Power of 3

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Scientist studies wild ancestors of domestic fruit to increase productivity

Going into his tomato project, Zachary Lippman expected something different. After all, over thousands of years, breeders had been growing the juiciest tomatoes they could.

A team of scientists from 14 countries had already put together a genetic blueprint of the 35,000 genes spread across 12 chromosomes for the “Heinz” tomato.

Lippman, meanwhile, led a group of scientists at Cold Spring Harbor, including Richard McCombie and Doreen Ware, to put together a similar genetic blueprint for the naturally occurring wild type. The tomato Lippman studied, which is an edible South American currant tomato, was much more like the original fruit our agricultural ancestors stumbled upon thousands of years ago.

Even before he finished the two-year effort to create his own genetic blueprint, Lippman suspected there would be plenty of genetic differences. After all, corn and rice, among others, had changed a great deal since its domestication.

“The expectation was that we’d see a lot of changes in the DNA,” offered Lippman. “What we found was the opposite. We see a remarkable similarity between the wild and domesticated tomato.”

Indeed, that scientific finding — and the years of work preparing and comparing the genetic libraries of the different tomato types — was flavorful enough for the scientific journal Nature to include it in its most recent issue.

Calling the genetic sequence of the two tomato types a “major first step,” David Spector, Cold Spring Harbor’s research director, explained that this type of research could help identify critical genes that scientists could manipulate to help improve the tomato, in terms of number of flowers that might give more fruit, or its ability to withstand drought conditions or insect infestations.

Longer term, identifying specific genes that could improve the quality and durability of the tomato could have implications for the world’s food supply, suggested Spector.

“Any developments that can be made to help increase yield and resistance to various conditions such as drought or insects will have a huge impact worldwide. What he’s doing is going to have huge global significance. He’s starting with the basics of the sequence of the plant and is working his way up from there.”

Lippman plans to use the information from the genetic sequences of the two tomato types   in several ways.

Using classical and modern genetics and breeding technologies, he studies tomato mutants that affect how many flowers are produced by a tomato plant on a branching structure called “inflorescence.” These mutants can cause tomato plants to produce either fewer than normal or more than normal flowers, by changing how many branches are produced on the inflorescence.

He then identifies the genes that are “not working properly” in the mutants and studies how these are turned on and off during growth of the tomato plant. He specifically looks at how these genes change in their activity as the tomato plant transitions from making leaves to making flowers.

He is also crossing wild species that produce a lot of branches and flowers with those that producer fewer flowers. He then “genetically maps” the location of the responsible genes. He studies how these genes change during the reproductive transition and what DNA changes occurred to cause the evolution of the different species that produced different numbers of flowers.

Lippman lives in North Bellmore with his wife Shira, a dentist, and their four children, who range in age from three to nine years old.

Lippman isn’t just a leading expert in the field of tomatoes: he’s also a consummate consumer, carting containers of V8 juice back from trips to Costco.

“It’s not a joke,” he insists. When he’s not working on tomatoes, he likes to eat, or drink, them.
Indeed, his favorite way to eat tomatoes is in a cold tomato salad, with basil and fresh mozzarella, and a pinch of salt and pepper.

Lippman, who was raised in Milford, Conn., first became interested in plants and agriculture, particularly pumpkins and tomatoes, when he took a summer job at Robert Treat Farm, a family-owned farm within a mile of his house.

Lippman hopes large-scale farmers, farm stands and backyard gardeners from around the world will benefit from his research on the genetic sequences and the genes of wild and domesticated tomatoes.

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Working on three stopping points, scientist tries to anticipate terrorists’ next move

One day, Joseph Brady hopes he’s unemployed. He doesn’t hate his job, but he wishes it weren’t necessary. Brady teams up with law enforcement — the Suffolk County Police Department and the Federal Bureau of Investigation — to prevent those bent on blowing things up from succeeding.

Brady, who joined the Nonproliferation and National Security Department staff at Brookhaven National Laboratory last summer, is a chemist who specializes in explosives. He explained that there are three potential points when law enforcement can stop the “bad guys” (a term he uses to describe would-be bombers).

First, law enforcement can prevent them from making explosives. They can interfere with one of the key ingredients — even a household product — in making deadly weapons. He calls this process denaturing explosive precursors.

Brady has put additives in hydrogen peroxide — yes, the same liquid parents apply to skinned knees after their kids fall off a bicycle — that make it less reactive with other chemicals. Those additives don’t interfere with the disinfectant’s intended use.

The second stopping point is in detection. Once an explosive is made, law enforcement may be able to detect it at airports, bridges, tunnels and other areas he calls “choke points.” Brady mimics the way bad guys manufacture explosives and studies the results. He looks at the properties, searching for byproducts that might be indicative of illicit activities. He examines how current detection technologies respond to these materials.

The third stopping point is to figure out how to get rid of a device once it’s detected — without allowing it to explode. Scientists can accomplish this by stabilizing the materials in the device or by introducing some new element that could “chemically digest the explosives.”

Brady has worked with triacetone triperoxide, the common homemade explosive that was part of the shoe bomber’s device. Attempting to move TATP could result in an unintended detonation because it’s so unstable. As part of Brady’s dissertation, he showed that chemists can destroy TATP on the 100-gram scale without detonation by using combinations of commonly available chemicals.

Brady, whose research is funded in part by the Department of Homeland Security, explained that “Bad guys are always finding new materials to use against us. A lot of times, they find old materials that have no value to military or commerce.”

He pointed to nitrate esters as one explosive he expects to see “on the scene.” Brady is working on ways to detect the presence of these homemade explosives.

Brady feels he’s playing a type of cat and mouse game with would-be terrorists, trying to anticipate what they’ll do next. Fortunately, he said, he’s working with a team of skilled law enforcement officials who offer suggestions.

“It’s a feedback loop,” he explained. Law enforcement “comes with a question, he provides an answer, then they have a new question.”

While Brady plans to conduct lab experiments with chemicals that can create explosives, the amount of materials he uses is on the order of milligrams — the equivalent of a few grains of salt. He’s unlikely to see explosive reactions that could cause any of the destruction he’s trying to prevent.

Brady, who worked on chemotherapeutic agents in college at the University of Rhode Island, studied explosives when he realized he could play a role in protecting people.

“You see that the bad guys are trying to do something and you can do something about it,” he said. “They are always working hard, so you try to work harder.”

Brady earned his Ph.D. from the University of Rhode Island. He’s been writing for grants to build his lab. The proximity of BNL to New York City and Washington, D.C. makes it an ideal resource for national law enforcement, he said.

Brady was involved with the FBI and the Suffolk County Police Department in presenting a class for Transportation Security Administration screeners on explosiveness awareness. Because BNL is on a former Army installation, the Suffolk County police could use an old grenade range to show TSA officials how the homemade, commercial and military explosives work.

Brady, who is not married, said when he’s not working to build his lab, he enjoys visiting beaches on the North and the South Shore.

Brady said his father, John, a counselor for troubled children, and his mother, Judi, a psychologist, are supportive of his work.

“They are proud,” he offered. “They say, ‘Good for you. Go get ’em.’”

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Post-doctoral student Attreyee Ghosh and Professor William Holt study plate tectonics

They only travel about four inches per year. That makes a sloth, which can achieve a top speed of 6.5 feet per minute, seem like a furry blur by comparison. And yet, when they move, they can change the face of the planet.

The slow shifting of the enormous tectonic plates — like puzzle pieces pressing against and pulling away from each other over the surface of the planet — can not only cause devastation through earthquakes, but can also build mountains and form deep-water ocean trenches.

Ever since the 1960s, when scientists accepted the theory of continental drift, they have been trying to understand and predict where those plates move. There has been a rift in the scientific community itself over what forces (and where those forces are located) that determine plate movement.

“Some people have been saying the deep Earth is everything and is the most important role and force in making the plates move,” said Attreyee Ghosh, a post-doctoral student at Stony Brook University’s Geosciences Department. “Another group has been saying that the deep Earth doesn’t have to play that much of a role and they can explain [the movements] looking at the top 100 kilometers of the Earth.”

As it turns out, both groups are right, depending on where you are on the planet, Ghosh explained.

The viscosity (or thickness) of the middle layer in between the top Earth and the deeper parts of the planet determines which contribution can be more important in driving the movement of the plates.

“A higher viscosity increases the contribution from the deeper mantle,” Ghosh suggested. “When the viscosity is weaker, there is a decoupling from the deeper mantle, so the [deeper Earth] doesn’t play as dominant a role” as the lithosphere, or the upper layer.

Working with professor William Holt, Ghosh created a mathematical model to predict movements of the plates. The scientists input readings from “literally hundreds if not thousands” of other researchers using data points from seismic records and earthquakes as they built and tested their computer model, Holt recalled.

The results were so much more effective than most of the models that one of the most prestigious journals in the country, Science, published their findings earlier this year.
Despite its effectiveness, the model, which was created on a relatively simple computer, can do better, Holt said.

“We are not very far away from having models that can predict surface observations at a level of accuracy that approaches the uncertainty in the measurements themselves,” Holt suggested.

What that means is that the models may become as accurate as the data they receive.

So, what does this increased accuracy mean for anticipating earthquakes?

While the science of predicting earthquakes is still years away, this is an important step toward building a better foundation for long-term earthquake forecast models. Holt explained. “We’re getting more accurate forecasts for the probabilities of earthquakes in particular regions,” he explained. “That enables one to prepare through proper retrofitting of buildings and construction for long-term mitigation of potential hazards from earthquakes.”
Holt, who has been working in this field for 20 years, said scientists have boosted dramatically the amount of information they gather about the Earth.

When he started, “we didn’t have observations to understand how the interior of Tibet was moving or how the interior of Nevada was moving, so there was this big revolution through the 1990s, with the advent of space geodesy,” he said. “I can see incredible progress over the last 20 years.”

When he’s not collecting and interpreting data about the planet, Holt is a busy father of two primary school daughters and the husband of Troy Rasbury, a geochemist at Stony Brook.
Holt enjoys sea kayaking and, more recently, fly fishing, although he said most of the time, he “catches nothing.”

As for Ghosh, she is a resident of Manhattan and commutes to Long Island. She expects to finish her post-doctoral work at Stony Brook in the next few months.

Inspired by her progress thus far, Ghosh expects to continue to look deep into the Earth to understand the movement of some of its larger pieces.

“I’m intrigued by how much of our Earth we still don’t know,” she offered.

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From fine tuning the synchrotron to authenticating a Rembrandt

In the late 1980s, just a few years after Peter Siddons started working at Brookhaven National Laboratory, a company called BASF ran ads with the line, “We don’t make a lot of the products you buy, we make the products you buy better.”

That idea is similar to the work Siddons does on BNL’s synchrotron: He doesn’t perform research, but he makes the research of other scientists better.

By being what he describes as a “gearhead,” Siddons, a native of Yorkshire, England, makes best use of the optics and the X-ray beams from the National Synchrotron Light Source to give scientists a fast, clear picture of small molecules and particles inside a wide range of objects.

When polymers melt, they go through a process called reptation, where they form long, linear entangled molecules (they look like a collection of snakes mixing together).
Andrei Fluerasu, a BNL scientist who has studied polymers, has worked with Siddons since he arrived three years ago and has been impressed with his colleague’s ability to fine-tune the detecting device.

He is “building a device that works exactly how it should,” Fluerasu said. “We can go 100 times faster and can detect things which move 100 times faster.”

Siddons has worked with scientists from all over the world, including Australian geologist Chris Ryan. The tandem first started collaborating a decade ago.

“We went through many generations of designs,” Ryan wrote in an email to the Times Beacon Record. Ryan praised Siddons, suggesting he had a “vision of new generations of detector technologies.”

Ryan said the enhanced detecting abilities have had applications in everything ranging from optimizing the availability of iron in rice, barley and wheat, to the study of organisms used as models for neurodegenerative diseases, to art.

Indeed, Siddons made headlines recently when he became involved in a debate over the effort to authenticate a painting called “Old Man with a Beard” that some art historians believed Rembrandt had created.

When he received the painting, it “took a while to figure out how to hold it without damaging it,” Siddons laughed. Once he worked out the logistics, Siddons used X-ray fluorescence on it to look deep inside the layers of the painting.

Using a detector called Maia, Siddons imaged the painting in eight hours. Using other technology, that analysis would have taken 30 days, Siddons said.

The approach showed there was a 400-year old image beneath the painting, likely of a younger self-portrait of Rembrandt. But that wasn’t where the effort ended. There was a third image hidden beneath the painting, of a person wearing a turban with a feather. There were enough similarities between these images and others done by the master painter to confirm that the “Old Man with a Beard” was an authentic Rembrandt.

“It was great fun,” concluded Siddons, who said he spent several evenings putting the data together.

One of his colleagues, noticing the similarity between the subject of the painting and Siddons, photoshopped the BNL scientist into a copy of the painting.

“It’s pretty convincing,” admitted Siddons, “except for the spectacles.”

While Siddons can appreciate a Rembrandt — and his role in authenticating one — the “gearhead” spends much more of his time in another cultural area, playing Renaissance music in a lecture room at BNL with his musically-inclined colleagues once a week on the guitar, recorder or other instruments.

Siddons lives in Cutchogue with his wife Elizabeth, who works across the street from his lab at the Physical Review. While they carpool to work, they rarely have lunch because she reserves that time for bridge.

They have three children: Giles, a vegan chef in Boston; Rebecca, a teacher in Providence, R.I. and Louise, an art professor at Oklahoma State University. Louise was the one who brought her father into the Rembrandt debate.

Siddons has a need to understand the benefits and limitations of technology, even outside the high-tech synchrotron where he works.

“I can’t use any instrument I haven’t taken to pieces,” he confesses. “It’s pathological. I used to do my own car maintenance. When I turn something on, I want to know where the warts are and what can go wrong.”

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Leaving the earth at least as good as he found it spurs his research

Jason Graetz’s friends want him to hurry up and build a better mousetrap or, more specifically, a better fuel-cell vehicle. When he socializes, Graetz is often urged to create an automotive alternative, especially as the cost of gas hovers near $4 a gallon.

As the head of the Energy Storage Group in the Sustainable Energy Technologies Department at Brookhaven National Laboratory, Graetz is working on developing fuel cells that use lithium or hydrogen.

“In both cases, we’re developing new materials,” Graetz offered. “The Holy Grail for these projects is developing systems for automotive applications.”

Creating a hydrogen system presents practical problems, including how to store the hydrogen. At room temperature, hydrogen gas is stored in compressed tanks, which take up so much space that they would occupy most of the trunk and part of the back seat in a typical car, Graetz explained.

Storing hydrogen in a solid state, however, provides a potential answer. “Hydrogen goes into metal very much like a sponge,” Graetz offered.

He hopes to find a material that’s lightweight and that might require a storage tank the size of a gas tank.

The key is finding the right material. Graetz has found promising results with aluminum hydride, which is five times better than other options, such as iron titanium hydride, at storing hydrogen.

Getting hydrogen into aluminum “takes extremely high pressure” Graetz said. “We need to come up with a more clever way.”

The recipe is complex and involves introducing another molecule that helps stabilize the aluminum hydride. That molecule, called a ligand, hangs off the aluminum hydride and gives it more stability.

While that procedure works, the process is still a matter of “keeping cost and energy inputs low for each step,” he explained. “It has to be a pretty inexpensive material to be viable.”
Scientists and auto manufacturers are years from using hydrogen in fuel-cell cars, Graetz suggested, but that only increases the need to conduct research now.

Cars that use lithium are further along, although there are still research challenges with them as well.

Tapping into the resources available through BNL, Graetz has been able to put a lithium battery into a synchrotron, which shoots X-rays through the battery as it’s operating. That allows him to see how the lithium changes as it charges and discharges.

“This informs us about how the material is working and how it’s not working,” he explained. “We can see things like where the degradation is occurring.”

He can then return to the lab to synthesize, or create, new materials and make alterations to improve the performance of the battery.

Graetz has used the synchrotron in the manufacture of lithium-related materials to see how different properties of his creations — such as their shape — change when reactions occur at different temperatures and pressures and over different amounts of time.

Using a clear chamber, Graetz can mix lithium with other elements and observe the process.
In a full-size reactor, making these molecules can take a day or two. After the reaction, the scientists may not have the product they sought. With the clear chamber, they can make adjustments to conditions as they’re building these materials.

“Most syntheses are done blind,” Graetz said. “This allows us to see what’s happening in real time and make changes on the fly.”

Graetz’s interest in improving and understanding the materials around him extends beyond the lab. He’s gone a few rounds with his washing machine and drier in the home in Calverton he shares with his wife Ronia and their son, who was born last summer.

And, when he’s not fixing or improving something, Graetz enjoys rowing as a crewmember of a six-man outrigger canoe. The BNL scientist has returned to Hawaii, where he went to high school, for a 42-mile competition with his New York-based friends.

Professionally, he doesn’t need his friends to encourage him to build a better fuel-cell car. He says he feels that urgency when he thinks about his son.

“I feel a certain responsibility for the classic idea of leaving a place as least as good as you found it to the next generation,” he offered. “To do that, I feel we need to transition to more sustainable fuels.”

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Recent research suggests how the brain puts together multisensory information

Rats are not only capable of learning a maze to get to a reward (the coveted cheese, for example), but they also have the ability to process a combination of slow or fast flashes and clicks to learn whether their prize will be on the left or right side of a cage.

Cold Spring Harbor neuroscientist Anne Churchland recently published a paper in the Journal of Neuroscience that shows that rats are capable of putting together combinations of sights and sounds and changing their behavior to fill their rat stomachs.

The results suggest rats may prove to be effective mammalian models for understanding the neuronal circuitry that other mammals (namely, say, humans) use to process information around them and make decisions about courses of action.

“Very little is known about how the brain puts together multisensory information,” Churchland said. “It’s a mystery how neural circuits of the brain make this happen. An animal model can really get at the neural mechanism that underlies multisensory integration.”

While Churchland’s study was a behavioral one — flash the lights, make the sounds and see where the rat goes — she also plans to add electrophysiological data. That means she will study the neurons that are active as a rat combines pieces of information. Neurons are cells that transmit information through chemical and electrical signals.

By looking closely at the responses of rats, she hopes to figure out how these signals come together.

For some people, reacting to and processing a combination of sights and sounds is sometimes “impaired when compared to typically developing peers,” Churchland explained. Some people, for example, struggle when they go into a multisensory environment, like a grocery store.

“If we understand the sensory side more, we’ll be in a better position to treat those aspects of the disorder,” she explained.

Some people with autism spectrum disorders have a hard time interpreting cues such as a tone of voice, body posture, or the look on someone’s face.

Understanding the sensory side of some of these disorders can put scientists and doctors “in a better position to treat” people, Churchland said.

The Cold Spring Harbor neuroscientist works much more on basic research and is not directly involved in clinical applications.

“I hope that our work might inform the ongoing foundation of knowledge that the community is starting to have about autism spectrum disorders,” she expounded.

Some of Churchland’s passion for addressing autism comes from her experience as a camp counselor and as a babysitter, where she took responsibility for a child with autism. While earning her undergraduate degree at Wellesley College, she took courses in child and cognitive development, even as she was earning a degree in math.

After college, she worked at the University of California at San Francisco, where she “fell in love with lab work,” she recalled. “Doing science captured my imagination. The big questions are so exciting.”

Aside from babysitting and camp, Churchland had plenty of opportunities to think about development and, specifically, neuroscience. Her parents, Anne and Paul Churchland, are neuroscientists and philosophers. Indeed, they met in a philosophy class.

“Their enthusiasm for the field was contagious, not just for me, but it inspired many people,” Churchland said. They addressed questions, she explained, such as, how our brains make us who we are, and how we navigate through the world.

She said her parents didn’t encourage her and her brother Mark to pursue careers in neuroscience.

“When we were undergraduates, NIH [National Institutes of Health] funding was at a low level, as it is now,” she explained.

Still, that didn’t keep either her or her brother Mark away, as both of them have now developed careers in experimental neuroscience.

“I feel really lucky to have a family with so many shared interests,” she said. Some day, she hopes to collaborate with her brother, who works at Columbia University.

As for her immediate family, Churchland is married to Michael Brodesky, who works at Bookish in Manhattan, lives at Cold Spring Harbor, and has two children who are in the early stages of primary school.

In her first experience of living in New York, she lauded Long Island for its hiking and biking trails and kayaking opportunities.

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Donald Porter, recipient of NSF Career Award, works on ‘cloud’ computing

Donald Porter was such a childhood fan of Sesame Street that he named his computer lab at Stony Brook OSCAR (for Operating System Security Concurrency and Architecture). His desktop is Kermit and his favorite 48-core test machine is Miss Piggy.

An assistant professor who joined Stony Brook just over a year ago, Porter, like the charming Muppets of his youth, is driven by a desire to teach.

Indeed, his promising research and dedication to teaching recently helped him win a prestigious Career award from the National Science Foundation, which recognizes promising junior faculty members around the country. The NSF will give his lab $400,000 over the course of five years.

“It’s very exciting,” he said. “This will give me funds to hire graduate research assistants, buy computing equipment and do other things that will help me get my research agenda going.”

Porter, who teaches a graduate course on operating systems, said when he explains something to students, it often winds up helping him with his research by forcing him to distill his thoughts.

“If you can’t teach someone else why things are the way they are, it may be hard to make them better in a clear way,” he suggested.

He said his teaching philosophy is to “demystify the computer, so people can really understand what’s going on.”

In a graduate-level operating systems course, he gives students a system developed at MIT in which there are “holes” in a source code. The students have to write the key pieces of the software themselves, including memory management, switching one running program to another, a network-card driver and the file system.

“There is no better way to understand how operating systems perform these central tasks than to write them yourself,” he advocates.

Associate professor Erez Zadok, who has been at Stony Brook for over a decade and has been teaching the popular graduate operating systems course since he arrived, applauded his colleague.

“There’s a small window when you can win this very prestigious award,” Zadok said. “We were delighted to hear he’d won it on the first shot, no less. It’s quite an achievement.”

As for his research, Porter works in an area called cloud computing, where a single computer can use several operating systems at the same time. The technique allows Apple computer users, for example, to run a Windows program at the same time they are also using a Mac operating system.

The process involves sharing resources, software and information. The concept not only allows those who own different hardware to use the software from other computers, but also allows businesses to adjust their technology resources to meet unpredictable demand.

“You can think of the cloud as very cheap, short-term computer rentals,” Porter said. “If you were launching a new product you could temporarily and affordably rent extra servers in the cloud to help meet peak demand for extra orders.”

Porter thinks about ways to divide the labor among the various parts of a computer functioning at the same time. He explained that the numerous systems — the hardware, the operating system, the language system, and the application library, to name a few — work at the same time and may interfere with each other. He wants to look closely at whether there are “better interfaces that make common problems less common.”

Porter hopes his research has a practical impact on industry and on the ways people use and interact with computers.

Porter doesn’t have a statue of Oscar or a puppet in his lab yet. If he needed one, he might borrow something from his wife, Lindsay Porter, a first- and second-grade teacher at Love of Learning Montessori School in Centerport.

“I owe a certain amount of my success to the support of my wife,” Porter acknowledges. “She put up with long hours and flak under deadline and also provided emotional and spiritual support.”

The Porters live in Setauket, an easy ten-minute bike ride to OSCAR and friends at his computer science lab. They moved just over a year ago after he earned his doctorate from the University of Texas at Austin.

“It’s easy to feel like this is home,” offered Porter.

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Understanding the basic properties of mixing fluids

As a child in France, Thomas Cubaud grew up watching rivers, waves in the ocean, tides, and even the vortex that formed as bathwater ran down a drain.

Fast forward to now and the assistant professor at Stony Brook University has turned his passion for understanding the way fluids move and interact with each other into an award-winning developing career in mechanical engineering.

Cubaud works in a field called microfluidics. That means he mixes tiny amounts of different kinds of fluids (often very viscous or thick liquids with less viscous liquids or solvents). In addition to producing magnificent images, he also tries to understand the nature of the way these liquids mix.

Microfluidics is a relatively new science that was developed about 30 years ago. It has applications in a wide range of fields and helped produce such products as inkjet printheads, DNA chips, and microthermal technologies.

While aware of the potential applications of his research, Cubaud is much more focused on understanding the basic properties of mixing.

When researchers like Cubaud mix a very viscous liquid with a solvent in small amounts, they maximize the surface area (or points of contact) between the two liquids. While that could be an advantage in mixing, they also see what’s called laminar flow, where those two liquids form parallel layers and glide past each other, rather than mixing.

Enter viscous buckling. To picture this, take honey from a pantry and pour it on toast. As it comes out of a jar held a few inches above the toast, the honey falls in lines back and forth, looking like coiled rope. If the honey were falling through another thick liquid instead of air, the buckling back and forth would promote turbulent flow (converting the laminar flow — not good for mixing — into turbulent flow — much better for mixing).

One of the goals of Cubaud’s research is to understand the role of different properties, such as viscosity and surface tension, on the flow of fluids on a small scale.

In his experiments, Cubaud varies the speed at which he injects one fluid into another, the pressure and the thickness of the liquids.

Cubaud’s research showed sufficient promise that he recently won the Career Award from the National Science Foundation, which will give him $400,000 over a five-year period.
The award is given to promising young faculty members at universities around the country to support their teaching and research.

“The challenge is to find the best operating condition. We need to do experiments with different materials and new methods to characterize the flows,” he said.

Jon Longtin, an associate professor at Stony Brook and Cubaud’s mentor, sees considerable promise in his junior colleague.

“He is a genuine top-notch scholar,” Longtin said. “When he gets his arms around an idea, he wrestles it to the ground until he figures out exactly what is going on.”

Longtin said microfluidics has become a hot topic in science, which means there is increased competition for funding.

“He has carved out a niche for himself,” Longtin described. “He’s looking at fluids that have disparities in thickness. He found interesting things that happen that are not necessarily obvious. He’s had a lot of success.”

Cubaud’s research also examines a process called carbon sequestration, where carbon dioxide is removed from the air and absorbed into liquids.

“Injecting carbon dioxide gas with liquids in microgeometries permits us to significantly increase the surface area of contact between the fluids,” he said. “The knowledge that will be gained during the project will help frame future carbon sequestration applications.”

Cubaud pointed to a biological system that already uses microscale interactions between gases and liquids: the lungs, where blood gives up carbon dioxide and takes in oxygen.

Microfluidics allows scientists to achieve a basic understanding of new physical interactions, he said.

“A key aspect of miniaturization technology is that, up until recently, we could only observe phenomena,” he said. “Today, not only can we observe, but we can also directly intervene on small-scale mechanisms.”

Echoing the observations of the young boy in France who watched rivers, oceans and whirlpools in a bathtub, Cubaud said: “When you just do an experiment, you find unexpected results. It’s very exciting to see something possibly unexpected occurring.”

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Cold Spring Harbor scientist’s discoveries also focus on cancer treatment

One Sunday in the fall of 2010, Alea Mills needed a break from one of her more mundane jobs — writing proposals to get money. She decided to check on her mice.

When she did, she couldn’t contain her excitement. She’d worked with mice for years and yet these were clearly different. She called her husband Ross Maddalena, an actor who doesn’t particularly enjoy visits to her lab — especially during a football Sunday.

“Please, please, please,” she begged. “You have to come. I need somebody else to observe this.”

Maddalena, an extra in movies like “Mr. Popper’s Penguins” and “Salt” who has taken cues from his wife’s career as he followed her from California to Texas to Long Island, drove to her lab at Cold Spring Harbor, where she has conducted research since 2001.

Even without any scientific expertise, Maddalena recognized the changes. Mills had created a mouse model for autism. Using a hand-held video camera, he recorded the mice. Mills said she has watched the movie dozens of times.

A researcher who has made important cancer discoveries, Mills took the unusual step of using her expertise in chromosome engineering — changing the genetic blueprint of an animal — to study autism.

“I saw [autism] as a genetic problem,” Mills said. “We can generate models where we can make the same precise changes as in various diseases.”

By using a form of molecular scissors, Mills took out a 27-gene region on chromosome 16 in mice.

“We didn’t know what to expect,” Mills recalled. “Could we see anything different with respect to the behavior or the brain anatomy of the mice? The answer is yes. Those genes are regulating fundamental processes that are evolutionarily conserved to some degree and are causing the same type of changes.”

Indeed, these genetically altered mice also showed eight regions in their brains that were larger than normal.

Her results, which were published last October in the prestigious journal Proceedings of the National Academy of Sciences, created a buzz in the world of autism research.

At this point, Mills, who is a resident of Lloyd Harbor, is fine-tuning her autism research to look at even smaller areas within that genetic region. She is also looking more closely at the brains of these mice to see if she can connect some of the more severe behaviors to the biggest changes in brain structures.

While extending this research to understanding the development of autism in humans remains a challenge and will require considerably more work, Mills said this could prove an important step in diagnosis and treatment.

People typically show signs of autism at around 2 or 3 years old, Mills said. In mice, Mills and her postdoctoral research fellow Guy Horev can often detect changes in one to two days after birth.

Researchers like Mills need to figure out the mechanism in which these genes might lead to autism and, once they do, work on a potential clinical model to correct it. Mills cautions that there is considerable work left to do to understand the pathways that lead to autism in humans.

While she will continue to oversee autism research, Mills will also direct and conduct studies on cancer, where she discovered Chd5 and p63. Scientists had long sought Chd5, a gene that produces a protein that prevents cancer. Indeed, the amount of Chd5 protein a patient has is a predictor of treatment outcome for cancer patients. The p63 gene, meanwhile, produces some proteins that suppress cancer, while it manufactures others that promote it. The effect of p63 depends on the type of cell.

Perhaps Mills’ upbringing on a 60-acre piece of property in upstate New York made her comfortable looking out to the horizon for answers to a wide range of questions. The only girl in a family of five children, she said she and her siblings “ran rampant.”

At the same time, when Mills was as young as 3, her mother often encouraged her to slow down and look closely at a small piece of grass, where she could study a flower or a worm.

Those days of watching worms brought her to Cold Spring Harbor, where she witnessed the excitement of her own breakthrough with the first mouse model of autism one Sunday in 2010.

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Working to lower heating bills, pollution and dependence on foreign oil

Tom Butcher doesn’t just stand around at the water cooler and complain every time he gets a heating oil bill — he’s doing something about it. The head of the Brookhaven National Laboratory’s Energy Resources Division, Butcher is conducting the kind of research he hopes will lower our heating oil bills, create less pollution, and reduce our dependence on foreign oil.

For starters, he is working on ways to displace import petroleum with domestic biodiesel. As it stands now, fuel that heats our homes can have 5 percent biodiesel — or fuel made from substances like soybeans and waste from restaurants. Butcher has his sights set on a much higher target.

“The legal definition of heating oil has changed so that it can have as much as 5 percent biodiesel,” Butcher explained. “Getting that done was a big step. Where our research is focused is on increasing that limit and going well beyond it. From a technology perspective, there are some challenges in doing that.”

Butcher and his colleagues at BNL and his counterparts at Stony Brook have been examining numerous technological hurdles. One of those. Butcher said, is looking at the reliability and safety of existing equipment designed to house oil-based fuels when liquid fuels, including fuels from soybeans and waste oils pass through them.

The “rubbers in a pump shaft may degrade and lead to leaking components,” Butcher said. “The key issue” in raising biofuel content is that there is a “lack of experience in some important areas, including the compatibility of field materials, including elastomers and rubbers,” Butcher said.

Butcher is also interested in examining how to reduce pollution and improve the efficiency of burning wood as a heat source.

“In rural New York state, wood burning is the number one source of air pollution,” he warned. “On the track we’re on, [wood burning] threatens to become a dominant source of air pollution in the Northeast.”

Burning wood is something consumers generally warm to because it “puts people to work and is a renewable energy source,” Butcher described. “A lot of our work is focused on how to burn wood cleanly. How do you develop test methods that can accurately capture the performance of the currently available leading-edge wood conversion combustion technology?”

Butcher is examining the effectiveness of electrostatic precipitators, which use a high-voltage field across the exhaust gas, where captured particles migrate to a wall, fall down and get removed. He is also examining heat exchangers that can be used to condense water vapor from the exhaust gas and wash the particles out.

“If we are going to continue to use wood for heating, this is a road we have to go down,” Butcher insists. “I don’t think we’re going to have a choice.”

The BNL investigator said there are already technologies on the market that are much better than the average pellet burners, some of which keep fuel from smoldering, especially during periods when a house doesn’t need heat. A key to this system is thermal storage, where systems run at their optimal condition and charge the storage. The stored energy can heat the home while the burning system is off.

Butcher and his wife Donna, who works in a dental office and as a real estate agent, have raised four children who have all shown interest in technical fields. Their eldest, Kim, is an aerospace engineer who works for NASA on the technology for future space travel. Matt is working on his Ph.D. in biology at Eastern Virginia Medical School and is focused on heart disease. Jon will complete his doctor of pharmacy degree at Long Island University at the Brooklyn campus in just over a year and is, in the words of his father, “a fanatic fisherman.”

Not to be outdone, Jamie, who worked at BNL last summer on radiation detectors, is at Geneseo and “will undoubtedly develop a career that involves something technical in collaboration with something international.”

As for Tom Butcher, who lives in Port Jefferson with Donna, the common theme for the work he’s tackling now is “given the high price of oil, what do we do?”

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