Demian Chapman has one of those jobs that turns heads at social gatherings: he’s a shark biologist. The New Zealand native, who is also an assistant professor in the School of Marine and Atmospheric Sciences at Stony Brook University, is in the middle of studying the oceanic whitetip sharks.

Known for living far from land, the whitetips, which eat tuna, mahi mahi, marlin and squid, have declined precipitously in numbers in the last few decades, in part because some people consider their fins a delicacy.

Chapman, his wife Debra Abercrombie — also a shark biologist — and several other researchers recently published results of a study on the whitetips. Starting in 2011, Abercrombie and other field biologists went to the Bahamas, where the waters are aggressively patrolled and the sharks are actively protected, to fit some sharks with pop-up satellite tags that could track their location.

As Chapman explained it, the researchers put bait in the water near the Bahamas at a time when the sharks are closer to land. If it’s alone, the first shark won’t typically approach a piece of bait. Once other sharks arrive for a meal, however, the shark’s competitive instincts take over and it becomes easier — albeit still a struggle — to reel them in.

The researchers slip a rope around the tail of the shark and then drive the boat slowly while they outfit the cartilaginous fish with a tag. Chapman said the tags, which weigh only a few grams, are probably barely noticeable to the sharks, which can be as long as eight feet and can weigh about 150 pounds.

What the tags showed was that one of the sharks traveled about 2,000 kilometers, or over 1,200 miles, in under a year. Five of the sharks traveled outside the exclusive economic zone (or EEZ) for the Bahamas, where they are better protected. This suggests that more countries might need to safeguard these sharks.

This March, the Convention on International Trade in Endangered Species of Wild Fauna and Flora is meeting in Bangkok, where representatives from several countries will consider whether to list this species. Such a listing would mean that permits would be required to trade the species across international boundaries. People caught trading the species without those permits would face penalties.

The sharks “do spend a lot of time in the Bahamas, where they are well protected,” Chapman said. “The fact that they do leave raises concerns. If you don’t have some parallel measures outside the Bahamas, that may undermine what the Bahamas has done.”

Chapman hopes that this paper, along with further research, helps to raise awareness of the delicate state of the shark population.

Countries vote to determine which species make it to different protected lists. A species has to get two-thirds of the vote.

“It’s difficult to get,” Chapman said. “Some countries that are pro-shark trade — if they consume fins — will never vote for a shark to be” on the list.

There’s definitely politicking at these meetings, he said, where some countries vote to list species in exchange for the votes of other countries on other organisms.

Chapman went to Asia in late February to help train customs agents to recognize the fins of different sharks.

Unusual for his combined expertise in DNA analysis and field work, Chapman made a remarkable find in 2005. A female hammerhead shark had been in an aquarium without any access to males for about three years. After all that time in isolation, it gave birth. The aquarium sent a copy of the mother and pup’s DNA to Chapman. He concluded that the shark had given a so-called virgin birth.

While impossible in mammals, animals like sharks, snakes and turkeys can somehow combine an unfertilized egg with the genetic code of a polar body, which essentially acts like a sperm.

The polar bodies are “cells that could have been an egg” but were produced during the production of eggs, he said.

Residents of Miller Place, where they recently purchased a house, Chapman and Abercrombie, who is originally from South Carolina and is a consultant for the New York Department of Environmental Conservation, met when they were at a field station in the Bahamas.

Chapman tries to avoid the “Shark Week” series on the Discovery Channel because of the frequent recreations of shark attacks.

“They try to add a conservation message,” Chapman said, “but it’s difficult to reconcile how the sharks need to be protected” after people have watched them attack swimmers.

As for working with sharks, he said he’s never had a “bad experience with them.”

Aaron Stein was hired to work at a place that existed only on paper. About a decade ago, the physicist agreed to work at Brookhaven National Lab’s Center for Functional Nanomaterials, even though BNL hadn’t started construction on the cutting edge facility.

“I see something that went from an idea to a hole in the ground to a place where lots of science is being done,” Stein said.

Indeed, Stein, who earned a Ph.D. in physics from Stony Brook University, was the first official hire at the CFN, which is one of only five nanoscale science research centers funded by the Department of Energy’s Office of Science.

The study of nanomaterials involves examining how to exploit or understand physical and chemical changes that occur at an incredibly small scale. While construction of a skyscraper follows certain laws of physics — such as how much weight a load-bearing wall can support — the manufacture of objects, such as fuel cells or computer parts, is guided by other forces and interactions.

“There are certain things you’d never see otherwise if not for shrinking them down to that size scale, either due to quantum effects, size effects — you have more surface area — or other things,” Stein explained. “Everything changes and gets weird and interesting on the nano scale.”

Stein has worked in nanomagnetism, X-ray optics and photovoltaics, among many others.

Working with nanomagnets isn’t all that different, he explained, from using the bar magnets children use in middle school, except that the scale, functionality and experiments are considerably altered.

“The side I’m on is in making these magnets,” he said. “We make millions of these magnets at a time and play with the physics. We’re building our own little playground to test theories and observe” the results.

Stein has worked with Kenneth Evans-Lutterrodt, a staff scientist at BNL, since his days as a Ph.D. candidate at Stony Brook. The two have worked for years developing and honing miniature lenses that could have applications ranging from creating higher resolution and better contrast diagnostic X-ray images all the way to looking at the stress, on an atomic level, of a helicopter bearing.

“We have spent many years developing the ideas behind this,” Evans-Lutterodt said. “We look at what new design to try. He does the e-beam lithography.”

In e-beam lithography, a tiny piece of silicon is coated with a material called a resist. The material scientists like Stein uses varies, depending on what they are trying to manufacture. The researcher shoots an electron beam at the resist. The resist is sensitive to electrons in the same way that film is sensitive to light: after exposure, it is developed and the contrast can be used to create structures or finely crafted objects that are of almost any shape and size, Stein said.

Evans-Lutterodt uses the lenses Stein makes in collaborations with other scientists. The lenses themselves, he said, are not like the ones that sit in prescription glasses: they have considerably more curvature.

“The shape is quite asymmetric,” Evans-Lutterodt said. “It’s very difficult to bend X-rays. The lenses are also made out of silicon, which is opaque to visible light, but somewhat transmissive to X-ray.”

As far as a commercial application, Evans-Luterrodt said he would expect it to take about three years, optimistically, before he and Stein had developed a commercial application from their research.

Stein’s goal is to “enable science.”

As for his own work, much of it is in understanding the limits of the tools and the materials he is employing.

“A big part of the job,” he said, “is to keep the lab humming.” That includes making sure the equipment is maintained, the supplies are available, and the tools are in the same condition for everyone.

Stein also spends considerable time focusing on the environmental components of nanofabrication, ensuring that everyone who comes into the lab goes home safely.

A resident of Huntington, Stein is married to Sasha Abraham, who is a member of an advocacy group that works on prostate awareness and screening. They have an 11-year-old daughter, Lily, and a 9-year-old son, Henry.

Stein grew up in Syracuse and said he never imagined coming to Long Island to build his life and career.

“There are a narrow set of places I could work,” he explained. “Probably, where I am now, is really an ideal situation for me.”

This is the second part of a two-part series on four Stony Brook University researchers who recently received an NSF Career Award. Designed to give researchers in the early part of their careers a financial boost before they compete against established scientists for the same dollars, the award funds projects, allows the scientists to expand their educational goals and offers recognition.

Last week, the Times Beacon Record Newspapers featured questions and answers with Radu Laza and Jonathan Rudick. This week, the paper will have insights from Alex Orlov and Emre Salman.

Alex Orlov

TBR: Are you excited to win this award?

Orlov: This was absolutely delightful news. Receiving this award, especially just before significant budget cuts to science, is even more amazing.

TBR: What will these funds enable you to do? Will you hire anyone new? Will you do more teaching?

Orlov: These funds will have a huge impact on my research focused on sustainable energy. It will also allow us to start new collaborations with Brookhaven National Lab and with other groups outside Stony Brook (University). I expect to hire several undergraduate and graduate students, who will be working on this project. There will be also a very significant impact on undergraduate and graduate teaching here.

Almost 80 graduate and undergraduate students are taking my courses and this project will allow me to introduce several innovative case studies based on this funded project into the classroom. We are also planning to develop new teaching techniques for engineering courses to help students (high school and university ones) to educate them on designing better consumer products while protecting the environment.

TBR: Is there anything new in your lab since we spoke? [The Times Beacon Record profiled Orlov on Dec. 18.]

Orlov: [He was named a fellow of the Royal Society of Chemistry in Britain in February.] The fellowship is something very exciting. There are also several interesting projects I am doing in collaboration with my colleagues (I am the principal investigator, but a significant player), such as developing a new computer game to educate students on environmental topics. There is a paper which was just accepted where we found a better way to get hydrogen fuel from water.

Emre Salman

TBR: How would you characterize the scope of your research?

Salman: Our research activities focus on high performance and energy efficient integrated circuits. We develop design techniques for next generation microprocessors, mobile computing devices as well as communication chips. We also investigate emerging integrated circuit technologies to overcome the fundamental limitations of current electronic systems such as high power consumption. At the NanoCAS Lab, our workstations are equipped with the latest electronic design automation software that allow us to verify our algorithms, models and design techniques.

Our ultimate objective is to develop future integrated circuits that are more portable, can interact with the environment, consume low power, yet still offer significant computing capability.

TBR: How will you use the funds from the award?

Salman: The NSF Career funds will support between one and two Ph.D. students in my research group (NanoCAS Lab) for five years. Part of the funds will be used to fabricate and test a three-dimensional integrated circuit to demonstrate and validate our methodologies. Furthermore, a scholarship will be available to an undergraduate student each year. Our objective is to provide undergraduate students with real research experience in our lab. These research activities will be integrated with multiple educational initiatives such as developing new course modules and outreach events for high school students within Long Island.

TBR: What would you tell those who are considering a career in research?

Salman: I would encourage them. It is fascinating to spend time on something that is not yet known by anybody. The hard part is to ask the right questions. If the questions are right, I believe the answers are likely to come, even though it may take some time. It is also very rewarding to share these experiences through teaching.

TBR: Where do you live?

Salman: I have been on Long Island since September 2010 and currently live in Sound Beach. I grew up in a small town on the Mediterranean coast in Turkey, so I enjoy being close to water. I like the nature of Long Island, hiking trails and its close proximity to New York City.

Children were falling through the cracks. A decade ago, when a child developed signs of a problem that primarily affects adults, their pediatricians generally had little or no experience, while the medical care workers who did hadn’t worked with children.

It was a problem Lauren Krupp decided needed action. A professor in clinical neurology and a practicing physician at Stony Brook University, Krupp founded the National Pediatric Multiple Sclerosis Center, which was recently renamed the Lourie Center for Pediatric MS.

“We saw parents who were frightened and who were told that multiple sclerosis can’t occur in children, which is obviously not true, or they were told, ‘Yes, it is multiple sclerosis, but I’m an adult neurologist,’” Krupp recalled. “It makes a real difference to parents if they can take their child somewhere where there’s experience with something that’s rare.”

About 3 percent to 5 percent of the MS population has a disease that begins before age 18. Among children, MS occurs once for about every 100,000 people, Krupp estimated.

Krupp has been working with some of the other facilities designated as Regional Centers of Excellence by the National Multiple Sclerosis Society to develop a better understanding of the way MS progresses in children. Recently, she joined with several other researchers to publish research about the potential cognitive effects of the disease.

“This was the first time a uniform approach to looking at kids and their cognitive functioning was taken across the country,” she said. “We also included children at a very early stage of the disease.”

Children who had only one attack had an 18 percent frequency of cognitive problems. In children with more than one attack, the cognitive problems rise to about 33 percent.

As an example, she cited the case of a teenager who loved playing in her school band. All of a sudden, she was getting failing grades in music. The problem had nothing to do with music — she couldn’t remember her locker combination.

Some children with MS don’t need additional services (and may need a locker with a key instead of a combination lock), while others could need anything from having someone take notes in class, to getting extra time for tests, Krupp suggested.

“Cognition needs to be considered,” she explained. “We’re very eager to come up with interventions” to improve treatment.

She’s exploring the possibility of developing strategies that don’t necessarily involve medication.

“There’s a lot of promise in innovative computer-based training programs,” she said. She hopes to study some of these models in the next several months.

Krupp has also organized a camp called Teen Adventure, where children from 13 to 18 with multiple sclerosis can “go out there and do stuff and be like other kids.”

The camp enables networking among the children. Krupp says she doesn’t attend because she doesn’t want to “medicalize” the experience, although there is a team of experts, including nurse practitioners and recreational therapists, on site.

Krupp believes her efforts, as well as those of others in her field, including the National Multiple Sclerosis Society, have helped the medical community become aware of pediatric multiple sclerosis.

In people who have MS, the immune system attacks the myelin, or protective sheath around the axons of the brain and spinal cord, potentially leading to neurological, physical and cognitive problems.

The cause of MS, a disease in which the symptoms can include weakness, visual problems, numbness and trouble speaking, involves an interaction between a genetic predisposition and environmental factors.

Some studies have shown that the farther away people live from the equator, the higher the incidence of MS. Indeed, children born near the equator who move before the age of 15 develop MS at the same rate as those who have lived all their lives farther from the equator.

“We think the reason for this has to do with higher prevalence of sunlight exposure,” offered Krupp.

Sunlight is among the biggest sources of vitamin D. Doctors have different approaches to vitamin D. Many think the best strategy is to maintain a normal to high vitamin D level in the blood and use vitamin D doses as needed, she said.

Krupp and her partner live in Setauket. They have twin daughters, Gina and Alexa, who are on their respective sailing teams in college.

People who are interested in finding out more about the camp, Krupp’s research efforts, or ways to help can visit www.pediatricmscenter.org.

Krupp’s professional goal is simple: “To be put out of business. I would like to see the disease ended.”

Back when she was in Boston, Raffaella Sordella was a part of an incredible discovery. Some patients with non-small cell lung cancer had mutations that made their tumors sensitive to drugs such as Tarceva and Iressa.

When the patients took the medicine twice a day, “the tumor was shrinking,” recalled Sordella. “Within a couple of weeks, the patient could resume a normal life, more or less.”

To top it off, the drug didn’t have all the side effects of conventional chemotherapy.

“This was a turning point in my career,” explained Sordella, who is originally from Turin, Italy, and was conducting her research at Massachusetts General Hospital.

The promising therapy for these patients, however, wasn’t as effective as researchers, clinicians and patients had hoped. Within a year, the tumors in even these patients had developed a resistance to the drugs.

Undeterred, Sordella decided she would search for reasons for the change. Now an associate professor at Cold Spring Harbor, Sordella is pursuing several possible explanations which she hopes one day will extend the effectiveness of drugs.

Lung cancer is the leading cause of cancer deaths in the world. It was responsible for 160,340 deaths in the United States in 2012, according to the American Cancer Society. More than 226,000 cases were diagnosed last year.

Tarceva and Iressa were sometimes effective initially on the tumors that harbor specific mutations because they blocked the epidermal growth factor receptors (or EGFR). Without signals from the EGFR sites, the tumors either stopped growing or began shrinking.

As Sordella and others have observed, however, these drugs became less effective over time. One possible explanation was that the cancers were changing, developing a secondary mutation that altered the way the tumor grew or developed. That likely accounted for about half of the cases. In the rest, scientists now know that resistance can develop through other mechanisms, such as the expression of other genes.

“If we understand the mechanism, we can slow down the process,” she explained. Scientists may not find a cure in the short term, but they may be able to extend the period when the tumors are sensitive to the drug out from one year.

Sordella discovered that the interleukin-6 protein, which was produced during inflammation, was responsible for decreasing the sensitivity of the tumor to the drugs.

Resistance was increased “by factors secreted during inflammation,” Sordella observed.

By turning off or blocking interleukin-6, researchers may be able to create a combination of drugs that blocks the growth and spread of tumors.

This, Sordella offered, would be considerably easier than trying to anticipate and stop the next cancerous mutation.

When she first started exploring the ways tumors might develop drug resistance, the most obvious, and medically most challenging possibility was that the tumor was heterogeneous, which means that it had a mix of cells with different genetic codes that kept it several steps ahead of the available drugs.

Sordella feels a scientific urgency to continue with her research, in the hopes of helping those suffering with cancer.

“What we are doing is not just for us,” she said. “It can make a difference to patients.”

Sordella and her husband Manuel Barriola, a theoretical physicist who works as a consultant, live on campus at Cold Spring Harbor. They have two daughters, Victoria, who is in second grade and Alicia, who is in kindergarten.

Sordella and her husband, who is from Spain, miss their connection to Europe. She explained that the Italian culture she grew up with is considerably different from that for third-generation Italian Americans.

“When I was in Boston, there was this old guy that learned I was Italian,” she recalled. “He spoke to me in what he thought was Italian.” Sordella suspected that he was speaking a dialect from Sicily and wasn’t able to understand a single word.

Sordella enjoys going to Manhattan to people watch. She said she doesn’t think about her research when she’s in the city, even though she knows cancer is so prevalent that any medical breakthrough could make a difference for everyone.

African violets

Continued from page B16

Any number of small insect pests, including aphids and spider mites as well as mealybugs, can attack African violets. I find that the yellow sticky traps are very helpful in dealing with insect pests in the house in general. If that doesn’t work, you may have to resort to using a pesticide. Make sure that the one you select can be used on houseplants and that you follow directions carefully.

Prevention is the best route to take. Check any new acquisitions carefully before bringing them into the house. You may also want to quarantine them for a few weeks so that if there is a problem it won’t affect your entire houseplant collection.

For more information, the African Violet Society of America can be reached at www.avsa.org.

Ellen Barcel is a freelance writer and master gardener. To reach Cornell Cooperative Extension and its Master Gardener Program, call 727-7850.

By Daniel Dunaief

After searching in 40 other places — albeit from millions of miles away — Deanne Rogers and her scientific colleagues from the U.S. and U.K. found what they were seeking. Using images beamed back to Earth, they found minerals on rocks that typically form in the presence of water.

The discovery, in the McLaughlin Crater on Mars, where deposits are probably 3.8 billion years old or older, is consistent with an expanding body of knowledge about the Red Planet.

“I almost expected we should see something like this,” explained Rogers, an assistant professor of geoscience at Stony Brook. “A lot of recent observations point to groundwater in the subsurface. There was a hint of water deep in the subsurface.”

Without channels going into or out of the basin, scientists suggested that the water likely came from under the ground.

Much of the water on Mars is likely a result of volcanic activity, although comet impacts may have also carried some. The water likely percolated through soil that is much more porous on Mars than it is on Earth. It likely collected several kilometers below the surface. The water may have come back up in deep basins, such as the McLaughlin Crater.

Indeed, there could still be water in the Martian crust.

If manned missions went to Mars, experts have suggested that the astronauts might need to find water on the planet to drink while they’re there and to restock their supplies for the long journey back to Earth.

Rogers suggested that astronauts probably wouldn’t be able to drill deep enough to get any groundwater. Some scientists, however, have been working on how to free the water trapped in the minerals on the rocks. By heating the rocks, astronauts might be able to release water. They could also go to high latitudes, where there is water ice within centimeters of the surface.

So far, the McLaughlin crater “is the only place where we find evidence of these minerals” together in a basin setting, Rogers offered. Some are covered in dust, which obstructs the scientists’ view, while others may never have had water upwell in that region.

The presence of water, even long ago, might suggest that conditions on Mars could have supported life. Those extraterrestrial organisms could have lived in the subsurface, where they might be sheltered from the harsh environment on the surface.

Despite the pervasive dust, Mars presents a clearer picture in some areas of geological processes than the Earth. Plate tectonics — the slow movement of the enormous landmasses on which the continents rest — on our planet muddy the waters of interpreting how the planet may have changed over its history.

Mars, however, does not have any such movement of tectonic plates. Additionally, the meteorites that slammed into its surface have helped reveal what is and was beneath the surface.

“It’s a lot easier to study craters on Mars because they are well preserved,” explained Rogers. “On Earth, they are buried under vegetation or erased from Earth’s surface” by the movement of the plates and by erosion or weathering.

Rogers explained that she has divided her research into analyzing data sent from orbiters and studying the properties of similar rocks and minerals that other researchers at Stony Brook have created.

“We can look at the spectra of altered samples to compare it to Martian data,” she explained. “We can confirm it in the lab.”

She also does some remote sensing of the moon and asteroids.

Rogers lives in Selden with Tim Glotch, who is also an associate professor in the same department (see July 17, 2012 issue), and their two preschool-age children.

Glotch, Rogers and a few other Stony Brook faculty are working on a multidisciplinary proposal, which is due in April, that considers the possibility of human exploration of the moon and asteroids. Glotch is the lead investigator, while Rogers and others have responsibilities specific to their expertise.

Their research is benefiting from a resurgence of interest in Mars, in part because of the newest rover, Curiosity.

Rogers said she hopes to continue to participate in research on Mars because “there are so many things left unexplored at this point.”

Jonathan Liu wants to see inside people’s brains. Specifically, he is working on a way he hopes will eventually give neurosurgeons a clearer look at the difference between malignant cells they want to remove in a specific type of tumor and healthy cells they’d rather not touch.

Taking out too many cells can damage the health of a patient, while not removing enough can give the tumor a chance to grow.

An assistant professor in biomedical engineering at Stony Brook University, Liu has tapped into his background in engineering to create microscopes that, in connection with a chemical called a contrast agent that lights up cancer cells, surgeons may one day use to see the edges of a tumor.

A doctor would “spray the contrast agent on at the final stages of surgery,” he explained. “It’s a way to check if there are any residual tumor cells.”

At this point, Liu and his graduate students, Danni Wang, Steven Leigh and Ye Chen, in conjunction with Stanford University, where Liu started this work as a postdoctoral student, have developed a system in animal models of medulloblastoma, a type of brain cancer, that makes the tumor glow.

In those animal models, medulloblastoma cells have a higher than normal amount of protein on their surface called Vascular Endothelial Growth Factor Receptor 1 (or VEGFR-1). Liu and his colleagues looked for a contrast agent that would stick to this protein and make it easy to find for surgeons.

“This is a specific contrast agent that we believe is labeling the tumor cells very accurately,” Liu said. “Normal cells would not overexpress this particular protein.”

The transition from these animal models of medulloblastoma to human forms will likely involve considerable study. Cancers can be highly variable and Liu explained that he wouldn’t expect all medulloblastomas to express VEGFR-1.

While the contrast agent and microscope could be years away from use in an operating room, the choice of a topical chemical, rather than a dye injected into a patient, may expedite the review process through the Food and Drug Administration.

Using a dye means the overall dosage could be lower, which would limit the introduction of the dye into the patient’s circulation.

Surgery has not yet reached the point where doctors can choose single cells to remove, Liu offered. Many brain tumor margins are diffuse and the cells can infiltrate and migrate through the brain, he explained. The goal, however, is to give the surgeon better guidelines.

A patient typically goes through chemotherapy to handle the remaining tumor. When surgeons remove more of the tumor, the postoperative therapies are generally also more effective, he asserted.

While the contrast agent the Stony Brook scientist used is innovative, the strengths of the design come from building the three-dimensional microscopes.

Liu designed a tabletop system for the recent results that were published in Translational Oncology. He is also creating a miniature handheld version that would be considerably more compact, in the form of a pen-like device.

As either a tabletop version or a handheld type, the microscope is “highly customized,” he related. “There’s nothing there that you can buy and get off the shelf.”

At Stanford, Liu built a similar microscope for the gastrointestinal tract. At Stony Brook, he has a new grant to develop a microscope to help with the early detection of oral cancers.

Receiving approval from regulators to use the newest microscope designs in the brain will require careful steps to ensure the instrument remains sterilized.

“You have to be very stringent,” Liu assured. He may surround the microscope in a plastic sheath, as medical researchers have done with similar devices.

Liu lives in Port Jefferson with his wife, Evie, a violin teacher who works at the Stony Brook School and gives lessons from home. They are both of Chinese descent and grew up in Hawaii.

Liu is an amateur surfer and enjoys going to the South Shore when a storm along the coast kicks up larger waves.

If he weren’t a scientist, Liu said he might consider a career as a doctor. He appreciates a physician’s opportunity to have a positive impact on their patients’ lives.

Still, he recognizes that his translational research may one day help those same patients.

He takes over a team that has had a hand in everything from the creation of video games to the silicon drift detector (which is used in X-ray spectrometry and electron microscopy).

As the recently appointed head of the instrumentation group at Brookhaven National Laboratory, Graham Smith, who has led the Gas and Liquid Detector Group for 15 years, now takes over as the leader of 40 professionals, most of them scientists, engineers and technicians. Smith helps coordinate the development and refinement of technology designed to answer questions ranging from understanding why neutrinos have mass to determining the structure of complex protein molecules.

A part of the Nuclear and Particle Physics directorate, the instrumentation division also works with the other four units at BNL, which include Basic Energy Sciences, Photon Sciences, Global and Regional Solutions and Environmental and Life Sciences.

The division applies some of its work with gas-filled neutron detectors to national security. His group is developing instruments that can “identify contraband material being brought into the country,” which could include uranium or plutonium, he said. Those materials emit neutrons, which are hard to stop, even for a lead-lined shipping container.

“There are only certain materials in nature that are sensitive to neutrons,” he explained. “Hydrogen and Helium-3 are good at stopping thermal neutrons.”

The instrumentation division at BNL has collaborated with professionals in nonproliferation and national security to build neutron detectors that are many pinhole cameras in a single instrument, which can be placed at ports around the country to look for radioactive objects that generate neutrons.

The instrumentation division is also playing an important part in the Long Baseline Neutrino Experiment (or LBNE). The centerpiece of the LBNE will be a liquid argon detector and electronics that BNL’s expertise is making possible, Smith said.

BNL’s Milind Diwan (Power of Three, Jan. 10) has been working closely with the instrumentation group, as well as with the physics, chemistry, accelerator, nuclear engineering and magnet units at BNL.

“The instrumentation division is crucial because they are going to be responsible for the wire chambers and the electronics that must operate at very low temperatures and with a lifetime of several decades without any maintenance,” he explained. “The technological development is far-reaching and extraordinary.”

Diwan is confident the group is up to the task, suggesting that the Instrumentation Division is “considered the best in the world in developing such advanced technologies.”

Smith and his colleagues have also been involved in developing a medical imaging instrument called RatCAP (for Rat Conscious Animal Positron Emission Tomography).

It’s the same principle as a PET scan for humans. The innovation, however, is that it allows an animal to wear the monitor while engaging in its normal activities. Typically, animal PET scans have required anesthesia, to keep an animal still as scientists survey the brain or other areas of the body. The instrumentation group designed and integrated a detector system for annihilation gamma-rays that is compact, lightweight and low power, which benefits from microelectronics.

“When the animal is anesthetized,” suggested Smith, “the brain activity is compromised. The idea is to investigate brain activity without putting the rat under any drug-induced sleep.”

Smith lives in Port Jefferson with his wife, Anne, a teaching assistant at Setauket Elementary School. Their older son, Edward, works in Manhattan in information technology, while their younger son, Michael, is a building manager in Seattle.

The couple enjoy the similarities between the village of Port Jefferson and their home villages in the United Kingdom. They enjoy walking through town, grabbing a cup of coffee, observing the harbor and trekking back.

In addition to the potential professional collaboration with Stony Brook scientists, Smith also appreciates the chance to play squash at the university campus. He met his wife on a squash court when they were at the University of Leicester.

In leading the instrumentation group, Smith said he hopes to continue to create a positive atmosphere that he likens to an extended family.

As for following in the footsteps of William Higinbotham, who invented the video game “Tennis for Two” at BNL in 1958, Smith suggested: “My goal is to provide the motivation for our outstanding staff to continue making significant high technology contributions to new BNL programs, for a better understanding of nature and for an overall benefit to society.”

Finding new materials has been a field where industrious and determined workers mixed elements, hoping to come up with the right combination to form a structure that might meet their needs.

While their choices of ingredients weren’t random, their results often proved disappointing, as the process produced considerably more failures than breakthroughs.

About eight years ago, however, Artem Oganov tried to change that. He didn’t want to build a better workbench or come up with a way to test more materials in a lab. He wanted to come up with a more efficient approach. Armed with a computer and working in an office at Stony Brook University, Oganov hoped to improve the process.

Predicting the crystal structure of an element or molecule in its lowest possible energy state presented an enormous challenge.

“Mathematically, when you formulate this problem, it looks intractable,” explained Oganov.

“The number of possible structures can be boiled down to ten to the power of 20 or 10 to the power of 50. Technically, you can’t sample all those structures,” he continued.

In 2003, Swiss scientists developed a computational method called metadynamics. It provided the first hope that the problem of crystal structure prediction might not be totally hopeless. Still, the process had significant limitations, Oganov said.

Oganov and several graduate students over the years, including Colin Glass, Andriy Lyakhov, Qiang Zhu, Guangrui Qian and Salah Eddine Boulfelfel, attempted to create a computer program that would narrow down those possibilities.

When their first several efforts were unsuccessful, “we were ready to give up.”

By combining several innovative approaches, including uniting global optimization (looking for the most likely solution in the big picture) with local optimization (narrowing the choices down among more subtle differences), they came up with a program that worked.

“The whole trick is to invent an algorithm which can work efficiently and reliably for a nearly infinite size,” he offered. “The problem was so big that we were dreaming without really hoping to get it.”

Oganov’s work has become “the gold standard,” suggested Stony Brook Geosciences Chairman Richard Reeder. “Discovering structures before was kind of random trial and error. There’s no systematic way to do it.”

Using the computer model, Oganov and his team predicted that sodium would become transparent under pressure. They found a collaborator who would conduct the test and, as they predicted, the metal became transparent.

The Oganov lab also became involved in an important discovery about carbon. Under high temperatures and pressure, carbon becomes diamonds. Under the same pressure, but at room temperature, carbon becomes superhard, without turning into diamonds.

Scientists had made guesses about the structure of this superhard carbon, but had trouble narrowing down the list in part because of the low resolution of experimental data. Using his computer model, Oganov predicted its structure. With some experimental support, Oganov’s prediction of a so-called M Carbon proved accurate.

Because other forms of carbon have had applications in technology, Oganov suggested this form might become instrumental in future manufacturing breakthroughs.

Oganov’s discoveries “won’t be seen to be applicable immediately,” Reeder explained, but could impact a wide range of fields, from planetary sciences to drug design.

In his presentations about his work, Oganov includes numerous historical references.

Indeed, if he hadn’t become a scientist, the Russian-born Oganov would have become a historian.

“History,” he explained, “gives very valuable lessons of wisdom: what were the good decisions and the bad decisions people made. How does progress work? History gives you good perspective on that.”

It’s important, he suggested, for people to have historical role models. Some of his include Linus Pauling, whom he described as being the “greatest chemist of the 20th century,” as well as Lev Landau. A physicist, Landau could “throw more ideas on one page than in a whole book written by other people.”

Laudau worked on his couch, scribbling notes that became the basis for papers and books, including one that physicists are still using, Oganov said.

A resident of East Setauket, Oganov would like to become a role model to future generations.

Oganov’s chairman believes he already stands out in his field, not only for his accomplishments but also for his intelligence.

“He’s well on his way. His code is the best out there,” Reeder said. “He has the motivation and the drive to do it.”

This is the second in a two-part series that began last week on two scientists at Stony Brook Medical School who are working to unlock the secrets of different types of fungi that can cause significant health problems.

Like the cracks in the sidewalk that we don’t notice most of the time, Candida albicans is everywhere. Mostly, though, it’s on and around us. While this fungus is harmless much of the time, it has a dark side.

After prolonged catheterization (tubes entering the body) or in people with weakened immune systems, Candida can enter the bloodstream, where it can cause significant damage.

“It’s considered to be the fourth most commonly acquired hospital infection,” explained James Konopka, a professor in molecular genetics and microbiology at Stony Brook Medical School. It often targets the kidney. Even with current state-of-the-art antifungal drugs, Candida can become life threatening.

In most people, Candida often can’t get past the skin or the lining of the gastrointestinal tract. That, however, changes when, for example, patients have surgical procedures.

“A tube going into a patient can provide a site for a biofilm and can get it across the skin,” Konopka explained.

This can also be compounded, he explained, by the use of antibacterial drugs, which eliminate the bacteria and give the fungus more room to grow.

Patients with weakened immune systems, through AIDS, cancer treatments or immunosuppressive therapies, can also be the target of fungal infections.

Konopka is looking from the outside of Candida in, trying to alter the cell wall, or plasma membrane. Everything in the membrane is not randomly moving around, he explained. There are specialized sensors that can be instrumental in its life cycle.

He’s been studying genes that are responsible for 30 proteins in the membrane. He has deleted the genes for most of these proteins and plans to pick the best candidates for more study and drug development.

“If we disrupt the function of those proteins, that leads to a global defect in how the membrane is organized,” he said.

One of the challenges in fungal research is that humans and fungi are more closely related, evolutionarily, than humans and bacteria. On the positive side, that means research into basic cellular mechanisms of fungi may provide information about human cells.

On the downside, however, it provides a tricky type of Venn diagram for medical treatment. Doctors and researchers have to find drugs that only affect fungi and that don’t harm human cells at the same time.

The existing therapies have limitations. As with bacteria, some fungal strains have developed resistance.

Even finding a specific therapy that targets and eliminates Candida could lead to another unintended consequence. Because Candida lives within most of us without causing problems, eliminating all of the fungus could create an opening for an infection from another type of bacteria or fungus.

“There’s been some suggestion that that possibility may be occurring in certain patients in long-term drug therapy,” Konopka acknowledged.

He’s not convinced that’s the case, but it has caused some researchers to think Candida might be filling a niche that keeps worse invaders out.

The ideal therapy may involve a short-term treatment that clears Candida from internal organs, but resets the relationship to where the fungus lives within humans without doing any damage.

At the University of Washington in Seattle, Konopka had been doing basic fungal research under the guidance of Leland Hartwell, who shared the Nobel Prize in 2001 for discovering protein molecules that control the division of cells. When Konopka moved to Stony Brook, he transitioned to studying Candida.

In 2008, he discovered that deleting the proteins in the plasma membranes caused the cell wall to grow backwards.

“There’s a layer of regulation that keeps the cell wall on the inside,” he explained.

Konopka lives in East Setauket with his life, Susan Watanabe, a scientist who is studying HIV, the virus that causes AIDS.

He said he wades out into the water at West Meadow Beach, where he catches bluefish and striped bass.

As for working with fungus, there is an upside: yeast. In the fall, he hosts an Oktoberfest party for his entire building, where he and his guests sample each other’s home-brewed beer. Last fall, the offerings included Strong Island Ale, Rye Smile and Midnight Spice. Konopka provided Hoppy Oktoberfest, a beer he describes as a “classic,” which has “the taste of fresh grown hops, but brings with it a fair amount of sweetness.”