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.

It took a year to plan for something that would last about ten seconds. All the safeguards were in place, which meant no one could touch any of the seven spheres that were about 1/8 the size of a Ping-Pong ball.

The first five balls didn’t make it into the right spot, leaving the team with only two more attempts to make it work.

“It was the equivalent of the bottom of the ninth inning and there were two pitches left,” said John Parise, a distinguished professor in the department of geosciences at Stony Brook. “If you don’t hit a home run, you’re going away empty-handed.”

Instead of baseballs, the group was working with forms of uranium dioxide, the major nuclear fuel component of fission reactors, which produce nuclear power. Scientists at Argonne National Laboratory in Lemont, Illinois, and Stony Brook were trying to get a clearer picture of the structure of this compound at extreme temperatures. In nuclear reactor accidents, like Chernobyl in 1986 and Fukushima in 2011, uranium dioxide can reach temperatures of over 3,000 degrees Celsius. At that level, uranium dioxide can melt many of the containers designed to hold the radioactive liquid.

Scientists had come up with several theories about what the structure of this compound is at these extreme temperatures, but no experiments had provided direct evidence.

Fortunately, the team, led by Lawrie Skinner, a research assistant professor at Stony Brook, was able to get the final pellets in the correct spot, giving the researchers a chance to heat it to these extreme temperatures and then study its structure with specialized x-rays produced by the synchrotron at the Advanced Photon Source at Argonne.

The researchers discovered that each atom of uranium starts with 8 oxygen atoms nearby and, at extreme temperatures, has that number reduced to 6.7 oxygen neighbors. This, Skinner explained, affects the physical properties of the liquid, like its viscosity.

Parise, Skinner, scientists at Argonne National Laboratory and colleagues including Richard Weber, the founder of Materials Development Inc. in Evanston, Illinois, recently published their findings in Science.

Levitating the uranium dioxide pellets was critical because it prevented the compound from coming into contact with anything else. Skinner likened the process to keeping a ping pong ball afloat by using a hair dryer. To heat the compound in the experiment, which was not radioactive, the scientists hit it with a carbon dioxide laser that is about 100,000 times more powerful than a bright laser pointer, Skinner offered.

Scientists and those involved with nuclear reactors need to understand the viscosity of uranium dioxide so they “know how it will behave in a reactor meltdown,” said Parise. “The chief motivation behind studying the structure of uranium dioxide is to provide theoreticians with an accurate set of data that they can use to derive the atomic interactions that’ll allow them to predict behavior,” Parise said.

Skinner and Parise started working together over four years ago, when Skinner was a postdoctoral researcher in Parise’s lab. Since then, Skinner has gone on to conduct his own research.

Parise explained that he and his colleague will continue to try to understand how atomic interactions give rise to physical properties and behaviors. They would like to understand how liquids evolve as a function of pressure and temperature.

The next material Parise is planning to study is iron-containing liquids, including those involved in steelmaking.

Parise sees considerable potential for work with lava. The hot magma that comes from the center of the Earth behaves differently depending on the conditions and location where it erupts. In Hawaii, for example, lavas are much more liquid, while those in the Pacific Northwest are more explosive.

The next challenge, Parise said, is to understand how the composition of gas that’s over the liquids affects the viscosity and internal structure of those liquids.

Parise and Skinner each grew up far from Long Island. A native of Far North Queensland, Australia, Parise now lives in Poquott with his wife Alyse, who is the owner of a business- coaching company called Power Outcomes.

Skinner, who spends much of his time in Illinois at Argonne National Laboratory, grew up in the United Kingdom. He is married to Sonia, who works as an engineer for S&C Electric Company, which makes parts for an electric power grid.

As for the experiment, Skinner said he was “a little tense,” when the first few uranium dioxide balls didn’t make it into the levitator, but he “had faith.” It’s important, he urged, to stay positive in the face of failure. “If we just did things that were easy, we would not progress [in] our knowledge as much.”

Imagine a pizza restaurant. Every day, the chef cooks a certain number of pies. At a specific point, the kitchen reaches a maximum. What if that restaurant could double its production?

That’s what Zachary Lippman, an associate professor at Cold Spring Harbor Laboratory, and colleagues in Israel did, except that instead of doubling his pizzas, he doubled the amount of fruit his tomato plants produced.

Lippman used the same kind of mutations that agriculturalists have employed for centuries to increase crop yields.

“The approach we took was to find new mutations and design specific screens” that would favor flowering instead of bushiness, Lippman said.

Lippman and collaborators from Israel created a tool kit of genes that balance between the hormones florigen and anti-florigen. The first one, florigen, promotes flowering and flower and fruit production. The second one, anti-florigen, promotes shoot and leaf production.

Florigen and anti-florigen are “like this yin and yang,” Lippman said. “We found mutations in genes that affect the florigen/anti-florigen paradigm.”

By cross breeding these mutations, Lippman and his associates were able to pinpoint what he described as “an optimal architecture,” which originates from an optimal balance of flowering signals, he said.

This genetic tool kit could have applications to other agricultural crops, such as soybeans, which, Lippman explained, share many growth similarities to tomatoes.

With the world population expected to reach 9 billion by the middle of this century, these kinds of discoveries could prove important in increasing food production, Lippman said. He is thinking of testing this tool kit in cowpea, a major crop related to soybean that is grown in Africa.

“The major advance in the present work is the illustration that fine tuning of signals from these hormones can help improve tomato field performance and thus, similar, directed changes can be applied in other plants,” explained Yuval Eshed a professor in the Department of Plant and Environmental Sciences at the Weizmann Institute of Science in Israel who collaborated with Lippman on this study. Eshed has worked with Lippman for almost a decade and called his partner “an outstanding scientist” who is “original, thorough and trustable.”

The approach Lippman and his team took does not involve inserting DNA into the plant but rather comes from the development of mutations, Lippman said.

“It’s the standard idea of classic genetic modification,” Lippman said. “We were able to design a way to find and select for mutations much faster than what Mother Nature has given us by using what people have been doing for decades.”

The genetic tool kit, with several specific mutations, gives scientists and, potentially, tomato producers a chance to boost the production without compromising the plant or the taste of the tomato.

At the same time there is no difference in the fruit quality or the plant, he said. “Sugar is unaffected,” he offered.

To be sure, like some animals bred in a zoo or plants farmers have used for hundreds or even thousands of years, these new tomato plants, with their collection of mutations designed to increase yield, would not fair as well outside of the confines of a farm. “What’s optimal in nature is not what’s optimal in agriculture,” Lippman explained. “We’re selecting for growing in greenhouses or fields.”

Lippman used this tool kit in cherry, plum and beefsteak tomatoes. He is hoping to test all major varieties of tomato, including slicing tomatoes for burgers, grape tomatoes and cocktails. This approach should work across the types of tomatoes, but he hasn’t conducted those tests yet. He has had some contact from companies that grow tomatoes and will likely enter a collaboration soon.

Lippman said introducing these new mutations into the elite breeding lines of tomato farmers may create some complications. “We don’t know how those mutations will respond” in the designer tomatoes agricultural companies use, he said. “One combination might work in one variety, whereas another combination might work in another variety.” The tool kit, however, provides a genetic resource.

“This summer, we repeated the experiment for a fourth time,” he said. He organized these plants in a row according to their mutations. “If you walk down the row, you could see the progressive quantitative increase,” with the plants going from bushy to less bushy to almost a tree. To see the yield [change] was even more impressive.”

Lippman, who has been working for for six years at CSHL, said these results are “by far the most important work to come out of my lab. This is the most fun” he’s had conducting research.

This group will not let pain or loss defeat them. Instead, they are banding together to fight a common enemy.

Several foundations, the Friends of T.J. Foundation, the Christina Renna Foundation, the Michelle Paternoster Foundation for Sarcoma Research and the Clark Gillies Foundation, are contributing about $300,000 to fund research into a rare form of deadly pediatric cancer called rhabdomyosarcoma. RMS is a tumor of the connective tissue that typically involves muscle cells attached to bones.

The groups are backing a research partnership between Cold Spring Harbor Laboratory Assistant Professor Chris Vakoc and Charles Keller, the scientific director at the Children’s Cancer Therapy Development Institute, Fort Collins, Colo., to find a cure for a disease that afflicts adults and children equally. For children who get cancer, it is the most common soft tissue cancer.

The directors from these groups got together at a special Banbury conference of world leaders in RMS in May and pooled their resources.

The foundations “all gelled,” said Phil Renna, the director of operations for public affairs at CSHL and the co-founder of the Christina Renna Foundation. Renna’s foundation is named after his daughter, who died in 2007, a year after her diagnosis. Renna is “happy to say that we are able to put together” this research focus.

Vakoc and Keller have “hit it off” after CSHL president and CEO Bruce Stillman helped form the collaboration, Vakoc said. The research team hopes to “leverage what my lab does with epigenetics with [Keller’s] expertise in the clinical realm.”

Vakoc said his lab is invested in the discovery of cancer drug targets. He asks “cancer cells what they need to grow,” while they also explore what makes cancer cells different from normal cells.

Working on leukemia, Vakoc has already found a drug target, called Brd4. He plans to take a similar approach to RMS.

Vakoc explained that his lab uses a technique called RNA interference, in which he methodically searches for protein targets. He also uses a gene knockout technique called CRISPR. Vakoc is inhibiting parts of proteins in animal models of this disease and examining how the sarcoma responds.

“This is a way to provide a road map for where drug discovery should be,” Vakoc said.

Once he and his lab finds these targets, they can look for existing drugs approved for other clinical applications that might work against this cancer. His first round of screens have nominated some targets, although it is too early to know if these will prove useful in treating RMS, Vakoc said.

With Brd4, Vakoc found a target in which an inhibitor already existed. Based on his research, scientists are now conducting a clinical trial to study its effects.

Keller used to see patients but now conducts research full time. Any discovery with RMS might have implications for other diseases, he said. The most commonly known inherited predisposition to cancer, called Li-Fraumeni syndrome, was originally reported as a condition of inherited RMS. This syndrome, Keller added, has mutations in the p53 genes, which is one of the most well-studied genes in cancer of any type.

“Pediatric cancers can lead to fundamental types of discoveries that are later paradigms for adults cancers,” Keller explained. Keller also recognized Stillman’s role in creating the partnership with Vakoc. “There is something very personal about [Stillman’s] desire to make a change for this disease,” Keller offered.

Indeed, after meeting with some of the families affected by RMS, the members of Vakoc’s lab have contributed more of their time to seeking a cure. Vakoc said his lab members attended a one-hour talk Keller gave that included people from the foundations. Keller discussed the unique challenges of this cancer.

“Seeing the reactions and hearing the questions families have puts a different perspective on cancer research” from what scientists who study molecules in a lab “normally encounter,” Vakoc said.

He praised his lab mates for coming in on the weekends for a few extra hours of work. They are also planning to volunteer at the Morgan Center, a group that supports preschool children with cancer.

Keller said he’s thrilled with his collaborator. He said his mentor, Nobel Prize winner Mario Capecchi had a saying: “Go with the best, no matter where they are.” That, he explained, is Vakoc.

Keller and Vakoc are using the philanthropic support to involve Novartis in a grant they have submitted to the National Institutes of Health, Keller said.

Paul Paternoster, who lost his wife Michelle to RMS last year, explained that it is “nice to drive by Cold Spring Harbor Laboratory every day and think about” how researchers are working toward a cure. “We took all the pain and negative energy” that comes from battling this disease “and turned it into something positive.”

Joel Saltz lives in a world of numbers. The first chairman of biomedical informatics at Stony Brook recently hit a number that will help him continue to develop a department he arrived to lead last year: $3.2 million. That’s how much the National Cancer Institute pledged to support Saltz’s efforts.

“This grant is related to developing methods and tools for analyzing tissue data, in particular pathology, as it relates to genetics and genomics,” Saltz said. That means he will try to understand more about the complex patterns of interactions between cancer cells, surrounding and distant tissues. By studying these interactions, Saltz and his collaborators hope to help develop diagnostic and treatment methods.

A powerful enemy with ways of evading different kinds of treatment, cancer can present prognoses that vary from one person to another — even when the cancer is in the same area or affects the same organs or systems.

“In some cases, the relationship varies from one part of the tumor to another,” said Saltz. “If one part of the tumor has ‘x,’ they treat it like ‘x,’ but if it has some ‘y,’ the heterogeneity can be indicative of another diagnosis. What you want to do is look at the distribution of proteins or nucleic acids, and then do an image analysis.”

Saltz has programmed computers to scan tumors to get a consistent, quick and reproducible understanding of the underlying cancer or tumors. This effort will provide data that the international community of academic and commercial algorithm developers can study.

This effort to count different types of cells to get a mathematical handle on the type of disease can “reduce the variability from one pathologist to another,” Saltz said. “That is critical for any study.” He also hopes to learn new relationships among various components that may not be obvious.

By understanding the nature of the specific cancer, scientists and doctors hope to get a better handle on a specific treatment for each patient.

Saltz is “working with a number of translational researchers” who have patient populations or are working with animal models of cancer, he said.

The kind of analysis Saltz does in his biomedical informatics world may eventually lead to individualized or precision medicine. At this point, this is a longer-term hope for the effort.

Saltz described the process as taking an image analysis and adding a machine learning component. While convinced of the value of this type of computer-aided analysis, Saltz is not advocating developing a diagnostic or treatment regime by relying exclusively on the analysis of a computer.

“The sort of information a machine can give you complements what two people trained in different parts of the country” conclude, he said. “It can help reduce the level of unanticipated disagreement.”

At this point, these methods are not directly used to treat patients. They are a part of a research effort to improve the quality of the scientific studies.

Saltz credited Ken Kaushansky, the dean of the School of Medicine, with committing Stony Brook to integrate the latest research into improvements in the care and treatment of patients.

Other Stony Brook scientists shared their appreciation for Saltz’s approach. Saltz “brings in unique and urgently needed expertise in cancer informatics,” said Yusuf Hannun, the director of the Stony Brook Cancer Center. “This is a discipline engaged in collating, organizing and analyzing large data sets obtained in the course of cancer studies. Saltz brings internationally recognized expertise in this field.”

Saltz said there were numerous steps researchers needed to take before this approach has a clinical application.

To build out the expertise in biomedical informatics at Stony Brook, Saltz is applying to add a Ph.D., Master’s and certificate program. He said the program will build a bridge between pathology and computer science.

A resident of Huntington, Saltz moved to Long Island with his wife Mary, a clinical associate professor of radiology. The couple have four children, who range in age from 19 to 26.

Saltz said he was impressed with the natural beauty of Long Island. He had visited the area before when his brother, David Saltz, who is now at the Department of Theatre and Film at the University of Georgia, worked at Stony Brook from 1994 to 1996.

As for his work, Saltz said he is “delighted” with the NCI grant. “We’ve got a great team.”

While the United States was celebrating Independence Day two years ago, a group of people were cheering the discovery of something they had spent almost half a century seeking. Physicists around the world were convinced the so-called Higgs boson particle existed, but no one had found clear-cut evidence of it.

At a well-attended press conference, scientists hailed the discovery, while recognizing the start of a new set of experiments and questions.

As a part of the ATLAS team, Marc-Andre Pleier knew what the group was set to announce. He was very excited “to see the signal confirmed by an independent measurement.” Two years later, Pleier, a physicist at Brookhaven National Laboratory and a part of a group of more than 3,000 scientists from around the world, are tackling the next set of questions.

The discovery “points to the Standard Model [of particle physics] being correct, but to know this we need to understand this new particle and its properties a lot better than we do now.”

According to the Standard Model of particle physics, the Big Bang beginning to the universe should have created equal parts matter and antimatter. If it did, the two opposite energies would have annihilated each other into light. An imbalance, however, resulted in a small fraction of matter surviving, forming the visible universe. The origin of this imbalance, however, is unknown, Pleier said.

“We know the Standard Models is incomplete,” he said, because there are observations of dark matter, dark energy and the antimatter/matter asymmetry in the universe that can’t be explained by this model. “We can test this” next chapter.

The process Pleier studies allows him to test whether the particle is doing its job as expected. In addition to analyzing data, Pleier also has “major responsibility in upgrading the detector,” said Hong Ma, a group leader in the Physics Department at BNL who recruited Pleier to join BNL in 2009.

Scientists at the Hadron Collider in Switzerland and at BNL and elsewhere are studying interactions that are incredibly rare among particles.

Pleier is searching for interactions of vector bosons, which have spin values of one and are extremely large in the world of bosons. He is looking for cases where two W bosons interact with each other.

“Only one event out of a hundred trillion events will be of interest to me,” said Pleier. Comparing those numbers to the world of biology, Pleier likened that to finding a single cell in an entire human body.

In 2012, the Hadron Collider produced 34 such interactions. The collider produces about 40 million pictures per second. To find the ones that might hold promising information, scientists like Pleier need to use a computing grid. BNL is one of only 10 tier 1 centers for ATLAS and the only one in the United States. Thus far, scientists have been able to look at these collisions from energies at 8 trillion electron volts. They hope to measure similar data at 13 trillion electron volts next year.

Ma said the increased energy of the collider will “put the Standard Model to an unprecedented level of tests,” allowing scientists to “measure the properties of Higgs boson to a higher precision.”

Growing up in Germany, Pleier said he loved playing with Legos to see how things worked. He helped fix his own toys. When he was older, he worked to repair a motor bike his uncle had.

What he’s doing now, he said, is exploring the fundamental building blocks of matter and their interactions. He likened it to examining the “construction kit” for the universe. While he’s a physicist, Pleier explained that he’s a Christian. “Some people think it has to be in conflict, but, for me, it clearly is not,” he said. “Each discovery adds to my admiration for God’s creation.”

A resident of Middle Island, Pleier lives with his wife Heather, an English teacher who is staying home for now to take care of their three children.

Pleier and Ma emphasized that the work at the collider is a collaborative effort involving scientists from institutions around the world.

Michael Kobel, a professor at TU Dresden, head of the Institute for Particle Physics and Dean of Studies in the Department of Physics who has known Pleier for about nine years, likened the process of studying the high energy particles to exploring a cave, where scientists “get more light to look deeper” into areas that were in the dark before. Researchers, he said, are just entering this cave of knowledge, with “a lot of corners yet to be explored.”

Human mistakes occur everywhere, from a driver who runs a red light to a professional athlete who literally drops a ball, to an accountant who adds the wrong numbers. Even scientists, with their lab coats, their scientific method and their careful review process make errors.

So it was, in 2013, when scientists in Switzerland published a research paper suggesting that boron could exhibit a similar behavior to a topological insulator. If true, that could have implications for nanotechnology.

Recently, however, postdoctoral student Xiang-Feng Zhou at Stony Brook University, working with his lab director Artem Oganov, discovered that their fellow researchers had made a mistake. The Swiss scientists had “suggested metallicity for boron’s surface and this turned out to be an incorrect suggestion,” said Oganov.

Typically, topological insulators are made up of heavier elements. The Swiss scientists believed that the surface atom rearrangements in boron would enable the lighter element to exhibit the same conducting properties.

Zhou was able to test this theory by using a high-powered computer system created by Oganov and his colleagues. Called USPEX, for Universal Structure Predictor: Evolutionary Xtallogaraphy, the prediction code uses a set of principals driven by quantum mechanics.

Zhou and Oganov, who is a professor of theoretical crystallography at Stony Brook University, published their results recently in the journal Physical Review Letters, a journal of the American Physical Society.

“Topological insulators must include heavy elements and metallicity of their surfaces does not come from structural reconstructions,” Oganov said. “For boron, a similar effect was predicted (as we now know, incorrectly) due to the reconstruction of the surface.”

The Swiss scientists knew that breaking a solid causes a cleaving of many bonds, Oganov said. Atoms near the surface try to compensate for the lost bonds. Often, this results in unusual chemistry, he continued. The Swiss scientists thought this would lead to metallicity, he said.

Using their computer model, Zhou and Oganov found that boron would have a much more stable structure if it avoided a metallic state. Instead, it forms a semiconducting surface.

When Zhou, who is also an associate professor of physics at Nankai University in Tianjin, China, and Oganov sent their results for publication, the editors at Physical Review Letters did what they always do: they sent the paper to several experts in the field for review. One of the groups overseeing the analysis of the Stony Brook scientists’ results was the original team from Switzerland. Oganov wasn’t sure how they’d react.

“Usually, people are upset when their results are disproven,” Oganov said. “They checked our calculations and found that our result is correct. They gracefully admitted a mistake. Often, people would fight even knowing they are wrong.”

The Swiss scientists said they didn’t find the right surface because they didn’t have enough computing power, Oganov said. They suggested to Oganov that they finished their calculations “too soon.”

Another reviewer confirmed the result was correct, while a third one suggested the result might not even be worth publishing because it was something a scientist might be able to come up with using a pencil and paper.

“I take this as a compliment,” said Oganov. “Simple and beautiful are sometimes hard to come by. Heavy computations like the ones we have done are often the best way to find the simple reality. Reality is not always simple.”

Oganov credits Zhou, whom he met over five years ago and recruited to join his lab on one of his annual trips to China, with pursuing this work.

What Zhou found was “absolutely surprising and unexpected. I couldn’t expect the Swiss paper would be so far from the solution. I give [Zhou] credit for his inquisitiveness. It is hard and beautiful work.” Zhou said he met Oganov when he was a Ph.D. student. He found that the two of them had similar interests. “I love predicting crystal structures,” Zhou said.

Oganov was born in the Ukraine and raised and educated in Russia. He has worked in the UK, Switzerland and the United States. While science has a discipline and approach that keeps researchers from making unsupported claims, scientists still make mistakes. “Nobody,” he offered, “is insured from making mistakes.”