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

By Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Gabor Balazsi in his lab. Photo by Aleksandrs Nasonovs

By Daniel Dunaief

It started with a bang. When he was young and living with his parents, Gabor Balazsi’s curiosity sometimes got the better of him, at the expense of his parents’ house.

The future Henry Laufer associate professor of physical and quantitative biology at Stony Brook University was holding bare wires in his native home in Transylvania when he plugged in an appliance. The current surged through his body, preventing him from releasing the wires. Fortunately, his mother came in and “unplugged me.”

These days, Balazsi, is much more focused on the kinds of behavior that turns the instructions for a cell into something more dangerous, like cancer or a drug-resistant strain of a disease.

Balazsi recently received a $1.8 million, five-year grant from the National Institutes of Health to study how gene networks change, often to the detriment of human health, as is the case when they are active in cancer or when they are resisting treatment. The grant is called Maximizing Investigators’ Research Award.

“Cancer cells often don’t look the same in a matter of months and drug-resistant microbes may look the same in a matter of days,” Balazsi said. He would like to know “what causes them to change and how can we prevent them from changing to their advantage and our disadvantage?”

In a way, Balazsi is trying to figure out a code that is akin to the popular 1970s game Simon in which a player has to repeat a growing number of flashing lights and sounds. With each turn, the game increases the number of flashing lights and sounds, going from a single red, to red, green, yellow and green until the player can no longer recall the entire code.

He is looking for a similar key to a sequence of events that transforms a cell, except that in the cancer, there are millions of interacting lights, many of which are invisible. The cancer biologist tries to reconstruct the sequence in which some of these lights turned on by observing visible lights that are currently on.

He is exploring the “pattern that leads to the outcome” through changes of networks in yeast cells, he said. He is also hoping to explore pathogenic fungi. The pattern, he said, will change depending on the circumstances, which include the environment and initial mutations.

Scientists who have collaborated with Balazsi suggested his understanding of several scientific disciplines enables him to conduct innovative research.

“He bridges two fields, biology and biophysics, allowing him not only to describe biological processes but also to model them and make predictions that can then be tested,” Marsha Rosner, the Charles B. Huggins professor at the University of Chicago, wrote in an email.

While Balazsi doesn’t treat patients, he is focused on understanding and controlling the processes that lead a cell or group of cells to change from a uniform function and task to a heterogeneous one, where the cells may follow a different path using a previously inactive network of genes.

By understanding what causes these changes, he hopes to find ways to slow their progress or prevent the kind of deviations that lead to combinations that are destructive to humans, such as when the cellular machinery copies itself uncontrollably.

Balazsi and Rosner collaborated on one paper and are continuing to work together. “Our work demonstrates one mechanism by which cells move from a homogeneous population to a more complex population that contains cells that promote cancer,” Rosner explained. “This mechanism is not based on mutations in genes, but rather on changes in the way that genes interact with each other in cells.”

On a fundamental level, Balazsi explained that researchers have developed considerable understanding, but still not enough, of what happens in normal conditions. He is seeking to discover the logic cells use to survive under stressful conditions.

Balazsi would like to determine if there is “anything we can do to decrease the tendency of cells to deviate from normality,” he said.

Balazsi welcomes this new funding, which will give him the freedom to pursue research questions at a basic level. Instead of supporting a single project, this financial support contributes to multiple projects.

The next step in funding his lab will be to approach the National Cancer Institute. Without much experience in applying for cancer grants, Balazsi plans to attend a think tank workshop in June in Seattle. Attendance at this meeting, which is hosted by Sage Bionetworks and the NCI, required an application and selection of participants.

To some degree, Balazsi may be able to relate to the heterogeneity that he hopes to study in cells. A physicist by training, Balazsi explained that he “wandered into biology.” He would like to steer away from major trends that mobilize many researchers. If many people are working on something, he does not want to be enriching big crowds but would prefer to try new things and test new ideas.

A resident of East Setauket, Balazsi lives with his wife Erika and their daughter Julianna, who is 6. Julianna is already doing some experiments at home and is exploring the yard.

When Balazsi was young, his parents tried to encourage him to become a doctor, which didn’t work because he didn’t like blood or hospitals as a child. In addition to his unexpected electric shock, Balazsi also explored how ethanol burns while flowing, which caused some additional damage to his house. “My parents,” he recalled, “weren’t happy.”

As for his work, Balazsi would like his work with these first steps, in understanding cellular processes, will have a translational element for people some time down the road.

“Whatever we do, hopefully, they can be implemented in actual cancer cells that are coming from patients one day,” he said, or they could have some relevance for people who are attempting to fight off “pathogenic microbes.”

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

By Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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By Daniel Dunaief

First responders, soldiers or those exposed to any kind of chemical weapons attack need a way to remove the gas from the air. While masks with activated carbon have been effective, the latest technological breakthrough involving a metal organic framework may not only remove the gas, but it could also disarm and decompose it.

That’s the recent finding from research led by Anatoly Frenkel in a study on a substance that simulates the action of sarin nerve gas.

Frenkel, who is a senior chemist at Brookhaven National Laboratory and a professor in the Department of Materials Science and Chemical Engineering at Stony Brook University, worked with metal organic frameworks, which contain zirconium cluster nodes that are connected through a lattice of organic linkages.

Anatoly Frenkel with his son, Yoni, at Lake Hopatcong in New Jersey. Photo by Mikhail Loutsenko.

These structures would “do the job even without any catalytic activity,” Frenkel said, because they are porous and capture gases as they pass through them. “It’s like a sponge that can take in moisture. Its high porosity was already an asset.”

Frenkel and his colleagues, which include John Morris and Diego Troya from Virginia Tech, Wesley Gordon from Edgewood Chemical Biological Center and Craig Hill from Emory University, among other contributors, suspected that these frameworks might also decompose the gas.

Theoretically, researchers had predicted this might be the case, although they had no proof. Frenkel and his team used a differential method to see what was left in the structure after the gas passed through. Their studies demonstrated a high density of electrons near the zirconium atoms. “These were like bread crumbs congregated around a place where the zirconium nodes with the connecting linkers were,” Frenkel said.

While this work, which the scientists published in the Journal of the American Chemical Society, has implications for protecting soldiers or civilians in the event of a chemical weapons attack, Frenkel and his colleagues, who received funding from the Defense Threat Reduction Agency, can share their results with the public and scientific community because they are not working on classified materials and they used a substance that’s similar to a nerve gas and not sarin or any other potentially lethal gas.

“This knowledge can be transferred to classified research,” Frenkel said. “This is a stepping stone.” Indeed, Frenkel can envision the creation of a mask that includes a metal organic framework that removes deadly nerve gases from the air and, at the same time, disarms the gas, providing a defense for first responders or the military after a chemical weapons attack. Even though he doesn’t work in this arena, Frenkel also described how manufacturers might use these frameworks in treating the fabric that is used to make clothing that can prevent gases that can be harmful to the skin from making contact.

A physicist by training, Frenkel’s work, which includes collaborations on five other grants, has a common theme: He explores the relationship between structure and function, particularly in the world of nanomaterials, where smaller materials with large surface areas have applications in a range of industries, from storing and transmitting energy to delivering drugs or pharmaceuticals to a targeted site.

Eric Stach, a group leader in electron microscopy at BNL, has collaborated with Frenkel and suggested that his colleague has helped “develop all these approaches for characterizing these materials.” Stach said that Frenkel has “an outstanding reputation internationally” as an expert in X-ray absorption spectroscopy, and, in particular, a subarea that allows scientists to learn about extremely subtle changes in the distance between atoms when they are subjected to reactive environments.

Frenkel said some of the next steps in the work with metal organic frameworks include understanding how these materials might become saturated with decomposed gas after they perform their catalytic function. “It’s not clear what can affect saturation,” he said, and that is something that “needs to be systematically investigated.” After the catalyst reaches saturation, it would also be helpful to know whether it’s possible to remove the remaining compound and reuse the catalyst.

“The next question is whether to discard” the framework after it’s trapped and deactivated the chemicals or regenerate it, Frenkel said. He is also exploring how temperature ranges might affect the performance of the framework. Ideally, it would function as well in an arctic environment as it would in a desert under extreme heat. A commercial application might require the synthesis of a material with different physical characteristics for a range of temperature conditions.

Frenkel has been working on this project for about one and a half years. A colleague approached him to become a part of this new collaboration. “My role was to bring this work to a national lab setting,” where the scientists could use the advanced tools at BNL to study the material as it was working, he said.

A resident of Great Neck, Frenkel, who grew up in St. Petersburg, Russia, lives with his wife Hope Chafiian, a teacher at the Spence School in Manhattan for almost 30 years. He has three children: Yoni lives in Manhattan and works at JP Morgan Chase, Ariela is a student at Binghampton and Sophie is in middle school in Great Neck.

Frenkel appreciates the opportunity to explore the broader world of nanomaterials, which, he said, are not constrained by crystal structures and can be synthesized by design. “They show a lot of mysteries that are not understood fully,” he said. Indeed, Frenkel explained that there are numerous commercial processes that might benefit from design studies conducted by scientists. As for his work with metal organic frameworks, he said “there’s no way to overestimate how important [it is] to do work that has a practical application that improves technology, saves costs, protects the environment” and/or has the potential to save lives.

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Esther Takeuchi with photo in the background of her with President Obama, when she won the 2009 National Medal of Technology and Innovation. Photo courtesy of Brookhaven National Laboratory

By Daniel Dunaief

Pop them in the back of a cell phone and they work, most of the time. Sometimes, they only do their job a short time, discharge or generate so much heat that they become a hazard, much to the disappointment of the manufacturers and the consumers who bought electronic device.

Esther Takeuchi, a SUNY distinguished professor in the Departments of Chemistry and Materials Science and Engineering and the chief scientist in the Energy Sciences Directorate at Brookhaven National Laboratory leads a team of scientists who are exploring what makes one battery work while another falters or fails. She is investigating how to improve the efficiency of batteries so they can deliver more energy as electricity.

Esther Takeuchi with a device that allows her to test batteries under various conditions to see how they function. Photo courtesy of Brookhaven National Laboratory

The process of manufacturing batteries and storing energy is driven largely by commercial efforts in which companies put the ingredients together in ways that have, up until now, worked to produce energy. Scientists like Takeuchi, however, want to know what’s under the battery casing, as ions and electrons move beneath the surface to create a charge.

Recently, Takeuchi and a team that includes her husband Kenneth Takeuchi and Amy Marschilok, along with 18 postdoctoral and graduate students, made some progress in tackling energy storage activity in iron oxides.

These compounds have a mixed track record among energy scientists. That, Takeuchi said, is what attracted her and the team to them. Studying the literature on iron oxides, her graduate students discovered “everything from, ‘it looks terrible’ to, ‘it looks incredibly good,’” she said. “It is a challenging system to study, but is important to understand.”

This offered promise, not only in finding out what might make one set of iron oxides more effective in holding a charge without generating heat — the energy-robbing by-product of these reactions — but also in providing a greater awareness of the variables that can affect a battery’s performance.

In addition to determining how iron oxides function, Takeuchi would like to “determine whether these [iron oxides] can be useful and workable.” Scientists working with iron oxides didn’t know what factors to control in manufacturing their prospective batteries.

Takeuchi said her group is focusing on the linkage between small-scale and mesoscale particles and how that influences battery performance. “The benefit of iron oxides is that they are fairly inexpensive, are available, and are nontoxic,” she said, and they offer the potential of high energy content. They are related to rust in a broad sense. They could, theoretically, contain 2.5 times more energy than today’s batteries. “By understanding the fundamental mechanisms, we can move forward to understand their limitations,” she said, which, ultimately, could result in making these a viable energy storage material. T

akeuchi is also looking at a manganese oxide material in which the metal center and the oxygen connect, creating a tube-like structure, which allows ions to move along a track. When she started working with this material, she imagined that any ion that got stuck would cause reactions to stop, much as a stalled car in the Lincoln Tunnel leads to long traffic delays because the cars behind the blockage have nowhere to go.

Takeuchi said the ions don’t have the same problems as cars in a tunnel. She and her team believe the tunnel walls are porous, which would explain why something that looks like it should only produce a result that’s 5 percent different instead involves a process that’s 80 percent different. “These escape points are an interesting discovery, which means the materials have characteristics that weren’t anticipated,” Takeuchi said. The next step, she said, is to see if the researchers can control the technique to tune the material and make it into the constructs that take advantage of this more efficient flow of ions.

Through a career that included stops in Buffalo and North Carolina and West Virginia, Takeuchi, who has over 150 patents to her name, has collected numerous awards and received considerable recognition. She won the 2009 National Medal of Technology and Innovation, a presidential award given at a ceremony in the West Wing of the White House. Takeuchi developed compact lithium batteries for implantable cardiac defibrillators.

Takeuchi is currently a member of the National Medal of Technology and Innovation Nomination Evaluation Committee, which makes recommendations for the medal to the president. Scientists who have known Takeuchi for years applaud the work she and her team are doing on Long Island. “Dr. Takeuchi and her research group are making great advances in battery research that are very clearly promoted by the strong relationship between Stony Brook and BNL,” said Steven Suib, the director of the Institute for Materials Science at the University of Connecticut.

Indeed, at BNL, Takeuchi has used the National Synchrotron Light Source II, which became operational last year. The light source uses extremely powerful X-rays to create incredibly detailed images. She has worked with three beamlines on her research. At the same time, Takeuchi collaborates with researchers at the Center for Functional Nanomaterials at BNL.

Although she works with real-world experiments, Takeuchi partners with scientists at Stony Brook, BNL and Columbia University who focus on theoretical possibilities, offering her an insight into what might be happening or be possible. There are times when she and her team have observed some interaction with batteries, and she’s asked the theorists to help rationalize her finding. Other times, theorists have suggested what experimentalists should search for in the lab.

A resident of South Setauket, Takeuchi and her husband enjoy Long Island beaches. Even during the colder weather, they bundle up and enjoy the coastline. “There’s nothing more mentally soothing and energizing” than going for a long walk on the beach, she said.

In her research, Takeuchi and her team are focused on understanding the limitations of battery materials. Other battery experts believe her efforts are paying dividends. Suib said the recent work could be “very important in the development of new, inexpensive battery materials.”

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Alan Alda received the Double Helix Award from Cold Spring Harbor Laboratory this month. Photo by Constance Brukin, Cold Spring Harbor Laboratory

By Daniel Dunaief

In a world of tirades and terrifying tweets, the Alan Alda Center for Communicating Science at Stony Brook University is encouraging its professors and students to do something the center’s namesake urges: Listen.

Tough as it is to hear what people mean behind an explosive expression that fuses reason and emotion, the scientists in training, established researchers and others who attend some of the lectures or workshops at the center go through an exercise called “rant” in which each person listens for two minutes to something that drives their partner crazy. Afterward, the scientist has to introduce their partner to the group in a positive way.

Alan Alda. Photo by Constance Brukin, Cold Spring Harbor Laboratory

The staff at the Alan Alda Center finds inspiration, a role model and a humble but willing listener in Alda, the highly decorated actor of “MASH” who has spent the last several decades drawing scientists out of dense shells constructed of impenetrable jargon and technical phrases.

For his dedication to forging connections for scientists, Times Beacon Record News Media is pleased to name Alan Alda a 2016 Person of the Year.

“He’s doing a wonderful job,” said Jim Simons, the former chairman of the Stony Brook Mathematics Department and hedge fund founder who shared the stage with Alda this summer as a part of a Mind Brain Lecture at Stony Brook. “I can’t think of anyone better to be an honoree.”

Simons described a moment with Alda, who is not a scientist nor does he play one on TV, when he was sharing some abstruse mathematics. Alda’s eyes “glazed over when I was first talking to him. He’s teaching scientists not to get a glaze over their audience’s eyes.”

Alda works tirelessly to share a method that blends scientific communication with the kind of improvisational acting he studied early in his career.

“Improv is not about being funny,” said Laura Lindenfeld, the director at the center. “It’s about being connected.”

Last June, Alda was a part of a team that traveled to California to share an approach that is in demand at universities and research institutions around the world. The day of the workshop, three people who were supposed to help lead the session were delayed.

Alda suggested that he run the event, which would normally involve several instructors and break-out groups. Learning about the art of connecting with an audience from someone who reached people over decades through TV, movies and Broadway performances, the attendees were enchanted by their discussion.

“He’s the master,” said Lindenfeld, who was at the campus when the team received news about the delay for the other instructors.

As soon as the session ended, Alda headed for Los Angeles to conduct a radio interview.

“I handed him a granola bar,” recalled Lindenfeld, who joined the center last year. “I was afraid he hadn’t eaten.”

Alda celebrated his 80th birthday earlier this year and shows no signs of slowing down, encouraging the spread of training techniques that will help scientists share their information and discoveries.

“He’s teaching scientists not to get a glaze over their audience’s eyes.”

— Jim Simons

The Alda Center is planning a trip to Scotland next year and has been invited to go to Norway, Germany and countries in South America, Lindenfeld said.

When the University of Dundee received a grant from the Leverhulme Trust to create the Leverhulme Research Centre for Forensic Science, officials in Scotland, one of whom knew Lindenfeld personally, researched the Alan Alda Center’s mission and decided to forge a connection. Lindenfeld helped coordinate a congratulatory video Alda sent that the Scottish centre played at its opening ceremony.

“Everyone present from the highest Law Lord in Scotland, through to the principal of the university and the Leverhulme trustees did not know it was going to happen, and so it was a huge surprise that stunned the room into complete silence,” recalled Sue Black, the director of the centre in an email. “Brilliant theatre of which Mr. Alda would have been proud.”

Established and internationally known scientists have expressed their appreciation and admiration for Alda’s dedication to their field.

The training sessions “drag out of people their inhibitions and get them to think about interacting with the public in ways that they might not have felt comfortable doing before,” said Bruce Stillman, the president and CEO of Cold Spring Harbor Laboratory. This month, Cold Spring Harbor Laboratory gave Alda the Double Helix Medal at a ceremony at the American Museum of Natural History in New York City.

Stillman described the public understanding and perception of science as “poor.” To bridge that gap, Alda’s programs “induce scientists to feel comfortable about talking to the public about their ideas and progress.”

Nobel Prize winner Eric Kandel suggested that Alda’s accomplishments exceed his own.

“There ain’t many Alan Aldas, but there are a lot of Nobel Prizes out there,” Kandel said. While Kandel is “extremely indebted to having won the Nobel Prize,” he said the totality of Alda’s accomplishments are “enormous.”

The Alda Center is working with Columbia University, where Kandel is the director of the Kavli Institute for Brain Science and a professor, to develop an ongoing program to foster scientific communication.

Alan Alda, left, at a ceremony at the American Museum of Natural History. Photo by Constance Brukin, Cold Spring Harbor Laboratory

Kandel, who considers Alda a friend, appreciates his support. Kandel said Jeff Lieberman, the chairman of the Department of Psychiatry at Columbia, asked Alda and Kandel to give a talk on issues related to neuroscience. Lieberman “was my boss,” Kandel said, “I had to be there, but [Alda] didn’t have to be there. He goes out of his way for people.”

In 2017, the center will not only share its communication techniques around the world, but it will also create conferences for timely scientific topics, including climate change and women in science.

The glass ceiling is a “real issue for women in science,” said Valerie Lantz Gefroh, the improvisation program leader at the center. “We’re hoping to give [women] better communication tools so they can move forward in their careers.”

The center is also adding new courses. Next fall, Christine O’Connell, who is a part of a new effort at Stony Brook called the Science Training & Research to Inform Decision and is the associate director at the center, will teach a course on communicating with policy and decision makers.

That will include encouraging scientists to invite state senators to see their field work, going to Congress, meeting with a senator or writing position papers. In political discussions, scientists often feel like “fish out of water,” O’Connell said. The course will give scientists the “tools to effectively engage” in political discussions.

Scientists don’t have to be “advocates for or against an issue,” O’Connell said, but they do have to “be advocates for science and what the science is telling us.”

Given an opportunity to express her appreciation directly to Alda, Black at the University of Dundee wrote, “Thanks for having the faith to collaborate with our centre so far away in Scotland, where we are trying to influence the global understanding of forensic science in our courtrooms — where science communication can make the difference between a guilty or an innocent verdict and in some places, the difference between life and a death sentence.”

To borrow from words Alda has shared, and that the staff at the center believe, “Real listening is a willingness to let the other person change you.” Even if, as those who have gone through some of the sessions, the speaker is ranting.

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Athi Varuttamaseni. Photo couresty of BNL

By Daniel Dunaief

Athi Varuttamaseni is like an exterminator, studying ways pests can gain entry into a house, understanding the damage they can cause and then coming up with prevention and mitigation strategies. Except that, in Varuttamaseni’s case, the house he’s defending is slightly more important to most neighborhoods: They are nuclear power plants.

The pests he’s seeking to keep out or, if they enter, to expel and limit the damage, are cyberattackers, who might overcome the defenses of a plant’s digital operating system and cause a range of problems.

Varuttamaseni, an assistant scientist in the Nuclear Science & Technology Department at Brookhaven National Laboratory, started his career at BNL by modeling the failure of software used in nuclear power plant protection systems. Last year, he shifted toward cybersecurity. “We’re looking at what can go wrong with nuclear power plants” if they experience an attack on the control and protection systems, he said.

Varuttamaseni is part of a team that received a grant from the Department of Energy to look at the next generation of nuclear power plants, which are controlled and managed mostly by digital systems. A few existing plants are also looking to replace some of their analog systems with digital. “We asked what can go wrong if a hacker somehow managed to breach the outer perimeter and get in to control the system, or even if that is possible at all,” he said. By looking at potential vulnerabilities in the next generation of power plants, engineers can find a problem or potential problem ahead of time and can “go back to the drawing board to put in additional protection systems that could save the industry significant cost in the long run,” Varuttamaseni said.

Robert Bari, a physicist at BNL and a collaborator on the cybersecurity work, said Varuttamaseni, who is the lead investigator on the Department of Energy project, played “a major role” in putting together a recent presentation Bari gave at UC Berkeley that outlined some of the threats, impacts and technical and institutional challenges. The presentation included a summary and the next steps those running or designing nuclear power plants can take. Bari said it was a “delight” to collaborate with Varuttamaseni.

A colleague, Louis Chu, had recruited Varuttamaseni to work at BNL in another program, and Bari said he “recognized his abilities” and “we started to collaborate.” Varuttamaseni and Bari are going through a systematic analysis using logic trees and other approaches to explore vulnerabilities. The BNL team, which is collaborating with scientists at Idaho National Laboratory, shared the information and analysis they conducted with the Department of Energy and with an industrial collaborator.

In his second year of the work, Varuttamaseni said he is looking at the system level and is pointing out potential weaknesses in the design. He then shares that analysis with designers, who can shore up any potential problems. In the typical analysis of threats to nuclear power plants, the primary concern is of the release of radioactive material that could harm people who work at the plants or live in the communities around the facility.

Varuttamaseni, however, is exploring other implications, including economic damage or a loss of confidence in the industry. That includes the headline risk attached to an incident in which an attacker controlled systems other than a safety function and that are not critical to the operation of a plant. In addition to exploring vulnerabilities, Varuttamaseni is studying a plant’s response. Most of the critical systems are air-gapped, which means that the computer has no physical or wireless connection. While this provides a layer of protection against cyberattacks, it isn’t flawless or impenetrable. An upgrade of the hardware or patching of a hardware system might create just the kind of opening that would enable a hacker to pounce.

The Nuclear Regulatory Commission and the industry are “aware of those scenarios,” Varuttamaseni said. “There are procedures in place and mitigation steps that are taken to prevent those kinds of attacks.” Ideally, however, the power plant would catch any would-be attacker early in the process. Varuttamaseni is working on three grants that are related to systems at nuclear power plants. In addition to cyberattacks, he is also analyzing software failures in the protection system and, finally, he’s also doing statistical testing of protection systems.

Varuttamaseni, who was born in Thailand, lives in Middle Island. He appreciates that Long Island is less crowded than New York City and describes himself as an indoor person. He enjoys the chance to read novels, particularly science fiction and mysteries. He also likes the moderate weather on Long Island compared to Bangkok, although threats from hurricanes are new to him. Next June, Varuttamaseni will present a paper on cybersecurity at the American Nuclear Society’s Nuclear Plant Instrumentation, Control & Human-Machine Interface Technology Conference in San Francisco.

Varuttamaseni is “always on the lookout for insights into possible attack pathways that an attacker could come up with,” he said. “The mitigating factor of my work is that we’re looking at a longer-term problem. There’s still time to [work with] many of these potential vulnerabilities.”

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Maureen O’Leary on an expedition in Mali. Photo by Eric Roberts

By Daniel Dunaief

At their greatest depths, oceans hold onto their secrets. With layers of light-blocking water between the surface and the bottom, they hide the kind of clues that might reveal more about who, or what, lived or traveled through them.

What if a sea dried up millions of years ago? And, what if that sea left behind pieces of information — some of them small and subtle and others larger and easier to spot? That’s what happened in a part of Africa that long ago gave up any signs of flowing water. The Sahara desert was, millions of years ago, home to an inland sea called the trans-Saharan seaway.

Maureen O’Leary, a professor in the Department of Anatomical Sciences in the School of Medicine at Stony Brook University, has been to Mali, a country in the northwest of Africa, three times on expeditions, most recently in 2008. There, she collected fossils that are members of extinct groups that are part of larger evolutionary units with living members today.

O’Leary has explored and cataloged a number of remnants from the region, including a turtle and crocodile skull. She and her collaborators have also discovered sting ray fossils. Originally considered likely residents after an asteroid hit Earth that caused a massive extinction, these fossils now suggest that these sting rays lived in the area earlier than previously believed.

“This suggests that the sting rays did survive” the asteroid impact, said O’Leary. “Often extinction events are described in very broad terms but specific studies like this help us” hone in on the kind of species that survived.

She also found intriguing deposits in fossilized feces. Invertebrates burrowed through these fossilized remains, leaving a cast of the shapes of their bodies. The group that left traces of their activities in fossilized feces includes Pholadidae, which has living members. “A careful inspection of a whole fauna of fossils allows you to find invertebrates you had no record of,” said O’Leary.

Leif Tapanila, the director of the Idaho Museum of Natural History and an associate professor of geosciences at Idaho State University, joined O’Leary on an expedition to Mali in 1999, where he was the invertebrate expert. Tapanila said the feces of sharks, crocodiles and turtles have bone fragments that tend to preserve well. Some of these fossilized feces can be four- to five-feet-thick deposits. A prehistoric diver from 30 million years ago would have found that the bottom of the seaway, which was probably 50 to 70 meters at its deepest points, was covered in these hard feces, Tapanila said.

Tapanila described O’Leary as an effective collaborator who ensured scientists formed effective partnerships. “She brings people together,” Tapanila said. “One of her biggest strengths is that she finds pieces of the puzzle that are needed for a particular scientific question. She sets up the infrastructure to make a research project work.”

In one of the blocks of limestone recovered in 1999, O’Leary found a crocodile skull with well-preserved ear bones. That level of detail is unusual in a fossil because of the relatively small and fine nature of those bones. Robert Hill, who was a doctoral student in O’Leary’s lab and is now a professor at Hofstra University, noticed that the ear bones had bite marks on them. A closer examination suggested that the marks were made by a shark, either during a prehistoric battle or after the crocodile had died.

O’Leary is currently working with Eric Roberts, the head of Geoscience at James Cook University in Australia, to write a review paper on Mali that would contain some reconstructions of the region and the species. The paper would emphasize a big picture story using the specialized details she and others collected. This will not only help people see the world as it was but also may help them see the Earth as a changing place, where rising sea levels could cause another transition in a dry and arid region.

While O’Leary would like to return to Mali, she and numerous other scientists have kept their distance amid the political instability in the area. In 2008, Canadian diplomat Robert Fowler was taken hostage for 60 days. “There were some diplomats there who seemed unflappable and serious” who suggested that O’Leary and her colleagues return home during their expedition. “The American Embassy was instrumental in leaning on me to leave.” O’Leary said the politics of these areas, despite the rich story they may have to tell about the past, “can play into whether science can even be done.”

In addition to her research in Mali, O’Leary raised the money and created an online system called MorphoBank, which enables scientists studying anatomy all over the world to collect their information in one place. MorphoBank encourages those interested in anatomy of any kind to find data in one place. Tapanila credits O’Leary for creating a valuable resource. For the time, MorphoBank was “totally new. It takes a lot of effort and vision to pull that off,” he said.

O’Leary is married to Michael Novacek, an author and senior vice president and curator in the Division of Paleontology at the American Museum of Natural History. He is one of the team leaders of the joint American Museum of Natural History/Mongolian Academy of Sciences ongoing expeditions to the Gobi Desert. The duo, who collaborated on an expedition in Morocco, have co-authored papers on the philosophy of science, placental mammal evolution and a team-based study of mammal evolution that was published in the journal Science.

O’Leary watches the political scene in and around Mali from afar.“I do keep an eye on it and would love to return,” she said.

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John Parise Photo courtesy of BNL

By Daniel Dunaief

Finding a proverbial needle in a haystack isn’t as hard as it once was. In fact, finding a needle with specific qualities has also become easier. Manufacturers and drug companies are constantly searching for a specific substance, whether it’s a drug that targets one part of an invading fungus or bacteria or a molecule that binds to a particularly harmful gas.

Indeed, it is in this latter category where John Parise, a distinguished research professor with joint appointments in geosciences and chemistry at Stony Brook University, and a team from Stony Brook, Brookhaven National Laboratory, the Lawrence Berkeley National Laboratory and Pacific Northwest National Laboratory recently shared their use of a metal organic framework, called SBMOF-1, that selectively binds to xenon, a gaseous by-product of nuclear reactions. Their findings, which were published recently in the journal Nature Communications, may point to a more effective and environmentally friendly way to manage nuclear waste.

“This [substance] is 70 times more effective than the current way scientists remove this dangerous gas,” said Parise, who has a joint appointment in photon sciences at BNL. “It allows krypton to pass through, but it retains xenon.” Parise said it acts like a sponge absorbing water until all the pores are filled, which can then be wrung out by passing a gas like nitrogen over it.

Researchers at Pacific Northwest National Laboratory, including Debasis Banerjee, who helped create this molecule when he was a graduate student at SBU, are continuing to work on this material.

The route SBMOF-1 took to becoming a potential xenon filter underscores the collaborative nature of a process that blends basic science with engineering, manufacturing, theory and potential commercial application.

Banerjee won the President’s Award as a distinguished doctoral student at Stony Brook for his research, which involved creating this framework in 2012. When Banerjee designed this material, he didn’t have xenon or nuclear energy on his mind — he was focused on trying to extract carbon dioxide at room temperatures in a humid environment during industrial processes. “We tested this material on numerous gases except xenon,” Parise said.

What they did that led to the next step, however, was critical to the search scientists at Berkeley were conducting to find their proverbial needle. The Berkeley researchers were looking for a better way to remove xenon from nuclear waste. The Stony Brook scientists put their compound in a searchable database online, which met the criteria the Berkeley scientists had established in their search.

Instead of trying to create something new, however, the Berkeley scientists did the equivalent of digging through massive piles of haystacks to search for something that already existed, perhaps for a different purpose, that might be a candidate for the job. Sure enough, they found SBMOF-1.

“While experimentally we need to sift through a fair amount of ‘hay’ — the computer, once programmed correctly (and this is nontrivial) works rapidly to locate the needle,” Parise said.

Indeed, when the theory met the reality, krypton passed through in 10 to 15 minutes, while xenon remained trapped for close to an hour. A nuclear facility can blow air back through the material and recover most of the xenon, Parise explained.

“It’s a beautiful compound and is so much better than anything else,” Parise said, although he cautioned that “it’s not to say something else can’t do better.”

In making the material, Bernjee started looking at sodium and calcium and phenyl ring compounds. He set out to create something that was environmentally friendly.

Banerjee is continuing to work on nuclear energy at PNNL. He reflected positively on his experiences at Stony Brook University, where he conducted research from 2007 to 2012. “Stony Brook is a great place to work, particularly for research,” he explained in an email. “I still actively collaborate with [Parise’s] group.”

He described Parise as a “great mentor” and said many of his current collaborators share a similar background of working in Parise’s lab. Banerjee’s scientific teammates are either in different national laboratories or are at other universities.

Parise is a strong advocate of the process that led to this uniting of theory and practice. This procedure will give the United States a research and development edge, because the theory makes the experiments more effective and the more effective experimental results reinforce the theory.

Parise works together with people like Artem Oganov, a professor in the Department of Geosciences at Stony Brook. They are exploring new compounds to split water from sunlight. “Computational materials discovery is an ongoing scientific revolution,” explained Oganov in an email. “Calculations are playing an increasingly critical role in materials science.”

Oganov said Parise is “known as a very creative and most versatile synthetic chemist.” Banerjee added that Parise “has major contributions in the field of materials characterization using X-ray and neutron diffraction.”

A native of North Queensland, Australia, Parise started working at SBU in 1989. He is married to Alyse Parise, who is a business coach and psychotherapist, who has a private practice in Setauket. Residents of Poquott, the Parises enjoy the beaches and kayaking on Long Island. At the end of July, they will join friends to raft down the Salmon River in Idaho.

As for his work, Parise said he is dedicated to determining how the structure of compounds are arranged. “We’re interested in where the atoms are” in a wide range of materials, he said.

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Christopher Vakoc in his lab at Cold Spring Harbor Laboratory. Photo courtesy of CSHL

We create buildings that climb into a sky crowded with airplanes and supersonic jets. We harness the energy of the atom, design intricate artwork, compose and perform inspirational music, travel miles below the surface of the ocean and send satellites deep into space. Sometimes, we tap into unlikely sources to learn new ways to improve our lives, even in the fight to understand and attack cancer.

Bacteria have been battling against viruses for so long that they have evolved to disarm these intruders. The bacterial immune system uses a gene-editing system called CRISPR. Researchers have taken some of the CRISPR machinery from bacteria and are using it in human cells. CRISPR was named the American Association for the Advancement of Science’s Breakthrough of the Year for 2015.

Using a bacterial enzyme called Cas9, which isn’t found naturally in humans but can be used in our genetic code, scientists can edit out DNA that contributes to the proliferation of cancer.

Christopher Vakoc, an associate professor at Cold Spring Harbor Laboratory, has used his expertise with CRISPR to study cancer.

Starting in the fall of 2014, he and Charles Keller, the scientific director at Children’s Cancer Therapy Development Institute in Oregon, collaborated to study the disease rhabdomyosarcoma, a rare form of deadly pediatric cancer of the connective tissue that typically involves muscle cells attached to bones. Vakoc’s lab is using CRISPR to discover new vulnerabilities in RMS.

At this point, Keller has found a potential treatment in animal models that shows positive results, while Vakoc has determined how that specific drug is working. They have submitted their work for publication in a scientific journal and are awaiting word back from reviewers.

Starting this fall, Vakoc will add Ph.D. scientist Bryan Lanning, who will try and identify new targets in RMS using CRISPR.

“It’s great to contribute more resources to this effort,” Vakoc said.

In an email, Keller detailed how “we have more insight into how the drug for rhabdomyosarcoma works.” He credits Eric Wang from Vakoc’s lab for contributing “instrumental” results to the early findings. Keller is “grateful for the support of [Vakoc’s] lab and the collaboration it empowers.”

At the same time, Vakoc’s lab continues to work in an area where they have made some breakthroughs with CRISPR, on a site called BRD4. Collaborating with several other labs, Vakoc showed that chemical inhibition of BRD4 provides a therapeutic benefit in mouse models of leukemia, which has led to clinical trials in humans. Using a drug called JQ1, scientists have generated positive results with humans in Phase I of the Food and Drug Administration’s process for therapeutic approval.

Christopher Vakoc/photo courtesy of CSHL
Christopher Vakoc/photo courtesy of CSHL

“Some of the patients at tolerated doses have had complete remission,” he said. He called those early findings “encouraging.”

A major area of focus, Vakoc explained, involves continuing to try to understand on a molecular level how these drugs are working and why BRD4 is a drug target. “It was not clear in the beginning, but we are slowly revealing the special properties of BRD4,” he said.

As the tests move into the next stage, called Phase 2, an important question in order for this therapy to work, Vakoc said, is to anticipate “how we are going to overcome these resistant states.”

While he doesn’t have an answer yet, he said, he hopes a combination of agents can be more active than any one treatment individually. “A lot of what we’ve been doing, while we are waiting for clinical trials to get under way, is to study resistance and therapies in animal and culture models,” Vakoc said.

Vakoc and Johannes Zuber, a group leader at the Research Institute of Molecular Pathology in Vienna, Austria, recently published a paper in which they outlined how some cells become resistant through nongenetic changes. As they described, the cells are rewiring gene expression without introducing new DNA. A cell can evolve to this new state, Vakoc said. In the battle to defeat the disease, this requires a readiness to defeat what he expects will be some level of resistance to this new treatment.

The inhibitors Vakoc and Zuber have worked on have “very broad and desired activity,” but to find a cure “we have to find effective combination therapies,” explained Zuber, who collaborated on BRD4 projects at Cold Spring Harbor when he was a postdoctoral researcher in Scott Lowe’s lab as early as 2008.

“Assuming that cancer drugs can be well-tolerated enough to be combined and administered as chronic therapy, I hold out hope that we can combine numerous agents and apply them upfront, based on information in the lab and real-life information from patients,” Vakoc said. This could mean a cocktail of three, four or five well-tolerated drugs that he hopes won’t increase chemotherapy toxicity.

In an email, Zuber wrote that Vakoc’s CRISPR system will allow systematic CRISPR screens that point toward domains and identify structures for drug development.

Vakoc lives on campus at CSHL with his wife Camila Dos Santos, who studies epigenetic changes that occur after pregnancy. The couple is collaborating in their research. “CRISPR technology is useful for all biologists and my wife is no exception,” he said.

As for his own work, Vakoc expressed an appreciation for the scientific tools bacteria are providing.“Biologists have always been learning from naturally occurring mechanisms used by various organisms” and using them to approach a range of challenges, Vakoc explained.

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