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Patricia Thompson photo from Stony Brook University

By Daniel Dunaief

Patricia Thompson gets a call from her sister Kathy Hobson when people in San Angelo, Texas — where Thompson grew up and where her sister and brother live — when someone has cancer. They want to know what Thompson thinks of their treatment.

While Thompson is not a medical doctor, she has been working as a scientist to develop ways to discriminate high-risk patient populations from low-risk patients to limit “toxic treatments in low-risk individuals” and improve the efficacy of aggressive treatment in high risk-patients. The goal, she said, is to better treat patients based on the specific pathobiology of their disease.

Thompson, who came to Stony Brook University last October as a professor of pathology and associate director of Basic Research at the Cancer Center, is pleased with the support from the university.

“There’s a real convergence of factors, including a strong commitment from the leadership, the Simons Center and the university medical school faculty and staff at Stony Brook,” she said. “We all want to see the Stony Brook Cancer Center bring prestige to our community, attract the finest talent in cancer research and clinical care and attract innovators and job builders.”

Thompson said Cancer Center Director Yusuf Hannun, Medical School Research Dean Lina Obeid, Pathology Department Chairman Ken Shroyer, and Dean of the Medical School Ken Kaushansky have all led the charge.
Shroyer is pleased Thompson joined the effort. “Bringing her here was an incredible coup,” he said. She brings “real national prominence” and led one of the “most important clinical and translational research programs in breast and colorectal cancer.”

Thompson is committed to furthering her own research studies, while balancing between critical basic science discoveries and their clinical impact.

For some scientists, she wants to assist researchers as they move from the bench to the first human study. She helps them understand who needs to be involved to advance a potential diagnostic tool or novel treatment.

Still, she endorses the benefits of basic research. “Application is always an important long-term goal, but scientific exploration for new discovery is critical to advancements,” she said. Applied and basic research are “neither mutually exclusive approaches.”

Thompson studies colorectal and breast cancer because both have an inflammatory component and an immune element. She’s exploring what is shared between these two cancers as common targets for prevention and treatment.

Colon cancer provides a window that helps scientists and doctors understand the way cancer progresses.
“Our ability to study the premalignant to malignant progression in colorectal cancer has provided important basic knowledge of how cancers develop and taught us about how cells defend against tumorigenesis and how these systems fail,” she said.

Thompson went through some formative professional and personal experiences during graduate school that shaped her career. In the mid-1990s, she was studying an autoimmune disease in which she worked on an animal model with a neuroimmunologist.

“I wanted to know that all this work I was doing with animals was contributing to the disease in humans,” she said.

Around the same time, her father, Jim Thompson, who owned and operated Angelo Tool Company, learned he had stage IV colorectal cancer. He was diagnosed in 1995, before major advances in colorectal cancer treatment. Her father received compassionate care use of a new therapy, enabling him to live for three more years, considerably longer than his initial two-month prognosis. If he had been diagnosed five years later and received a platinum-based regimen, he would have “gained even more time,” she said.

Thompson said she and her family struggle with the fact that her father showed symptoms he kept to himself, largely out of fear. If his cancer had been detected earlier, she believes it is likely he could have been cured.

She suggests people not be “afraid of a cancer diagnosis” and recommends “routine screening” and consultation with a doctor if they show symptoms.

Thompson lives in Rocky Point with her husband, Michael Hogan, who is the vice president of life sciences at Applied DNA Sciences.

As for her work, Thompson believes her research might help physicians and their patients.
Her research aims to develop “diagnostic tests that help in prognosis” while identifying “patients that may achieve more benefit from aggressive chemotherapy,” she said.

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John Haley photo from SBU

By Daniel Dunaief

Once they reach their destination, they wreak havoc, destroying areas critical to life. All too often, when cancer spreads, or metastasizes, through the body, it becomes fatal.

John Haley, a Research Associate Professor in the Pathology Department at Stony Brook, is trying to figure out how cancer become metastatic and, even further, what they do to avoid recognition by the immune system.

Haley is “working on the mechanisms by which metastasis occurs,” he said. He is also studying the “immune recognition of tumor cells and, in the near future, wants to link the two.”

Understanding the way metastasis works can greatly reduce mortality in cancer, Haley said. Researchers are currently attempting to develop therapies that target metastatic cells, but these are often more difficult to kill than their primary counterparts, Haley explained.

The stakes are high, as 90 percent of cancer deaths are due to complications from the spread of cancer rather than the primary tumor itself, he said.

About 80 percent of human cancers are carcinomas, which are derived from epithelial cells. Those are the cells that make up the skin, and line the stomach and intestines.

“As cancers become metastatic, those cells have the ability to shape shift,” he said.

They become much more like fibroblasts, which are underneath the skin and glue the skin to bone and make up connective tissue layers. Haley said he has made some progress in understanding the molecular mechanism that allows cells to shift from epithelial to fibroblastic cells. They have “defined factors which promote” this transition, with differences in survival and growth pathways.

Haley works with a machine called a mass spectrometer, in which he identifies proteins in complex biological samples and measures how changes in composition alters function. He spends about half his time working on his own research and the other half assisting other researchers who are seeking to get a clearer view of key changes in proteins in their work.

In his own research, he wants to understand how cancers modify a cell’s proteins. He has helped define how cancers can change their protein signaling pathways to become drug resistant, which suggests targets for drug therapies.

Haley is tapping into an area of science that many other researchers are exploring, called bioinformatics. Using statistics and mathematical models, these scientists are cutting down on the number of genes and proteins they study, honing in on the ones that have the greatest chance to cause, or prevent, changes in a cell.

“We’re taking the data sets we’ve generated and trying to predict what we should look for in human patient samples,” Haley said. “We can find a tumor cell that have mutations or this expression profile and find drugs they are sensitive to.” Once scientists find those drugs, researchers can test them in cell cultures, then in mouse models and eventually in people, he said.

“We try to isolate someone’s cancer to understand what the molecular drivers are that occur in that cancer,” Haley said. The approach, as it is much of modern medicine, is to understand the patient’s genetics and biochemistry to select for a drug that would be effective against the particular mutations present in their tumor.

A resident of Sea Cliff, Haley is married to Lesley, whom he met while he was pursuing his PhD at Melbourne University. A native Australian, Lesley was completing her Masters in Opera when the couple met at a tennis match. They still play today. Lesley has sung at New York premieres for several living composers at concert venues including Avery Fischer Hall. She teaches music at her studio in Sea Cliff. Their children share their interests. John is a freshman studying biochemistry at Stony Brook University and Emma, who is a senior at North Shore High School, plans to study science and singing.

As for his work, Haley would like to see his efforts culminate in cancer therapies and diagnostics. Any novel therapy might also become a product for a start up company which could create jobs on Long Island. “There are some fabulous scientists” at the university, he said. “A major goal of the Center for Biotechnology and Diane Fabel, its director, is to create small businesses here in New York. I’m trying to help them in that goal.”

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Scott Powers with his wife Diane at a recent Cancer Research Gala. Photo by Julie Skarratt

By Daniel Dunaief

He spent 20 years looking at the problem in one way. Now, he’s ready for a change and Stony Brook officials stand behind him. After working in genomics at several locations, including for a decade as director of human cancer genomics at Cold Spring Harbor Laboratory to find therapeutic targets for human tumors, Scott Powers recently embraced the opportunity to find better ways to diagnose different types of cancer.

“A major driver for me coming to Stony Brook was to work on earlier detection,” Powers said.

Working with pathology department Chairman Ken Shroyer and Stony Brook obstetrician/gynecologist Michael Pearl, Powers is hoping to develop a prototype test for early detection of ovarian cancer so it can be removed by “simple surgery,” he said.

Powers has worked in numerous ways to isolate or identify mutations that might lead to cancer. That work focused on finding drug targets or developing therapies. One of the many challenges in studying genomics is that some mutations are bystanders, which means they likely don’t have a role in causing cancer or even, necessarily, in enabling cancer to spread. They make it harder to know whether they have a role or are merely different from the range of normal in a genetic sequence.

Some of the ways Powers has understood the potential part mutations play is by taking a computational approach, which can take many forms, including finding gene networks that are frequently altered. This approach has helped find various targets for therapies and improve the classification of tumors.

Powers said the “poster child” for success of this method was the development of the Oncotype DX test for breast cancer, which allows patients with node-negative, ER-positive breast cancer to determine whether they need to take chemotherapy.

He has also compared the gene sequences for similar cancer types across different species. He and Scott Lowe, who is now at Memorial Sloan Kettering Cancer Center, found this approach could “help identify drivers and, in a sense, help filter out passengers,” he said. This has been successful on a basic science level but hasn’t yet led to the identification of a viable new therapeutic strategy, he said.

Powers’ focus now is to direct his expertise toward developing a test that might address early detection and, in some cases, improved diagnosis.

“It’s a brand new set of things for me to think about,” Powers said. The effort, he believes, should prove reinvigorating. The intellectual challenge of coming up with a solution that improves or enhances someone’s life motivates him.

Powers supports Stony Brook’s effort to add staff and develop a pool of researchers who can develop techniques and tools to aid in the diagnosis and treatment of cancer. “I am very hopeful for Stony Brook to build up an intellectually interesting environment that will attract a new generation of cancer scientists to come on board,” he said.

Powers believes cancer is a complex disease that has many different variations. “Many random events occur that sometimes give the cancer cell a competitive survival advantage,” he explained. “Everyone’s tumor has its own unique combination of 10 to 25 genetic alterations that are driving it.”

In addition to working with Shroyer on developing diagnostic tools for the genomics of cancer, Powers has turned his attention toward other researchers on the campus with different backgrounds. He is planning a collaboration with Sasha Levy, who works at the Laufer Center for Physical and Quantitative Biology and is an assistant professor of biochemistry and cell biology, to study cancer evolution. He said they’ll be using experimental methods Levy has developed on yeast.

Yusuf Hannun, the director of the Cancer Center, has recruited Powers to participate on the tumor board, which is where physicians from different areas come to discuss specific patients in a multidisciplinary fashion.

“There are numerous discussions and plans to expand upon this growing trend to use genetic testing in developing a personalized strategy for each patient,” Powers said.

Powers and his wife Diane, who works in fundraising with Patricia Wright at Stony Brook in the anthropology department, live in Greenlawn with their daughter Camille, who is a sophomore at Harborfields High School. Their other children are Alexander, 25, who works for a nonprofit in Brooklyn called the Social Science Research Council, and Douglas, 21, who is a junior studying applied math at Harvard.

Powers was looking for two things that he found when he came to Stony Brook: “the chance to develop diagnostic tests” and to “enter new fields by finding new collaborators with scientists doing interesting things.”

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Geoffrey Girnun hiking in the White Mountains of New Hampshire. Photo from Girnun

By Daniel Dunaief

He hopes to use their addictions against them. By taking away what they depend on for survival, he would like to conquer a disease that ravages and, all too often, kills its victims.

Geoffrey Girnun, an associate professor in the pathology department and the director of cancer metabolomics at Stony Brook University, is looking closely at the addictions cancer has to certain pathways that normal cells do not. “It is really about starving the cancer,” he explained. “Perhaps what you feed the patient can starve the cancer.”

Cancer has a ramped-up metabolism that handles nutrients differently, Girnun explained. Differences between normal cells and cancer can provide scientists and doctors with opportunities to develop selective treatments.

Using mouse models, Girnun is exploring the role of different proteins that either promote or prevent various cancers. Recently, he has been studying one particular protein in the liver cell. This protein classically regulates the cell cycle, which is why finding it in the liver, which has non-dividing cells under normal conditions, was unusual.

Girnun discovered that it promotes how the liver produces sugar, in the form of glucose, to feed organs such as the brain under normal conditions. In diabetic mice, the protein goes back to its classic role as a cell cycle regulator.

“We’re using genetic and pharmaceutical mechanisms to dissect out whether increases in liver cancer associated with obesity in diabetics is dependent on this protein,” Girnun said. If he and other scientists can figure out how the protein that functions in one way can take on a different role, they might be able to stop that transformation.

“It’s like a linebacker becoming a quarterback,” Girnun said. He wants to figure out “how to turn it back” into a linebacker.

Girnun is exploring the metabolic pathways and signatures for liver cancer. If doctors are targeting one particular pathway, they might develop “personalized therapy that would help avoid treatments that wouldn’t be effective.”

Girnun’s peers and collaborators said he has contributed important research and insights in his laboratory.

Girnun is “considered a rising star, especially in the area of the downstream signaling events that modulate gluconeogenic gene expression,” explained Ronald Gartenhaus, a professor of medicine and co-leader of the Molecular and Structural Biology Program at the University of Maryland Cancer Center. Gartenhaus, who has known Girnun for seven years and collaborated with him, said metabolomics is “rapidly exploding with novel insights into the perturbed metabolism of cancer cells and how this information might be exploited for improved cancer therapeutics.”

What encouraged Girnun to consider the professional move to Stony Brook was the opportunity to create something larger. “I want to build a program in cancer metabolism,” he said. “I want to build something beyond my own lab.”

When he first spoke to the leadership at Stony Brook, including Ken Shroyer, the head of the pathology department, Yusuf Hannun, the director of the Cancer Center, and Lina Obeid, the dean of research at the School of Medicine, he felt as if he’d found a great match.

Girnun has been so busy working with other researchers that managing collaborations has become a part-time job, albeit one he finds productive and exciting.

Hannun said Girnun has identified “key investigators who are working on developing the field of nutrition and metabolomics.” Girnun is heading up a symposium on May 13th that focuses on innovations in basic and translational cancer metabolomics. The keynote speaker is Harvard Professor Pere Puigserver.

While Girnun changed jobs, he hasn’t moved his family yet from Baltimore. Every week, he commutes back and forth. Girnun and his wife Leah have five children, who range in age from preschool to high school. He hopes his family will move within the next year or so.

Girnun enjoys Stony Brook, where he said he has an office that overlooks the Long Island Sound and where he can run. When he’s hiking on Long Island, he said he has a chance to “think through my experiments.”

His commute from several states away shows “how much I was sold on Stony Brook,” he said. “We believe Stony Brook is moving up to the next level.”

He remains focused on the applications of his research toward people. “Something may be cool mechanistically, but, unless it’ll have a biologically meaningful result and affect how patients are treated or diagnosed, to me, it doesn’t matter,” he said.

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Counterclockwise from front row left, John Haley, Geoffrey Girnun, Scott Powers and Patricia Thompson. Photo from Stony Brook University

When local teams bring in superstars, the typical sports fan salivates at the prospect of winning a national championship. At the player level, success often breeds success, as other stars and talented players are eager to join teams where they believe in the philosophy of management and the talent of their teammates.

With considerably less fanfare to the typical Suffolk County resident, Stony Brook University has lured some promising researchers from around the country to its growing pathology department. What’s more, the newest members of the team not only have big plans for themselves and their department — they want to help Long Islanders who are battling cancer.

Their research aims to give doctors tools to make a more informed cancer diagnosis, create jobs by developing start-up companies and contribute to the Cancer Center’s goal of receiving a National Cancer Institute designation, which would allow Stony Brook to bid on multimillion dollar grants.

“We are looking for new ways to advance the practice of pathology that will improve the quality of health care nationwide and worldwide,” said Ken Shroyer, the head of the pathology department.

When Shroyer arrived in 2007, he said his first goal was to bring together the talent that was already working at the university. Like siblings who grow apart after they leave home, the clinical research and basic research efforts were working in parallel, rather than together.

After finding common ground for those groups, Shroyer added staff on the clinical side. His next priority, he said, was to boost the research department, which had only one externally funded investigator. That number now stands at 12, with four of the new staff coming in the last 18 months.

The newest researchers joined the pathology department and became leaders in the Cancer Center. “Each of these four individuals has a national reputation and special expertise in a particular area of cancer research,” Shroyer explained, saying he combed the research landscape to find the right experts in their field.

For their part, the new staff share an enthusiasm for the department and a vision for where it’s heading. An expert in finding biomarkers that help identify patients at risk of cancer recurrence, Patricia Thompson plans to encourage basic scientists to make discoveries that affect patient care.

Geoffrey Girnun, meanwhile, continues to study how cancer’s metabolism works, hoping to find differences between cancer cells and normal cells that can become targets for intervention and therapy.

After two decades searching for therapeutic targets for cancer, Scott Powers shifted gears and is now looking for ways to detect cancer earlier.

John Haley is concentrating on exploring how cancer cells escape detection from the immune system and become metastatic.

The director of the Cancer Center, Yusuf Hannun said the partnership with the pathology department is “key to bridging basic research discoveries to cancer specific research and then to human applications,” which could include biomarker discoveries, new therapeutics and individualized and personalized genomic cancer research.

Hannun believes the Cancer Center will continue to push the envelope in diagnosis, treatment and prevention. “We want to bring more special and unique abilities in the war against cancer,” Hannun said. “The inroads in cancer are happening.”

Stony Brook could become involved in prevention, where doctors and scientists work with patients before they develop any signs of the disease. “That domain is clearly within the scope of the Cancer Center,” Hannun said. “We are working on novel biomarkers that could detect very early cancer.”

Hannun described Shroyer as his “alter ego” in the Cancer Center. “He is a very capable leader and does very exciting cutting edge research with a steeped history in early diagnostics.”

Shroyer focuses his work on the discovery of biomarkers that can be used to improve diagnostic accuracy, provide prognostic information and identify more effective treatments for cancer, he said.

Five years from now, the success of the effort will be reflected by the extent to which the group can enhance the national standing of Stony Brook Medicine and the Cancer Center as leading institutions in basic and translational cancer research, Shroyer said.

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Emily Krainer can hear the excitement in her father’s voice when she calls. After she gets off the phone, she tells her classmates about his work, which, one day, could influence their lives. Like Emily, they attend Vanderbilt University School of Medicine and, once they graduate, may use his work to help their patients.

The younger Krainer has “high hopes” for a promising new treatment her father developed for a potentially fatal disease.

Adrian Krainer, a professor and program chair of Cancer and Molecular Biology at Cold Spring Harbor Laboratory, has developed a drug for a pediatric neurological condition called spinal muscular atrophy, which is the leading genetic case of death among infants and affects about 1 in 6,000 newborns.

The drug, called an antisense oligonucleotide, is in phase III trials, which is the final stage before the Food and Drug Administration considers approving it.

SMA is a genetic disorder caused by a defective SMN1 gene. Patients with SMA rely on the SMN2 gene, which can produce normal survival of motor neuron protein but in low quantities because alternative splicing results in a shorter, unstable form of the protein.

Splicing is the process where important genetic information, exons, are joined together, while less important genetic parts, introns, are removed. The process starts with an RNA that is a copy of the gene, Krainer explained. For the SMN2 RNA, splicing leaves out the next to last exon. Krainer has found a way to encourage the splicing machinery to include exon 7 more efficiently.

These phase III trials involve two separate groups of patients. The first includes infants with type 1 SMA, which is the most severe version and has an average life expectancy of two years. Working with Isis Pharmaceuticals in California, doctors in these clinical trials will determine if the drug increases survival and reduces the need for ventilation.

In the second group, patients who are from two years of age up to 14 with type 2 SMA, which is an intermediate form of the disease, will receive the drug. Doctors will monitor improvements in neuromuscular function, Krainer said.

His Ph.D. advisor at Harvard, Tom Maniatis, praised his former student.

“This is beautiful and highly original work, which has already shown great promise for SMA therapy,” explained Maniatis, who is now chairman of the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center.

While Krainer is awaiting results of these trials, he is making new discoveries that may also affect future treatments.

In mouse models of SMA, Krainer has found that injecting the drug under the skin was even more effective than inserting it directly into the spinal chord.

Additionally, neutralizing the drug in the central nervous system didn’t prevent its effectiveness. The drug enabled spinal chord motor neurons to continue to function, even when it wasn’t active in that area.

“Surprisingly, the effect of the drug given that way is still dramatic,” he said.

Krainer cautioned that results in mice may not display a similar pattern in humans.

Still, the mouse data suggest treatment with this drug might be more effective if administered beneath the skin.

If this drug becomes an accepted treatment for SMA, the approach of creating a synthetic antisense oligonucleotide could also become an effective weapon against other diseases, such as familial dysautonomi, in which a mutation causes a reduction in the expression of a protein.

“It is estimated that 10 to 15 percent of all human disease causing mutations affect RNA splicing, so the tool [Krainer] has developed should have wide applications,” Maniatis suggested.

Maniatis has seen firsthand how Krainer has “a deep passion for science and a strong work ethic. More importantly, in my view, he has an incisive critical mind, which leads to the development of novel approaches and rigorous science.”

In addition to Emily, Krainer has two sons: Andrew, 22, who is in his last semester at CUNY-Baruch College, and Brian, 20, who is a junior at Carnegie-Mellon.

When she was young, Emily Krainer said she met children with SMA at conferences. These interactions “shaped my interest.”

Emily said her father is a role model and “hopes whatever I do in the future, I enjoy as much as he enjoys his work.”

As for the drug trials, the younger Krainer said her fellow future doctors want to know how this treatment works. She said her classmates hope he is “going to change the lives of so many patients.”

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In winters like this one, most people focus on the weather for the day or week. That’s not the case for Minghua Zhang, who is much less concerned about whether to buy more salt for the next snowstorm than he is about global changes in the weather over the last 100 years.

The dean of the School of Marine and Atmospheric Sciences at Stony Brook University, Zhang studies weather around the globe, exploring changes in temperature, precipitation, clouds, convection and atmospheric and oceanic circulations.

Working with a team of scientists from Britain, Switzerland and Germany, Zhang recently discovered that the industrial revolution has had severe consequences in the northern tropics in the Atlantic.

Zhang, who worked with graduate student Tingyin Xiao on the study, said precipitation in that area decreased by 10 percent in the last 100 years. This decrease could have implications for farming in Central America, experts said.

“These findings may help to reveal shifts in seasonal rainfall in Central America, which is critical for agriculture in the area and may, therefore, have potential impacts on agricultural and environmental policies in the region,” wrote Provost Dennis Assanis in response to emailed questions.

Zhang said sulfate aerosols in the atmosphere moderated temperatures in the northern hemisphere by reflecting radiation from the sun. This shifted the intertropical convergence zone, which is a tropical rainfall belt near the equator, toward the southern hemisphere.

Led by Harriet Ridley from the Department of Earth Sciences at Durham University in the United Kingdom, the scientists published their work in the journal Nature Geoscience.

Zhang addressed the challenge of predicting or understanding global patterns even as computer models, which are at the center of predicting and understanding weather, raised alarms in New York City for a record-breaking blizzard that never came.

“The fluid system is chaotic,” he suggested, “which prevents a deterministic prediction with long lead time.”

The predictive ability of the model for approaching storms are limited by the computing power to resolve key processes, the lack of understanding of turbulence and condensed water processes, such as ice crystal aggregation and the lack of sufficient data in remote areas, such as over the ocean.

“In the short term, the weather is chaotic and there is a limit” to how well these models predict the movement of approaching storms, he said.

More broadly, Zhang, whose research contributed to the Nobel Peace Prize in 2007 headlined by former Vice President Al Gore, said his research goal is to improve global climate models.

“We have uncertainties in the models, especially those related to clouds,” Zhang said.

Indeed, despite advances in technology, computers are still not powerful enough to resolve large cloud systems, he said. The current fastest computer in the United States can do about 27,000 trillion calculations per second, he said, which is the equivalent of the speed of about one million desktop PCs. That only resolves the climate in units that are about 25 kilometers apart.

Zhang said the scientific understanding of liquid clouds is much better than before, but the knowledge of ice clouds in a turbulent environment is “still not sufficient.”

When he’s not conducting research, Zhang oversees a school that has 120 faculty and staff, with about 150 graduate students and 350 undergraduates.

While the Ph.D. program is ranked sixth in the category of marine and atmospheric sciences by the National Research Council, Zhang wants to continue to move up the ladder. He also wants to improve the teaching at Stony Brook and has put the syllabus for all the courses on the website and  urges all faculty to be involved in advising undergraduate students.

Zhang has established a faculty mentoring program that allows junior faculty to receive tips from senior faculty.

Zhang “has helped to grow the school” of faculty that are “working together to better understand how our marine, terrestrial, and atmospheric environments function and are related to one another,” Assanis explained in an email. “The current expertise [at the school] places them in the forefront in addressing and answering questions about immediate regional problems, as well as long-term problems relating to the global oceans and atmosphere.”

Zhang and his wife Ying live in East Setauket, where they raised their daughters Grace, who is studying art at Brown University, and Harley, who works for the Singapore branch of a consulting firm based in New York.
Born and raised in China, Zhang said that, in his rare free time, he enjoys visiting the beaches through all the seasons.

As for his work, Zhang finds his role as the dean of the school and as a researcher rewarding. In his research, he focuses on “improving the mathematical formulas that go into the models.”

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Looking through binoculars from the bleachers at a baseball game, at an eagle as it alights on a distant tree or at a constellation in a cloudless night are all much easier with a clear lens. A smudge, crack or even a hair on the lens can make that long-distance gazing considerably more challenging, as the images become blurry and our eyes struggle to interpret the difference between what’s out there and the defect in our binoculars.

The same holds true for radiation detectors. Constructed with bars of crystals, the detectors have applications in everything from medical imaging to see tumors to peering deep into the universe for signature radiation signals to detecting the movement of nuclear materials to help prevent an attack or accident.

A significant challenge with these detectors has been the defects that appear as the crystal grows. Scientists work on two fronts to deal with these imperfections: They improve the quality of the crystals, and they develop ways to compensate for the imperfections.

At Brookhaven National Laboratory, physicist Aleksey Bolotnikov has made significant contributions to improving detector performance despite the flaws in the crystal.

“We veto the interactions in the ‘bad’ regions of the crystals,” Bolotnikov explained.

Working with a team of scientists at BNL, including Giuseppe Camarda, Utpal Roy, Anwar Hossain and Ge Yang, Bolotnikov has been able to measure the coordinates of these defects with high accuracy. This allows the researchers to improve the detecting capability and reduce the cost by increasing the acceptance rates of the crystals.

Recently, Bolotnikov authored a paper in Applied Physics Letters in which he increased the size and thickness of the crystals. The thicker crystals are important in detecting weak sources.

Bolotnikov has “been able to establish new records for the thickness of semiconductor gamma-ray detectors operating at room temperature,” offered Ralph James, who heads Bolotnikov’s department and has collaborated with him ever since he arrived 20 years ago. “This is a critical step in the move to replace many traditional radiation-sensing instruments used today.”

The biggest market for these detectors with thicker crystals is in nuclear medical instruments for oncology and cardiology, James said.

Bolotnikov explained that the team at BNL combines researchers with expertise in a range of areas. Roy grows the crystals, while a group from the instrumentation division led by Gianluigi De Geronimo facilitates the work as a “top expert in readout electronics.” By tapping into his expertise in nuclear physics and nuclear engineering, Bolotnikov is  also able to design and develop new detectors.

James credits his colleague with significant advances in detector technology. “His new position-sensitive device design has rendered outstanding results that have approached the theoretical limits for energy resolution,” James said.

The work of Bolotnikov and the team has earned them national recognition. Bolotnikov was a part of three R&D Magazine’s R&D 100 Awards, in 2006, 2009 and 2014.

Last fall, he received the Room Temperature Semiconductor Detector Scientist Award from the Institute of Electrical and Electronics Engineers. The award recognized a scientist who had done the most to impact room temperature semiconductor detectors and could be given either for a lifetime of work or for a single accomplishment.

The award is “well earned,” James said. Bolotnikov’s votes among the awards committee “surpassed others by far.”

Like other members of his team, James said Bolotnikov works most waking hours. “I can count on a quick response from him via emails during the evenings,” James said.

Born in a small city near Moscow, Bolotnikov first came to Long Island around 1991. He now lives in Setauket with his wife Mila, who is a teacher for North Shore Montessori. His daughter Dasha works at BlackRock, while his son Vassili works for a small management company affiliated with Stony Brook Hospital.

Bolotnikov, who said he enjoys his work, suggested that the effort to improve technology generates new ideas, which “creates the new background or basis for writing proposals for the next cycle of work.”

Bolotnikov continues to work on increasing the size of the crystals in the detectors. At some point, the larger sizes can become prohibitively expensive. An alternative, he suggested, is to use gamma-ray focusing optics, concentrating gamma rays coming from large areas toward a reasonably sized detector. “This, he said, “is a new horizon.”

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If imitation is the highest form of flattery, there should be plenty of blushing moths. A group of scientists is working on a new way to create a structure similar to the moth eye, albeit with several important differences, to build a better solar cell.

Unlike human eyes, the compound moth’s eyes have a collection of miniature posts across their surface.

These posts allow the moth to absorb a wide range of light without reflecting it back. This prevents the “moth in the headlights” appearance, enabling the insect to blend in without sending a reflection predators might notice.

While Lord Rayleigh worked out the mathematics for why the moth eye geometry eliminates reflection in the 1800s, a team at Brookhaven National Laboratory has come up with a new approach to creating an anti-reflective silicon.

“Our advance is in coming up with a tricky new way” to make a silicon surface that absorbs instead of reflects light, said Chuck Black, a scientist and group leader at the Center for Functional Nanomaterials at BNL. “We think it has practical advantages in applying this” to things like solar cells or even, some day, anti-reflective windshields on cars or windows in buildings.

Companies have been using multilayer coatings to increase the ability of silicon solar cells to absorb light. By etching a nanoscale texture onto the material, researchers including Black and Atikur Rahman, a postdoctoral researcher, were able to create an anti-reflective surface that works as well as multilayer coatings, while outperforming single antireflective film by about 20 percent.

The researchers coated the top of a silicon solar cell with a substance Black has worked with for more than 15 years, called a block copolymer. The advantage to this substance is that it can self-organize into a surface pattern with dimensions of only about 10 nanometers. This pattern enabled the development of posts that are similar to those of a moth’s eyes, even though the features in their structures are much smaller than those in the insect eye.

The challenge in trying to reduce reflections is that sunlight has a wide range of colors at different wavelengths. Substances designed to absorb one color won’t be as effective at capturing a different one.

That’s where the moth enters the picture.

“Nature has learned how to create this anti-reflection,” by using spikes, Black said. “This promotes anti-reflection not just in one but in all wavelengths of light.”

The way this works is somewhat akin to the proverbial frog in a pot of water. In the frog story, a frog sitting in a pot of water that slowly heats up doesn’t jump out of the water even when it’s boiling because it’s adjusted to the changing temperature. Similarly, these spikes draw light of different wavelengths in because the distances between them are all smaller than the wavelength of light. The light effectively reacts to their average properties, Black explained.

When the light travels through these spikes, which are not cylindrical but, rather are thinner at the top and flair at the bottom, it reacts as if it hits something that is a combination of something small and insignificant and air. As the light travels towards the silicon surface, it interacts less with air and more with the spike, where it becomes absorbed by the thicker base before it can reflect back out.

“You’re softening this transition between air and whatever you’re trying to couple the light into,” Black said. Instead of a sharp boundary between the air the light is traveling through and the surface, the spikes ease that interaction, gradually capturing the light.

To demonstrate its effect, Black held a small photograph of his lab above a reflecting surface in which a small square is coated with the anti-reflective material. In the reflection, the square with the anti-reflective substance appears black.

Black and Rahman, who was the lead author on the study, published their results in Nature Communications. They don’t know whether this approach is more economical or efficient than the current multilayer coating for solar cells. They are working with external partners to understand the economic or performance advantages of this approach, he said.

Black and his wife Theresa Lu, who is a physician scientist at the Hospital for Special Surgery, live in Manhattan with their two primary school children, Marina and Charlotte.

As for his work, Black and Rahman filed a patent for this technology last year. “It’s something we’re very proud of,” he said.

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In the blistering heat of the summer, when the three H’s — hazy, hot and humid — dominate the weather forecast, people gravitate toward the refreshing stream of comfort from an air conditioner. Similarly, when a polar vortex descends, people seek the warmth from a heater to help unfurl frozen fingers.

Ya Wang, an assistant professor in the Department of Mechanical Engineering at Stony Brook University, is working on a type of vent that will direct the soothing air toward people wherever they are, whether they’re cozying up on a couch, dropping down at a desk, or resting in a recliner.

Teaming up with professor Lei He and professor Qibing Pei at the University of California, Los Angeles, Wang and her partners recently received a $2 million grant from the U.S. Department of Energy for a proposal that will make the vents for these air conditioners and heaters more efficient, lowering the cost to heat or cool a room.

Wang and her collaborators are developing a vent that will enable the air conditioner or heater to work less hard at changing the temperature in the parts of a room where a filing cabinet, a ficus tree, or a fireplace is, targeting the soothing air at the room’s occupants.

The new vent could generate 30 percent savings through such directed flow, SBU estimates. “We can regulate the airflow velocity by a special design and adjust the temperature to whatever is needed,” Wang said. “This will adjust automatically to regulate the airflow velocity back to the occupant.”

Wang is the principal investigator on the project, which means she collaborated on the idea and put it together.

Unlike academic funds, which require researchers to conduct experiments and produce data, this grant was awarded to produce a product.

Aside from coordinating the effort, Wang will also focus on developing the harvesters, which will provide a power supply for the on-board sensors and actuators. Wang and her collaborators estimate a cost of less than $20 per unit, with a $60 per year per unit electricity savings.

Jeff Ge, chairman of the Department of Mechanical Engineering at SBU, said Wang is one of six new faculty members hired in the past two years. He said she received positive reviews for her research and teamwork.

“The work of Dr. Wang and her colleagues to enhance energy efficiency is one of the most important research endeavors for our state and society,” Samuel Stanley, president of SBU, said in a statement.

Apart from her work on the new vent, Wang spends about a quarter of her time teaching, 65 percent of her time on academic research, advising graduate and undergraduate students, and about 10 percent of her time in community service. She participates in a seminar for women in science and engineering, and encourages women to enter these fields.

She is working through other grants on energy-related research. With the U.S. Department of Transportation, she is developing ways to tap into the vibrational energy from subway trains and from the wind these cars generate to power sensors that monitor the track. As it stands, the DOT sends people to the tracks to make sure they are functioning correctly. By reusing other forms of energy, the department can create a more extensive monitoring system that won’t involve as many potentially hazardous trips onto the tracks for transit workers.

Wang said soldiers in the field often carry a few hundred tons of batteries to power electronics and communication systems. She is working with the U.S. Navy to generate power by walking or running. To be sure, that won’t provide all the necessary energy, but it can supply some of the power for electronics or communications.

A Smithtown resident, Wang woke up one night to the sounds of her smoke alarm battery indicating it needed replacing.

She’s working on a circuit that will use vibrational energy for the detector. She has a one-year old nephew and sees an opportunity to create batteries that tap into vibrational energy or the temperature difference between a toy and the air to provide power.

With all her interests in energy for commercial applications, Wang would be a compelling candidate to work in industry. Why, then, did she choose to come to SBU, an academic home where she’s worked for 18 months?

“My dream, since I was a kid,” in Shandong Province in China, was “to be a teacher,” she said. “I enjoy working with new students.”

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