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  • richardmitnick 8:59 am on April 21, 2017 Permalink | Reply
    Tags: , , BNL, OpenMP (for Multi-Processing) Architecture Review Board (ARB)   

    From BNL: “Brookhaven Lab Joins the OpenMP Architecture Review Board’ 

    Brookhaven Lab

    April 20, 2017
    Ariana Tantillo
    atantillo@bnl.gov

    Lab to help evolve the standard for OpenMP, the most popularly used shared-memory parallel programming model.

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    (Left to right) Lingda Li, Abid Malik, and Verinder Rana of Brookhaven Lab’s Computational Science Initiative (CSI) will collaborate with members of the OpenMP Architecture Review Board to help shape the OpenMP programming standard for high-performance computing. Not pictured: Kerstin Kleese van Dam, CSI director, and Barbara Chapman, director of CSI’s Computer Science and Mathematics research team who led the Brookhaven initiative to join the OpenMP ARB.

    The U.S. Department of Energy’s (DOE) Brookhaven National Laboratory has joined the OpenMP (for Multi-Processing) Architecture Review Board (ARB). This nonprofit technology consortium manages the OpenMP application programming interface specification for parallel programming on shared-memory machines, in which any processor can access data stored in any part of the memory.

    As part of this consortium of leading hardware and software vendors and research organizations, Brookhaven Lab will help shape one of the most widely used programming standards for high-performance computing—the combination of computing power from multiple processors working simultaneously to solve large and complex problems. Brookhaven’s participation in the OpenMP ARB is critical to ensuring the OpenMP standard supports scientific requirements for data analysis, modeling and simulation, and visualization.

    “Advancing the frontiers of high-performance and data-intensive computing is central to Brookhaven’s mission in scientific discovery. Our membership in the OpenMP ARB recognizes the importance we place upon OpenMP for our science portfolio, both now and in the future,” said Robert Harrison, chief scientist of the Computational Science Initiative (CSI) at Brookhaven Lab and director of the Institute for Advanced Computational Science at Stony Brook University, which joined OpenMP ARB at the end of 2016.

    Barbara Chapman, director of CSI’s Computer Science and Mathematics research team at Brookhaven and a professor of applied mathematics and statistics and of computer science at Stony Brook, led the initiative to join the OpenMP ARB. Chapman, whose research focuses on programming models for large-scale computing, has been involved with the evolution of OpenMP since 2001.

    Abid Malik, a senior technology engineer on Chapman’s team, and research assistant Verinder Rana will represent Brookhaven during monthly meetings with the ARB. They plan to join several of the subgroups that focus on evolving specific aspects of the OpenMP programming model, including those for computational accelerators (such as graphics processing units, or GPUs), the C++ programming language, and memory management.

    Each ARB member organization makes suggestions on how OpenMP should be evolved to meet their specific requirements. In turn, the vendors decide which suggestions to implement, depending on how relevant they are to a wide range of applications.

    According to Malik, OpenMP will benefit from Brookhaven’s expertise in tackling big data challenges, especially those posed by its DOE Office of Science User Facilities—the Center for Functional Nanomaterials, National Synchrotron Light Source II, and Relativistic Heavy Ion Collider.

    BNL Center for Functional Nanomaterials

    BNL NSLS-II

    BNL NSLS-II

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    BNL RHIC Star detector

    BNL RHIC Campus

    Using this expertise, Brookhaven will help advance the OpenMP standard for next-generation supercomputers, which will help scientists tackle increasingly complex problems by performing calculations at unprecedented speed and accuracy.

    “The OpenMP language subgroup is actively working with the scientific community to prepare OpenMP for exascale computing,” said Malik. “Brookhaven’s big data experience will help expand OpenMP to include features useful for porting big data programs on multicore CPUs [central processing units] and GPUs.”

    See the full article here .

    Please help promote STEM in your local schools.

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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 4:26 pm on April 20, 2017 Permalink | Reply
    Tags: , , BNL,   

    From BNL: “Q&A with CFN User Davood Shahrjerdi” 

    Brookhaven Lab

    April 18, 2017
    Ariana Tantillo
    atantillo@bnl.gov

    Combining the unique properties of emerging nanomaterials with advanced silicon-based electronics, NYU’s Shahrjerdi engineers nano-bioelectronics

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    Davood Shahrjerdi in the scanning electron microscope facility at Brookhaven Lab’s Center for Functional Nanomaterials (CFN). The image on the screen is a Hall bar structure for measuring carrier transport in a semiconductor wire.

    Davood Shahrjerdi is an assistant professor of electrical and computer engineering at New York University (NYU) and a principal investigator at the NYU Laboratory for Nano-Engineered Hybrid Integrated Systems. Shahrjerdi, who holds a doctorate in solid-state electronics from The University of Texas at Austin, engineers nanodevices for sensing and life science applications through integrating the unique properties of emerging nanomaterials with advanced silicon-based electronics. For the past two years, he has been using facilities at the Center for Functional Nanomaterials (CFN)—a U.S. Department of Energy (DOE) Office of Science User Facility at Brookhaven National Laboratory—to fabricate and characterize these nanodevices.

    What is the mission of the NYU Laboratory for Nano-Engineered Hybrid Integrated Systems?

    My lab’s mission is to create new electronic devices for sensing and life science applications. To achieve this goal, we combine the benefits of emerging nanomaterials—such as two-dimensional (2D) materials like graphene—and advanced silicon integrated circuits. These nano-engineered bioelectronic systems offer new functionalities that exist in neither nanomaterials nor silicon electronics alone. At the moment, we are leveraging our expertise to engineer new tools for neuroscience applications.

    We are also doing research for realizing high-performance flexible electronics for bioelectronics applications. Our approach is two pronged: (1) flexible electronics using technologically mature materials, such as silicon, that are conventionally mechanically rigid, and (2) flexible electronics using atomically thin 2D nanomaterials that are inherently flexible.

    Given the resources of NYU and the plethora of nanotechnology research centers in the surrounding New York City area, why bring your research to CFN?

    Before I joined academia, I was a research staff member at the IBM Thomas J. Watson Research Center, where I had easy access to advanced fabrication and characterization facilities. When I joined NYU in September 2014, I began to look for research facilities to pursue my research projects. In my search, I discovered CFN and reached out to its scientists, who were very helpful in explaining the research proposal process and the available facilities for my research. In the past two years, my research projects have evolved tremendously, and access to CFN laboratories has been instrumental to this evolution. Because research-active scientists maintain CFN labs, I can conduct my research without major hiccups—a rare occurrence in academia, where equipment downtime and process changes could set back experiments.

    It is not only the state-of-the-art facilities but also the interactions with scientists that have made CFN invaluable to my research. I could use other fabrication facilities in Manhattan, but I prefer to come to CFN. At IBM, I could walk out of my office and knock on any door, gaining access to the expertise of chemists, physicists, and device engineers. This multidisciplinary environment similarly exists at CFN, and it is conducive to driving science forward. Bringing my research to the CFN also means that my doctoral students and postdocs have the opportunity to use state-of-the-art facilities and interact with world-class scientists.

    What tools do you use at CFN to conduct your research, and what are some of the projects you are currently working on?

    We synthesize the 2D nanomaterials at my NYU lab, with subsequent device fabrication and some advanced material characterization at CFN. After device fabrication, we perform electrical characterization at my NYU lab.

    In addition to using the materials processing capabilities in CFN’s clean room, we use advanced material characterization capabilities to glean information about the properties of our materials and devices at the nanoscale. These capabilities include transmission electron microscopy (TEM) to study the structure of the materials, X-ray photoelectron spectroscopy to examine their chemical state, and nano-Auger electron spectroscopy to probe their elemental composition.

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    The 5,000-square-foot clean room at CFN is dedicated to state-of-the-art processing of thin-film materials and devices. Capabilities include high-resolution patterning by electron-beam and nanoimprint lithography methods, plasma-based dry etch processes, and material deposition.

    One of our projects is the large-area synthesis of 2D transition metal dichalcogenide semiconductors, which are materials that have a transition metal atom (such as molybdenum or tungsten) sandwiched between two chalcogen atoms (sulfur, selenium, or tellurium). Using a modified version of chemical vapor deposition (referring to the deposition of gaseous reactants onto a substrate to form a solid), my team synthesized a monolayer of tungsten disulfide that has the highest carrier mobility reported for this material. I am now working with CFN scientists to understand the origin of this high electrical performance through low-energy electron microscopy (LEEM). Our understanding could lead to the development of next-generation flexible biomedical devices.

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    The single-atom-thick tungsten disulfide (illustration, left) can absorb and emit light, making it attractive for applications in optoelectronics, sensing, and flexible electronics. The photoemission image of the NYU logo (right) shows the monolayer material emitting light.

    Recently, our team together with CFN scientists published a paper on studying the defects in another 2D transition metal dichalcogenide, monolayer molybdenum disulfide. We treated the material with a superacid and used the nano-Auger technique to determine which structural defects were “healed” by the superacid. Our electrical measurements revealed the superacid treatment improves the material’s performance.

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    Shahrjerdi and his team fabricated top-gated field-effect transistors (FETs)—devices that utilize a small voltage to control current—on as-grown and superacid-treated molybdenum disulfide films. A schematic of the device is shown in (a). As seen in the graph (b), the chemical treatment (TFSI, red line) improves the electronic properties of the device. From Applied Physics Letters 110, 033503 (2017).

    Another ongoing project in my NYU lab involves a collaborative effort with the NYU Center for Neural Science to develop next-generation neuroprobes for understanding not only the electrical signaling in the brain but also the chemical signaling. This problem is challenging to solve, and we are excited about the prospects of nanotechnology for realizing an innovative solution to it.

    In fabricating nanoelectronic materials and components, what are some of the challenges you face?

    Nanomaterials are usually difficult to handle—they are often very thin and are highly sensitive to defects or misprocessing. As a result, reproducibility could be a challenge. To understand what is causing a particular observed behavior, we have to fabricate many samples and try to reproduce the same result to understand the physical origin of an observed behavior.

    Also, it often happens that you expect to observe a certain behavior but you might end up observing an anomalous behavior that could lead to new discoveries. For example, I accidentally stumbled on the epitaxial growth of silicon on silicon at 120-degrees Celsius while playing around with hydrogen dilution during the deposition of amorphous silicon. This temperature is much lower than the usual temperature required by the traditional approach. My IBM collaborators and I published the work, and it actually led to a best paper award from the Journal of Electronic Materials!

    What is the most exciting thing on the horizon for nanoelectronics? What do you personally hope to achieve?

    Over the next 5 to 10 years, the field of nanoelectronics has great potential to transform our lives—especially in the areas of bioelectronics and bio-inspired electronics, with the marriage between nanomaterials and conventional electronics leading to new discoveries in the life sciences.

    Biosensing is the area that I am most passionate about. The research community still has a limited understanding of how the brain functions, hindering the progress for developing treatments and drugs for neurological disorders such as Parkinson’s. Developing next-generation sensors that advance our understanding of the brain will have tremendous economic and societal impact. I am very excited about our neuroprobe project.

    Also, better understanding of the brain could lead to new discoveries for realizing next-generation computing systems that are inspired by the brain. For example, nanoscale memory devices that could mimic the synapses of the brain would open new horizons for brain-inspired computing. I am engaged in a collaborative effort with The University of Texas at Austin to explore the prospects of nanoscale memristors (short for memory resistor, a new class of electrical circuits with memories that retain information even after the power is shut off) for such an application.

    NYU is home to the second-highest number of international students in the United States, representing more than 130 different countries, and CFN employs staff and hosts users from around the world. How has being in these multicultural environments impacted your research?

    I believe science has no boundaries because it is shared by people who are driven by their curiosity to discover unknowns and have the desire to better humanity. These sentiments are at the core of scientific communities. Though we may have different backgrounds, our common ground is working on problems that have not yet been solved or discovering the undiscovered.

    How did you become interested in science in general and specifically neuroscience?

    As a kid, I was fascinated with science, particularly physics, and building things. By high school, I had also developed an interest in biology and particularly the brain. When I completed high school in Iran, I had to make the decision of whether I wanted to pursue an undergraduate degree or attend medical school. In Iran, there are no pre-med programs—you start medical school directly after high school, and you cannot enroll in medical school after you have taken the undergraduate route.

    My passion at the time was electrical engineering, so I went for the undergraduate degree. This passion evolved into device physics, my PhD field. After a few years at IBM as a device physicist, my love of bioelectronics was rekindled. I started studying neuroscience and even contemplated attending medical school in the United States. Finally, I decided to join academia and apply my knowledge of physics and electronics to the area of bioelectronics. I feel fortunate to have found a career in which I can combine my expertise and interests.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 11:15 am on March 31, 2017 Permalink | Reply
    Tags: BNL, , Methanol, , NSLS-II   

    From BNL: “Chemists ID Catalytic ‘Key’ for Converting CO2 to Methanol” 

    Brookhaven Lab

    March 23, 2017
    Karen McNulty Walsh,
    (631) 344-8350
    kmcnulty@bnl.gov

    Peter Genzer
    (631) 344-3174
    genzer@bnl.gov

    Results will guide design of improved catalysts for transforming pollutant to useful chemicals.

    1
    Jingguang Chen and Jose Rodriguez (standing) discuss the catalytic mechanism with Ping Liu and Shyam Kattel (seated).

    Capturing carbon dioxide (CO2) and converting it to useful chemicals such as methanol could reduce both pollution and our dependence on petroleum products. So scientists are intensely interested in the catalysts that facilitate such chemical conversions. Like molecular dealmakers, catalysts bring the reacting chemicals together in a way that makes it easier for them to break and rearrange their chemical bonds. Understanding details of these molecular interactions could point to strategies to improve the catalysts for more energy-efficient reactions.

    With that goal in mind, chemists from the U.S. Department of Energy’s Brookhaven National Laboratory and their collaborators just released results from experiments and computational modeling studies that definitively identify the “active site” of a catalyst commonly used for making methanol from CO2. The results, published in the journal Science, resolve a longstanding debate about exactly which catalytic components take part in the chemical reactions—and should be the focus of efforts to boost performance.

    “This catalyst—made of copper, zinc oxide, and aluminum oxide—is used in industry, but it’s not very efficient or selective,” said Brookhaven chemist Ping Liu, the study’s lead author, who also holds an adjunct position at nearby Stony Brook University (SBU). “We want to improve it, and get it to operate at lower temperatures and lower pressures, which would save energy,” she said.

    But prior to this study, different groups of scientists had proposed two different active sites for the catalyst—a portion of the system with just copper and zinc atoms, or a portion with copper zinc oxide.

    “We wanted to know which part of the molecular structure binds and breaks and makes bonds to convert reactants to product—and how it does that,” said co-author Jose Rodriguez, another Brookhaven chemist associated with SBU.

    To find out, Rodriguez performed a series of laboratory experiments using well-defined model catalysts, including one made of zinc nanoparticles supported on a copper surface, and another with zinc oxide nanoparticles on copper. To tell the two apart, he used an energetic x-ray beam to zap the samples, and measured the properties of electrons emitted. These electronic “signatures” contain information about the oxidation state of the atoms the electrons came from—whether zinc or zinc oxide.

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    Brookhaven chemist Ping Liu

    Meanwhile Liu, Jingguang Chen of Brookhaven Lab and Columbia University, and Shyam Kattel, the first author of the paper and a postdoctoral fellow co-advised by Liu and Chen, used computational resources at Brookhaven’s Center for Functional Nanomaterials (CFN) and the National Energy Research Scientific Computing Center (NERSC)—two DOE Office of Science User Facilities—to model how these two types of catalysts would engage in the CO2-to-methanol transformations. These theoretical studies use calculations that take into account the basic principles of breaking and making chemical bonds, including the energy required, the electronic states of the atoms, and the reaction conditions, allowing scientists to derive the reaction rates and determine which catalyst will give the best rate of conversion.

    “We found that copper zinc oxide should give the best results, and that copper zinc is not even stable under reaction conditions,” said Liu. “In fact, it reacts with oxygen and transforms to copper zinc oxide.”

    Those predictions matched what Rodriguez observed in the laboratory. “We found that all the sites participating in these reactions were copper zinc oxide,” he said.

    But don’t forget the copper.

    “In our simulations, all the reaction intermediates—the chemicals that form on the pathway from CO2 to methanol—bind at both the copper and zinc oxide,” Kattel said. “So there’s a synergy between the copper and zinc oxide that accelerates the chemical transformation. You need both the copper and the zinc oxide.”

    3
    Ping Liu and Shyam Kattel with the x-ray source used in this study.

    Optimizing the copper/zinc oxide interface will become the driving principal for designing a new catalyst, the scientists say.

    “This work clearly demonstrates the synergy from combining theoretical and experimental efforts for studying catalytic systems of industrial importance,” said Chen. “We will continue to utilize the same combined approaches in future studies.”

    For example, said Rodriguez, “We’ll try different configurations of the atoms at the copper/zinc oxide interface to see how that affects the reaction rate. Also, we’ll be going from studying the model system to systems that would be more practical for use by industry.”

    An essential tool for this next step will be Brookhaven’s National Synchrotron Light Source II (NSLS-II), another Office of Science User Facility. NSLS-II produces extremely bright beams of x-rays—about 10,000 times brighter than the broad-beam laboratory x-ray source used in this study. Those intense x-ray beams will allow the scientists to take high-resolution snapshots that reveal both structural and chemical information about the catalyst, the reactants, and the chemical intermediates that form as the reaction occurs.

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    Brookhaven scientists identified how a zinc/copper (Zn/Cu) catalyst transforms carbon dioxide (two red and one grey balls) and hydrogen (two white balls) to methanol (one grey, one red, and four white balls), a potential fuel. Under reaction conditions, Zn/Cu transforms to ZnO/Cu, where the interface between the ZnO and Cu provides the active sites that allow the formation of methanol.

    “And we’ll continue to expand the theory,” said Liu. “The theory points to the mechanistic details. We want to modify interactions at the copper/zinc oxide interface to see how that affects the activity and efficiency of the catalyst, and we’ll need the theory to move forward with that as well.”

    An additional co-author, Pedro Ramírez of Universidad Central de Venezuela, made important contributions to this study by helping to test the activity of the copper zinc and copper zinc oxide catalysts.

    This research was supported by the DOE Office of Science.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 9:37 am on March 31, 2017 Permalink | Reply
    Tags: Andrei Nomerotski, , BNL, TimepixCam   

    From BNL:”A New Ultrafast Camera for Use Across the Sciences” 

    Brookhaven Lab

    March 29, 2017
    Lida Tunesi
    ltunesi@bnl.gov

    1
    Andrei Nomerotski with a recent model of TimepixCam

    Andrei Nomerotski joined the U.S. Department of Energy’s Brookhaven National Laboratory to build a three-gigapixel camera for the Large Synoptic Survey Telescope (LSST), a massive instrument that will be installed in the mountains of Chile to capture the deepest and widest snapshots of the cosmos to date.



    LSST/Camera being built at SLAC


    LSST telescope, currently under construction at Cerro Pachón Chile, a 2,682-meter-high mountain in Coquimbo Region, in northern Chile, alongside the existing Gemini South and Southern Astrophysical Research Telescopes.

    The LSST is Nomerotski’s main focus, yet he manages to find time to run a side project at Brookhaven: developing an ultrafast camera, called TimepixCam, that can detect either single photons or ions for more down-to-earth studies in fields from biology to quantum computing.

    “To our knowledge, these are the first experiments that involve imaging single photons with simultaneous time stamping at the pixel level with 10 nanosecond time resolution,” Nomerotski said in a recent paper illustrating TimepixCam’s capabilities.

    The idea for the superfast shooter sprouted when Nomerotski was working at Oxford University, developing a camera for chemists that could image and timestamp the flying molecular fragments produced in mass spectrometry, a common chemical-identification technique used in laboratories.

    “When I came to Brookhaven I figured out how to make this type of camera in a much simpler way,” Nomerotski said.

    His latest rendition has a modest 256 by 256 pixel array, but its speed sets it apart, running roughly 4 million times faster than an iPhone shooting slow-motion video.

    Putting the pieces together

    Part of the key to this incredible speed is the camera’s silicon sensor, which Nomerotski designed himself. It has a very thin surface conductive layer and an antireflective coating that allows it to absorb every possible speck of light and efficiently convert incoming photons into readable signals.

    “The optical characteristics of image sensors we make for the LSST camera are similar to those of the silicon sensors we use in TimepixCam. I used my new expertise in optical sensors and astronomy to come up with a new sensor that we can attach to an existing readout chip,” he explained.

    The rest of the camera’s parts are an amalgamation of pre-existing technology from scattered fields of science. The sensors are manufactured at a foundry in Barcelona. But the eponymous Timepix readout chip, bonded underneath the sensor in each camera, hails from the European Center for Nuclear Research (CERN) laboratory in Geneva.

    “There are a lot of similarities between this readout chip-silicon sensor combination and the pixel detectors in ATLAS and CMS, two detectors for large particle physics experiments at CERN’s Large Hadron Collider,” said Nomerotski. “The camera’s electronics are made by yet another company that develops detectors for x-ray imaging,” he added.

    After buying lenses on eBay and creating a casing using a 3D printer, Nomerotski’s team assembles the various parts and tests each TimepixCam in their lab at Brookhaven. So far the group has made three cameras.

    A myriad of uses

    When the cameras are ready, the group collaborates with other scientists who want to use TimepixCam in their own experiments. Michael White’s group in Brookhaven’s chemistry department and Thomas Weinacht’s group at Stony Brook University already use the camera for innovations in imaging mass spectrometry, the same chemistry technique Nomerotski was working on at Oxford.

    “For a while I was only thinking of applications in chemical imaging,” said Nomerotski, “but then I read a couple of papers that guided me in a new direction. It occurred to me that by placing an image intensifier in front of the camera it could be used to image single photons. That opens a completely different domain of applications.”

    A single photon is too faint for the camera to see on its own. So the intensifier takes incoming photons and passes them through a series of materials that turn each particle of light into a brighter flash. As the camera picks up this flash, it also records the time.

    “The intensifier is like a pair of very fast night vision goggles,” Nomerotski explained.

    With this addition, TimepixCam can act as a fluorescent imaging tool, as Nomerotski demonstrated in a recent paper. These sorts of tools can, for example, help biologists look at oxygen concentrations in living cells to track metabolic processes, or help characterize new materials such as the light-harvesting layers used in solar cells.

    In addition, because single photons can be used as ‘qubits,’ the quantum version of the binary bits that carry information in today’s computers, Nomerotski also thinks TimepixCam could play a role in quantum computing and advances in cryptography. He is testing this with collaborator Eden Figueroa of Stony Brook University.

    Figueroa, who specializes in quantum information technology, wants to use TimepixCam in imaging experiments using “entangled photons.” Entangled photons are not, as it might seem, physically wrapped around one another. They are simply aware of each other, a peculiar quantum phenomenon in which any measurement of one photon immediately affects the other, even over long distances. Thus when either photon is measured, information about that measurement is “teleported” from one photon to the other. Researchers like Figueroa can create entangled photons in laboratories and send them along regular fiber optic cables.

    “Entangled photons are created simultaneously, so checking that they have the same timestamp is a powerful tool to distinguish the pair from the background photons,” Nomerotski said. “TimepixCam can also be used to measure the spatial distribution of photons and to keep track of the actions of entanglement sources and quantum memories in real time.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 9:11 am on March 31, 2017 Permalink | Reply
    Tags: , BNL, , Wei Xu,   

    From BNL: Women in STEM “Visualizing Scientific Big Data in Informative and Interactive Ways” Wei Xu 

    Brookhaven Lab

    March 31, 2017
    Ariana Tantillo
    atantillo@bnl.gov

    Brookhaven Lab computer scientist Wei Xu develops visualization tools for analyzing large and varied datasets.

    1
    Wei Xu, a computer scientist who is part of Brookhaven Lab¹s Computational Science Initiative, helps scientists analyze large and varied datasets by developing visualization tools, such as the color-mapping tool seen projected from her laptop onto the large screen.

    Humans are visual creatures: our brain processes images 60,000 times faster than text, and 90 percent of information sent to the brain is visual. Visualization is becoming increasingly useful in the era of big data, in which we are generating so much data at such high rates that we cannot keep up with making sense of it all. In particular, visual analytics—a research discipline that combines automated data analysis with interactive visualizations—has emerged as a promising approach to dealing with this information overload.

    “Visual analytics provides a bridge between advanced computational capabilities and human knowledge and judgment,” said Wei Xu, a computer scientist in the Computational Science Initiative (CSI) at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and a research assistant professor in the Department of Computer Science at Stony Brook University. “The interactive visual representations and interfaces enable users to efficiently explore and gain insights from massive datasets.”

    At Brookhaven, Xu has been leading the development of several visual analytics tools to facilitate the scientific decision-making and discovery process. She works closely with Brookhaven scientists, particularly those at the National Synchrotron Light Source II (NSLS-II) and the Center for Functional Nanomaterials (CFN)—both DOE Office of Science User Facilities.


    NSLS-II

    By talking to researchers early on, Xu learns about their data analysis challenges and requirements. She continues the conversation throughout the development process, demoing initial prototypes and making refinements based on their feedback. She also does her own research and proposes innovative visual analytics methods to the scientists.

    Recently, Xu has been collaborating with the Visual Analytics and Imaging (VAI) Lab at Stony Brook University—her alma mater, where she completed doctoral work in computed tomography with graphics processing unit (GPU)-accelerated computing.

    Though Xu continued work in these and related fields when she first joined Brookhaven Lab in 2013, she switched her focus to visualization by the end of 2015.

    “I realized how important visualization is to the big data era,” Xu said. “The visualization domain, especially information visualization, is flourishing, and I knew there would be lots of research directions to pursue because we are dealing with an unsolved problem: how can we most efficiently and effectively understand the data? That is a quite interesting problem not only in the scientific world but also in general.”

    It was at this time that Xu was awarded a grant for a visualization project proposal she submitted to DOE’s Laboratory Directed Research and Development program, which funds innovative and creative research in areas of importance to the nation’s energy security. At the same time, Klaus Mueller—Xu’s PhD advisor at Stony Brook and director of the VAI Lab—was seeking to extend his research to a broader domain. Xu thought it would be a great opportunity to collaborate: she would present the visualization problem that originated from scientific experiments and potential approaches to solve it, and, in turn, doctoral students in Mueller’s lab would work with her and their professor to come up with cutting-edge solutions.

    This Brookhaven-Stony Brook collaboration first led to the development of an automated method for mapping data involving multiple variables to color. Variables with a similar distribution of data points have similar colors. Users can manipulate the color maps, for example, enhancing the contrast to view the data in more detail. According to Xu, these maps would be helpful for any image dataset involving multiple variables.

    3
    The color-mapping tool was used to visualize a multivariable fluorescence dataset from the Hard X-ray Nanoprobe (HXN) beamline at Brookhaven’s National Synchrotron Light Source II. The color map (a) shows how the different variables—the chemical elements cerium (Ce), cobalt (Co), iron (Fe), and gadolinium (Gd)—are distributed in a sample of an electrolyte material used in solid oxide fuel cells. The fluorescence spectrum of the selected data point (the circle indicated by the overlaid white arrows) is shown by the colored bars, with their height representing the relative elemental ratios. The fluorescence image (b), pseudo-colored based on the color map in (a), represents a joint colorization of the individual images in (d), whose colors are based on the four points at the circle boundary (a) for each of the four elements. The arrow indicates where new chemical phases can exist—something hard to detect when observing the individual plots (d). Enhancing the color contrast—for example, of the rectangular region in (b)—enables a more detailed view, in this case providing better contrast between Fe (red) and Co (green) in image (c).

    “Different imaging modalities—such as fluorescence, differential phase contrasts, x-ray scattering, and tomography—would benefit from this technique, especially when integrating the results of these modalities,” she said. “Even subtle differences that are hard to identify in separate image displays, such as differences in elemental ratios, can be picked up with our tool—a capability essential for new scientific discovery.” Currently, Xu is trying to install the color mapping at NSLS-II beamlines, and advanced features will be added gradually.

    In conjunction with CFN scientists, the team is also developing a multilevel display for exploring large image sets. When scientists scan a sample, they generate one scattering image at each point within the sample, known as the raw image level. They can zoom in on this image to check the individual pixel values (the pixel level). For each raw image, scientific analysis tools are used to generate a series of attributes that represent the analyzed properties of the sample (the attribute level), with a scatterplot showing a pseudo-color map of any user-chosen attribute from the series—for example, the sample’s temperature or density. In the past, scientists had to hop between multiple plots to view these different levels. The interactive display under development will enable scientists to see all of these levels in a single view, making it easier to identify how the raw data are related and to analyze data across the entire scanned sample. Users will be able to zoom in and out on different levels of interest, similar to how Google Maps works.

    4
    The multilevel display tool enables scientists conducting scattering experiments to explore the resulting image sets at the scatterplot level (0), attribute pseudo-color level (1), zoom-in attribute level (2), raw image level (3), zoom-in raw image level (4), and pixel level (5), all in a single display.

    The ability to visually reconstruct a complete joint dataset from several partial marginal datasets is at the core of another visual analytics tool that Xu’s Stony Brook collaborators developed. This web-based tool enables users to reconstruct all possible solutions to a given problem and locate the subset of preferred solutions through interactive filtering.

    “Scientists commonly describe a single object with datasets from different sources—each covering only a portion of the complete properties of that object—for example, the same sample scanned in different beamlines,” explained Xu. “With this tool, scientists can recover a property with missing fields by refining its potential ranges and interactively acquiring feedback about whether the result makes sense.”

    Their research led to a paper that was published in the Institute of Electrical and Electronics Engineers (IEEE) journal Transactions on Visualization and Computer Graphics and awarded the Visual Analytics Science and Technology (VAST) Best Paper Honorable Mention at the 2016 IEEE VIS conference.

    At this same conference, another group of VAI Lab students whom Xu worked with were awarded the Scientific Visualization (SciVis) Best Poster Honorable Mention for their poster, “Extending Scatterplots to Scalar Fields.” Their plotting technique helps users link correlations between attributes and data points in a single view, with contour lines that show how the numerical values of the attributes change. For their case study, the students demonstrated how the technique could help college applications select the right university by plotting the desired attributes (e.g., low tuition, high safety, small campus size) with different universities (e.g., University of Virginia, Stanford University, MIT). The closer a particular college is to some attribute, the higher that attribute value.

    5
    The scatter plots above are based on a dataset containing 46 universities with 14 attributes of interest for prospective students: academics, athletics, housing, location, nightlife, safety, transportation, weather, score, tuition, dining, PhD/faculty, population, and income. The large red nodes represent the attributes and the small blue points represent the universities; the contour lines (middle plot) show how the numerical values of the attributes change. This prospective student wants to attend a university with good academics (>9/10). Universities that meet this criterion are within the contours lines whose value exceeds 9. To determine which universities meet multiple criteria, students would see where the universities and attributes overlap (right plot).

    According to Xu, this kind of technique also could be applied to visualize artificial neural networks—the deep learning (a type of machine learning) frameworks that are used to address problems such as image classification and speech recognition.

    “Because neural network models have a complex structure, it is hard to understand how their intrinsic learning process works and how they arrive at intermediate results, and thus quite challenging to debug them,” explained Xu. “Neural networks are still largely regarded as black boxes. Visualization tools like this one could help researchers get a better idea of their model’s performance.”

    Besides her Stony Brook collaborations, Xu is currently involved in the Co-Design Center for Online Data Analysis and Reduction at the Exascale (CODAR), which Brookhaven is partnering on with other national laboratories and universities through DOE’s Exascale Computing Project. Her role is to visualize data evaluating the performance of computing clusters, applications, and workflows that the CODAR team is developing to analyze and reduce data online before the data are written to disk for possible further offline analysis. Exascale computer systems are projected to provide unprecedented increases in computational speed but the input/output (I/O) rates of transferring the computed results to storage disks are not expected to keep pace, so it will be infeasible for scientists to save all of their scientific results for offline analysis. Xu’s visualization will help the team “diagnose” any performance issues with the computation processes, including individual application execution, computation job management in the clusters, I/O performance in the runtime system, and data reduction and reconstruction efficiency.

    Xu is also part of a CSI effort to build a virtual reality (VR) lab for an interactive data visualization experience. “It would be a more natural way to observe and interact with data. VR techniques replicate a realistic and immersive 3D environment,” she said.

    For Xu, her passion for visualization most likely stemmed from an early interest in drawing.

    “As a child, I liked to draw,” she said. “In growing up, I took my drawings from paper to the computer.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 8:46 am on March 31, 2017 Permalink | Reply
    Tags: BNL, Gnome X Scanning Microscopy or GXSM, Next-Generation Software Supports Explorations Beyond the Nanoworld into the Intramolecular Picoworld   

    From BNL: “Next-Generation Software Supports Explorations Beyond the Nanoworld into the Intramolecular Picoworld” 

    Brookhaven Lab

    March 30, 2017
    Ariana Tantillo
    atantillo@bnl.gov

    A recent upgrade to data acquisition and visualization software more than 20 years in the making enhances scientists’ ability to observe and control individual atoms and molecular interactions.

    1
    Brookhaven physicist Percy Zahl at the Center for Functional Nanomaterials, where he uses scanning microscopy and the Gnome X Scanning Microscopy (GXSM) open-source software he developed to image and manipulate individual atoms and molecules. On the computer screens in front of him are simulated non-contact atomic force microscopy (NC-AFM) images of a trimesic acid (TMA) dimer (left) and a structural model overlaid on the dimer (right). He generated the simulations with a new plug-in that is part of the recently updated GXSM software. Zahl is using NC-AFM to look at hydrogen bonding between TMA molecules that self-assemble on a copper substrate. These hydrogen bonds (the dotted lines between the blue hydrogen atoms and red oxygen atoms, right screen) play a key role in the formation of metal organic-frameworks, which are 3D porous materials of interest for a variety of applications, including catalysis, gas capture, and biomedical sensing.

    For physicist Percy Zahl, traversing surfaces is not only a long-time hobby of his but also the focus of his research. An avid cyclist who is part of the Green Arm Bandits of the East End Cycling Team, he has pedaled more than 10,000 miles in 2016 alone, competing in races as close to home as the New York tri-state area and touring in places as far away as Chile. Weather permitting, he bikes the 20 miles it takes each day to make the round trip between his home and the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, where he covers terrain of a different kind—mapping the atomic structure and electronic properties of material surfaces through scanning probe microscopy (SPM).

    Since 2005, Zahl has been working as an associate scientist at Brookhaven’s Center for Functional Nanomaterials (CFN), a DOE Office of Science User Facility. He came to Brookhaven from a postdoc position at IBM Zurich, where SPM was founded, with the invention of the scanning tunneling microscope in 1981.

    In 1994, Zahl began developing control software for scanning tunneling microscopy (STM). At the time, he was attending the Institute for Solid State Physics at Leibniz Universität Hannover, working on his thesis with a group in Germany that had microscopes but lacked the financial means for a full-scale commercial system. This software later evolved into what is known today as Gnome X Scanning Microscopy, or GXSM, an open-source software that enables scientists to acquire and interactively visualize data from digitally controlled scanning probe microscopes and similar instruments, in real time and offline.

    2
    The GXSM software logo shows a molecule of phthalocyanine simulated with non-contact atomic force microscopy, a technique that scientists use to study the detailed internal structure of single molecules. Phthalocyanines are brilliant blue-green colored compounds that are widely used as dyes and pigments.

    With GXSM, scientists not only can explore and image the atomic structure and electronic properties of material surfaces in multiple dimensions and at atomic resolution but also manipulate individual atoms and molecules.

    Now, Zahl has recently completed a major upgrade to GXSM that makes use of the latest computer technologies and incorporates new features.

    “This upgrade involved a lot of behind-the-scenes work,” said Zahl, who re-coded roughly half of the original 300,000 lines of source code and, in the process, reduced the amount of code by nearly 20 percent. “The software’s GUI was totally redesigned not only in its look and feel but also its function. I also added several features for enhancing data acquisition and visualization.”

    The modernized GUI is based on GNOME-3, a desktop environment for computers using the Linux operating system.

    One of the new features is a function to export visualizations in publication-quality vector format (PDF and SVG files). Previously, GXSM users relied on bitmap-based export (PNG files) to save their images, plots, and other graphics.

    Another new feature is a remote-control console for automating complex or time-consuming scanning and manipulation tasks. In particular, the automation is useful for mapping electronic properties and force fields on the molecular scale within a multidimensional space above a sample’s surface.

    3
    This screenshot provides a typical view of the GXSM software in action. The open windows include control panels for setting the microscope’s operating parameters, such as the scan geometry, and selecting data channels; a console for writing and executing scripts to automate tasks; images of the scan in progress; and a frequency detection display.

    A new non-contact atomic force microscopy (NC-AFM) simulation plug-in module helps scientists understand the imaging process and makes data acquisition more efficient. The NC-AFM technique involves measuring the force between atoms and molecules on the surface of a sample and a highly sensitive single-molecule probe that oscillates with a controlled amplitude (at a fraction of an atom’s diameter). The resulting “force” images resolve the internal structure of single molecules in great detail—for example, revealing carbon rings and “shadows” of hydrogen bonds.

    However, getting the probe molecule in the right position to get these detailed images can take days of preparation work and is largely a trial-and-error process. The new simulation module is a valuable tool for scientists to explore imaging modes before and during an experiment to get an idea of what the molecules should ideally look like. Post-experiment, the module can be used to overlay the simulated molecules onto the actual microscopy images for comparison and optimization in future scans.

    “In force imaging, the probe needs to be close enough to the surface that it “feels” the repulsive force of the surface molecules, but if the probe gets too close, it loses its probing molecule and the probe-forming process must start all over again,” explained Zahl. “Using this plug-in module has helped me to better understand the imaging process so that I could operate the microscope most efficiently and under the best imaging conditions.”

    4
    The image of the trimesic acid (TMA) molecule dimer (a, left) was generated by simulating the probe force under a scenario in which the probe is positioned very close to the molecules on the surface. The molecule on the left is in a network formation; the one on the right is unbound. A structural model overlaid on the dimer (a, right) shows these networked and unbound molecules and the hydrogen bonds between TMA molecules, which are 93 picometers (a picometer is equal to one trillionth of a meter) apart, center to center. The “large” (5500 x 5500 picometers) non-contact atomic force microscopy image (b) is of a double-hydrogen-bonded TMA molecular network on a copper surface. The hertz (Hz) frequency scale indicates the molecular force “felt” by the probe, with the darker regions corresponding to the most attractive forces and the white approaching the repulsive force range. Close-up images of a dimer network junction are shown in experimental (c) and simulation (d) form, with an overlaid molecule sketch.

    A full list of the new features can be found on the GXSM website, and the software is available for download through SourceForge, an online service where software developers can manage their projects and source code. A project discussion forum allows for interaction with users and provides user support and the latest software information. Since 2000, GXSM has been available under the GNU General Public License, which guarantees that users can freely access, share, and modify the source code. Zahl’s collaborator, Thorsten Wagner of the Institute for Experimental Physics in Austria, packages the software and offers support to the more than 50 organizations around the world that use GXSM.

    According to Zahl, though the major software overhaul is done, he will continue to make tweaks.

    “As the GXSM project administrator and software developer, a GXSM user, and a microscopy instrument developer, I have the best possible combination of perspectives from which I can continuously make improvements,” said Zahl. “I am always looking for feedback and ideas from users across the world, and, if a novel experiment presents the need for new functionality, it most likely can be made to work, as long as the instrument/hardware is capable.”

    In fact, Zahl purposely used a modular approach to design the original software so that it could be adapted to different types of data acquisition hardware and next-generation experimental techniques or data analysis tasks by adding new plug-in modules instead of modifying the large-scale code. Since its inception, GXSM has supported a line of commercially available data acquisition hardware optimized for scanning probe microscopy and instrument control, including hardware to amplify output signals from the control unit.

    However, GXSM can be used for any kind of point-by-point scanning multichannel data acquisition on any scale. A laser laboratory at the CFN is currently using GXSM to measure optical signals directly via counting pulses. Zahl imagines GXSM could be used for various x-ray, ultraviolet, and infrared imaging techniques at Brookhaven’s National Synchrotron Light Source II, also a DOE Office of Science User Facility. Via a customized control plug-in, users could even manage camera images with GXSM.

    “I am very thrilled about the software’s new features, particularly the mechanical probe particle simulation module for generating NC-AFM images from a molecular model. Plus, the new technologies that I have incorporated into the software provide the next level of ease and operational comfort for long experimental immersions into the intramolecular picoscale world,” said Zahl.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 12:50 pm on March 24, 2017 Permalink | Reply
    Tags: , BNL, , Producing Radioisotopes for Medical Imaging and Disease Treatment   

    From BNL: “Producing Radioisotopes for Medical Imaging and Disease Treatment” 

    Brookhaven Lab

    March 21, 2017
    Karen McNulty Walsh

    Brookhaven’s high-energy proton accelerator and a group led by Cathy Cutler team up to meet the nation’s demand for medical isotopes.

    1
    Cathy Cutler, Lisa Muench, Tatjana Klaric, Weimin Zhou, Vicky Litton, and Anna Goldberg in the hot cell area where BLIP targets are processed to extract desired isotope products.

    The before and after images are stunning: A prostate cancer patient riddled with metastatic tumors that disappear after just three, potent treatments.

    “Two patients underwent these treatments and they were cured,” said Cathy Cutler, director of the Medical Isotope Research and Production Program at the U.S. Department of Energy’s Brookhaven National Laboratory. “Their cancer was gone.

    “This is what we want to do—supply this material so that more patients can get this treatment,” she said.

    3
    Medical applications of isotopes produced at BLIP Top: BLIP produces Strontium-82, a relatively stable isotope that can be transported and used in hospitals to generate Rubidium-82, a radiotracer that reveals reduced blood flow in heart muscle under stress. This precision scanning points physicians to coronary arteries that need treatment. Credit: Washington University School of Medicine. Bottom: Before and after images show how a molecule labeled with Actinium-225 delivers cell-killing alpha particles directly to tumors, eradicating metastatic prostate cancer. The BLIP team aims to increase the production of Ac-225 so scientists can conduct large-scale trials and get this potentially lifesaving treatment to more patients. Credit: ©SNMMI: C. Kratochwil. J. Nucl. Med., 2016; 57 (12); 1941.

    The material is a molecule tagged with Actinium-225, a radioactive isotope. When designed to specifically bind with a protein on the surface of cancer cells, the radiolabeled molecule delivers a lethal, localized punch—alpha particles that kill the cancer with minimal damage to surrounding tissues.

    Actinium-225 can only be produced in the large quantities needed to support clinical applications at facilities that have high-energy particle accelerators.

    “This is why I came to Brookhaven,” Cutler said in a recent talk she gave to highlight her group’s work.* “We can make these alpha emitters and this is really giving doctors a chance to treat these patients!”

    Radiochemistry redux

    Brookhaven Lab and the Department of Energy Isotope Program have a long history of developing radioisotopes for uses in medicine and other applications. These radioactive forms of chemical elements can be used alone or attached to a variety of molecules to track and target disease.

    “If it wasn’t for the U.S. Department of Energy and its isotope development program, I’m not sure we’d have nuclear medicine,” Cutler said.

    Among the notable Brookhaven Lab successes are the development in the 1950s and 60s, respectively, of the Technetium-99m generator and a radioactively labeled form of glucose known as 18FDG—two radiotracers that went on to revolutionize medical imaging.

    As an example, 18FDG emits positrons (positively charged cousins of electrons) that can be picked up by a positron emission tomography (PET) scanner. Because rapidly growing cancer cells take up glucose faster than healthy tissue, doctors can use PET and 18FDG to detect and monitor the disease.

    “FDG turned around oncology,” Cutler said. Instead of taking a drug for months and suffering toxic side effects before knowing if a treatment is working, “patients can be scanned to look at the impact of treatment on tumors within 24 hours, and again over time, to see if the drug is effective—and also if it stops working.”

    Symbiotic operations

    While Tc-99m and 18FDG are now widely available in hospital settings and used in millions of scans a year, other isotopes are harder to make. They require the kind of high-energy particle accelerator you can find only at world-class physics labs.

    “Brookhaven is one of just a few facilities in the DOE Isotope Program that can produce certain critical medical isotopes,” Cutler said.

    Brookhaven’s linear accelerator (“linac”) was designed to feed beams of energetic protons into physics experiments at the Relativistic Heavy Ion Collider (RHIC), where physicists are exploring the properties of the fundamental building blocks of matter and the forces through which they interact.

    6
    Brookhaven’s linear accelerator (“linac”)

    7
    The Solenoidal Tracker at the Relativistic Heavy Ion Collider (RHIC) is a detector which specializes in tracking the thousands of particles produced by each ion collision at RHIC. Weighing 1,200 tons and as large as a house, STAR is a massive detector. It is used to search for signatures of the form of matter that RHIC was designed to create: the quark-gluon plasma. It is also used to investigate the behavior of matter at high energy densities by making measurements over a large area. | Photo courtesy of Brookhaven National Lab.

    But because the linac produces the protons in pulses, Cutler explained, it can deliver them pulse-by-pulse to different facilities. Operators in Brookhaven’s Collider-Accelerator Department deliver alternating pulses to RHIC and the Brookhaven Linac Isotope Producer (BLIP).

    “We operate these two programs symbiotically at the same time,” Cutler said. “We combine our resources to support the running of the linear accelerator; it’s cheaper for both programs to share this resource than it would cost if each of us had to use it alone.”


    Access mp4 video here .

    Tuning and targets

    BLIP operators aim the precisely controlled beams of energetic protons at small puck-shaped targets. The protons knock subatomic particles from the targets’ atoms, transforming them into the desired radioactive elements.

    “We stack different targets sequentially to make use of the beam’s reduced energy as it exits one target and enters the next in line, so we can produce multiple radionuclides at once,” Cutler said.

    Transformed targets undergo further chemical processing to yield a pure product that can be injected into patients, or a precursor chemical that can easily be transformed into the desired isotope or tracer on site at a hospital.

    “A lot of our work goes into producing these targets,” Cutler said. “You would be shocked at all the chemistry, engineering, and physics that goes into designing one of these pucks—to make sure it survives the energy and high current of the beam, gives you the isotope you are interested in with minimal impurities, and allows you to do the chemistry to extract that isotope efficiently.”

    Cutler recently oversaw installation of a new “beam raster” system designed to maximize the use of target materials and increase radioisotope production. With this upgrade, a series of magnets steers BLIP’s energetic particle beam to “paint” the target, rather than depositing all the energy in one spot. This cuts down on the buildup of target-damaging heat, allowing operators to increase beam current and transform more target material into the desired product.

    Meeting increasing demand

    The new raster system and ramped up current helped increase production of one of BLIP’s main products, Strontium-82, by more than 50 percent in 2016. Sr-82 has a relatively long half-life, allowing it to be transported to hospitals in a form that can generate a short-lived radiotracer, Rubidium-82, which has greatly improved the precision of cardiac imaging.

    4
    Weimin Zhou, Anna Goldberg, and Lisa Muench in the isotope-processing area.

    “Rb-82 mimics potassium, which is taken up by muscles, including the heart,” Cutler explained. “You can inject Rubidium into a patient in a PET scanner and measure the uptake of Rb-82 in heart muscle to precisely pinpoint areas of decreased blood flow when the heart is under stress. Then surgeons can go in and unblock that coronary artery to increase blood flow before the patient has a heart attack. Hundreds of thousands of patients receive this life-saving test because of what we’re doing here at Brookhaven.”

    BLIP also produces several isotopes with improved capabilities for detecting cancer, including metastatic tumors, and monitoring response to treatment.

    But rising to meet the demand for isotopes that have the potential to cure cancer may be BLIP’s highest calling—and has been a key driver of Cutler’s career.

    5
    Jason Nalepa, a BLIP operator, prepares targets to be installed in the BLIP beamline for irradiation

    “This is where I started as a chemist at the University of Missouri—designing molecules that have the right charges, the right size, and the right characteristics that determine where they go in the body so we can use them for imaging and therapy,” she said. “If we can target receptors that are overexpressed on tumor cells, we can selectively image these cells. And if there are enough of these receptors expressed, we can deliver radionuclides to those tumor cells very selectively and destroy them.”

    Radionuclides that emit alpha particles are among the most promising isotopes because alpha particles deliver a lot of energy and traverse very small distances. Targeted delivery of alphas would deposit very high doses—“like driving an 80-ton semi truck into a tumor”—while minimizing damage to surrounding healthy cells, Cutler said.

    “Our problem isn’t that we can’t cure cancer; we can ablate the cancer. Our problem is saving the patient. The toxicity of the treatments in many cases is so significant that we can’t get the levels in to kill the cancer without actually harming the patient. With alpha particles, because of the short distance and high impact, they are enabling us to treat these patients with minimal side effects and giving doctors the opportunity to really cure cancer.”

    Making the case for a cure

    One experimental treatment Cutler developed using Lutetium-177 while still at the University of Missouri worked favorably in treating neuroendocrine tumors, but didn’t get to a cure state. Actinium-225, one of the isotopes that is trickier to make, has shown more promise—as demonstrated by the prostate cancer results published in 2016 by researchers at University Hospital Heidelberg.

    Right now, according to Cutler, DOE’s Oak Ridge National Laboratory (ORNL) makes enough Ac-225 to treat about 50 patients each year. But almost 30 times that much is needed to conduct the clinical trials required to prove that such a strategy works before it can move from the laboratory to medical practice.

    “With the accelerator we have here at Brookhaven, the expertise in radiochemistry, and experience producing isotopes for medical applications, we—together with partners at ORNL and DOE’s Los Alamos National Laboratory—are looking to meet this unmet need to get this material out to patients,” Cutler said.

    The work at BLIP is funded by the DOE Isotope Program, managed by the Office of Science’s Nuclear Physics program. RHIC is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 10:04 am on March 10, 2017 Permalink | Reply
    Tags: , , BNL, , , , , , , , Xiaofeng Guo   

    From Brookhaven: Women in STEM – “Secrets to Scientific Success: Planning and Coordination” Xiaofeng Guo 

    Brookhaven Lab

    March 8, 2017
    Lida Tunesi

    1
    Xiaofeng Guo

    Very often there are people behind the scenes of scientific advances, quietly organizing the project’s logistics. New facilities and big collaborations require people to create schedules, manage resources, and communicate among teams. The U.S. Department of Energy’s Brookhaven National Laboratory is lucky to have Xiaofeng Guo in its ranks—a skilled project manager who coordinates projects reaching across the U.S. and around the world.

    Guo, who has a Ph.D. in theoretical physics from Iowa State University, is currently deputy manager for the U.S. role in two upgrades to the ATLAS detector, one of two detectors at CERN’s Large Hadron Collider that found the Higgs boson in 2012.


    CERN ATLAS Higgs Event


    CERN/ATLAS detector

    Brookhaven is the host laboratory for both U.S. ATLAS Phase I and High Luminosity LHC (HL-LHC) upgrade projects, which involve hundreds of millions of dollars and 46 institutions across the nation. The upgrades are complex international endeavors that will allow the detector to make use of the LHC’s ramped up particle collision rates. Guo keeps both the capital and the teams on track.

    “I’m in charge of all business processes, project finance, contracts with institutions, baseline plan reports, progress reports—all aspects of business functions in the U.S. project team. It keeps me very busy,” she laughed. “In the beginning I was thinking ‘in my spare time I can still read physics papers, do my own calculations’… And now I have no spare time!”

    Guo’s dual interest in physics and management developed early in her career.

    “When I was an undergraduate there was a period when I actually signed up for a double major, with classes in finance and economics in addition to physics,” Guo recalled. “I’m happy to explore different things!”

    Later, while teaching physics part-time at Iowa State University, Guo desired career flexibility and studied to be a Chartered Financial Analyst. She passed all required exams in just two years but decided to continue her research after receiving a grant from the National Science Foundation.

    Guo joined Brookhaven Lab in 2010 to fill a need for project management in Nuclear and Particle Physics (NPP). The position offered her a way to learn new skills while staying up-to-date on the physics world.

    Early in her time at Brookhaven, Guo participated in the management of the Heavy Flavor Tracker (HFT) upgrade to the STAR particle detector at the Relativistic Heavy Ion Collider (RHIC), a DOE Office of Science User Facility for nuclear physics research. The project was successfully completed $600,000 under budget and a whole year ahead of schedule.


    BNL/RHIC Star Detector

    “This was a very good learning experience for me. I participated in all the manager meeting discussions, updated the review documents, and helped them handle some contracts. Through this process I learned all the DOE project rules,” Guo said.

    While working on the HFT upgrade, Guo also helped develop successful, large group proposals for increased computational resources in high-energy physics and other fields of science. She joined the ATLAS Upgrade projects after receiving her Project Management Certification, and her physics and finance background as well as experience with large collaborations have enabled her to orchestrate complex planning efforts.

    For the two phases of the U.S. ATLAS upgrade, Guo directly coordinates more than 140 scientists, engineers, and finance personnel, and oversees all business processes, including finance, contracts, and reports. And taking her job one step further, she’s developed entirely new management tools and reporting procedures to keep the multi-institutional effort synchronized.

    “Dr. Guo is one of our brightest stars,” said Berndt Mueller, Associate Lab Director of NPP. “We are fortunate to have her to assist us with many challenging aspects of project development and execution in NPP. In the process of guiding the work of scores of scientists and engineers, she has single-handedly created a unique and essential role in the development of complex projects with an international context, demonstrating skills of unusual depth and breadth and the ability to apply them across a wide array of disciplines.”

    Guo’s management of Phase I won great respect for the project from the high-energy physics community and the Office of Project Assessment (OPA) at the DOE’s Office of Science. The OPA invited her to participate in a panel discussion to share her expertise and help develop project management guidelines that can be used in other Office of Science projects. Guo also worked with BNL’s Project Management Center to help the lab update its own project management system description to meet DOE standards and lay down valuable groundwork for future large projects.

    As the ATLAS Phase I upgrade proceeds through the final construction stage, Guo is simultaneously managing the planning stages of HL-LHC.

    “We haven’t completely defined the project timeline yet, but it’s projected to go all the way to the end of 2025,” Guo said.

    Like Phase I, HL-LHC will ensure ATLAS can perform well while the LHC operates at much higher collision rates so that physicists can further explore the Higgs as well as search for signs of dark matter and extra dimensions.

    Although she admits to missing doing research herself, Guo is not disheartened.

    “I’m still in the physics world; I’m still working with physicists,” she said. “I enjoy working and interacting with people. So I’m happy.”

    Brookhaven’s work on RHIC and ATLAS is funded by the DOE Office of Science.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 4:07 pm on January 27, 2017 Permalink | Reply
    Tags: BNL, Regeneron Science Talent Search (STS) Competition, Science & Technology, Siemens Competition in Math, What is wrong with this picture?   

    From BNL: “Six Brookhaven Lab-Mentored Students Garner Awards at Regeneron and Siemens Science Competitions” 

    Brookhaven Lab

    January 27, 2017
    Jane Koropsak
    jane@bnl.gov

    [I WOULD LIKE TO KNOW IF ANYONE SEES SOMETHING WRONG WITH THIS PICTURE.]

    Awardees include Regeneron finalist Emily Peterson, Smithtown High School East, who completed her work at Brookhaven.

    Since 1942, students have competed in one of the nation’s most prestigious pre-college science competitions, first in partnership with Westinghouse, then with Intel from 1998 to 2016, and now with Regeneron.

    Regeneron has named the top 300 scholars for its 2017 Science Talent Search (STS) Competition, and three of the selected scholars conducted their research at Brookhaven Lab. One of them—Emily Peterson from Smithtown High School East—has been named a finalist and will be invited to Washington, D.C. in March to participate in final judging and compete for the top award of $250,000. Students compete for more than $3 million in awards, with each scholar receiving a $2,000 award from Regeneron with an additional $2,000 going to his or her school.

    In addition to the Regeneron STS scholars, four Brookhaven students were also named as semifinalists in the annual Siemens competition. The Siemens Foundation established the Siemens Competition in Math, Science & Technology in 1999 to promote excellence by encouraging high school students to undertake individual or team research projects. It fosters intensive research that improves students’ understanding of the value of scientific study and their consideration of future careers in these disciplines.

    “These six students reflect the extraordinary scientific talent being developed on Long Island,” said Kenneth White, manager of the Lab’s Office of Educational Programs. “We have been privileged to host them and many other highly capable students here at the Lab, introducing them to U.S. Department of Energy research. Our congratulations to the six awardees, and many thanks to our Lab mentors.”

    Meet the Regeneron Scholars:

    1
    Finalist Emily Peterson – Woman in STEM

    Finalist Emily Peterson: Smithtown High School East
    Mentor: David Biersach, Information Technology Division
    Title of Project: “Lecithin-Retinol Acyltransferase in Squamous Cell Carcinoma: The Relationship Between Oncology and Wound Repair”

    Emily Peterson met mentor David Biersach at a scientific computing seminar he was giving at her high school, where he learned of her research on skin cancer. Emily’s initial research focused on the possibility that a gene expression problem might inhibit the production of an enzyme responsible for strengthening cell walls. As cancer is invasive, skin cells with weak walls are more susceptible to becoming tumorous. Dave showed Emily how a classic computer algorithm that looks for repeated substrings can be used in a novel way to determine if DNA sequences are likely to have important biological functions. This is accomplished by searching the human genome for other occurrences of these repeated sequences. They discovered that this enzyme’s sequence also occurs in an enzyme involved in blood clotting. When blood clots form to heal a wound, the human body knows to leave the clot alone until the wound is fully repaired. After healing, a chemical signal triggers the body to break down the clot. The similarity in gene sequences that Peterson discovered suggests that cancer cells potentially use the same “don’t bother me” signaling mechanism as blood clots, thus allowing the tumor to continue to grow in stealth mode. This collaboration is an excellent example of how students can apply skills in scientific computing directly to their research projects. Peterson hopes to continue her research by studying the enzyme’s 3D atomic structure.

    2
    Semifinalist Vishrath Kumar

    Semifinalist Vishrath Kumar: Smithtown High School East
    Mentor: Haixin Huang, Collider-Accelerator Department
    Title: “Tune Jump Quadrapole Strength Optimization for AGS Polarization Preservation”

    The spin physics program at Brookhaven Lab’s Relativistic Heavy Ion Collider (RHIC) requires high-energy protons spinning in the same direction. By controlling the direction of the protons’ spins and keeping them aligned, or “polarized,” physicists can tease apart how the protons’ inner building blocks, quarks and gluons, contribute to its spin. A pair of specialized magnets at the Alternating Gradient Synchrotron, the accelerator that injects proton beams into RHIC, helps to mitigate polarization loss. Vishrath’s work is focused on using computer simulations to determine the optimal strength of this pair of magnets and should lead to more precise results.

    Kumar is a participant in the High School Research Program administered by the Lab’s Office of Educational Programs.

    3
    Semifinalist Rushabh Mehta

    Semifinalist Rushabh Mehta: Syosset High School
    Mentor: William Morse, Physics Department
    Title: “Exact Radial Muon Orbit Distortion with E821 BETA-function”

    Rushabh Mehta was named both a Siemens and Regeneron semifinalist for his work with Brookhaven physicist Bill Morse to develop a mathematical formula for calculating how best to control a beam of particles called muons for an upcoming experiment at the U. S. Department of Energy’s Fermilab—one that builds upon Brookhaven Lab’s historic g-2 experiment, which concluded in 2001. Mehta’s research will help in achieving an expected 400-percent improvement in beam quality with 20 times more muons. Using the same ring from the earlier g-2 experiment at Brookhaven, and with far greater precision, scientists from Brookhaven, Fermilab, and other institutions around the world will test a discrepancy between the muon g-2 particle’s theorized “magnetic moment” and the magnetic moment actually measured in the original experiment.

    Mehta is a participant in the High School Research Program administered by the Lab’s Office of Educational Programs.

    Meet the Siemens Semifinalists:

    4
    Semifinalist Daniel Lee
    5
    Semifinalist Brandon Feng

    Mentor: Shinjae Yoo, Computational Science Initiative
    Title of Project: Sensor Network Based Wind Field Detection

    Under the mentorship of Shinjae Yoo, Brandon Feng and Daniel Lee conducted research on sensor network analysis on the Long Island Solar Farm located at Brookhaven Lab. As part of their project, they built a realistic solar irradiance sensor simulator to detect multi-layered wind fields. Feng and Lee also developed robust wind field detection algorithms to determine various properties of data, such as time lag and the correct way to determine the wind field. These meaningful results can be integrated with the sensor network based solar irradiance forecasting framework and possibly applied to real-world data. Under the direction of Yoo, the students will contribute a paper on their findings.

    Feng and Lee are participants in the High School Research Program administered by the Lab’s Office of Educational Programs.

    6
    Semifinalist Bart Voto

    Bart Voto: Manhasset High School
    Mentor: Laura Fierce, Environmental and Climate Sciences Department
    Title of Project: Validating a Parameterization for Absorption by Black Carbon Through Comparisons with Observations

    Black carbon strongly absorbs solar radiation, causing a warming effect on the climate, but absorption per black carbon mass remains uncertain. To evaluate this uncertainty, Voto was tasked with validating a parameterization for light absorption by black carbon against observations. To do this, he used Python (a high-level programming language) to code a parameterization for black carbon’s absorption coefficient (developed previously by Fierce). He then used his code to evaluate the sensitivity of absorption by black carbon to different input parameters and compared the output from the parameterization with the corresponding values from field observations.

    For more information on the Regeneron STS Competition:

    https://www.regeneron.com/science-talent-search

    For more information on the Siemens Competition: https://siemenscompetition.discoveryeducation.com/

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 3:26 pm on January 20, 2017 Permalink | Reply
    Tags: BNL, Center for Data-Driven Discovery (C3D), Line Pouchard,   

    From BNL: Women in STEM – “Turning Research Data into Scientific Discoveries” Line Pouchard 

    Brookhaven Lab

    January 17, 2017
    Ariana Tantillo

    Line Pouchard, an information specialist in computational science, brings her expertise in big data management and curation to Brookhaven Lab’s Center for Data-Driven Discovery.

    1
    Line Pouchard is a senior researcher at the Center for Data-Driven Discovery, part of Brookhaven Lab’s Computational Science Initiative. No image credit.

    This week, the Center for Data-Driven Discovery (C3D) at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory welcomed its newest member: Line Pouchard, a computational science information specialist. Pouchard joins C3D as a senior researcher.

    Since 2014, Pouchard had been an assistant professor at Purdue University, where she led the investigation of the “scientific big data landscape”—referring to the large number of unique datasets that researchers are generating at unprecedented rates. Her research at Purdue focused on aspects of data management and curation for the storing, sharing, and re-using of research data. Pouchard, who spent 10 years at the beginning of her career as a research scientist at DOE’s Oak Ridge National Laboratory, returns to the DOE complex ready to accelerate data-driven discovery in high-energy physics, nanoscience, biology, and other fields.

    “As an information scientist with a passion for making connections between people and data to discover new knowledge for evidence-based decision-making, I am excited by the opportunity to take on the complex data curation challenges produced by experiments at Brookhaven Lab,” said Pouchard. “I look forward to helping scientists with the discovery, integration, and re-use of data and to providing efficient and effective data delivery systems that advance the state of the art in data curation at DOE and beyond.”

    Part of Brookhaven’s Computational Science Initiative (CSI), C3D is a multidisciplinary center for the development of tools and services—in areas such as machine-learning algorithms, visual analytics approaches, and easily reusable knowledge repositories—to improve the scientific discovery process. C3D’s staff of computational scientists, applied mathematicians, and computer scientists work closely with physicists, biologists, and other scientists to identify and address the challenges of scientific data management and analysis.

    Over her career, Pouchard has designed, developed, and deployed many systems to help scientists discover and integrate the vast wealth of scientific data. Her expertise is in the areas of metadata, semantics, ontologies, and provenance—all ways of “tagging” the data with information about their origins, such as when and how the data were generated, and encoding meaning into the data to facilitate their interrelation and integration. With an MS in information science from the University of Tennessee and a PhD in comparative literature from the City University of New York, Pouchard has a background and skillset that has enabled her to determine and serve the needs of users in a wide variety of domains, including environmental science, high-performance computing, and medicine.

    One of the systems she developed is an online repository of ontology entities for describing satellite and remote-sensing observations, climate simulations, and other earth science datasets. This ontology repository provides detailed descriptions and annotations that help scientists search for and share data, building upon each other’s work. Pouchard also developed a system that collects data on the “health” of a high-performance computing cluster—its temperature, voltage, and power. Collecting machine health data is important in monitoring power consumption, improving resource management, and detecting malware.

    “An experienced scholar in metadata, ontologies, and data provenance, Line will help lead C3D’s efforts to research and create new approaches for gaining, managing, and sharing insights from extreme-scale data collections,” said CSI Director Kerstin Kleese van Dam. “DOE’s large-scale experimental facilities and computing resources are creating unprecedented volumes of data, and Line will play a key role in turning these data into scientific discoveries at Brookhaven.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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