientists involved in this paper used micro-CT scans and 3D scanning to compare lagerpetid and pterosaur skeletal fossils to demonstrate overlaps in their anatomy. The shape and size of the brain and inner ear of these lagerpetid fossils share similarities with pterosaurs.

The inner ear, Turner explained, is particularly important for animals like the pterosaur, which likely used it the way modern birds do when they are in flight to help determine their location in space and to keep their balance.

Lagerpetids, however, didn’t fly, so paleontologists aren’t sure how these ancient rabbit lizards used their inner ear.

Turner said the Dromomeron discovery was initially more of a curiosity. In fact, when researchers found it, “we had a blackboard in this collection space where we were working,” Turner recalled. “It was unceremoniously referred to as ‘Reptile A.’ There weren’t a lot of things to compare it to. At that point we knew we had a thing but we didn’t know what it was.”

A colleague of Turners, Randall Irmis, Chief Curator and Curator of Paleontology, Associate Professor of Geology and Geophysics at the University of Utah, traveled to Argentina, where he noticed a creature that was similar to the find in New Mexico.

Irmis’s trip “allowed our team to confirm our comparison [between Dromomeron and Lagerpeton] first-hand. From there, we were able to build out the larger evolutionary context,” Turner explained in an email.

Falcatakely

Meanwhile, Turner and Patrick O’Connor, Professor of Anatomy and Neuroscience at Ohio University and lead author on the study, shared their discovery of a bird they located in Madagascar that they called Falcatakely.

The bird’s name is a combination of Latin and Malagasy, the language of the island nation of Madagascar, which means “small scythe” and describes the beak shape.

Right, an artist reconstruction of the Late Cretaceous enantiornithine bird Falcatakely forsterae with its unique beak/Sketch by Mark Witton

The scientists found a partial skull in a quarry in Madagascar. The fossil was embedded in rocks. Turner and O’Connor analyzed it through CT scanning and through careful physical and digital preparation by their colleague Joe Groenke, laboratory coordinator for the O’Connor lab.

The discovery of grooves on the side of the face for a beak took the researchers by surprise.

“As the face began to emerge from the rock, we immediately knew that it was something very special, if not entirely unique,” O’Connor said in a press release. 

“Mesozoic birds with such high, long faces are completely unknown, with Falcatakely providing a great opportunity to reconsider ideas around head and beak evolution in the lineage leading to modern birds.”

As with the Dromomeron find, the discovery of Falcatakely didn’t provide a eureka moment when the scientists found it 10 years ago.

“We didn’t know [what we had] when we collected this material,” Turner said. “It wasn’t until we CT scanned the block in an effort to begin the preparation that we said, ‘Wait a second. There’s something really weird in this block. The flat part turned out to be the side of the face.”

Turner originally thought it could have been the breast bone of a larger dinosaur. During the pandemic, he has come back to projects that have been sitting around for several years. Some have “probably danced on the periphery that have now come to the dance,” in terms of his focus.

In looking back on the ingredients that made these two Nature papers possible, Turner added another element. These publications underline “the importance of investing in long term field work expeditions,” he said.

Cars line up at the Stony Brook coronavirus testing site. Photo by Kyle Barr

New York State has partnered with Stony Brook University to provide drive-through testing for the coronavirus at Stony Brook University’s South P Lot off Stony Brook Road. Residents must make appointments in advance by phone at 888-364-3065 or online at covid19screening.health.ny.gov.

Hours of Operation
Monday through Friday, 8 am to 6 pm
Saturday and Sunday, 8 am to 3 pm

Please note: The hours of the testing site during the New Year’s Day holiday are as follows:

Thursday, Dec. 31: 8 am to 6 pm
Friday, Jan. 1: Closed
Saturday, Jan. 2: 8 am to 5 pm
Sunday, Jan. 3: 8 am to 3 pm

Anyone who believes they’re at risk should call the Department of Health Hotline, 888-364-3065, and talk to experts to determine if and how they should be tested.

Walk-ins are not accepted and will not be seen.

All test results will be provided by the Department of Health. Call the DOH Hotline at 888-364-3065.

Click here for a map and directions to the testing site.

Corals in the Gulf of Aqaba in the Red Sea. Photo by Maoz Fine

A paper published in Frontiers in Marine Science on December 15 is calling for action to remove the oil from a decaying and inactive tanker in the Red Sea that holds approximately one million barrels of oil – four times the amount of oil contained in the Exxon Valdez, the tanker that had a disastrous environmental oil spill in 1989 –  before its current seepage turns into a massive oil spill into the sea. The paper, a policy brief, is authored by a team of international scientists led by Karine Kleinhaus, MD, MPH, an Associate Professor of the School of Marine and Atmospheric Sciences (SoMAS) at Stony Brook University.

Scientists produced a computer simulation of the spread of oil from the abandoned tanker in the Red Sea. The projection shows mass spread during winter compared to summer due to current patterns. The data shown was produced by running the model for 30 days. Oil spread even further from the tanker when the model ran for a longer period of time. Photo from SBU

Called the Safer, the tanker is a floating storage and offloading unit (FSO) abandoned for years, and with access controlled by Yemen’s Houthis. The paper, titled “A Closing Window of Opportunity to Save a Unique Marine Ecosystem,” comes shortly after The New York Times reported on November 24 that the Houthis will grant permission to a United Nations (UN) team to board the Safer to inspect and repair the vessel in the near future.  

“The time is now to prevent a potential devastation to the region’s waters and the livelihoods and health of millions of people living in half a dozen countries along the Red Sea’s coast,” says Dr. Kleinhaus. “If a spill from the Safer is allowed to occur, the oil would spread via ocean currents to devastate a global ocean resource, as the coral reefs of the northern Red Sea and Gulf of Aqaba are projected to be among the last reef ecosystems in the world to survive the coming decades.”

She explained that the reason the coral reefs of the northern Red Sea are unique is because they survive in much warmer waters than today’s ocean temperatures, which are becoming too high for most coral to tolerate (over half of the Great Barrier Reef has degraded due to marine heat waves caused by climate change). Additionally, the fish living on the reefs off Yemen in the southern Red Sea are a major resource of food for the populations of the region, and the entire sea and its coral reefs are a highly biodiverse and rich ecosystem.

Dr. Kleinhaus and co-authors point out that in May 2020 seawater breached the Safer and entered the engine compartment, and news agencies have reported oil spots next to the tanker, indicating likely seepage. The tanker has been abandoned since 2015, which the authors emphasize is a long advance warning of a decaying tanker poised to degrade to the point of a mass oil leak into the Red Sea.

The paper reveals a computer model of how the oil will disperse if a major leak begins this winter. The model shows that the oil will reach much further if the spill occurs now rather than in summer, due to the typical winter currents in that region of the Red Sea. A spill now will cause much broader and more extensive devastation as a result.

Despite the signs of the Safer’s structural deterioration, access to the tanker has yet to be achieved and concrete steps to repair or to prevent an oil spill have yet to been taken, the authors point out. Dr. Kleinhaus adds that winter is the worst time to have an oil spill in that region, as winter currents will disperse oil much more widely.

The authors urge that “Emergent action must be taken by the UN and its International Maritime Organization to address the threat of the Safer, despite political tensions, as a spill will have disastrous environmental and humanitarian consequences, especially if it occurs during winter. With millions of barrels of oil, a day passing through the Red Sea, a regional strategy must be drafted for leak prevention and containment that is specific to the Red Sea’s unique ecosystems, unusual water currents, and political landscape.”

 

Fotis Sotiropoulos displays a slide during Zoom presentation. Photo from Stony Brook University

The CDC has issued its strongest mask guidance yet during the COVID-19 pandemic, calling for “universal mask wearing” in all activity outside of one’s home. The new guidance lists “universal wearing of face masks” as the first recommendation to help stop the spread of the disease. It says masks should be worn for all indoor activity outside of an individual’s home, as well as during all outdoor activity when at least 6 feet of social distancing can’t be maintained.  

Fotis Sotiropoulos

Fotis Sotiropoulos, the Stony Brook University Interim Provost and Dean of the College of Engineering and Applied Sciences addressed the importance of face coverings and social distancing in the midst of the pandemic during a virtual lecture “How Far Is Far Enough and Can Masks Curb the Spread of COVID-19?” on December 2. He also described the importance of fluid mechanics to the spread of a virus like COVID-19.

“Larger, heavy saliva particles can in fact settle within the recommended six-foot CDC guidelines and could contaminate surfaces. However, the greater concern is the smallest particles, or “aerosols,” that can be transported by the airflow several feet away from the body and stay suspended for longer periods of time,” said Sotiropoulos. 

“A virus is primarily spread by respiratory droplets produced by exhalation. As we exhale, sneeze and cough it creates a range of particles at a range of scales,” said Sotiropoulos. “Airborne transmission occurs more easily when droplets are very small and stay suspended for a long period of time and can be inhaled and penetrate lung tissues, which is the case with coronavirus.”

These findings led a team in the Department of Civil Engineering, including assistant professor Ali Krosronejad, research associate Christian Santoni and PhD students Kevin Flora and Zexia Zhang, to study the effectiveness of social distancing and face coverings.

The research used computational fluid dynamics modeling for coughing and breathing, indoors and outdoors, with masks and without. High-fidelity numerical simulations of respiratory particulate transport on high-performance supercomputers provided strong evidence that even the simplest masks are effective in protecting others by dissipating the forward momentum of expiratory jets, especially in indoor environments. The details of the study were published in a paper, entitled “Fluid dynamics simulations show that facial masks can suppress the spread of COVID-19 in indoor environments,” in American Institute of Physics (AIP) Advances.

“The difference is stunning,” Sotiropoulos said. “Masks can modify the structure of a cough and dramatically diminish its energy and forward propagating momentum. The bottom line is: Wear a mask, any mask, and stay six feet apart to both protect yourself and others around you.” 

President Maurie McInnis
Pulitzer-Prize Winning Cartoonist Jules Feiffer Receives Honorary Degree

After months of hybrid  learning during the COVID pandemic, thousands of Stony Brook University students were awarded degrees at the Winter Virtual Degree Conferral Celebration. The Degree Conferral was webcast on Friday, December 18 at 6:30pm, ET.

Candidates, with their families and friends, were invited to participate in the live-streamed celebration as Bachelors, Masters, Doctoral and Professional, Medical Degrees and Graduate Certificates were bestowed.

During her first graduation address, President Maurie McInnis commended the newly-designated alumni for their fearlessness during these trying times.

“You were brave enough to start at a new school; brave enough to make mistakes, learn new things, and share your opinions. You were brave enough to take risks and allow your minds to change. You were brave enough to excel through this most difficult year in contemporary memory. And you were brave enough to take the leap of faith that is inherent in any commencement,” she said.

In addition, former Stony Brook Southampton faculty member and internationally renowned Pulitzer Prize and Academy Award winning cartoonist Jules Feiffer received an Honorary Doctor of Humane Letters Degree, recognizing his talents that also include achievements as a celebrated playwright, screenwriter, satirist, children’s book author and graphic novelist. After he left the Village Voice where he worked for 42 years, Feiffer joined Stony Brook’s MFA program in Creative Writing and Literature where he taught ”Humor and Truth,” one of the program’s most popular classes.

After receiving his honorary degree this evening, Feiffer said, “When I started on that first day [of teaching at Stony Brook Southampton], I said ‘You have a license to fail and if you don’t take advantage of that license, you really will fail. But if you take chances; if you fall flat on your face; if you just reach out to what you can’t do, I’m going to help you learn how to do it and we’re going to have a very good time together’ and in the years that I taught, we did have a very good time together failing our way upward.”

Pre-recorded remarks for the Conferral Celebration were provided by Interim Provost Fotis Sotiropoulos and Deans from each of Stony Brook University’s Schools and Colleges. For the first time in history, several students from the Renaissance School of Medicine (RSOM) at Stony Brook University conferred their degrees and took their Hippocratic oath during a December ceremony, administered by Dr. Kenneth Kaushansky, Dean, RSOM and Sr. Vice President of the Health Sciences.

Carlos Simmerling

By Daniel Dunaief

They know what happens. They’re just not sure how it happens.

Carlos Simmerling, Marsha Laufer Endowed Professor of Physical and Quantitative Biology and Professor of Chemistry at Stony Brook University, has spent over 22 years trying to answer the question of how processes at a molecular level occur.

Using chemistry, physics and computer programs he helped create, Simmerling determines the intermediate structural changes that occur with biomolecules such as nucleic acids and proteins, which would be extremely difficult to impossible to do at a bench or in a laboratory.

In March, as the United States was in the beginning of various school and office lockdowns in response to the spread of the pandemic, Simmerling endured the same discomfort and loss of control.

Researchers at Brookhaven National Laboratory, including Kerstin Kleese van Dam, Director of the Computational Science Initiative, reached out to Simmerling to see if his lab might use their experience and tools to understand the spike protein on the coronavirus that causes COVID-19.

Except for two people who were on the cusp of finishing their PhD’s, everyone else in the lab “shifted to work on this instead. We put everything else on hold and it’s been nonstop since March.”

Simmerling said he and his lab group decided at a special lab meeting on March 13th that it was important to contribute whatever they could to this unprecedented crisis.

Without the same kind of restrictions or limitations that lab groups that depend on working at a bench or conducting in-person experiments might have, the Simmerling group could work every day, forging ahead to understand the way the protein operates and to look for critical steps or weaknesses that might assist doctors down the road.

Recently, Simmerling and his lab group exchanged emails over Thanksgiving, during which the group felt this commitment to COVID research gave them a “shared purpose” and helped them feel as if they were “doing something.”

While the Simmerling lab appreciated the opportunity to contribute to efforts to combat COVID-19, they also recently received a national award in high-performance computing. Called the Gordon Bell Special Prize, the award recognizes “outstanding research achievement towards the understanding of the COVID-19 pandemic through the use of high-performance computing.”

The award, which was announced at the virtual SuperComputing 2020 Conference and recognizes the work of the Simmerling lab and some collaborators they worked with since early in the pandemic, includes a $10,000 prize.

The kind of research Simmerling and his team conducted may help either with this specific virus or with any others that might threaten human health again.

“We were not well prepared in science and humanity in general,” Simmerling said. “We have to come up with better tools.”

While he is pleased that pharmaceutical companies are getting closer to introducing vaccines for COVID-19, Simmerling said any such solutions would apply to this specific virus and not to any subsequent forms of coronavirus or other potential threats to human health.

People who contracted SARS or MERS, which are coronavirus cousins, didn’t develop an immunity to COVID-19.

“Even if we all get vaccinated, that won’t help us for the next one, and we’ll likely have other ones,” Simmerling explained. “Science needs to do a better job getting deeper into how these work.”

At this point, the models Simmerling and his staff have created are working and are providing the kind of clues that could contribute to providing suggestions for future experiments. The lab is “now at the stage where we are seeing new things not seen in the experiments and suggesting new experiments to test our hypotheses,” said Simmerling.

His lab has focused on the dynamics of proteins and other biomolecules to see how they move around in time. He simulates the shape changes when molecules interact, including in the 2000s when he worked on proteins in the human immunodeficiency virus.

Simmerling likens the study to the process of shaking other people’s hands. When two people come together, their hands adapt to each other when they interact, changing shape as they move up and down.

With the spike protein in COVID-19, scientists have seen what it looks like before it interacts. The structure after it unlocks the cell is fuzzier and scientists aren’t sure if they are relevant to the actual virus or something vaguely similar to it.

“We only get snapshots at the beginning and the end,” he said. “What we need to do is figure out how it works.”

He uses software his lab has developed with a few other labs in the country. Scientists around the world use this Amber system. They take steps in time and calculate the forces on the atom, which requires millions of iterations.

Simmerling said other people sometimes think he and his team download the structure, plug it into a computer, run it and then publish a paper. That’s far from the case, as the computer does the number crunching, but people like Simmerling spend considerable time trying to understand a molecule like the spike protein well enough to develop ideas about how it might move and change.

Simmerling took a circuitous route to the world of using chemistry and physics on a computer. When he entered college at the University of Illinois at Chicago, he wanted to be a chemist. The only problem was that he didn’t enjoy working in the lab with all the chemicals.

Half way through his college education, he left school and started working at a computer company. Eight years later, he decided to return to college, where he planned to earn his chemistry degree.

“When I went back to school, I told my [teaching assistant] that I wish I could do [chemistry] on computers rather than experiments,” Simmerling said. “He introduced me to the professor [Ron Elber] who became my PhD advisor. That brought together things I was interested in.”

He knew programming and how to use computers.

“Sometimes, you’re the sum of your choices,” Simmerling said.

He and his wife Maria Nagan, who also does computer modeling at Stony Brook University, live in Port Jefferson. In non-pandemic times, Simmerling enjoys sailing throughout the year.

As for the prize, Simmerling said the “recognition is nice” and he would like his lab to contribute to “models to change how we combat infectious disease.”