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.”

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.”

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.

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.”

The solar panels on his house in Dix Hills help provide about a third of the energy he and his family use. When he drives around Long Island and sees plumes of smoke from power plants, he looks to see where it’s heading.

Energy and environmental conservation aren’t just hobbies or personal philosophies ­— they are part of what Vasilis Fthenakis teaches as a senior scientist at Brookhaven National Laboratory and an adjunct professor at Columbia University.

Fthenakis helped improve the environmental impact of solar cells, working several years ago to eliminate lead, which can be dangerous to humans and to the environment, from the manufacture of solar panels. He has helped guide the industry to minimize the environmental, health and safety risks of solar cells.

Fthenakis recently returned from a trip to Chile, where he is encouraging the use of solar panels in a country that is often bathed in sunlight. “It’s the best place in the world for solar,” he said. It rarely rains and most of the land that is available for installation is up on high altitudes, he said.

Fthenakis, who was born and raised in Greece, has worked for about a year with several Chilean organizations to discuss the benefits and realities of solar energy.

Chile now imports coal, natural gas and diesel fuel. If the country produced its own energy, it could cut its energy costs, he said. It could take up to five years to see significant effects on the national economy, he estimated.

The South American nation has been ramping up its solar efforts. A few years ago, Chile generated no power from sunlight. That rose to 10 megawatts in 2012, 189 megawatts in August last year and currently stands at about 500 megawatts.

“We’re talking about tremendous growth,” Fthenakis said. Chile has a plan to boost renewable energy, which includes solar, wind and some hydroelectric plants, to 12 percent by 2020 and 20 percent by 2025. Fthenakis believes solar will be the biggest constituent in the mix.

While Chile doesn’t have the same oil, gas, coal and nuclear lobbies as the United States does, it does present some challenges to boosting solar energy, including inertia, Fthenakis said. “Most people don’t want to change,” he added, including people in other countries around the world.

In 2008, Fthenakis and two other authors wrote a cover story for Scientific American, titled “A Solar Grand Plan,” about the benefits and reliability of solar energy. At the time, solar was contributing 0.1 percent of energy to the capacity in the U.S. That number has climbed to 2 percent.

The article was translated into 11 languages and has raised his profile around the world. He has also traveled to Abu Dhabi to discuss the feasibility of tapping into the sun-driven renewable resource. As with Chile, these interactions have developed through a combination of approaches from other countries and an interest on Fthenakis’ part.

In addition to his work at BNL, Fthenakis teaches two environmental courses at Columbia: Air Pollution Prevention and Control, and Photovoltaics Systems Engineering and Sustainability.

As for his research at BNL, Fthenakis said he is involved in all aspects and impacts in evaluating energy alternatives. That can include affordability, which addresses direct and hidden costs, resource availability and environmental impact.

Fthenakis has been working at BNL for 34 years, where he has earned the respect of his colleagues. He is “a world-renowned expert in issues of safety of photovoltaic systems and, more broadly, in issues of deployment, efficiency, practicality and the like,” said Stephen Schwartz, a senior scientist in the Biological, Environmental & Climate Sciences Department at BNL, who has known Fthenakis for about 20 years.

Fthenakis’ wife, Christina, is an executive director in research and development at Estée Lauder Companies. The couple have a daughter, Antonia, who is doing her residency in dermatology at Stony Brook and a 21-year-old son Michael who is exploring his career options.

Fthenakis said he and his family visit beaches on Long Island or wherever they travel. When they find litter, they help dispose of it in a safe place.

“Solar energy and the environment defines the way I live,” Fthenakis said.

They help start car engines, provide light in the darkness, keep music playing as joggers circumnavigate their towns, and help send signals to hearts that might otherwise have irregular beats. They are, of course, batteries.

The fact that they work is something everyone understands as soon as they flip a switch. What no one can see completely yet, though, is what happens on a small scale as a battery discharges.

Mostly encased in stainless steel, the inner workings of a battery have been difficult to measure directly. A much-heralded hire from two years ago, who divides her time between Stony Brook and Brookhaven National Laboratory, Esther Takeuchi has teamed up with several other scientists to gather new clues about the changes in a battery as it discharges.

“We’re looking at the internal anatomy of a battery without taking it apart,” said Takeuchi, a distinguished professor with an appointment in the department of chemistry and the department of materials Science and engineering at Stony Brook and a chief scientist at BNL’s Basic Energy Sciences Directorate.

Takeuchi and her team worked at BNL’s National Synchrotron Light Source, where they stopped batteries at various times and measured them with the kind of x-rays that penetrate the steel casing. These provide a resolution on the scale of 20 microns, which is about 1/4 the width of a human hair.

By understanding on a more precise level what happens inside a battery, scientists may provide insight that enables a greater understanding of the best architecture or design for a battery.

“The way we understand a battery could change dramatically,” said study co-author Amy Marschilok, a research associate professor in materials science and engineering at Stony Brook. “We’re taking” the inner workings of a battery “from black box science to more [open] science, where we can see and understand what’s happening. We’re on the verge of that type of discovery right now.”

In general, Takeuchi said batteries may work at about 80 percent efficiency, depending on the type of battery or its use. That, she said, could increase with a design that makes best use of the developing environment in the battery as it functions.

The results of the study, which included Takeuchi’s husband Kenneth, who is a distinguished teaching professor at Stony Brook, Marschilok, BNL scientist Zhong Zhong, BNL postdoc Kevin Kirshenbaum and Stony Brook graduate student David Bock, were published in the prestigious journal Science.

The research team used these bright x-ray beams to study lithium batteries that have a special silver material at the cathode, the place from which current departs, that has high stability, high voltage and spontaneous matrix formation.

As the batteries, which Bock created, discharge, lithium ions from the anode travel to the cathode, displacing silver ions in the process. Coupling with free electrons and unused cathode material, the displaced silver forms a conductive silver metal matrix that enables electrons to flow.

The research demonstrated that a slow discharge rate early in the battery’s life creates a more uniform network.

“When we started activating the battery, the cathode spontaneously, within its own structure, starts forming small parts, or ions, of silver metal,” Takeuchi said. “The silver ions are reduced to silver metal. What’s really interesting is that, because we’re forming silver metal, we have something we can measure.”

The results of the experiment provided a clearer understanding of the steps the battery goes through. The last part of the battery to activate is the center.

In some batteries, the flow of electrons may just reach the edges and never have access to the middle.

Takeuchi, who left the University at Buffalo to come to Long Island, said she is excited by the opportunities at Stony Brook and BNL. This past June, Stony Brook led a multi-institution group that received a $10 million Energy Frontier Research Center Award from the Department of Energy.

Takeuchi is convinced she made the right decision to move to Long Island.

“The willingness of Stony Brook and BNL to commit to this field was appealing to me,” Takeuchi said. “They recognize how important it is, to Long Island, nationally, and globally. We have the opportunity to make a difference.”

Lottery winners don’t get to keep all their money — they have to pay a sizable federal tax. Similarly, solar energy involves a tax, albeit a very different kind. The light that becomes heat in solar cells doesn’t make its way into homes or stores.

Employing a new polymer, however, scientists at Brookhaven National Laboratory and Columbia University have started a process that may enable them to keep more energy from sunlight.

Using something called “singlet fission,” they figured out a way to cut down on solar energy lost as heat.

Through a multiplication process, one absorbed unit of light creates two electrical charge carriers.

Other researchers had produced materials that benefited from singlet fission. They hadn’t, however, created a substance that works while dissolved in liquids, which creates the potential for industrial-scale manufacturing.

“Not many materials do singlet fission,” said Matthew Sfeir, a scientist at BNL and one of the leaders on the project. The material Sfeir and co-investigator Luis Campos of Columbia University used can be made through solution processing, which includes material such as ink.

Sfeir explained that the discovery of this polymer was something of a fortunate accident. Campos, whom he describes as a “great organic chemist,” was attempting to create a molecule for an application that did not work. “It failed spectacularly,” Sfeir recalled.

Campos and Sfeir took a closer look at what was happening. As it turns out, by examining the materials with a strobe laser at the Center for Functional Nanomaterials at BNL, Sfeir and Campos recognized that this polymer was “behaving like nothing else with this class of organics.” They were, indeed, creating singlet fission.

Campos and Sfeir tested how well their sensitizer might work to tap into the heat energy. “A failure in one context [was turned into] a spectacular success in another,” Sfeir said.

Sfeir and Campos, along with John Miller at the Laser-Electron Accelerator Facility and postdoctoral student Erik Busby in Sfeir’s lab and postdoctoral student Jianlong Xia in Campos’s lab, started these experiments in September, 2013. They recently published their results online in the journal Nature Materials.

Sfeir explained that the technology at BNL enables scientists to test materials and ideas. “My research lab uses ultrafast lasers to evaluate how well materials might perform in actual devices, without building actual devices,” Sfeir explained.

Using lasers, he puts light energy into a system and then tries to measure where the energy goes and how fast it gets there.

Sfeir and Campos are looking at a material that works even better than the one for which they published their recent results. The original polymer included a small amount of a minority project that they are trying to minimize.

A resident of Bethpage, Sfeir lives with his wife Margot, their 6-year-old daughter Katy and their son Jonah, who will be 2 in a few months.

Sfeir was born in Buffalo while his wife was born in Minnesota. When they first met in Chicago, he said Margot would only use a scarf and mittens instead of a winter coat, even in cold weather. Living in the New York City area since 2000 has reduced their resistance to frigid temperatures.

When he was younger, Sfeir learned some lessons in a seemingly unrelated field when he worked at Hector’s Hardware, a small chain owned by his father Ken’s extended family. While he did other jobs like unloading concrete bags, mixing paint and cutting and threading pipe, Sfeir developed an expertise in window and screen repair.

In college, Sfeir discovered a passion for quantum mechanics and was fascinated by light and the way it interacts with matter.

In Sfeir’s first job at a research lab, one of his first responsibilities was fixing the water cooling lines on a laser. “I called my dad right away to thank him for the lessons about compression fittings,” Sfeir said.

As for his work, he said he thoroughly enjoys the opportunities. “I love working at BNL because its mission resonates strongly with me,” he said. “Sometimes, this research evolves into readily identifiable technological applications and sometimes it evolves our understanding of some of the most basic questions about our world. Both are very important to me.”

Two groups lived at about the same time. At around 40,000 years ago, one of them died off, while the other grew, changed and developed, becoming individuals who build airplanes, send text messages instantaneously over thousands of miles and harvest and replant crops that become high fructose corn syrup.

The winner was Homo sapiens, or wise man. Neanderthals, with their muscular frames, prominent brows and wide noses, came up short. Scientists on the winning team have been asking everything from how Neanderthals and Homo sapiens coexisted to why one group is still around, while the other left clues including fossils, cave drawings and genetic evidence.

Using mathematical and computational techniques to study DNA sequences, Adam Siepel, a professor at Cold Spring Harbor Laboratory, teams up with numerous collaborators to paint a clearer picture of what happened all those years ago.

“We try to reconstruct aspects of human history by comparing these sequences,” said Siepel, who joined CSHL this summer as chair of the new Simons Center for Quantitative Biology. The center, which started with a $50 million donation from the Simons Foundation, uses a combination of applied mathematics, computer science, theoretical physics and engineering to make sense of the explosion of data produced in labs on Long Island and throughout the world.

In his research, Siepel is trying to “make sense of how much gene flow” there was between Neanderthals and Homo Sapiens, he said. He is reconstructing models of ancient human demography based on a joint analysis of genome sequences from the two groups. He is currently seeing signatures of gene flow in both directions.
Scientists have been finding that the size of the Neanderthal population declined steadily over time. By using statistical models, researchers can look at patterns of genetic variation and can reconstruct the size of the population.

“There is a clear signal of the population shrinking over time, reaching precipitously low levels in anticipation of extinction,” Siepel said. This can be interpreted as signaling a steady decline, arguing against a cursory event where Neanderthals suddenly all died out.

In building these statistical models to reconstruct the Neanderthal story, scientists recognize numerous challenges. Researchers try to consider as many model violations as possible and cross check their results carefully, he added.

Siepel also conducts research into gene transcription, or the process through which DNA is copied into RNA, which is needed for a wide range of assembly and regulatory functions.

About a month ago, in conjunction with John Lis, a professor and former colleague of Siepel’s at Cornell University, Siepel published a paper in Nature Genetics in which the team showed that the first steps in transcribing genes and their regulatory elements are highly similar. This, he said, suggests that the differences between promoters and enhancers must occur downstream through mechanisms that cause an abrupt termination of transcription at enhancers.

This research and Siepel’s work on Neanderthals underscores the two major focuses of his lab: the process of transcriptional regulation and natural selection and human evolution. These disciplines “intersect in various ways,” Siepel said. He has, for example, studied the “influence of natural selection on transcription factor binding sites in the human genome.”

Siepel and his wife Amber bought a Victorian house in Huntington that has become a “fun project” for the family, which includes their 12-year-old daughter Ella and their 9-year-old son Charlie.

Siepel said he had never planned on living on Long Island, where he had a “vision of a big strip mall,” but he’s been “pleasantly surprised by Huntington” where he and the family can walk their two labradoodles along the streets by the harbor and visit nearby parks.

Siepel has enjoyed his first few months at Cold Spring Harbor Laboratory, where he said it is easy “to make changes.” The group has promoted Justin Kinney to assistant professor and Michael Schatz to associate professor. Siepel is also reviewing applications of researchers who are seeking to fill an open assistant professor job.

As for his work, Siepel said he is “fascinated by the idea of being able to reconstruct the past through the analysis
of present-day and fossil
genome sequences.”

When he was 15, Raju Venugalapan spent what was then a considerable sum of money to buy three books on what his parents thought was an obscure subject. Living in India, where he was born and raised, Venugalapan bought the Feynman lectures, books that were based on lectures delivered to students at the California Institute of Technology by Nobel laureate Richard Feynman. These lectures were designed to make physics more vibrant and inspirational.

The books worked for Venugalapan, who was determined to enter the field of physics. The would-be physicist, however, had a problem — his parents weren’t sure this represented a viable career choice. For them, studying physics was like writing poetry, he said. While it might have value, it could be difficult to earn a living and support a family.

His parents’ opinion changed, however, when he received a full scholarship to study physics at the University of Chicago.

Over a quarter of a century later, Venugalapan is a senior scientist and group leader of the Nuclear Theory Group in the Physics Department at Brookhaven National Laboratory.

“I love getting up in the morning and going to work,” said Venugalapan. His daily pursuits are something that are “very natural to me, like breathing.” What makes his work so exciting, Venugalapan said, is that he can address questions about some of the unknown structural elements of matter.

“I see various data as pieces of a jigsaw puzzle that, together with theoretical insight, can provide a larger picture of the sub-nuclear scale matter,” he explained.

Larry McLarren, a senior scientist and a group leader at the Riken BNL Center, said Venugalapan’s approach and theories have proven successful.

“He’s developed many of the ideas that are hot right now,” he said. Venugalapan is “somebody who has done a lot of good work and is full of energy.”

Venugalapan studies data that comes out of the Relativistic Heavy Ion Collider at BNL, where scientists collide protons and neutrons almost to the speed of light. The heat generated from these collisions is 100,000 times hotter than the center of the sun, although they last for an unimaginably small amount of time.

Feynman — the physicist who inspired Venugalapan — described this process as being similar to smashing two Swiss watches together. At this point, he said, “we don’t have the luxury of taking apart” subatomic particles such as gluons and quarks.

A few years ago, he and his colleagues had developed a theory about the correlations of gluons and how they would behave. One of the team members made a prediction for proton-proton collisions at the Large Hadron Collider near Geneva, Switzerland.

Because the signal was too small, the group published its result as a curiosity in a conference proceeding rather than in a scientific journal. When the LHC experimentalists found this phenomenon, Venugalapan and his team were able to put out a paper within a week of the announcement.

The event they described was about a one in a million occurrence in a proton-proton collision. “It was extremely exciting,” he recalled. “It was the biggest high you can imagine.”

After the original result, the science progressed as it often does in the face of new information and a new theory: Other researchers performed similar experiments to confirm the data — and to test the idea behind it.

“I’d go to bed at night with a mixture of anticipation and trepidation,” Venugalapan said. There might be a new paper out that “either killed or confirmed our idea.”

Venugalapan and his colleagues believed there could be two phenomena that could cause the effect: One was hydrodynamics and the other was a so-called quantum synchronicity of gluons.

A resident of Riverhead, Venugalapan enjoys sailing with his family on Peconic Bay. As for his work, Venugalapan said he still marvels at how the theories he and his colleagues create might describe events at a subatomic level.

“When you’re making up these mathematical edifices, there’s a certain level of disbelief that this can describe the world,” he said. “We’re playing with paper and equations and, on the other side of the world, there’s a 15-ton detector” that’s running experiments. He wonders: “What do my scribbles have to do with what they see there?”

As for his parents, he said they had a point: “The creative process in science and theoretical physics in particular is not unlike that in poetry.”

From finding prehistoric groundhog-like creatures to fostering mutations that help tomato plants produce more fruit to doubling the understanding of what causes a proton to spin, scientists on Long Island, working with teams from around the world, had a busy, productive and, in some cases, lucky year in 2014.

Experts from all three local institutions made waves well beyond their scientific peers, as their papers in Science, Nature to the Proceedings of the National Academy of Sciences generated headlines around the world.

While the researchers at Stony Brook University, Brookhaven National Laboratory and Cold Spring Harbor Laboratory answered important questions in their fields, they consider the achievements of the past year a starting point for the next set of questions, experiments and opportunities.

Times Beacon Record Newspapers will take a look back at the remarkable achievements, findings researchers working in our communities enjoyed in 2014.

Stony Brook
A long time ago on an island far, far away, a 20-pound mammal walked with dinosaurs, including the carnivorous 2,400-pound Majungasaurus. This mammal, which is much larger than the mammals that were mostly the size of shrews and rats at that time, was hidden in a 150-pound slab of sandstone for over 66 million years in Madagascar. That is, until David Krause, a distinguished service professor in the Department of Anatomical Sciences, and his graduate students brought back the creature.
Krause was fishing through the block for, well, fossil fish, but instead stared into the face of an unknown chapter in ancient history. Removing one grain of sand at a time, Krause and his colleagues spent six months extricating the extraordinary find. They named the mammal Vintana sertichi. Vintana comes from the Malagasy word for “luck,” because they had no idea what awaited them in the heavy rock. “It’s good to have strong graduate students,” Krause said.
On the same island nation of Madagascar, Patricia Wright had a year that would make the lemurs she studies and considers her extended family howl. Only two years after opening a state-of-the-art, five-story research facility called Namanabe Hall on the boundary of Ranomafana National Park, Wright and her research were featured in an Imax movie called “Island of Lemurs: Madagascar.” As if that weren’t enough, Wright became the first female scientist to win the top award in conservation: the Indianapolis Prize, which included a $250,000 cash gift.
Meanwhile, ecologist Heather Lynch used satellite images to study penguin poop in Antarctica. Lynch and Michelle LaRue from the University of Minnesota estimated that the population of Adelie penguins was considerably larger than expected. While some conservationists suggested such a result might run counter to concerns raised by global warming, Lynch said the story was more complicated than the overall number, with groups declining in some areas and increasing in others.
Studying temperatures that would make those in the Antarctic seem balmy by comparison, researchers in the Department of Physics and Astronomy sought to understand properties of metallic materials as they approached absolute zero. Liusuo Wu, a doctoral student, Moosung Kim and Keeseong Park worked with Professor Meigan Aronson to explore the start of ferromagnetism, which is the same property in electrical motors or refrigerator magnets, in a specially made iron compound near this extremely cold temperature.
Exploring the quantum phase transition allows researchers to predict and possibly boost the performance of new materials in practical ways that had previously been theoretical, explained Brookhaven Lab physicist Alexei Tsvelik, a co-author on the study.
Looking at how life copies itself on the genetic scale, Huilin Li, a professor of biochemistry and cell biology at Stony Brook and a biologist at BNL, teamed up with researchers from BNL and Cold Spring Harbor Laboratory. The group found structural details of an enzyme that unzips and splits the double helical DNA into two halves. This, Li explained, may help researchers explore how that process can go wrong and may one day lead to new treatments that stall or break runaway genetic machinery. The findings came from a close collaboration with lead author Jingchuan Sun at BNL, Bruce Stillman at CSHL and Christian Speck at Imperial College, London.

Cold Spring Harbor Laboratory
At CSHL, scientists made strides in gathering information about human diseases, like schizophrenia, Alzheimer’s and cancer. They also developed a new genetic toolkit for growing more productive tomato plants.
Looking at de novo mutations in a broader range of diagnoses, including schizophrenia, autism and intellectual disabilities, W. Richard McCombie and Shane McCarthy found overlapping genes. Some of these genes are involved in reading, writing and editing chemical marks on DNA and proteins that help control when specific genes are switched on or off. It is possible, a group that includes professor Aiden Corvin of Trinity College speculates, that the genes that affect the same biological function in some disorders are examples of those that contribute to normal brain development.
Associate Professor Bo Li, meanwhile, helped identify neurons that actively participate in fear conditioning. By studying a group of long-range neurons that extend from the central amygdala to an area of the brainstem called the midbrain periaqueductal gray in an animal model, he discovered a neural circuit that connects the site of fear memory with a part of the brainstem that controls behavior. His work could have applications to models of post-traumatic stress disorder.
Also studying the brain, Associate Professor Adam Kepecs asked rats how confident they were in their decisions. Designing experiments that required rodents to wait for a reward, Kepecs was able to show that a part of the brain called the orbitofrontal cortex plays a role in confidence and decision making. Animals with a blocked orbitofrontal cortex made decisions just as effectively, but their confidence, even with incorrect choices, remained high even when they didn’t get their desired reward.
Using a mouse model for prostate cancer, Associate Professor Lloyd Trotman studied the genetics of a disease that afflicts one in six men. In these mice, the typical driver of prostate cancer, PI 3-kinase, was absent in metastasized tumors. Instead, he and colleagues from Weill Cornell Medical College, Mt. Sinai School of Medicine and Dana-Farber Cancer Institute discovered that a cancer gene called Myc had become active. By lowering the amount of Myc in cells, they shrunk the metastases. Trotman hopes the model provides a fast and faithful way to test new approaches to find a cure for what is up to now an incurable disease.
Finally, associate professor and tomato expert Zachary Lippman, working with colleagues in Israel, discovered a genetic toolkit that allows researchers to double fruit production. The team found a collection of new gene mutations that allow scientists, and potentially farmers, to fine-tune the balance between the hormones florigen and anti-florigen. This has the potential to maximize fruit production without compromising the energy leaves need to support the fruit.
In the bigger picture, scientists at all three institutions showed considerable excitement for discoveries in the year, and years, ahead. Tribble pointed to the opening of the National Synchrotron Light Source II, the next-generation light source that cost about $900 million to build and that will provide images that are 10,000 times brighter than the original NSLS.
“NSLS II is poised to have some phenomenal information coming out,” Tribble said. “We can set a big battery in the beam and watch what’s happening” inside the battery without taking it apart.
At Stony Brook, the past year was “notable for the huge potential related to imaging,” said Lina Obeid, the dean for research at the Stony Brook Medical School. She said the university, with the construction of the new Medical and Research Translation building is “poised to have lots of great ideas and strong data.”
Cold Spring Harbor Laboratory is celebrating its 125th anniversary next year. Bruce Stillman, the president and CEO, said he hopes 2015 “will be a big year for expanding opportunities to apply our basic research to the medical clinic and other areas like food production and biofuels.”

Brookhaven National Laboratory
Scientists at BNL explored everything from the origins of the universe to nanoscale — i.e., very small — reactions in electric car batteries, to processes even more rare than the recently discovered Higgs boson, to increasing the production of oil in plants.
“It’s an enormously exciting time at BNL right now,” said Bob Tribble, the deputy director for science and technology, who joined the research center in February. A nuclear physicist, Tribble highlighted several studies that have broader implications.
Over the last decade, researchers could only account for a third of what gives a proton — that positively charged particle in the nucleus — its spin. As recently as six years ago, researchers believed subatomic particles called gluons had only a small effect. Now, “it’s clearer that the gluon field is playing a significant role in developing that spin,” Tribble said. Indeed, Elke Aschenauer, a leader in the spin program at the Relativistic Heavy Ion Collider, in collaboration with researchers at Star and Phenix, benefited from accelerator advances and added running time to collide polarized protons. The knowledge of gluon’s larger role in a proton’s spin, which no one had measured conclusively until now, could not only provide a better awareness of the internal structure of particles but could also affect optical, magnetic and electrical properties.
Scientists at the RHIC also learned about the phase transition of matter. Say what? Yes, that’s the equivalent of ice turning into water, although at a subatomic level. Zhangbu Xu, a spokesperson for RHIC’s Star collaboration, said RHIC provides the ability to explore what happens over a wide range of collisions. As Tribble put it, “now that we’ve been able to probe in some different regimes of the phase diagram, we’re seeing evidence that the first-order phase transition occurs in certain parts of the phase diagram. That’s new.”
Meanwhile, physicists at the ATLAS experiment at the Large Hadron Collider continue to test the Standard Model of particle physics. To do that, they are looking for incredibly rare events, where two same-charged particles called W bosons scatter off one another. Physicist Marc-Andre Pleier studied 34 such events that confirm that the Higgs boson particle does what physicists predicted.
In the world of superconductivity, senior physicist and director of the DOE’s Center for Emergent Superconductivity at BNL J.C. Seamus Davis helped lead a team that showed how electrons in a pseudogap are less free to move than they are in their superconductive state. By understanding these gaps, the team may be able to conduct the kind of science that leads to the speeding up of efficient power generators and transmission and computers at levels more than thousands of times faster than the machines currently in use.
John Shanklin, Jilian Fan and Changcheng Xu didn’t build a better mousetrap, but they did figure out how to encourage the development of a better plant, at least in the world of biofuel. The researchers found the detailed biochemical steps in the breakdown of oils. They disabled an enzyme that breaks down oil droplets to release fatty acids. The result was a 150-fold increase in oil content compared to the leaves of the naturally occurring counterpart. This could enhance production of biofuels.