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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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Huloin Xin. Photo courtesy of Brookhaven National Laboratory

By Daniel Dunaief

The unexpected appearance of Swiss cheese may be preferable to the predicted presence of a balloon. When it comes to the creation of catalysts for fuel-cell-powered vehicles, the formation of a structure that has miniature holes in it may reduce costs and improve energy efficiency.

Using a state-of-the-art facility where he also supports the work of other scientists around the world, Huolin Xin, an associate materials scientist at the Center for Functional Nanomaterials at Brookhaven National Laboratory, recently made the discovery about the structure of a cheaper catalyst. Xin and his collaborators published their work in Nature Communications.

Huloin Xin. Photo courtesy of Brookhaven National Laboratory

The finding “goes against conventional wisdom,” Xin said. “If you have a precursor that’s nanometers in size that’s a metal and you heat it up in oxygen, normally, it would grow into a hollow structure, like a balloon.” Instead, Xin and his colleagues discovered that mixing nickel and cobalt produces a structure that has porosity but is more like spherical Swiss cheese than a balloon. The new architecture has more material crammed into a smaller region than the hollow balloon. It is also stronger, creating a broader range of potential applications.

Scientists at Brookhaven and at other institutions around the world are seeking ways to take advantage of the growing field of nanotechnology, in which physical, electrical or other types of interactions differ from the macromolecular world of hammers, nails and airplane wings. These nanomaterials take advantage of the high surface area to volume ratio, which offers promise for future technologies. What that means is that these materials contain numerous surfaces without taking up much space, like an intricate piece of origami, or, in Xin’s case, a sphere with higher packing density.

The potential new catalyst could be used as a part of an oxygen reduction reaction in an alkaline environment. In a car that uses hydrogen, the reaction would produce water with zero emissions, Xin said. To see the structure of this catalyst, Xin used environmental transmission electron microscopy and electron tomography. The TEM uses computed axial tomography. This is similar to the CAT scan in a hospital, except that the sample Xin studied was much smaller, about 100 nanometers in size, which is 100 times thinner than the width of a human hair.

In addition to determining and defining the structure of the final product, scientists are trying to understand the process that led to that configuration. They can use the environmental transmission electron microscope, which allows gas flowing to study the formation of the catalyst.

Charles Black, the director at the Center for Functional Nanomaterials, said Xin is “off the charts talented” and is a “world leader” in figuring out ways to get more information from the electron microscope. Xin, Black said, has helped create a three-dimensional picture by tilting a two-dimensional sample at different angles in the microscope. “He had already made great strides in improving the speed with which this could be done,” Black said. “He’s also improved the process to the point where you don’t have to be a super expert to do it anymore.”

By slowing the reaction in the nickel-cobalt catalyst down and studying how it forms, Xin uncovered that the shell is not solid: It has pinholes. Once those small holes form, the oxygen infiltrates the pores. The process repeats itself, as shells form, then break up, then oxygen forms another shell, which breaks up, until the process leads to a spherically stacked collection of Swiss cheese structures. The process is ready for industrial-scale applications, Xin said, because the whole synthesis involves putting the elements into a furnace and baking it. While this could have applications in fuel cells, the catalyst still awaits a breakthrough technology with alkaline fuel cells.

The technological breakthrough Xin awaits is an alkaline membrane that can conduct a hydroxyl group. “We are definitely doing research for the future,” he said. “We’re still awaiting the essential element, which is the ionic conductive membrane, to become a technologically mature product.” Xin isn’t focused on creating that membrane, which is a task for organic chemists. Instead, his main focus is on inorganic materials.

As a member of the BNL staff at the Center for Functional Nanomaterials, which is a facility that provides technical support to other scientists, Xin spends half of his time with other researchers on the TEM and half of his time on his own research. “We really have been fortunate to have found someone like [Xin] who wants to excel in both sides of his mission,” Black said “Someone as talented as [Xin], who is very smart with big ideas and increasingly ambitious in terms of what he wants to accomplish for himself … checks his ego at the door and he helps others accomplish their goals.” To improve his ability as a colleague, Xin reads about what the users of the TEM are doing and talks with them about their work.

Xin has been working at BNL for over three years. When he’s not in the lab, Xin enjoys traveling to snorkel in the U.S. Virgin Islands, including his favorite destination, St. John. A skier, Xin’s favorite winter recreational mountain is Lake Placid. Xin grew up in Beijing, where his father is a professor in a business school and his mother is an engineer. He appreciates the opportunity to engage in a broad universe of fields through the work he does at BNL and  appreciates the scientific partnerships he’s formed. “My primary focus is on creating novel microscope techniques that can advance the electron microscopy field,” he explained. “I apply them to a variety of materials projects.” Xin estimates that half of his materials application projects come from collaborators.

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By Daniel Dunaief

In medieval times, armies needed to understand the structure of the castles they were about to attack. Enough information could enable a leader to find a weakness and exploit it, giving his troops a plan to take over the castle. Today, researchers use advanced tools to study the molecular structure of everything from tumors to the protein plaques involved in neurodegenerative conditions like Alzheimer’s disease.

Recently, William Van Nostrand and Steven Smith, scientists at Stony Brook University who have worked together for over 10 years, discovered subtle differences in amyloid fibril structures that surround blood vessels and neurons. Many forms of the structures likely have some contributory effect to cognitive declines, although researchers debate the extent of that contribution, Van Nostrand said.

Above, William Van Nostrand completes a triathlon this past September in Lake George. Photo courtesy of William Van Nostrand
Above, William Van Nostrand completes a triathlon this past September in Lake George. Photo courtesy of William Van Nostrand

Amyloid fibrils in plaques in the space between neurons have subunits lined up side by side in a head-to-head manner. Van Nostrand and Smith’s new work, which was published in Nature Communications, showed that vascular amyloid subunits, which are on the vessel’s surface, have a different configuration, lining up side by side in an alternating head-to-toe pattern.

This structural difference generates a new set of questions that might provide insight into ways to diagnose or treat diseases or cognitive declines. The structural difference in the vascular forms may provide a way to determine how they uniquely contribute to cognitive decline, which could have implications for diagnostic and therapeutic intervention.

“We want to know if these different structures cause different responses,” said Van Nostrand, who was the co-lead investigator in the study with Smith and is a professor in the Department of Neurosurgery at Stony Brook. The research came from a close structural analysis of the amyloid buildup in mouse models of the disease. Van Nostrand provided the animal models and did the vascular amyloid isolation, while Smith, a professor and the director of structural biology in the Department of Biochemistry and Cell Biology, conducted the structural study.

“The more we understand about how these peptides assemble (and which components and structural motifs actually are toxic to neurons), the easier it is to target” the problem, Smith explained in an email. While the mouse models the scientists studied may have some differences from the human forms of the disease, Van Nostrand said the group also conducted some preliminary studies that showed that vascular amyloid from human vessels has the same structure as the vascular amyloid in isolated vessels from the mice.

Van Nostrand and Smith have “investigated the structure of vascular amyloid in one case of a transgenic mouse and from vessels isolated from the brain of one human patient that had spontaneous cerebral amyloid angiopathy,” Smith said. “In both cases, the structure was anti-parallel, which provides some confidence when we start investigating additional mouse and human samples, we will also find the structure is anti-parallel.”

Van Nostrand’s lab studies pathogenic mechanisms in neurodegenerative diseases, including cerebral amyloid angiopathy. In Alzheimer’s disease, patients have these amyloid or protein plaques around neurons. In about 90 percent of these, people also have protein buildup around blood vessels, where the amount can vary.

Amyloid plaques on the surface of blood vessels are “a lot more common than previously thought,” Van Nostrand said. The consequences of these amyloid fibrils on blood vessels can affect other conditions and treatments for medical challenges including an ischemic stroke. Typically, doctors can prescribe a tissue plasminogen activator. While the drug works to break up the blood clot in the brain, it can cause amyloid blood vessels, if they are present, to bleed, which is a serious side effect.

It would be particularly helpful for doctors and their patients if they knew with certainty before doctors gave any drugs whether the patient had any of these plaques around their blood vessels. The current state of the art in searching for these plaques around blood vessels is to look for any signs of bleeding.

Van Nostrand and Smith are searching for biomarkers that could indicate the presence of specific types of amyloids. “If you had a probe that would recognize a structure, can you also use that for imaging?” Van Nostrand asked. Such a probe might be able to distinguish between the parallel and anti-parallel orientation of the proteins in the plaques.

Van Nostrand said there are rare mutations that create blood vessel amyloids, without the plaque between the neurons. People with only blood vessel amyloids have cognitive impairments, Van Nostrand said, but it’s not the same as Alzheimer’s pathology. In addition to partnering with Smith, Van Nostrand works with Lisa Miller, a biophysical chemist at Brookhaven National Laboratory and collaborators in the Netherlands.

A resident of Poquott, Van Nostrand competes in triathlons and iron man events. During the offseason, when the weather isn’t particularly warm, he still does some training. Van Nostrand’s oldest son, Joffrey, who earned his undergraduate degree at Stony Brook, graduated from law school and is now working at a law firm in Wisconsin. His younger son, Kellen, is applying to graduate school to study psychology. Van Nostrand has an 11-year old daughter, Waela, with his wife Judianne Davis. Waela has done two triathlons and “puts me to shame in 100 yards swimming,” Van Nostrand proudly confessed.

As for his work, Van Nostrand, Smith and their collaborators are focused on understanding how to exploit any differences in the plaques, so they can make progress in the battle against neurodegenerative diseases. “We are interested in understanding structure and pathological functions” of different states of the subunits of amyloid fibrils, Van Nostrand said.

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Tesla Science Center at Wardenclyffe's Board of Directors President Jane Alcorn helps American Physical Society President Sam Aronson unveil the historic site plaque while American Physical Society chair member Paul Halpern looks on. Photo by Kevin Redding

The Tesla Science Center At Wardenclyffe, a lab of the former inventor Nikola Tesla, is the only one left of its kind, so it’s no surprise it’s historic.

To recognize this, a large crowd of local dignitaries and community members gathered in Shoreham Dec. 11 to witness the site be designated as a national historic physics site by the American Physical Society.

Back in 2013 a local not-for-profit known then as Friends of Science East Inc. raised over $1 million to purchase the property – Nikola Tesla’s last standing laboratory he conducted research in – when it was on the brink of being forgotten with the hopes of preserving its history. The site has since turned it into a hub for science education, “inspiring the Tesla’s of tomorrow.”

And while there’s still plenty of work to be done before the Science and Technology Center and Museum opens, the APS’s plaque presentation ceremony proved appreciation for Tesla is alive and well – due in large part to the determination of those in Shoreham to keep the legacy of the Serbian-born scientist and inventor of alternating current electricity and neon lighting energized.

“We wanted to have a place where children could build upon their science education, enhance what they learn in school, and have an opportunity to explore and develop a curiosity of how the world works.”

–Jane Alcorn

Members of the APS, the largest professional committee of physics in the U.S. that has deemed just 40 sites worthy of designation since 2004, presented the black stone plaque to Board of Directors President Jane Alcorn and Director Marc Alessi, because of the site’s commitment to raising awareness of Tesla and physics to Long Island and across the world.

Paul Halpern, a chair member with the society, said the site is of great value and interest in terms of history and science.

“There’s a lot of [renewed] interest in Tesla now, and we’re hoping this will help spur on the Tesla Science Center project to build a museum here,” Halpern said.

Speakers took to the podium in front of the historic brick building where Tesla built his laboratory in 1901 with the help of renowned architect Stanford White.

Unfortunately, his funders had given up on the project a few years later and a tower he was using to send wireless power across the world was demolished in 1917, leaving his grand vision to go unexplored.

But, as the plaque reads in gold lettering, “while long-distance wireless power transmission remains a dream, worldwide wireless communication was achieved within a century.”

Alcorn, who has been an especially instrumental force in saving the site, said she and the rest of the volunteers at the center are humbled to be listed among the other notable institutions and people who’ve received the prestigious recognition in the past.

“We work to educate the public about Tesla and his work,” Alcorn said. “We also work to educate the public about the importance of science education for children … so when we set out to create this place, we wanted to have a place where children could build upon their science education, enhance what they learn in school, and have an opportunity to explore and develop a curiosity of how the world works.”

Tescla Science Center at Wardenclyffe Director Marc Alessi speaks during the national historic site designation ceremony. Photo by Kevin Redding
Tescla Science Center at Wardenclyffe Director Marc Alessi speaks during the national historic site designation ceremony. Photo by Kevin Redding

In the future, the 16-acre campus plans to include a children’s playground, an entrepreneurial lab, an exhibit space and a gathering space for community events and programs.

Alessi said he and the center raised upwards of $1.37 million in 2012 in collaboration with internet cartoonist Matt Inman through an internet fundraising campaign that had the support of over 33,000 people in 108 countries. They obtained the property from the Agfa Corporation officially in May 2013.

“For quite some time, [Tesla] was almost forgotten,” Alessi said. “If it wasn’t for the work of many of the people here in this community and across the country we would have lost this location, historic lab and beautiful building behind us. With all of that hard work we’ve been able to secure the property and pay testament to the history of this property and Tesla’s legacy here by establishing the museum and science center.”

Alessi said the site belongs to the public and the center wants to open as soon as possible and will continue to fundraise. Just that day, he said he was informed somebody in attendance of the ceremony who wished to remain anonymous donated $5,000.

He said the center hopes to have two buildings up by early 2018 and intends to eventually have something to the scale of the Liberty Science Center in New Jersey or the Franklin Institute in Philadelphia.

Just before the official register was signed to seal the designation, Alessi called Brookhaven Town Supervisor Ed Romaine (R) said the science center being developed is desperately needed in a nation that needs to focus more on science and fact.

“We are standing here – long after Tesla’s death in 1944, long after his emigration to this country in 1884 – to remind people that the power of ideas doesn’t die with the person who thought those ideas,” Romaine said. “We envision this to be one our best institutes.”

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PSEG employees volunteered time to help clean up the grounds of the Tesla Science Center at Wardenclyffe in Shoreham Dec. 10. Photo by Kevin Redding

Long Island PSEG employee Meredith Lewis wanted to help clean up the grounds of the Tesla Science Center at Wardenclyffe in Shoreham, so she organized volunteer efforts to do just that.

The cleanup was part of PSEG’s Community Partnership Program, which provides sponsorship to any employees passionate about contributing within their community.

PSEG volunteers rake leaves at the Tesla Science Center at Wardenclyffe in Shoreham Dec. 10. Photo by Kevin Redding
PSEG volunteers rake leaves at the Tesla Science Center at Wardenclyffe in Shoreham Dec. 10. Photo by Kevin Redding

As a Shoreham resident, Lewis said she wanted to help make Wardenclyffe – which has become something of an eyesore the past few decades – a place the community can go to and be proud of, especially the area that will become the center’s welcome site.

The location where Serbian-born inventor Nikola Tesla’s last remaining laboratory in the world stands was designated as a world historic site the following day, so timing couldn’t have been more perfect for Lewis and her merry band of helpers – made up of about 25 people between those from PSEG and the Tesla Science Center.

“It feels really great that people want to take time out of their personal schedules and give back to the community,” Lewis said. “We want a nice place for people to go and honor Tesla. It’s very exciting to have somebody who has such a historical significance be in our community and to be able to clean up the site, which really was a dumb beforehand, and make it what it is today. It’s nice and helps the community.”

Her volunteers rakes leaves, trimmed low brush and shrubs, cleared out vines attached to the fence that separates the grounds and the road, and got the area ready for planned irrigation in the spring.

PSEG volunteers rake leaves at the Tesla Science Center at Wardenclyffe in Shoreham Dec. 10. Photo by Kevin Redding
PSEG volunteers rake leaves at the Tesla Science Center at Wardenclyffe in Shoreham Dec. 10. Photo by Kevin Redding

Even her kids Brayden, 7, and Brooke, 5, were taking part.

Karl Sidenius, a longtime volunteer for the center, said he got involved in the effort because he was sick of seeing what had become of the property.

“I knew this had been Tesla’s lab and to drive by here every day or so and see the mess really disturbed me,” he said. “If we can get this cleaned up today, it would be a big help in maintaining the property.”

Gene Genova, vice president of the Tesla Science Center, said the help was great. Ever since the property was bought in 2013, he said, hundreds of volunteers come out to the site and help clean up.

He said there are big plans to turn the abandoned house and building on the property into a visitor’s center and a community events center, respectively.

“When we get volunteers who are passionate about helping us,” Genova said, “it furthers our cause to make things happen faster.”

 

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Above, Shyamalika Gopalan. The image on the screen shows methylation levels with age. Photo by Casey Youngflesh

By Daniel Dunaief

The Museum of Natural History in New York City features a slice of a 1,400-year-old sequoia tree that was cut down in California in 1891. The cross section of the tree offers a testament to history on its inside. That’s where the tree rings that grow every year mark the passing of another year. As it turns out, humans have something in common with trees. While people may not have rings in bones that an observer can see, they do have age-related changes in their genetic material, or DNA.

Human genes go through a process called methylation in which a methyl group comprised of a carbon and three hydrogens attaches to DNA. Methylation upstream of a gene generally reduces transcription, or the copying of that gene into messenger RNA that can then begin the process of building proteins.

gopalanlab2
Shyamalika Gopalan demonstrates how she prepares to extract DNA. Photo by Casey Youngflesh

Using broad time-based methylation changes, Shyamalika Gopalan, who is earning her doctorate at Stony Brook University in the Department of Ecology and Evolution, recently received a three-year grant from the Department of Justice to refine an understanding of methylation and aging. The DOJ would like to use this kind of analysis to gather more information from a scene at which the remaining clues include DNA that isn’t in one of its databases.

Gopalan isn’t the first scientist to study genetic methylation and aging. Other scientists have used blood, saliva and other tissues. She is starting with one type of tissue in the bone. “I’m trying to make” the analysis “more specific to bones,” she said. She doesn’t know how much variation she will find in the age-related methylation patterns depending on ethnicity and lifestyle. “It does appear that some sites are remarkably ‘clock-like,’” she said. “It is these types of sites I’m hoping to find and use in my research.”

Gopalan explained that millions of sites can be methylated. She’s hoping to hone in on those that act more like a clock and that change in a linear manner with time. She’s not sure how many sites she’ll use and said some changes in methylation involve removing methyl groups. “Some methylation increases and some decreases,” she said. “If you know the pattern with age at any site, you can start to build an estimate from those.”

Methylation occurs with age for several possible reasons. “A major theory for these changes in methylation level with age is that the epigenetic patterns are drifting from the optimum,” she said. “This may explain some, or even most, of the changes we observe, but I don’t think it is universally true for all sites in the genome.” Still, there probably is a biologically relevant reason why some of these sites are changing, she suggested.

Gopalan said we know that these methylation patterns are crucial in early development, from conception to birth and she suggested it probably doesn’t completely stop changing there. Some sites are probably regulated throughout life.

Gopalan is hoping to have the bone data prepared by this summer and then believes she’ll be able to get methylation types and start working on a computer algorithm to build a predictor for the next year. After her initial work, she will also shift to saliva and blood.

Like a scene from “Law & Order” or other crime shows, the DNA methylation test may be another clue for police officers or prosecutors to use to rule in or out potential suspects from a crime scene where DNA, but not a driver’s license, is left behind. If the genetic material is not in a database, “you could build a profile and it could be useful for narrowing down suspects,” Gopalan said. At this point, she is taking data for people of age classes but with different ethnicities and lifestyles and comparing them to people of a different age with a similar range of backgrounds and lifestyles.

Gopalan is using samples from medical schools around the New York area, borrowing from anatomy departments where people have donated their bodies to research or teaching. More broadly, she is interested in studying diverse populations, especially in Africa. She has worked with her thesis advisor Brenna Henn, exploring methylation from two different populations. These are the ‡Khomani San of South Africa and the Baka of Cameroon.

Gopalan was interested in working with methylation as a biomarker for aging when she came across this funding opportunity from the DOJ. “It was a good fit for what I had already been studying,” she said, adding that she hopes this method will be used in the future in forensics to assist in criminal investigations.

Krishna Veeramah, an assistant professor of primate genomics at Stony Brook and the chair of her thesis committee, described Gopalan as an “intellectually engaged student who is always eager to absorb information.” Veeramah explained in an email that he thinks “there is scope for this work to transition from basic research” to an application “in criminal forensics and related areas. It will certainly require more work and testing.”

Gopalan has been at SBU for over three years. She lives in Crown Heights, Brooklyn, and commutes about 90 minutes each way most days. She enjoys the beaches, farms, apple picking and the natural beauty of the area. Gopalan would like to continue to perform research after she earns her doctorate, whether that’s with a company, a research institution or with a university. She is excited about extracting and working with DNA, particularly from archeological sites. These samples “come from a field and, once you dust them off, it makes it personal. This is a part of a story.”

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Most snakes ... have no sign of limb development when X-rayed or when their skeletons are studied by anatomists.

By Elof Axel Carlson

Elof Carlson
Elof Carlson

The re-discovery of Mendelism in 1900 greatly enhanced breeding for new varieties of animals and plants. Similarly, the discovery of sex chromosomes and the chromosome theory of heredity enhanced Mendelism five years later. The discovery in the 1970s of genes controlling embryonic organs and body plans enhanced both embryology and genetics.

Also in the late 20th century a molecular approach was worked out that allows detection of genes and their functions using DNA sequencing and tools for isolating and inserting genes from one species into another. A good example of this is the analysis of limb development in vertebrates.

We are vertebrates because we have a spinal column and so do fish, frogs and tetrapods (four-limbed organisms like mice, humans, deer and lizards).

But some vertebrates lack limbs. Snakes are the best example of this. Boas and pythons do have internal vestigial hind limbs but totally lack any rudiments of limbs for their forelimbs. Most snakes, like vipers, have no sign of limb development when X-rayed or when their skeletons are studied by anatomists.

How did the snakes lose their limbs? The earliest ancestors of snakes did have hind limbs. Those ancestral types are only known from the fossil record. In the 1970s Hox genes, which determine development from the head to the tail, were found in vertebrates. The Hox gene for limb development is Hox C-6. It is regulated by another gene called sonic hedgehog or Shh. In vipers the Shh gene regulating Hox C-6 is mutated for both fore and hind limb production. In pythons it is nonfunctional for forelimbs but mutated with an aborted development preventing full growth of the hind limb buds.

Just this year, molecular biologists used the new techniques of gene removal and transfer (using a tool called CRSPR) and removed the Shh gene from a mouse fertilized egg. It resulted in a limbless baby mouse. When they put a python’s Shh gene in a mouse embryo whose Shh gene was removed, the resulting baby mouse had vestigial nubbins. When a mouse fertilized egg had its own Shh gene removed and replaced by that of a fish or human Shh gene, the baby mouse had perfectly normal limb development.

This work by Axel Visel and colleagues at Lawrence Biology Laboratories in Berkeley was published in the journal Cell. What makes science so attractive to scholars is its convincing logic, tested by experiments, to explore, confirm or rule out different interpretations of a puzzle. The puzzle of nature in this case is why snakes lost their limbs.

Those who see it in human terms (because we often use the ancient Greek dictum “Man is the measure of all things”) may invoke that the snake was punished for its role in corrupting humans. The scientist, however, likes to see things in more detail. There is comparative anatomy, the fossil record, experimental embryology, gene identification for function, sequencing for recognizing the gene, molecular tools for isolating the gene and experimental means of altering fertilized eggs to follow their fate.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Dept.of Biochemistry and Cell Biology at Stony Brook University.

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Shinjae Yoo with his son Erum

By Daniel Dunaief

He works with clouds, solar radiation and nanoparticles, just to name a few. The subjects Shinjae Yoo, a computational scientist at Brookhaven National Laboratory, tackles span a broad range of arenas, primarily because his focus is using large pieces of information and making sense of them.

Yoo helps refine and make sense of searches. He develops big data streaming algorithms that can apply to any domain where data scalability issues arise. Integrating text analysis with social network analysis, Yoo did his doctoral research at Carnegie Mellon University, where he also earned a master’s degree, on creating systems that helped prioritize these electronic messages.

“If you are [traveling and] in the airport, before you get into your plane, you want to check your email and you don’t have much time,” he said. While this isn’t the main research work he is doing at the lab, this is the type of application for his work. Yoo developed his technical background on machine learning when he was at Carnegie Mellon. He said he continues to learn, improve and develop machine learning methods in various science domains. By using a statistical method that combines computational science skills, statistics and applied math, he can offer a comprehensive and, in some cases, rapid analysis of information.

Colleagues and collaborators suggested Yoo has made an impact with his work in a wide range of fields. His “contribution is not only in the academic field, but also means a lot on the industrial and academic field,” Hao Huang, a machine learning scientist at GE Global Research, wrote in an email. “He always focuses on making good use of data mining and machine learning theory on real world [areas] such as biology, renewable energy and [in the] material science domain.”

Yoo explained how a plant biologist can do stress conditioning for a plant with one goal in mind. That scientist can collect data over the course of 20 years and then they can “crunch the data, but they can’t always analyze it,” which might be too unwieldy for a bench scientist to handle. Using research from numerous experiments, scientists can study the data, which can provide a new hypothesis. Exploring the information in greater detail, and with increased samples, can also lead to suggestions for the best way to design future experiments.

Yoo said he can come to the scientist and use machine learning to help “solve their science data problem,” giving the researchers a clearer understanding of the broad range of information they collected. “Nowadays, generated data is very easy,” but understanding and interpreting that information presents bigger challenges. Take the National Synchrotron Light Source II at BNL. The $912 million facility, which went live online earlier this year, holds considerable promise for future research. It can look at the molecules in a battery as the battery is functioning, offering a better understanding of why some batteries last considerably longer than others. It can also offer a look at the molecular intermediaries in biochemical reactions, offering a clearer and detailed picture of the steps in processes that might have relevance for disease, drug interactions or even the creation of biological products like shells. He usually helps automate data analytics or bring new hypotheses to scientists, Yoo said. One of the many challenges in experiments at facilities like the NSLS II and the Center for Functional Nanomaterials, also at BNL, is managing the enormous flow of information that comes through these experiments.

Indeed, at the CFN, the transmission electron microscopy generates 3 gigabytes per second for the image stream. Using streaming analysis, he can provide an approximate understanding of the information. Yoo received a $1.9 million, three-year Advanced Scientific Computer Research grant this year. The grant is a joint proposal for which Yoo is the principal investigator. This grant, which launched this September, is about high-performance computing enabled machine learning for spatio-temporal data analysis. The primary application, he said, is in climate. He plans to extend it to other data later, including, possibly for NSLS II experiments.

Yoo finds collaborators through emails, phone calls, seminars or anywhere he meets other researchers. Huang, who started working with Yoo in 2010 when Huang was a doctoral candidate at Stony Brook, appreciates Yoo’s passion for his work. Yoo is “dedicated to his research,” Huang explained. “When we [ran] our proposed methods and got results that [were] better than any of the existing work, he was never satisfied and [was] always trying to further explore to get even better performance.”

When he works with collaborators in many disparate fields, he has found that the fundamental data analysis methodologies are similar. He needs to do some customization and varied preprocessing steps. There are also domain-specific terms. When Yoo came to BNL seven years ago, some of his scientific colleagues around the country were not eager to embrace his approach to sorting and understanding large pools of data. Now, he said other researchers have heard about machine learning and what artificial intelligence can do and they are eager to “apply those methods and publish new papers.”

Born and raised in South Korea, Yoo is married to Hayan Lee, who earned her PhD at Stony Brook and studies computational biology and specializes in genome assembly. They have a four-year old son, Erum. Yoo calls his son “his great joy” and said he “gives me a lot of happiness. Hanging around my son is a great gift.”

When Yoo was entering college in South Korea, he said his father, who had worked at the National Institute of Forest Science, played an important role. After his father consulted with people about different fields, he suggested Yoo choose computer science over chemistry, which would have been his first choice. “He concluded that computer science would be a new field that would have a great future, which is true, and I appreciate my dad’s suggestion,” Yoo said.

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Dr. Hal Walker, co-director of the New York State Center for Clean Water Technology, speaks during a symposium at Stony Brook University Thursday, June 23, 2016. Photo by Barry Sloan

By Daniel Dunaief

Water, water everywhere and Harold “Hal” Walker is making sure there’s more than a few drops on Long Island to drink. The head of the new Department of Civil Engineering at Stony Brook is one of two co-directors of the Center for Clean Water Technology. The center received a $5 million commitment from New York State to pilot test a variety of ways to remove contaminants from drinking water.

“The center will be working with water authorities and water utilities to do pilot testing of new technology to deal with emerging contaminants,” Walker said. “One goal of the testing will be to collect information needed to assess new technologies and, if they are effective, to get them approved so they can be used by water utilities.”

Contaminants the center will explore include 1,4-dioxane and perfluorinated compounds, which have “turned up in some regions of Long Island,” Christopher Gobler, the co-director of the center and an associate dean for research and professor at the School of Marine and Atmospheric Sciences, explained in an email.

’One lesson we have learned is that it is critically important to protect the environment, since the environment serves as a natural buffer to these large storms.’ — Harold Walker

The technologies the center will test likely include novel membrane processes, advanced oxidation, novel absorbents and advanced oxidation processes. The center will explore “how these compounds are removed in conventional drinking water treatments processes,” Walker said. “If they are not removed sufficiently, what do novel technologies use and are they ready for the pilot stage?” Walker acknowledges that staying ahead of the curve in being prepared to protect drinking water requires an awareness of numerous new compounds that are a part of modern manufacturing.

Gobler said the center’s findings would be made public. New York State had previously committed $3.5 million from the Environmental Protection Fund to support the center. With an additional $5 million in funding, the center will develop new technologies to improve drinking water and wastewater quality on Long Island, according to the State Department of Environmental Protection.

The center was formed originally to focus on innovative alternative individual onsite treatment systems for reduction of nitrogen and pathogens. That was broadened this year to focus on the impact of emerging contaminants on water supplies, a representative from the DEC explained in an email.

Walker has built an expertise in developing and applying membrane processes for drinking and wastewater. At Ohio State University, where he worked from 1996 until 2012, when he came to Stony Brook, he spent considerable time analyzing drinking water in the Great Lakes. Gobler appreciates Walker’s expertise.“

He has worked with many federal and state agencies on these topics across the United States,” Gobler explained. “He is also well-versed in wastewater treatment technologies.”

Jennifer Garvey, the associate director for the center, meets with Garvey and Walker at least once a week. She also connects weekly for a call or meeting to discuss administrative and strategic issues. Walker is “at the leading edge of water treatment approaches and he understands where opportunities and obstacles lie,” Garvey said. The center has a sense of urgency about the work because “there is such a clear and immense need for wastewater infrastructure improvements,” she continued. The targeted and strategic work emphasizes near-term solutions. A leading focus is a nonproprietary passive system known as a nitrogen removing biofilter that they will be piloting in Suffolk County soon. “Our hope is that we can make systems available for widespread deployment within the next two to three years,” she said.

Apart from his work at the center, which Walker estimates takes about a third of his time, he is also a professor and the founding chair of the Department of Civil Engineering, which conferred bachelor’s degrees on its inaugural 13 undergraduate students this summer. Those students have all found engineering jobs within their field of interest or continued to pursue additional schooling. The civil engineering department has 10 faculty and is at the end of the first phase of its growth and development, Walker said.

Phase II will include building out the faculty and staff, developing new research and teaching labs and enhancing the recently approved master’s of science and doctoral programs in civil engineering, Walker explained. Resiliency of the coastal communities is a major thrust of his department. He said he recently hired a number of faculty in this area and launched an Advanced Graduate Certificate in Coastal Zone Management and Engineering in partnership with the School of Marine and Atmospheric Sciences. “One lesson we have learned is that it is critically important to protect the environment, since the environment serves as a natural buffer to these large storms,” he explained.

Apart from water and the resilience of the coastal community, the civil engineering department is also involved in transportation. The department works with Farmingdale State College in a new Infrastructure, Transportation and Security Center. In that effort, the department collaborates with the Department of Computer Science, among others at Stony Brook, to bring new approaches to “improving the efficiency, sustainability and safety of our transportation system.”

For his part, Gobler welcomes the talent and expertise the civil engineering department brings to Stony Brook. “This is a tremendous asset” for Stony Brook, Gobler explained in an email. “Civil engineers solve complex problems and I have found that [Walker] and the people he has hired have the skill set and mind-set to address many environmental problems that are important on Long Island.

A resident of Port Jefferson, Walker lives with his wife Alyssa, who is a writer, and their three children, Abby, 14, Halliway, six, and Northie, who is five. They enjoy visiting the beach and traveling east to go apple and pumpkin picking. A native of Southern California, Walker started surfing at the age of 10. He was a four-year varsity letterman in surfing when he was in high school. He has surfed in Hawaii, Costa Rica, Japan, Portugal and Mexico.

As for the department, he said he feels excited by the responsibility for building only the second civil engineering program in the SUNY system. “I’d like the department to quickly become nationally recognized and be the leading source of expertise for the state on infrastructure issues, especially in the downstate area,” he said.

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