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Qiang Li. Photo courtesy of BNL

By Daniel Dunaief

Decades ago, most people could only tune to shows like The Jetsons to imagine interactive televisions in which people could see each other during conversations.

Qiang Li. Photo courtesy of BNL

In modern times, hand held devices and laptop computers have turned those science fiction ideas into everyday realities, as people can tell their phones to call their mom, to provide the outdoor temperature or to help them recall the name of a movie they saw decades ago.

These helpful technological devices, however, may some day go the way of the clunky desktop computers of yesteryear, as scientists around the world work to turn the vision of a quantum computer into a reality.

Scientists hope to develop a next generation of quantum computer that is faster, smarter, more flexible and more energy-efficient than current technological devices. They hope these devices could be the key to future technological breakthroughs, inspiring them to figure out how to bring the theory to life.

Collaborating with scientists at Ames Laboratory in Iowa, Qiang Li, SUNY Empire Innovation Professor in the Department of Physics and Astronomy at Stony Brook University and Leader of the Advanced Energy Materials Group at Brookhaven National Laboratory, recently published a study in the journal Nature Materials that provided fundamental information that might contribute to the field of quantum computers.

The group of scientists, which included Li’s PhD student Pedro Lozano, discovered a light-induced switch that twists the crystal lattice of a semimetal, turning on an electron current that the team believes is nearly dissipationless.

When currents move through wires between utilities and people’s homes and offices, that current encounters resistance, losing energy along the way, as if the movement towards the home created a tax on the journey. Similarly, dissipation inside an electronic device can sap some of the energy needed to transmit information or a signal, reducing the effectiveness of the process.

Li and BNL physicist Genda Gu synthesized, patterned and characterized the material at BNL, while Jigang Wang, a senior scientist at Ames Laboratory, performed the light-induced lattice twisting. The team helped create the light-induced switch.

Li described the effort as “fundamental research” and cautioned that any such advancement is more of a principal study, rather than a step closer to making any new qubit (the basic unit of quantum information) device.

“This is an experimental study to show that this is possible,” Li said. “It’s a demonstration of feasibility that you can harness chirality for building quantum information systems.”

With chirality, electrons have a handedness based on whether their spin and momentum are aligning in the same or opposite direction.

Once electrons have chirality, they can travel much easier, enabling a more direct and predictable route from one place to another.

Scientists like Li would like to create physical systems that enable them to control the chirality, preventing the spin from switching from one direction to the other.

Numerous factors can disrupt the chirality of an electron, including imperfections in the material.

A pulse-triggered light-induced switch can change the topology of a Weyl semimetal, making it possible to enable the movement of electrons that are nearly dissipationless. “For pure electronics, even computer chips, electrons consume a lot of energy because of electrical resistance,” Li said. “A chiral current [however] will travel without resistance, in ideal cases without chirality flipping.”

Chiral electrons travel through the semimetal at a speed as high as 1/300th of the speed of light and can travel considerably further before a collision that alters its direction, speed, or other particle properties. The mean free path, which is the average distance a particle will travel between such disruptive events, for a typical metal is nanometers. By contrast the chiral electrons can move micrometers, which is thousands of times longer.

An unperturbed chiral electron could travel further distances over shorter intervals, carrying preserved coded information without losing much energy during movement. 

Scientists have sought ways to create a path through which electrons travel with this predictable spin. They can break chiral symmetry by applying a magnetic field, which led to the discovery of the chiral magnetic effect by a team of scientists from BNL and Stony Brook University, including Dmitri Kharzeev, in 2014.  

For this work, Li received the Brookhaven Science and Technology Award in 2019.

“Using a magnetic field is problematic for some computations,” he said. Besides, people don’t want a “big magnet around your computers.”

Another way is to send in the laser pulse, creating left-handed or right-handed polarization.

To determine the ideal pulse to change the material, Li and Wang partnered with several theorists from Ames Lab and Ilias Perakis, Professor and Chair of Physics at the University of Alabama — Birmingham.

The theorists conducted detailed analysis of the lattice vibrations and the ideal pulse energy needed to break symmetry in the Weyl semimetal. “There is a very strong collaboration between the theorists and the experimentalists,” Li said.

While the research remains fundamental and is unlikely to generate a specific product any time soon, Li said it has “attracted a lot of attention” from other scientists and is a significant step forward in establishing the basic principles for topology-enabled quantum logic and information systems.

Li and Wang have been collaborating on this project for about two years as scientists around the world are in a “horse race” to produce results in the arena of quantum computing.

A resident of Setauket, Li and his wife Meiling Shih, have two children. Shih, who worked in the Stony Brook Pharmacological Science Department and later at Morgan Stanley, is retired and is now a volunteer instructor of a Tai Chi class for local seniors, 

Li enjoys jogging and runs a few miles every other day.

Down the road, Li hopes to address how to make the two quantum bits talk to each other.

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Results from a study of clouds and aerosols conducted in the Azores revealed that new particles can seed the formation of clouds in the marine boundary layer—the atmosphere up to about a kilometer above Earth's surface—even over the open ocean, where the concentration of precursor gases was expected to be low. Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

Understanding previously undocumented source of new particle formation will improve models of aerosols, clouds, and their impact on Earth’s climate

New results from an atmospheric study over the Eastern North Atlantic reveal that tiny aerosol particles that seed the formation of clouds can form out of next to nothingness over the open ocean. This “new particle formation” occurs when sunlight reacts with molecules of trace gases in the marine boundary layer, the atmosphere within about the first kilometer above Earth’s surface. The findings, published in the journal Nature Communications, will improve how aerosols and clouds are represented in models that describe Earth’s climate so scientists can understand how the particles—and the processes that control them—might have affected the planet’s past and present, and make better predictions about the future.

“When we say ‘new particle formation,’ we’re talking about individual gas molecules, sometimes just a few atoms in size, reacting with sunlight,” said study co-author Chongai Kuang, a member of the Environmental and Climate Sciences Department at the U.S. Department of Energy’s Brookhaven National Laboratory. “It’s interesting to think about how something of that scale can have such an impact on our climate—on how much energy gets reflected or trapped in our atmosphere,” he said.

Using an aircraft outfitted with 55 atmospheric instrument systems, scientists traversed horizontal tracks above and through clouds and spiraled down through atmospheric layers to provide detailed measurements of aerosols and cloud properties. The aircraft data were supplemented by measurements made by ground-based radars and other instruments. Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

But modeling the details of how aerosol particles form and grow, and how water molecules condense on them to become cloud droplets and clouds, while taking into consideration how different aerosol properties (e.g., their size, number, and spatial distribution) affect those processes is extremely complex—especially if you don’t know where all the aerosols are coming from. So a team of scientists from Brookhaven and collaborators in atmospheric research around the world set out to collect data in a relatively pristine ocean environment. In that setting, they expected the concentration of trace gases to be low and the formation of clouds to be particularly sensitive to aerosol properties—an ideal “laboratory” for disentangling the complex interactions.

“This was an experiment that really leveraged broad and collaborative expertise at Brookhaven in aerosol observations and cloud observations,” Kuang said. Three of the lead researchers—lead authors Guangjie Zheng and Yang Wang, and Jian Wang, principal investigator of the Aerosol and Cloud Experiments in the Eastern North Atlantic [https://www.arm.gov/publications/backgrounders/docs/doe-sc-arm-16-020.pdf] (ACE-ENA) campaign—began their involvement with the project while working at Brookhaven and have remained close collaborators with the Lab since moving to Washington University in St. Louis in 2018.

Land and sea

Brookhaven Lab atmospheric scientist Chongai Kuang (center) with Art Sedlacek (left) and Stephen Springston (right) aboard ARM’s Gulfstream-159 (G-1) aircraft during a 2010 atmospheric sampling mission that was not part of this study. Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

The study made use of a long-term ground-based sampling station on Graciosa Island in the Azores (an archipelago 850 miles west of continental Portugal) and a Gulfstream-1 aircraft outfitted with 55 atmospheric instrument systems to take measurements at different altitudes over the island and out at sea. Both the ground station and aircraft belong to the DOE Office of Science’s Atmospheric Radiation Measurement (ARM) user facility [https://www.arm.gov/], managed and operated by a consortium of nine DOE national laboratories.

The team flew the aircraft on “porpoise flights,” ascending and descending through the boundary layer to get vertical profiles of the particles and precursor gas molecules present at different altitudes. And they coordinated these flights with measurements taken from the ground station.

The scientists hadn’t expected new particle formation to be happening in the boundary layer in this environment because they expected the concentration of the critical precursor trace gases would be too low.

“But there were particles that we measured at the surface that were larger than newly formed particles, and we just didn’t know where they came from,” Kuang said.

The aircraft measurements gave them their answer.

Many of the choreographed flight paths for this study traversed the open ocean and also crossed within the ranges of the ground-based scanning radars at DOE’s Atmospheric Radiation Measurement (ARM) Climate Research Facility on Graciosa Island in the Azores. Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

“This aircraft had very specific flight patterns during the measurement campaign,” Kuang said. “They saw evidence that new particle formation was happening aloft—not at the surface but in the upper boundary layer.” The evidence included a combination of elevated concentrations of small particles, low concentrations of pre-existing aerosol surface area, and clear signs that reactive trace gases such as dimethyl sulfide were being transported vertically—along with atmospheric conditions favorable for those gases to react with sunlight.

“Then, once these aerosol particles form, they attract additional gas molecules, which condense and cause the particles to grow to around 80-90 nanometers in diameter. These larger particles then get transported downward—and that’s what we’re measuring at the surface,” Kuang said.

“The surface measurements plus the aircraft measurements give us a really good spatial sense of the aerosol processes that are happening,” he noted.

At a certain size, the particles grow large enough to attract water vapor, which condenses to form cloud droplets, and eventually clouds.

Both the individual aerosol particles suspended in the atmosphere and the clouds they ultimately form can reflect and/or absorb sunlight and affect Earth’s temperature, Kuang explained.

Study implications

Framed by a brilliant rainbow, ARM’s Gulfstream-159 (G-1) research aircraft sits on the tarmac on Terceira Island during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) winter 2018 intensive operation period in the Azores. Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

So now that the scientists know new aerosol particles are forming over the open ocean, what can they do with that information?

“We’ll take this knowledge of what is happening and make sure this process is captured in simulations of Earth’s climate system,” Kuang said.

Another important question: “If this is such a clean environment, then where are all these precursor gases coming from?” Kuang asked. “There are some important precursor gases generated by biological activity in the ocean (e.g., dimethyl sulfide) that may also lead to new particle formation. That can be a nice follow-on study to this one—exploring those sources.”

Understanding the fate of biogenic gases such as dimethyl sulfide, which is a very important source of sulfur in the atmosphere, is key to improving scientists’ ability to predict how changes in ocean productivity will affect aerosol formation and, by extension, climate.

The research was funded by the DOE Office of Science, DOE’s Atmospheric System Research, and by NASA. In addition to the researchers from Brookhaven Lab and Washington University, the collaboration included scientists from Pacific Northwest National Laboratory; Missouri University of Science and Technology; the University of Washington, Seattle; NASA Langley Research Center; Science Systems and Applications Inc. in Hampton, Virginia; the Max Planck Institute for Chemistry in Mainz, Germany; and the Scripps Institution of Oceanography, University of California, San Diego.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy.  The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.  For more information, please visit science.energy.gov [https://www.energy.gov/science/office-science].

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Accelerator physicist Chuyu Liu, the run coordinator for this year's experiments at the Relativistic Heavy Ion Collider (RHIC), in the Main Control Room of the collider-accelerator complex at Brookhaven National Laboratory.

Final stage of Beam Energy Scan II will collect low-energy collision data needed to understand the transition of ordinary nuclear matter into a soup of free quarks and gluons

Accelerator physicists are preparing the Relativistic Heavy Ion Collider (RHIC), a DOE Office of Science user facility for nuclear physics research at DOE’s Brookhaven National Laboratory, for its 21st year of experiments, set to begin on or about February 3. Instead of producing high-energy particle smashups, the goal for this run is to maximize collision rates at the lowest energy ever achieved at RHIC.

STAR co-spokesperson Lijuan Ruan noted that this year’s run is the third and final leg of Beam Energy Scan II, a systematic study of RHIC collisions at low energies.

“Run 21 is the final step of Beam Energy Scan II (BES-II), a three-year systematic study of what happens when gold ions—gold atoms stripped of their electrons—collide at various low energies,” said Brookhaven physicist Lijuan Ruan, co-spokesperson for RHIC’s STAR experiment collaboration.

Nuclear physicists will examine the BES-II data, along with data from RHIC’s high-energy collisions, to map out how these collisions transform ordinary protons and neutrons into an extraordinary soup of free quarks and gluons—a substance that mimics what the early universe was like some 14 billion years ago. By turning the collision energy down, RHIC physicists can change the temperature and other variables to study how these conditions affect the transition from ordinary matter to early-universe hot quark-and-gluon soup.

“Out of the five energies of BES-II—9.8, 7.3, 5.75, 4.6, and 3.85 billion electron volts, or GeV—this year’s run at 3.85 GeV is the most difficult one,” said Brookhaven Lab accelerator physicist Chuyu Liu, the run coordinator. That’s because “RHIC’s beams of gold ions are really difficult to hold together at the lowest energy,” he explained.

In Run 21, the accelerator team will use a variety of innovative components and schemes to maintain the lifetime and intensity of the colliding ion beams under challenging conditions. Read on to learn more about RHIC’s Run 21 science goals and the accelerator features that will make the science possible.

Scanning the transition

Mapping nuclear phase changes is like studying how water changes under different conditions of temperature and pressure (net baryon density for nuclear matter). RHIC’s collisions “melt” protons and neutrons to create quark-gluon plasma (QGP). STAR physicists are exploring collisions at different energies, turning the “knobs” of temperature and baryon density, to look for signs of a “critical point.” That’s a set of conditions where the type of transition between ordinary nuclear matter and QGP changes from a smooth crossover observed at RHIC’s highest energies (gradual melting) to an abrupt “first order” phase change that’s more like water boiling in a pot.

As Ruan explained, the quest to map out the phases of nuclear matter and the transitions between them is somewhat similar to studying how water molecules transform from solid ice to liquid water and gaseous steam at different temperatures and pressures. But nuclear matter is trickier to study.

“We need a powerful particle collider and sophisticated detector systems to create and study the most extreme forms of nuclear matter,” she said. “Thanks to the incredible versatility of RHIC, we can use the ‘knob’ of collision energy and the intricate particle-tracking capabilities of the STAR detector to conduct this systematic study.”

RHIC’s highest collision energies (up to 200 GeV) produce temperatures more than 250,000 times hotter than the center of the Sun. Those collisions “melt” the protons and neutrons that make up gold atoms’ nuclei, creating an exotic phase of nuclear matter called a quark-gluon plasma (QGP). In QGP, quarks and gluons are “free” from their ordinary confinement within protons and neutrons, and they flow with virtually no resistance—like a nearly perfect liquid.

But QGP lasts a mere fraction of a second before “freezing out” to form new particles. RHIC physicists piece together details of how the melting and refreezing happen by taking “snapshots” of the particles that stream out of these collisions.

By systematically lowering the collision energy, the physicists are looking for signs of a so-called “critical point.” This would be a set of conditions where the type of transition between ordinary nuclear matter and QGP changes from the smooth crossover observed at RHIC’s highest energies (picture butter melting gradually on a counter), to an abrupt “first order” phase change (think of how water boils suddenly at a certain temperature and holds that temperature until all the molecules evaporate).

As physicists turn RHIC’s collision energy down, they expect to see large event-by-event fluctuations in certain measurements—similar to the turbulence an airplane experiences when entering a bank of clouds—as conditions approach a “critical point” in the nuclear phase transition. This year’s run at the lowest collision energy will contribute to this search.

“Theorists have predicted that certain key measurements at RHIC will exhibit dramatic event-by-event fluctuations when we approach this critical point,” Ruan said.

Some RHIC physicists liken these fluctuations to the turbulence an airplane experiences when it moves from smooth air into a bank of clouds and then back out again. Measurements from phase I of RHIC’s Beam Energy Scan (BES-I, with data collected between 2010 and 2017) revealed tantalizing hints of such turbulence. But because collisions are hard to achieve at low energies, the data from BES-I aren’t strong enough to draw definitive conclusions.

Now, in BES-II, a host of accelerator improvements have been implemented to maximize low-energy collision rates.

Cooling the ions

One of the innovations that Chuyu Liu and the other Collider-Accelerator Department (C-AD) physicists managing RHIC operations will take advantage of in Run 21 is a first-of-its-kind beam-cooling system. This Low Energy RHIC electron Cooling  (LEReC) system operated at full capacity for the first time in last year’s RHIC run, making it the world’s first implementation of electron cooling in a collider. But it will be even more important for the lowest-of-low collision energies this year.

“The longer the beam stays at low energy, the more ‘intra-beam scattering’ and ‘space charge’ effects degrade the beam quality, reducing the number of circulating ions,” said Liu. Simplistic translation: The positively charged ions tend to repel one another. (Remember: The ions are atoms of gold stripped of their electrons, leaving a lot of net positive charge from the 79 protons in the nucleus.) The scattering and the repulsive space charge cause the ions to spread out, essentially heating up the beam as it makes its way around the 2.4-mile-circumference RHIC accelerator. And spread-out ions are less likely to collide.

A host of accelerator improvements have been implemented to maximize RHIC’s low-energy collision rates. These include a series of components that inject a stream of cool electron bunches into the ion beams in these cooling sections of the two RHIC rings. The cool electrons extract heat to counteract the tendency of RHIC’s ions to spread out, thereby maximizing the chances the ions will collide when the beams cross at the center of RHIC’s STAR detector.

“The LEReC system operates somewhat similar to the way the liquid running through your home refrigerator extracts heat to keep your food cool,” said Wolfram Fischer, Associate Chair for Accelerators in C-AD, “but the technology needed to achieve this beam cooling is quite a bit more complicated.”

A series of components (special lasers and a photocathode gun) produces bunches of relatively cool electrons, which are accelerated to match the bunching and near-light-speed pace of RHIC’s ions. Transfer lines inject the cool electrons into the stream of ion bunches—first in one RHIC ring, then, after making a 180-degree turn, into the other. As the particles mix, the electrons extract heat, effectively squeezing the spread-out ion bunches back together. The warmed-up electron bunches then get dumped and replaced with a new cool batch.

“To add more flexibility for cooling optimization during this year’s run at RHIC’s lowest energy, where the space-charge effects and beam lifetime degradation are concerns for both the electrons and the ions, we installed a new ‘second harmonic’ radiofrequency (RF) cavity in the electron accelerator,” said Alexei Fedotov, the accelerator physicist who led the LEReC project.

These cavities generate the radio waves that push the electrons along their path, with the higher (second harmonic) frequency helping to flatten out the longitudinal profile of the electron bunches. “This should help to reduce the space charge effect in the electron beams to achieve better cooling performance at low energy,” Fedotov said.

“We plan to commission the new electron beam transport line in late January and start cooling ions with the new electron beam setup in early February,” he added.

More accelerator advances

Similarly, third-harmonic RF cavities installed in the ion accelerator rings will help to flatten the longitudinal profile of the ion bunches, reducing their peak intensity and space charges, Liu explained. “With that, more bunch intensity can be injected into RHIC to produce higher luminosity—a measure closely tied to collision rates,” he said.

The accelerator team will also be commissioning a new bunch-by-bunch feedback system to help stabilize the beam for a better lifetime. “This system measures how each ion bunch deviates from the center of the beam pipe, and then applies a proportional correction signal through a component called a kicker to nudge each bunch back to where it should be,” Liu said.

All this cooling and nudging will counteract the ions’ tendency to spread, which maximizes chances of collisions happening when the two beams cross at the center of STAR.

“This run will bring together many of the advances we’ve been working on at RHIC to meet the challenging conditions of low-energy collisions,” said Fischer. “STAR would have preferred to test the lowest energy first, but we needed to learn everything possible (and develop the electron cooling system) before we could embark on operation at the most difficult energy.”

RHIC operations are funded by the DOE Office of Science.

Brookhaven National Laboratory is supported by the U.S. Department of Energy’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://www.energy.gov/science/ [https://www.energy.gov/science/].

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Dr. Christopher Vakoc. Photo from CSHL

On January 23, the Christina Renna Foundation (CRF), together with Cold Spring Harbor Laboratory, will host a free virtual celebration and sarcoma update to mark their 14th Annual Angel’s Wish Gala. Join us in celebrating 14 years of funding cutting edge research into rare pediatric cancer.

The gala will honor Christopher Vakoc, MD., Ph.D., Professor, Cold Spring Harbor Laboratory, 2020 CRF Research Award recipient for the Sarcoma Research Project

The Christina Renna Foundation is a 501(c)(3) public charity supporting children’s cancer research and furthering awareness and education through the support of cancer groups and outreach programs for the direct support of those in need. Funds raised through this event will go to continued research into rhabdomyosarcoma (RMS), a rare and often fatal form of pediatric cancer. In total, CRF has donated over $350,000 to research at CSHL. For more information, please visit: www.crf4acure.org

What: CRF Angel’s Wish Virtual Gala and Sarcoma Research Update

When: January 23, 2021 – 6 p.m. to 7 p.m.

RSVP: https://www.cshl.edu/mc-events/crf-angels-wish-virtual-gala-and-sarcoma-research-update/

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From left, Research Assistant Onur Eskiocak, CSHL Fellow Semir Beyaz and graduate student Ilgin Ergin. Photo by Gina Motisi, 2019/CSHL.

By Daniel Dunaief

It’s a catch-22: some promising scientific projects can’t get national funding without enough data, but the projects can’t get data without funding.

That’s where private efforts like The Mark Foundation for Cancer Research come in, providing coveted funding for promising high-risk, high-reward ideas. Founded and funded by Pamplona Capital Management CEO Alex Knaster in 2017, the Foundation has provided over $117 million in grants for various cancer research efforts.

Tobias Janowitz

This year, The Mark Foundation, which was named after Knaster’s father Mark who died in 2014 after contracting kidney cancer, has provided inaugural multi-million dollar grants through the Endeavor Awards, which were granted to three institutions that bring scientists with different backgrounds together to address questions in cancer research. 

In addition to teams from the University of California at San Francisco and a multi-lab effort from Columbia University, Memorial Sloan Kettering Cancer Center and Johns Hopkins University School of Medicine, Cold Spring Harbor Laboratory scientists Tobias Janowitz and Semir Beyaz received this award.

“We are absolutely delighted,” Janowitz wrote in an email. “It is a great honor and we are excited about the work.” He also indicated that the tandem has started the first set of experiments, which have produced “interesting results.”

The award provides $2.5 million for three years and, according to Janowitz, the researchers would use the funds to hire staff and to pay for their experimental work.

Having earned an MD and a PhD, Janowitz takes a whole body approach to cancer. He would like to address how the body’s response to a tumor can be used to improve treatment for patients. He explores such issues as how tumors interact with the biology of the host.

Semir Beyaz

Semir Beyaz, who explores how environmental factors like nutrients affect gene expression, metabolic programs and immune responses to cancer, was grateful for the support of the Mark Foundation.

Beyaz initially spoke with the foundation about potential funding several months before Janowitz arrived at Cold Spring Harbor Laboratory. When the researchers, whose labs are next door to each other, teamed up, they put together a multi-disciplinary proposal.

“If the risks [of the proposals] can be mitigated by the innovation, it may yield important resources or new paradigms that can be incorporated into research proposals that can be funded by the [National Institutes of Health] and other government agencies,” Beyaz said.

Janowitz wrote that he had a lunch together in a small group with Knaster, who highlighted the importance of “high-quality data and high-quality data analysis to advance care for patients with cancer.”

Michele Cleary, the CEO of The Mark Foundation, explained that the first year of the Endeavor program didn’t involve the typical competitive process, but, rather came from the Foundation’s knowledge of the research efforts at the award-winning institutions.

“We wanted to fund this concept of not just studying cancer at the level of the tumor or tumor cells themselves, but also studying the interaction of the host or patient and their [interactions] with cancer,” Cleary said. “We thought this was a fantastic project.”

With five people on the Scientific Advisory Committee who have PhDs at the Foundation, the group felt confident in its ability to assess the value of each scientific plan.

Scientists around the world have taken an effective reductionistic approach to cancer, exploring metabolism, neuroendocrinology and the microbiome. The appeal of the CSHL effort came from its effort to explore how having cancer changes the status of bacteria in the gut, as well as the interplay between cancer and the host that affects the course of the disease.

From left, Becky Bish, Senior Scientific Director, Ryan Schoenfeld, Chief Scientific Officer and Michele Cleary, CEO of The Mark Foundation at a workshop held at the Banbury Center at Cold Spring Harbor Laboratory in September 2019. Photo by Constance Brukin.

These are “reasonable concepts to pursue, [but] someone has to start somewhere,” Cleary said. “Getting funding to dive in, and launch into it, is hard to do if you can’t tell a story that’s based on a mountain of preliminary data.”

Beyaz said pulling together all the information from different fields requires coordinating with computational scientists at CSHL and other institutions to develop the necessary analytical frameworks and models. This includes Cold Spring Harbor Laboratory Fellow Hannah Meyer and Associate Professor Jesse Gillis.

“This is not a simple task,” Beyaz said. The researchers will “collaborate with computational scientists to engage currently available state-of-the-art tools to perform data integration and analysis and develop models [and] come up with new ways of handling this multi-dimensional data.”

Cleary is confident Janowitz and Beyaz will develop novel and unexpected insights about the science. “We’ll allow these researchers to take what they learn in the lab and go into the human system and explore it,” she said.

The researchers will start with animal models of the disease and will progress into studies of patients with cancer. The ongoing collaboration between CSHL and Northwell Health gives the scientists access to samples from patients.

With the Endeavor award, smaller teams of scientists can graduate to become Mark Foundation Centers in the future. The goal for the research the Foundation funds is to move towards the clinic. “We are trying to join some dots between seemingly distinct, but heavily interconnected, fields,” Beyaz said.

Beyaz has research experience with several cancers, including colorectal cancer, while Janowitz has studied colorectal and pancreatic cancer. The tandem will start with those cancers, but they anticipate that they will “apply similar kinds of experimental pipelines” to other cancer types, such as renal, liver and endometrial, to define the shared mechanisms of cancer and how it reprograms and takes hostage the whole body, Beyaz said. 

“It’s important to understand what are the common denominators of cancer, so you might hopefully find the Achilles Heel of that process.”

While Cleary takes personal satisfaction at seeing some of the funding go to CSHL, where she and Mark Foundation Senior Scientific Director Becky Bish conducted their graduate research, she said she and the scientific team at the foundation were passionate to support projects that investigated the science of the patient.

“No one has tried to see what is the cross-talk between the disease and the host and how does that actually play out in looking at cancer,” said Cleary, who earned her PhD from Stony Brook University. “It’s a bonus that an institution that [she has] the utmost respect for was doing something in the same space we cared” to support.

The CSHL research will contribute to an understanding of cachexia, when people with cancer lose muscle mass, weight, and their appetite. Introducing additional nutrition to people with this condition doesn’t help them gain weight or restore their appetite.

Janowitz and Beyaz will explore what happens to the body physiologically when the patient has cachexia, which can “help us understand where we can intervene before it’s too late,” Cleary said.

The CSHL scientists will also study the interaction between the tumor and the immune system. Initially, the immune system recognizes the tumor as foreign. Over time, however, the immune system becomes exhausted.

Researchers believe there might be a “tipping point” in which the immune system transitions from being active to becoming overwhelmed, Cleary said. People “don’t understand where [the tipping point] occurs, but if we can figure it out, we can figure out where to intervene.”

Scientists interested in applying for the award for next year can find information at the web site: https://themarkfoundation.org/endeavor/. Researchers can receive up to $1 million per year for three years. The Mark Foundation is currently considering launching an Endeavor call for proposals every other year.

 

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Brookhaven Lab Scientist Guobin Hu loaded the samples sent from researchers at Baylor College of Medicine into the new cryo-EM at LBMS. Photo from BNL

On January 8 the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory welcomed the first virtually visiting researchers to the Laboratory for BioMolecular Structure (LBMS), a new cryo-electron microscopy facility. DOE’s Office of Science funds operations at this new national resource, while funding for the initial construction and instrument costs was provided by NY State. This state-of-the-art research center for life sciences imaging offers researchers access to advanced cryo-electron microscopes (cryo-EM) for studying complex proteins as well as the architecture of cells and tissues.

Many modern advances in biology, medicine, and biotechnology were made possible by researchers learning how biological structures such as proteins, tissues, and cells interact with each other. But to truly reveal their function as well as the role they play in diseases, scientists need to visualize these structures at the atomic level. By creating high-resolution images of biological structure using cryo-EMs, researchers can accelerate advances in many fields including drug discovery, biofuel development, and medical treatments.

During the measurement of the samples, the LBMS team interacted with the scientists from Baylor College of Medicine through Zoom to coordinate the research. Photo from BNL

This first group of researchers from Baylor College of Medicine used the high-end instruments at LBMS to investigate the structure of solute transporters. These transporters are proteins that help with many biological functions in humans, such as absorbing nutrients in the digestive system or maintaining excitability of neurons in the nervous system. This makes them critical for drug design since they are validated drug targets and many of them also mediate drug uptake or export. By revealing their structure, the researchers gain more understanding for the functions and mechanisms of the transporters, which can improve drug design.  The Baylor College researchers gained access to the cryo-EMs at LBMS through a simple proposal process.

“Our experience at LBMS has been excellent. The facility has been very considerate in minimizing user effort in submission of the applications, scheduling of microscope time, and data collection,” said Ming Zhou, Professor in the Department of Biochemistry of Molecular Biology at Baylor College of Medicine.

All researchers from academia and industry can request free access to the LBMS instruments and collaborate with the LBMS’ expert staff.

“By allowing science-driven use of our instruments, we will meet the urgent need to advance the molecular understanding of biological processes, enabling deeper insight for bio-engineering the properties of plants and microbes or for understanding disease,” said Liguo Wang, Scientific Operations Director of the LBMS. “We are very excited to welcome our first visiting researchers for their remote experiment time. The researchers received time at our instruments through a call for general research proposals at the end of August 2020. Since September, we have been running the instruments only for COVID-19-related work and commissioning.”

LBMS has two cryo-electron microscopes—funded by $15 million from NY State’s Empire State Development—and the facility has space for additional microscopes to enhance its capabilities in the future. In recognition of NY State’s partnership on the project and to bring the spirit of New York to the center, each laboratory room is associated with a different iconic New York State landmark, including the Statue of Liberty, the Empire State Building, the Stonewall National Monument, and the Adam Clayton Powell Jr. State Office Building.

“By dedicating our different instruments to New York landmarks, we wanted to acknowledge the role the State played in this new national resource and its own unique identity within Brookhaven Lab,” said Sean McSweeney, LBMS Director. “Brookhaven Lab has a number of facilities offering scientific capabilities to researchers from both industry and academia. In our case, we purposefully built our center next to the National Synchrotron Light Source II, which also serves the life science research community. We hope that this co-location will promote interactions and synergy between scientists for exchanging ideas on improving performance of both facilities.”

Brookhaven’s National Synchrotron Light Source II (NSLS-II) is a DOE Office of Science User Facility and one of the most advanced synchrotron light sources in the world. NSLS-II enables scientists from academia and industry to tackle the most important challenges in quantum materials, energy storage and conversion, condensed matter and materials physics, chemistry, life sciences, and more by offering extremely bright light, ranging from infrared light to x-rays. The vibrant structural biology and bio-imaging community at NSLS-II offers many complementary techniques for studying a wide variety of biological samples.

“At NSLS-II, we build strong partnership with our sister facilities, and we are looking forward to working closely with our colleagues at LBMS. For our users, this partnership will offer them access to expert staff at both facilities as well as to a versatile set of complementary techniques,” said NSLS-II Director John Hill. “NSLS-II has a suite of highly automated x-ray crystallography and solution scattering beamlines as well as imaging beamlines with world-leading spatial resolution. All these beamlines offer comprehensive techniques to further our understanding of biological system. Looking to the future, we expect to combine other x-ray techniques with the cryo-EM data to provide unprecedented information on the structure and dynamics of the engines of life.”

LBMS operations are funded by the U.S. Department of Energy’s Office of Science. NSLS-II is a DOE Office of Science user facility.

Brookhaven National Laboratory is supported by the U.S. Department of Energy’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://energy.gov/science.

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Illustration depicting Falcatakely amid nonavian dinosaurs and other creatures during the Late Cretaceous in Madagascar. (Credit: Mark Witton)

By Daniel Dunaief

Dromomeron and Falcatakely lived nowhere near each other. They also lived millions of years apart, offering the kind of evolutionary pieces to different puzzles that thrill paleontologists.

Left, Alan Turner holds a model of the maxilla of Falcatakely, with a CT reconstruction on his computer screen.

These two creatures, the first a three-foot long dinosaur precursor discovered in Ghost Ranch, New Mexico, and the second a crow-sized bird fossil discovered in Madagascar, have taken center stage in recent scientific circles.

What they have in common is Alan Turner, Associate Professor in the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook University.

The discoveries, which were made over a decade ago, were recently parts of publications in consecutive issues of the prestigious journal Nature. “It’s really exciting,” Turner said. “I definitely feel fortunate” to contribute to these two publications.

Turner, who is not the lead author in either study, emphasized that these papers were only possible through teamwork. “These large, collaborative efforts are one of the ways these really significant discoveries can happen,” he said.

The work that includes Dromomeron, in particular, is one that “any one of our groups couldn’t have done [alone]. It hinged on a series of discoveries across multiple continents.”

Each paper helps fill out different parts of the evolutionary story. The Dromomeron discovery helps offer an understanding of a major evolutionary transition from the Triassic Period, while the Falcatakely find offers a look at the diversification of birds during the Cretaceous Period.

Dromomeron

Starting with the paper in which Dromomeron appears, researchers used a collection of dinosaur precursor fossils to study a smaller group of animals called lagerpetids, whose name means “rabbit lizard” or “rabbit reptile.”

These creatures lived during the age of the earliest relatives of lizards, turtles and crocodylians.

Above, a reconstruction of a pterosaur, a lagerpetid from the Triassic Period/Rodolfo Nogueria

Pterosaurs, which have a characteristic elongated fourth finger that forms a large portion of their wing, lived 160 million years ago, which means that the earlier, flightless lagerpetids roamed the Earth about 50 million years before pterosaurs.

Turner discovered Dromomeron in Ghost Ranch, New Mexico 14 years ago. Since then, other scientists have unearthed new bones from this prehistoric rabbit lizard group in North America, Brazil, Argentina and Madagascar.

Scientists involved in this paper used micro-CT scans and 3D scanning to compare lagerpetid and pterosaur skeletal fossils to demonstrate overlaps in their anatomy. The shape and size of the brain and inner ear of these lagerpetid fossils share similarities with pterosaurs.

The inner ear, Turner explained, is particularly important for animals like the pterosaur, which likely used it the way modern birds do when they are in flight to help determine their location in space and to keep their balance.

Lagerpetids, however, didn’t fly, so paleontologists aren’t sure how these ancient rabbit lizards used their inner ear.

Turner said the Dromomeron discovery was initially more of a curiosity. In fact, when researchers found it, “we had a blackboard in this collection space where we were working,” Turner recalled. “It was unceremoniously referred to as ‘Reptile A.’ There weren’t a lot of things to compare it to. At that point we knew we had a thing but we didn’t know what it was.”

A colleague of Turners, Randall Irmis, Chief Curator and Curator of Paleontology, Associate Professor of Geology and Geophysics at the University of Utah, traveled to Argentina, where he noticed a creature that was similar to the find in New Mexico.

Irmis’s trip “allowed our team to confirm our comparison [between Dromomeron and Lagerpeton] first-hand. From there, we were able to build out the larger evolutionary context,” Turner explained in an email.

Falcatakely

Meanwhile, Turner and Patrick O’Connor, Professor of Anatomy and Neuroscience at Ohio University and lead author on the study, shared their discovery of a bird they located in Madagascar that they called Falcatakely.

The bird’s name is a combination of Latin and Malagasy, the language of the island nation of Madagascar, which means “small scythe” and describes the beak shape.

Right, an artist reconstruction of the Late Cretaceous enantiornithine bird Falcatakely forsterae with its unique beak/Sketch by Mark Witton

The scientists found a partial skull in a quarry in Madagascar. The fossil was embedded in rocks. Turner and O’Connor analyzed it through CT scanning and through careful physical and digital preparation by their colleague Joe Groenke, laboratory coordinator for the O’Connor lab.

The discovery of grooves on the side of the face for a beak took the researchers by surprise.

“As the face began to emerge from the rock, we immediately knew that it was something very special, if not entirely unique,” O’Connor said in a press release. 

“Mesozoic birds with such high, long faces are completely unknown, with Falcatakely providing a great opportunity to reconsider ideas around head and beak evolution in the lineage leading to modern birds.”

As with the Dromomeron find, the discovery of Falcatakely didn’t provide a eureka moment when the scientists found it 10 years ago.

“We didn’t know [what we had] when we collected this material,” Turner said. “It wasn’t until we CT scanned the block in an effort to begin the preparation that we said, ‘Wait a second. There’s something really weird in this block. The flat part turned out to be the side of the face.”

Turner originally thought it could have been the breast bone of a larger dinosaur. During the pandemic, he has come back to projects that have been sitting around for several years. Some have “probably danced on the periphery that have now come to the dance,” in terms of his focus.

In looking back on the ingredients that made these two Nature papers possible, Turner added another element. These publications underline “the importance of investing in long term field work expeditions,” he said.

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Corals in the Gulf of Aqaba in the Red Sea. Photo by Maoz Fine

A paper published in Frontiers in Marine Science on December 15 is calling for action to remove the oil from a decaying and inactive tanker in the Red Sea that holds approximately one million barrels of oil – four times the amount of oil contained in the Exxon Valdez, the tanker that had a disastrous environmental oil spill in 1989 –  before its current seepage turns into a massive oil spill into the sea. The paper, a policy brief, is authored by a team of international scientists led by Karine Kleinhaus, MD, MPH, an Associate Professor of the School of Marine and Atmospheric Sciences (SoMAS) at Stony Brook University.

Scientists produced a computer simulation of the spread of oil from the abandoned tanker in the Red Sea. The projection shows mass spread during winter compared to summer due to current patterns. The data shown was produced by running the model for 30 days. Oil spread even further from the tanker when the model ran for a longer period of time. Photo from SBU

Called the Safer, the tanker is a floating storage and offloading unit (FSO) abandoned for years, and with access controlled by Yemen’s Houthis. The paper, titled “A Closing Window of Opportunity to Save a Unique Marine Ecosystem,” comes shortly after The New York Times reported on November 24 that the Houthis will grant permission to a United Nations (UN) team to board the Safer to inspect and repair the vessel in the near future.  

“The time is now to prevent a potential devastation to the region’s waters and the livelihoods and health of millions of people living in half a dozen countries along the Red Sea’s coast,” says Dr. Kleinhaus. “If a spill from the Safer is allowed to occur, the oil would spread via ocean currents to devastate a global ocean resource, as the coral reefs of the northern Red Sea and Gulf of Aqaba are projected to be among the last reef ecosystems in the world to survive the coming decades.”

She explained that the reason the coral reefs of the northern Red Sea are unique is because they survive in much warmer waters than today’s ocean temperatures, which are becoming too high for most coral to tolerate (over half of the Great Barrier Reef has degraded due to marine heat waves caused by climate change). Additionally, the fish living on the reefs off Yemen in the southern Red Sea are a major resource of food for the populations of the region, and the entire sea and its coral reefs are a highly biodiverse and rich ecosystem.

Dr. Kleinhaus and co-authors point out that in May 2020 seawater breached the Safer and entered the engine compartment, and news agencies have reported oil spots next to the tanker, indicating likely seepage. The tanker has been abandoned since 2015, which the authors emphasize is a long advance warning of a decaying tanker poised to degrade to the point of a mass oil leak into the Red Sea.

The paper reveals a computer model of how the oil will disperse if a major leak begins this winter. The model shows that the oil will reach much further if the spill occurs now rather than in summer, due to the typical winter currents in that region of the Red Sea. A spill now will cause much broader and more extensive devastation as a result.

Despite the signs of the Safer’s structural deterioration, access to the tanker has yet to be achieved and concrete steps to repair or to prevent an oil spill have yet to been taken, the authors point out. Dr. Kleinhaus adds that winter is the worst time to have an oil spill in that region, as winter currents will disperse oil much more widely.

The authors urge that “Emergent action must be taken by the UN and its International Maritime Organization to address the threat of the Safer, despite political tensions, as a spill will have disastrous environmental and humanitarian consequences, especially if it occurs during winter. With millions of barrels of oil, a day passing through the Red Sea, a regional strategy must be drafted for leak prevention and containment that is specific to the Red Sea’s unique ecosystems, unusual water currents, and political landscape.”

 

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Long Island Explorium

The Long Island Explorium, 101 E. Broadway, Port Jefferson has been selected by the Museum Association of New York (MANY) with 98 museums from across New York State to participate in “Building Capacity, Creating Sustainability, Growing Accessibility”, an IMLS CARES Act grant project designed to help museums impacted by the COVID-19 pandemic share their collections and reach audiences who cannot physically visit their museums. Staff will be trained to use new hardware and software to develop programs that will engage their communities and reach new audiences.

The grant is an in-depth partnership for two years designed to strengthen museum virtual programs. In addition to the training, museums will receive hardware and software equivalent to a $5,000 in-kind donation.

“We are honored to be awarded IMLS CARES act funding and excited to be able to make an impact on the work of our colleagues and their museums across New York State,” said Erika Sanger, MANY Executive Director. “We are living in an age of transition, experiencing a radical shift in our ways of learning and communicating. The group selected captures the diversity of our shared history in NY and our nation. The stories embodied in the museums’ collections and the storytelling talents of their interpretive staff are the heart of the project.”

In this two-year program, museums will identify a program to virtually deliver to their audiences, focusing on developing programs from stories found in their collections that reveal cultural and racial diversity in their communities.“We are ecstatic to receive this award to continue to be responsive and reflective of the diverse communities we aim to reach. We aim to build ​upon a current exhibit, “​Rain Gardens: Linking Water, Wildlife, and Wisdom,” and use technology to develop a video/ audio series that focuses on the rich heritage of the indigenous peoples of Long Island and their contributions to Long Island”, said Angeline Judex, MPA, Executive Director, Long Island Explorium.

“The Long Island Explorium was selected due to our perseverance in the face of the devastating COVID-19 pandemic and our commitment to STEM and those in our communities on Long Island and in New York,” explained Lisa Collet Rodriguez, M.S. Director, Digital Media/Marketing, Long Island Explorium. “We are excited to begin working with the Museum Association of New York serving high need communities through this initiative. The program is geared to assist and successfully respond to one of the biggest challenges created by the pandemic: how we reach audiences that cannot visit the Long Island Explorium in person. ​The pandemic has provided the Explorium with an opportunity to re-imagine our program delivery methods and engage our online audiences through meaningful content on a much larger scale.”

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Michael Schatz and Aspyn Palatnick. Photo by Lauryl Palatnick

By Daniel Dunaief

Michael Schatz, Adjunct Associate Professor at Cold Spring Harbor Laboratory, saw some similarities to his own life when he met the then 14-year old Aspyn Palatnick.

Palatnick, who was a student at Cold Spring Harbor High School, had been developing games for the iPhone. When he was that age, Schatz, who is also a Bloomberg Distinguished Associate Professor of Computer Science and Biology at Johns Hopkins University, stayed up late into the evening programming his home computer and building new software systems.

Meeting Palatnick eight years ago was a “really special happenstance,” Schatz said. He was “super impressed” with his would-be young apprentice.

When he first met Schatz, Palatnick explained in an email that he “realized early on that he would be an invaluable mentor across research, computer science, and innovation.”

Palatnick was looking for the opportunity to apply some of the skills he had developed in making about 10 iPhone games, including a turtle racing game, to real-world problems.

Knowing that Palatnick had no formal training in computer science or genetics, Schatz spent the first several years at the white board, teaching him core ideas and algorithms.

“I was teaching him out of graduate student lecture notes,” Schatz said.

Schatz and Palatnick, who graduated with a bachelors and master’s from the University of Pennsylvania and works at Facebook, have produced a device which they liken to a “tricorder” from Star Trek. Using a smart phone or other portable technology, the free app they created called iGenomics is a mobile genome sequence analyzer.

The iPhone app complements sequencing devices Oxford Nanopore manufactures. A mobile genetic sequencer not only could help ecologists in the field who are studying the genetic codes for a wide range of organisms, but it could also be used in areas like public health to study the specific gene sequences of viruses like SARS-CoV-2, which causes COVID-19.

In a paper published in GigaScience, Schatz and Palatnick describe how to use iGenomics to study flu genomes extracted from patients. They also have a tutorial on how to use iGenomics for COVID-19 research.

While developing the mobile sequencing device wasn’t the primary focus of Schatz’s work, he said he and others across numerous departments at Johns Hopkins University spent considerable time on it this summer, as an increasing number of people around the world contracted the virus.

“It very rapidly became how I was spending the majority of my time,” said Schatz.

Palatnick is pleased with the finished product.

“We’ve made DNA sequence analysis portable for the first time,” he explained in an email.

Palatnick said the app had to use the same algorithms as traditional genomics software running on supercomputers to ensure that iGenomics was accurate and practical. Building algorithms capable of rendering DNA alignments and mutations as users tapped, scrolled and pinched the views presented a technical hurdle, Palatnick wrote.

While Schatz is optimistic about the vaccinations that health care workers are now receiving, he said a mass vaccination program introduces new pressure on the virus.

“We and everyone else are watching with great interest to see if [the vaccinations] cause the virus to mutate,” Schatz said. “That’s the big fear.”

Working with the sequences from Nanopore technology, iGenomics can compare the entire genome to known problematic sequences quickly. Users need to get the data off the Oxford Nanopore device and onto the app. They can do that using email, from Dropbox or the web. 

In prior viral outbreaks, epidemiologists traveled with heavier equipment to places like West Africa to monitor the genome of Ebola or to South and Central America to study the Zika virus genome.

“There’s clearly a strong need to have this capability,” Schatz said.

Another iGenomics feature is that it allows users to airdrop any information to people, even when they don’t have internet access.

Schatz urged users to ensure that they use a cloud-based system with strong privacy policies before considering such approaches, particularly with proprietary data or information for which privacy is critical.

As for COVID-19, people with the disease have shown enough viral mutations that researchers can say whether the strain originated in Europe or China.

“It’s kind of like spelling mistakes,” Schatz said. “There are enough spelling mistakes where [researchers] could know where it came from.”

Palatnick described iGenomics as an “impactful” tool because the app has increased the population of people who can explore the genome from institutional researchers to anyone with an iPhone or iPad.

In the bigger picture, Schatz is broadly interested in learning how the genome creates differences.

“It’s important to understand these messages for the foods we eat, the fuels we use, the medicines we take,” Schatz said. “The next frontier is all about interpretation. One of the most powerful techniques is comparing one genome to another.”

Schatz seeks out collaborators in a range of fields and at numerous institutions, including Cold Spring Harbor Laboratory.

Schatz and W. Richard McCombie, Professor at CSHL, are studying the genomes of living fossils. These are species that haven’t evolved much over millions of years. They are focusing on ancient trees in Australia that have, more or less, the same genetic make up they did 100 million years ago.

As for Palatnick, Schatz described his former intern and tricorder creating partner as a “superstar in every way.” Schatz said it takes considerable fortitude in science, in part because it takes years to go from an initial idea on a napkin to something real.

Down the road, Schatz wouldn’t be surprised if Palatnick took what he learned and developed and contributed to the founding of the next Twitter or Facebook.

“He has that kind of personality,” Schatz said.

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