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  • richardmitnick 2:26 pm on February 2, 2017 Permalink | Reply
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    From Caltech: “Protein Chaperone Takes Its Job Seriously” 

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    Caltech

    02/02/2017

    Whitney Clavin
    (626) 395-1856
    wclavin@caltech.edu

    1
    Structural rendering of a ribosomal protein (yellow and red) bound to its chaperone (blue). By capturing an atomic-resolution snapshot of the pair of proteins interacting with each other, Ferdinand Huber, a graduate student in the lab of André Hoelz revealed that chaperones can protect their ribosomal proteins by tightly packaging them up. The red region illustrates where the dramatic shape alterations occur when the ribosomal protein is released from the chaperone during ribosome assembly. Credit: Huber and Hoelz/Caltech

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    A diagram of the cell showing the process by which chaperone proteins (red) transport ribosomal proteins (beige) to the nucleus. The chaperones bind to the ribosomal proteins and usher them into the nucleus, while also protecting the proteins from liquidation machinery. Once a ribosomal protein reaches a growing ribosome (green and purple), the chaperone releases it. The nearly complete ribosome units exit the nucleus where they undergo final assembly. Credit: Huber and Hoelz/Caltech

    For proteins, this would be the equivalent of the red-carpet treatment: each protein belonging to the complex machinery of ribosomes—components of the cell that produce proteins—has its own chaperone to guide it to the right place at the right time and protect it from harm.

    In a new Caltech study, researchers are learning more about how ribosome chaperones work, showing that one particular chaperone binds to its protein client in a very specific, tight manner, almost like a glove fitting a hand. The researchers used X-ray crystallography to solve the atomic structure of the ribosomal protein bound to its chaperone.

    “Making ribosomes is a bit like baking a cake. The individual ingredients come in protective packaging that specifically fits their size and shape until they are unwrapped and blended into a batter,” says André Hoelz, professor of chemistry at Caltech, a Heritage Medical Research Institute (HMRI) Investigator, and Howard Hughes Medical Institute (HHMI) Faculty Scholar.” What we have done is figure out how the protective packaging fits one ribosomal protein, and how it comes unwrapped.” Hoelz is the principal investigator behind the study published February 2, 2017, in the journal Nature Communications. The finding has potential applications in the development of new cancer drugs designed specifically to disable ribosome assembly.

    In all cells, genetic information is stored as DNA and transcribed into mRNAs that code for proteins. Ribosomes translate the mRNAs into amino acids, linking them together into polypeptide chains that fold into proteins. More than a million ribosomes are produced per day in an animal cell.

    Building ribosomes is a formidable undertaking for the cell, involving about 80 proteins that make up the ribosome itself, strings of ribosomal RNA, and more than 200 additional proteins that guide and regulate the process. “Ribosome assembly is a dynamic process, where everything happens in a certain order. We are only now beginning to elucidate the many steps involved,” says Hoelz.

    To make matters more complex, the proteins making up a ribosome are first synthesized outside the nucleus of a cell, in the cytoplasm, before being transported into the nucleus where the initial stages of ribosome assembly take place.

    Chaperone proteins help transport ribosomal proteins to the nucleus while also protecting them from being chopped up by a cell’s protein shredding machinery. The components that specifically aim this machinery at unprotected ribosomal proteins, recently identified by Raymond Deshaies, professor of biology at Caltech and an HHMI Investigator, ensures that equal numbers of the various ribosomal proteins are available for building the massive structure of a ribosome.

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    Structural rendering of a chaperone called Acl4 bound to ribosomal protein L4

    Previously, Hoelz and his team, in collaboration with the laboratory of Ed Hurt at the University of Heidelberg, discovered that a ribosomal protein called L4 is bound by a chaperone called “Assembly chaperone of RpL4,” or Acl4. The chaperone ushers L4 through the nucleus, protecting it from harm, and delivers it to a developing ribosome at a precise time and location. In the new study, the team used X-ray crystallography, a process that involves exposing protein crystals to high-energy X-rays, to solve the structure of the bound pair. The technique was performed at Caltech’s Molecular Observatory beamline at the Stanford Synchrotron Radiation Lightsource.

    “This was not an easy structure to solve,” says Ferdinand Huber, a graduate student at Caltech in the Hoelz lab and first author of the new study. “Solving the structure was incredibly exciting because you could see with your eyes, for the very first time, how the chaperone embraces the ribosomal protein to protect it.”

    Hoelz says that the structure was a surprise because it was not known previously that chaperones hold on to their ribosomal proteins so tightly. He says they want to study other chaperones in the future to see if they function in a similar fashion to tightly guard ribosomal proteins. The results may lead to the development of new drugs for cancer therapy by preventing cancer cells from supplying the large numbers of ribosomes required for tumor growth.

    The study, called “Molecular Basis for Protection of Ribosomal Protein L4 from Cellular Degradation,” was funded by a PhD fellowship of the Boehringer Ingelheim Fonds, a Faculty Scholar Award of the Howard Hughes Medical Research Institute, a Heritage Medical Research Institute Principal Investigatorship, a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research, a Teacher-Scholar Award of the Camille & Henry Dreyfus Foundation, and Caltech startup funds.

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 1:43 pm on January 31, 2017 Permalink | Reply
    Tags: , , , Caltech, , , vortex coronagraph   

    From Caltech: “Keck Observatory’s New Planet Imager Delivers First Science” 

    Caltech Logo
    Caltech
    01/30/2017

    Whitney Clavin
    (626) 395-1856
    wclavin@caltech.edu

    1
    An image of the brown dwarf HIP 79124 B, which is separated from its host star by 23 astronomical units (an astronomical unit is the distance between our sun and Earth). The vortex coronagraph was used to suppress the much brighter host star, allowing its dim companion to be imaged for the first time. Credit: NASA/JPL-Caltech

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    An image of the dusty disk of planetary material surrounding the star called HD 141569, located 380 light-years away. It was taken using the vortex coronagraph on the W.M. Keck Observatory. The vortex suppressed the star in the center, revealing light from the innermost ring of planetary material around the star (blue). The disk is made of olivine particles and extends from 23 to 70 astronomical units from the star—around where the outer planets lie in our solar system. Credit: NASA/JPL-Caltech

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    A picture of a vortex mask (left), which is made out of synthetic diamond. The mask is 1 centimeter in diameter and 0.3 millimeters thick. The vortex’s engraved pattern of grooves is very similar to a compact disk, making it look like a miniature version of a CD. The image at right zooms into the mask’s center with a scanning electron microscope. This view reveals the microstructure of the mask, highlighting its concentric grooves, which have a thickness of about 1/100th that of a human hair. No image credit.

    A new instrument on the W. M. Keck Observatory in Hawaii has delivered its first images, showing a ring of planet-forming dust around a star and, separately, a cool star-like body, called a brown dwarf, lying near to its companion star.

    The device, called the vortex coronagraph, was recently installed inside the Near Infrared Camera 2 (NIRC2), the workhorse infrared imaging camera at Keck. The vortex coronagraph has the potential to image planetary systems and brown dwarfs closer to their host stars than was possible previously. It was invented in 2005 by Dimitri Mawet while he was at the University of Liège in Belgium. Mawet is currently associate professor of astronomy at Caltech and a senior research scientist at NASA’s Jet Propulsion Laboratory (JPL). The Keck vortex coronagraph was built by the University of Liège, Uppsala University in Sweden, JPL, and Caltech.

    “The vortex coronagraph allows us to peer into the regions around stars where giant planets like Jupiter and Saturn supposedly form,” says Mawet. “Before now, we were only able to image gas giants that are born much farther out. With the vortex, we will be able to see planets orbiting as close to their stars as Jupiter is to our sun, or about two to three times closer than what was possible before.”

    The new vortex results are presented in two papers, both published in the January 2017 issue of The Astronomical Journal. One study, led by Gene Serabyn of JPL, the overall lead of the Keck vortex project, presents the first direct image of the brown dwarf called HIP 79124 B. This brown dwarf is located 23 astronomical units from a star in a nearby star-forming region called Scorpius-Centaurus (an astronomical unit is the distance between our sun and Earth).

    “The ability to see very close to stars also allows us to search for planets around more distant stars, where the planets and stars would appear closer together. Having the ability to survey distant stars for planets is important for catching planets still forming,” says Serabyn, who also led team that tested a predecessor of the vortex device at the Hale Telescope at Caltech’s Palomar Observatory near San Diego.

    Caltech Palomar 200 inch Hale Telescope, at Mt Wilson, CA, USA
    Caltech Palomar 200 inch Hale Telescope interior
    Caltech Palomar 200 inch Hale Telescope, at Mt Wilson, CA, USA

    In 2010, the team took images of three planets orbiting in the distant reaches of the star system called HR 8799.

    The second vortex study, led by Mawet, presents an image of the innermost of three rings of dusty planet-forming material around the young star called HD 141569 A. The results, when combined with infrared data from NASA’s Spitzer and WISE missions, and the European Space Agency’s Herschel mission, reveal that the star’s planet-forming material is made up of pebble-size grains of olivine, one of the most abundant silicates in Earth’s mantle. In addition, the data show that the temperature of the innermost ring imaged by the vortex is around 100 Kelvin (or minus 173 Celsius degrees), a bit warmer than our asteroid belt.

    NASA/Spitzer Telescope
    NASA/Spitzer Telescope

    NASA/WISE Telescope
    NASA/WISE Telescope

    ESA/Herschel spacecraft
    “ESA/Herschel spacecraft

    “The three rings around this young star are nested like Russian dolls and undergoing dramatic changes reminiscent of planetary formation,” says Mawet. “We have shown that silicate grains have agglomerated into pebbles, which are the building blocks of planet embryos.”

    How the vortex sees planets

    The first science images and results from the vortex instrument demonstrate its ability to image planet-forming regions hidden under the glare of stars. Stars outshine planets by a factor of a few thousands to a few billions, making the dim light of planets very difficult to see. The closer a planet is to its star, the more difficult it is to image. To deal with this challenge, researchers have invented Instruments called coronagraphs, which typically use tiny masks to block the starlight, much like blocking the bright sun with your hand or a car visor to see better.

    What makes the vortex coronagraph unique is that it does not block the starlight with a mask, but instead redirects the light away from the detectors using a technique in which light waves are combined and canceled out. Because the vortex doesn’t require a mask, it has the advantage of taking images of regions closer to stars than other coronagraphs. Mawet likens the process to the eye of a storm.

    “The instrument is called a vortex coronagraph because the starlight is centered on an optical singularity, which creates a dark hole at the location of the image of the star,” says Mawet. “Hurricanes have a singularity at their centers where the wind speeds drop to zero—the eye of the storm. Our vortex coronagraph is basically the eye of an optical storm where we send the starlight.”

    A team at the University of Liège, led by Olivier Absil, designed a portion of the Keck vortex coronagraph called the phase mask, which consists of concentric microstructures that force the starlight waves to swirl about the mask’s center, creating the vortex singularity. This mask was forged at Uppsala University by Mikael Karlsson and his team, who etched the concentric microstructures into synthetic diamond. The etching is done in a plasma chamber where the diamond is bombarded by argon and oxygen ions, ripping the carbon atoms out of the diamond crystal.

    The vortex was installed at Keck in the spring of 2015 by Keith Matthews, chief instrument scientist at Caltech, who has worked on dozens of astronomical instruments in his more than 50-year career at the Institute. The coronagraph was optimized and is operated with the help of the Keck Observatory staff. “Once the device is in there, users can operate it remotely from the base of the mountain or even from their home universities,” says Matthews.

    What’s next for the vortex

    In the future, the vortex will look at many more young planetary systems, in particular planets near the “ice lines,” which are the region around a star where temperatures have become cold enough for volatile molecules, such as water, methane, and carbon dioxide, to condense into solid icy grains. Ice lines are thought to delineate the transition between rocky planets and gas giants.

    Surveys of the ice-line region by the vortex coronagraph will help answer ongoing puzzles about a class of hot, giant planets found extremely close to their stars—the “hot Jupiters” and “hot Neptunes.” Did these planets first form close to the ice lines and migrate in, or did they form in situ, right next to their star? “With a bit of luck, we might catch planets in the process of migrating through the planet-forming disk, by looking at these very young objects,” says Mawet.

    This month, a privately funded project called Breakthrough Initiatives announced that it is partnering with the European Southern Observatory to use similar vortex technology to find and image a putative Earth-like planet in the nearby Alpha Centauri star system. What’s more, results from Keck’s vortex coronagraph will help with a planet imager planned for the future Thirty Meter Telescope and with proposed NASA space missions, such as the Habitable Exoplanet Imaging Mission (HabEx) and the Large UV/Optical/IR Surveyor (LUVOIR), which would use next-generation vortex coronagraphs currently being designed in Mawet’s group at Caltech.

    The challenge of these facilities is to image planets even closer to their stars than those at the ice line, which includes Earth-like rocky planets. When combined with data from spectrograph instruments, which can identify molecules in planets’ atmospheres, the images could help astronomers identify possible signs of life.

    “The power of the vortex lies in its ability to image planets very close to their star, something that we can’t do for Earth-like planets yet,” says Serabyn. “The vortex coronagraph may be key to taking the first images of a pale blue dot like our own.”

    The Keck Observatory is managed by Caltech and the University of California. In 1996, the NASA joined as a one-sixth partner in the Keck Observatory. JPL is managed by Caltech for NASA.

    See the full article here .

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    Caltech campus
    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”

     
  • richardmitnick 3:07 pm on January 14, 2017 Permalink | Reply
    Tags: , , , Caltech, , , Keck Cosmic Web Imager   

    From Caltech via EurekaAlert: “New Caltech instrument poised to image the cosmic web” 

    Caltech Logo
    Caltech

    1

    EurekaAlert

    12-Jan-2017
    Whitney Clavin
    wclavin@caltech.edu
    626-395-1856

    Keck Cosmic Web Imager ships from Caltech to Keck Observatory

    2
    Hector Rodriguez, senior mechanical technician, works on the Keck Cosmic Web Imager in a clean room at Caltech. Caltech

    An instrument designed to image the vast web of gas that connects galaxies in the universe has been shipped from Los Angeles to Hawaii, where it will be integrated into the W. M. Keck Observatory.

    Keck Observatory, Mauna Kea, Hawaii, USA
    Keck Observatory, Mauna Kea, Hawaii, USA

    The instrument, called the Keck Cosmic Web Imager, or KCWI, was designed and built by a team at Caltech led by Professor of Physics Christopher Martin. It will be one of the best instruments in the world for taking spectral images of cosmic objects–detailed images where each pixel can be viewed in all wavelengths of visible light. Such high-resolution spectral information will enable astronomers to study the compositions, velocities, and masses of many objects, such as stars and galaxies, in ways that were not possible before.

    One of KCWI’s main goals, and a passion of Martin’s for the past 30 years, is to answer the question: What is the gas around galaxies doing?

    “For decades, astronomers have demonstrated that galaxies evolve. Now we’re trying to figure out how and why,” says Martin. “We know the gas around galaxies is ultimately fueling them, but it is so faint–we still haven’t been able to get a close look at it and understand how this process works.”

    Martin and his team study what is called the cosmic web–a vast network of streams of gas between galaxies. Recently, the scientists have found evidence supporting what is called the cold flow model, in which this gas funnels into the cores of galaxies, where it condenses and forms new stars.

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    The forming galaxy with binary quasars as it fits into the timeline of the Universe. We’re seeing it 10 billion years ago, during the epoch of galaxy formation. Credit: Caltech Academic Media Technologies

    Researchers had predicted that the gas filaments would first flow into a large ring-like structure around the galaxy before spiraling into it–exactly what Martin and his team found using the Palomar Cosmic Web Imager, a precursor to KCWI, at Caltech’s Palomar Observatory near San Diego.

    Caltech Palomar Cosmic Web Imager
    Caltech Palomar Cosmic Web Imager

    “We measured the kinematics, or motion, of the gas around a galaxy and found a very large rotating disk connected to a gas filament,” says Martin. “It was the smoking gun for the cold flow model.”

    With KCWI, the researchers will get a closer look at the gas filaments and ring-like structures around galaxies that range from 10 to 12 billion light-years away, an era when our universe was roughly 2 to 4 billion years old. Not only can KCWI take more detailed pictures than the Palomar Cosmic Web Imager, it has other advances such as better mirror coatings. The combination of these improvements with the fact that KCWI is being installed at one of the twin 10-meter Keck telescopes–the world’s largest observatory with some of the darkest known skies on Earth–means that KCWI will have an improved performance by more than an order of magnitude over the Palomar Cosmic Web Imager.

    KCWI will map the gas flowing from the intergalactic medium–the space between galaxies–into many young galaxies, revealing, for the first time, the dominant mode of galaxy formation in the early universe. The instrument will also search for supergalactic winds from galaxies that drive gas back into the intergalactic medium. How gas flows into and out of forming galaxies is the central open question in the formation of cosmic structures.

    “We designed KCWI to study very dim and diffuse objects, our main emphasis being on the wispy cosmic web and the interactions of galaxies with their surroundings,” says Mateusz (Matt) Matuszewski, the instrument scientist for the project.

    KCWI is also designed to be more a general-purpose instrument than the Palomar’s Cosmic Web Imager, which is mainly for studies of the cosmic web. It will study everything from gas jets around young stars to the winds of dead stars and supermassive black holes and more. “The instrument is really versatile,” says Matuszewski. “Observers can configure the optics to adjust the spatial and spectral scales and resolutions to suit their interests.”

    The nuts and bolts of KCWI

    Scientists and engineers have been busy assembling the highly complex elements of the KCWI instrument at Caltech since 2012. The instrument is about the size of an ice cream truck and weighs over 4,000 kilograms. The core feature of KCWI is its ability to capture spectral information about objects, such as galaxies, across a wide image. Typically, astronomers capture spectra using instruments called spectrographs, which have narrow slit-shaped windows. The spectrograph breaks apart light from the slit into each of the colors making up the target object, just like a prism that spreads light into a rainbow. But traditional spectrographs cannot be used to capture spectral information across an entire image.

    “Traditional spectrographs use multiple small slits to capture many stars or the cores of many galaxies,” says Martin. “Now, we want to look at features that are extended across the sky, such as stellar jets and galaxies, which have complex structures, velocities, and gas flows. If you can only look through a slit, you can only see a small part of what is going on. But we want to see the whole picture. That’s why we need an imaging spectrograph, a device that gives you an image for every single wavelength across a wide view.”

    To create a spectrograph that can image more extended objects like galaxies, KCWI uses what is called an integral field design, which basically divides an image up into 24 slits, and gathers all the spectral information at once.

    “If you’re looking at something big in the sky, it’s inefficient to just have one slit and step your way across that object, so an integral field spectrograph combines a number of slit-shaped mirrors together across a continuous field of view,” says Patrick Morrissey, the project scientist for KCWI who now works at JPL. “Imagine looking into a broken mirror–the reflected image is shifted around depending on the angles of the pieces. This is how the integral field spectrograph works. A series of mirrors works together to make a square-shaped stack of slits across an image appear as a single traditional vertical slit.”

    KCWI has the highest spectral resolution of any integral field spectrograph, which means it can better break apart the rainbow of light to see more colors, or wavelengths. The first phase of the instrument, now on its way to Keck, covers the blue side of the visible spectrum, spanning wavelength ranges from 3500 to 5600 Angstroms. A second phase, extending coverage to the red side of the spectrum, out to 10400 Angstroms, will be built next.

    KCWI to Climb Mauna Kea

    After KCWI arrives in Hawaii on January 18, engineers will guide it up to the top of Mauna Kea, where Keck is perched. A series of checkout and alignment tests is planned, and will be followed in a few months by the first observations through the Keck telescope.

    “There are train tracks around the telescope where the instruments are installed,” says Morrissey. “It’s like one of those old railroad roundhouses where the train would come in and they would spin it to an available space for storage. The telescope turns around, points to the instrument that the astronomer wants to use, and then they roll that instrument on. Soon KCWI will becomes part of the telescope.”

    KCWI is funded by the National Science Foundation, through the Association of Universities for Research in Astronomy (AURA) program, and by the Heising-Simons Foundation, the W.M. Keck Foundation, the Caltech Division of Physics, Mathematics and Astronomy, and the Caltech Optical Observatories.

    See the full article here .

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    Caltech campus
    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”

     
  • richardmitnick 12:56 pm on January 12, 2017 Permalink | Reply
    Tags: , Caltech, IC 3639, Monster black holes, , , NGC 1448, , , Type II supernova   

    From Space Science Laboratory at UC Berkeley: “NuSTAR – Black Holes Hide in our Cosmic Backyard” 

    UC Berkeley

    UC Berkeley

    SSL UC Berkeley

    Space Science Laboratory

    1
    No image caption. No image credit.

    NASA/NuSTAR

    NuSTAR

    January 12, 2017
    Christopher Scholz

    Monster black holes sometimes lurk behind gas and dust, hiding from the gaze of most telescopes. But they give themselves away when material they feed on emits high-energy X-rays that NASA’s NuSTAR (Nuclear Spectroscopic Telescope Array) mission can detect. That’s how NuSTAR recently identified two gas-enshrouded supermassive black holes, located at the centers of nearby galaxies.

    “These black holes are relatively close to the Milky Way, but they have remained hidden from us until now,” said Ady Annuar, a graduate student at Durham University in the United Kingdom, who presented the results at the American Astronomical Society meeting in Grapevine, Texas. “They’re like monsters hiding under your bed.”

    Both of these black holes are the central engines of what astronomers call “active galactic nuclei,” a class of extremely bright objects that includes quasars and blazars. Depending on how these galactic nuclei are oriented and what sort of material surrounds them, they appear very different when examined with telescopes.

    Active galactic nuclei are so bright because particles in the regions around the black hole get very hot and emit radiation across the full electromagnetic spectrum — from low-energy radio waves to high-energy X-rays. However, most active nuclei are believed to be surrounded by a doughnut-shaped region of thick gas and dust that obscures the central regions from certain lines of sight. Both of the active galactic nuclei that NuSTAR recently studied appear to be oriented such that astronomers view them edge-on. That means that instead of seeing the bright central regions, our telescopes primarily see the reflected X-rays from the doughnut-shaped obscuring material.

    “Just as we can’t see the sun on a cloudy day, we can’t directly see how bright these active galactic nuclei really are because of all of the gas and dust surrounding the central engine,” said Peter Boorman, a graduate student at the University of Southampton in the United Kingdom.

    Boorman led the study of an active galaxy called IC 3639, which is 170 million light years away.

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    IC 3639, a galaxy with an active galactic nucleus, is seen in this image combining data from the Hubble Space Telescope and the European Southern Observatory.

    This galaxy contains an example of a supermassive black hole hidden by gas and dust. Researchers analyzed NuSTAR data from this object and compared them with previous observations from NASA’s Chandra X-Ray Observatory and the Japanese-led Suzaku satellite.

    NASA/Chandra Telescope
    NASA/Chandra Telescope

    JAXA/Suzaku satellite
    JAXA/Suzaku satellite

    The findings from NuSTAR, which is more sensitive to higher energy X-rays than these observatories, confirm the nature of IC 3639 as an active galactic nucleus that is heavily obscured, and intrinsically much brighter than observed.

    Researchers analyzed NuSTAR data from this object and compared them with previous observations from NASA’s Chandra X-Ray Observatory and the Japan-led Suzaku satellite. NuSTAR also provided the first precise measurement of how much material is obscuring the central engine of IC 3639, allowing researchers to determine how luminous this hidden monster really is.

    More surprising is the spiral galaxy that Annuar focused on: NGC 1448.

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    NGC 1448 (also designated NGC 1457 and ESO 249-16) is a spiral galaxy located about 60 million light-years away in the constellation Horologium. It has a prominent disk of young and very bright stars surrounding its small, shining core. The galaxy is receding from us with 1168 kilometers per second.

    NGC 1448 has recently been a prolific factory of supernovae, the dramatic explosions that mark the death of stars: after a first one observed in this galaxy in 1983 (SN 1983S), two more have been discovered during the past decade.

    Visible as a red dot inside the disc, in the upper right part of the image, is the supernova observed in 2003 (Type II supernova SN 2003hn), whereas another one, detected in 2001 (Type Ia supernova SN 2001el), can be noticed as a tiny blue dot in the central part of the image, just below the galaxy’s core. If captured at the peak of the explosion, a supernova might be as bright as the whole galaxy that hosts it.

    A Type Ia supernova is a result from the violent explosion of a white dwarf star. This category of supernovae produces consistent peak luminosity. The stability of this luminosity allows these supernovae to be used as standard candles to measure the distance to their host galaxies because the visual magnitude of the supernovae depends primarily on the distance.

    A Type II supernova results from the rapid collapse and violent explosion of a massive star. A star must have at least 8 times, and no more than 40–50 times the mass of the Sun for this type of explosion. It is distinguished from other types of supernova by the presence of hydrogen in its spectrum. Type II supernovae are mainly observed in the spiral arms of galaxies and in H II regions, but not in elliptical galaxies.

    This image was obtained using the 8.2-metre telescopes of ESO’s Very Large Telescope. It combines exposures taken between July 2002 and the end of November 2003.

    ESO/VLT at Cerro Paranal, Chile, ESO/VLT at Cerro Paranal, with an elevation of 2,635 metres (8,645 ft) above sea level
    ESO/VLT at Cerro Paranal, Chile, ESO/VLT at Cerro Paranal, with an elevation of 2,635 metres (8,645 ft) above sea level

    Credit: ESO

    The black hole in its center was only discovered in 2009, even though it is at the center of one of the nearest large galaxies to our Milky Way. By “near,” astronomers mean NGC 1448 is only 38 million light years away (one light year is about 6 trillion miles).

    Annuar’s study discovered that this galaxy also has a thick column of gas hiding the central black hole, which could be part of a doughnut-shaped region. X-ray emission from NGC 1448, as seen by NuSTAR and Chandra, suggests for the first time that, as with IC 3639, there must be a thick layer of gas and dust hiding the active black hole in this galaxy from our line of sight.

    Researchers also found that NGC 1448 has a large population of young (just 5 million year old) stars, suggesting that the galaxy produces new stars at the same time that its black hole feeds on gas and dust. Researchers used the European Southern Observatory New Technology Telescope to image NGC 1448 at optical wavelengths, and identified where exactly in the galaxy the black hole should be. A black hole’s location can be hard to pinpoint because the centers of galaxies are crowded with stars. Large optical and radio telescopes can help detect light from around black holes so that astronomers can find their location and piece together the story of their growth.

    “It is exciting to use the power of NuSTAR to get important, unique information on these beasts, even in our cosmic backyard where they can be studied in detail,” said Daniel Stern, NuSTAR project scientist at NASA’s Jet Propulsion Laboratory, Pasadena, California.

    NuSTAR is a Small Explorer mission led by Caltech and managed by JPL for NASA’s Science Mission Directorate in Washington. NuSTAR was developed in partnership with the Danish Technical University and the Italian Space Agency (ASI). The spacecraft was built by Orbital Sciences Corp., Dulles, Virginia. NuSTAR’s mission operations center is at UC Berkeley, and the official data archive is at NASA’s High Energy Astrophysics Science Archive Research Center. ASI provides the mission’s ground station and a mirror archive. JPL is managed by Caltech for NASA.

    See the full article here .

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    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 9:50 am on January 12, 2017 Permalink | Reply
    Tags: , Auroral Displays at Brown Dwarfs, , , Caltech   

    From astrobites: “Auroral Displays at Brown Dwarfs” 

    Astrobites bloc

    Astrobites

    Title: Magnetospherically driven optical and radio aurorae at the end of the stellar main sequence
    Authors: G.Hallinan, S. P. Littlefair, G. Cotter, et al.
    First Author’s Institution: California Institute of Technology
    Caltech Logo
    Status: Published in Nature (2015), open access

    Auroras are the spectacular light shows visible in the polar regions at Earth and other planets. In 2015 they were detected for the first time outside of the solar system. Brown dwarfs are objects often described as “failed stars”, meaning they are insufficiently massive to ignite hydrogen fusion in their cores. Today’s paper reports on the remarkable discovery that a particular brown dwarf plays host to auroral displays far more powerful than those found anywhere in the solar system.

    Brown dwarfs

    Artist's concept of a Brown dwarf [not quite a] star. NASA/JPL-Caltech
    Artist’s concept of a Brown dwarf [not quite a] star. NASA/JPL-Caltech

    Brown dwarfs occupy the region between giant planets and the lowest mass stars. It is generally accepted that they form in a manner similar to stars, i.e. the gravitational collapse of interstellar gas, but never reaching a mass sufficient to sustain hydrogen fusion in the core. As such, brown dwarfs are extremely cool, faint objects, making their detection much more difficult than ordinary stars. However, they provide an excellent opportunity to for us to better understand the physics that differentiates the stellar and planetary domains. Since their discovery many surveys have been performed which have revealed, amongst other things, the existence of complex weather systems and strong global magnetic fields.

    Auroras

    Understanding the interaction of the magnetic field at a brown dwarf with its nearby space environment is a key scientific goal. At Earth, space scientists observe the aurora as a means of revealing the structure and dynamics of the magnetic field, and the plasma which interacts with it. Before turning to auroras at brown dwarfs we shall briefly review at what we know about auroras from our studies at Earth and other solar system planets.

    The vibrant displays that we see are a result of charged particles (i.e. electrons and ions) from the plasma population around the Earth raining down along magnetic field lines, and colliding with molecules in the atmosphere. These collisions excite the atmospheric constituents to a higher energy state, causing the emission of a photon as they return to their original state.

    Auroral emissions aren’t just confined to Earth; they are found at other magnetised planets in the solar system, with Jupiter being a particularly spectacular example.

    3
    JUNE 30, 2016: Astronomers are using NASA’s Hubble Space Telescope to study auroras — stunning light shows in a planet’s atmosphere — on the poles of the largest planet in the solar system, Jupiter. The auroras were photographed during a series of Hubble Space Telescope Imaging Spectrograph far-ultraviolet-light observations taking place as NASA’s Juno spacecraft approaches and enters into orbit around Jupiter. The aim of the program is to determine how Jupiter’s auroras respond to changing conditions in the solar wind, a stream of charged particles emitted from the sun. Auroras are formed when charged particles in the space surrounding the planet are accelerated to high energies along the planet’s magnetic field. When the particles hit the atmosphere near the magnetic poles, they cause it to glow like gases in a fluorescent light fixture. Jupiter’s magnetosphere is 20,000 times stronger than Earth’s. These observations will reveal how the solar system’s largest and most powerful magnetosphere behaves. The full-color disk of Jupiter in this image was separately photographed at a different time by Hubble’s Outer Planet Atmospheres Legacy (OPAL) program, a long-term Hubble project that annually captures global maps of the outer planets.
    Date 30 June 2016
    Source http://hubblesite.org/newscenter/archive/releases/2016/24
    Author NASA, ESA, and J. Nichols (University of Leicester)

    Neither are they confined only to the visible part of the spectrum; auroral emissions occur from radio frequencies through to UV and X-ray.

    Now we return to brown dwarfs. Since 2006 it has been known that a handful of brown dwarfs emit very regular and persistent radio bursts. These burst are pulsed at the rotation period of the dwarf, leading some researchers to suggest that they may be caused by auroras that are generated in a similar manner to Jupiter’s main auroral oval. The pulsing in this case may be due to the magnetic axis being tilted from the spin axis, so that as the dwarf rotates the auroral emission cones into our line of sight. This motivated the authors of today’s paper to target a particular brown dwarf, LSR J1835 + 3259, with simultaneous radio and optical observation, pursuing a possible relation between the two.

    4
    LSR J1835 + 3259. Image: http://images.zeit.de/ http://www.theweeklyobserver.com/ailed-star-shows-dazzling-display-of-northern-lights/5575/

    Radio observations were made using the Very Large Array (VLA) radio telescope, while simultaneously, optical measurements were made with the 5.1 m Hale telescope at the Palomar Observatory with follow-up observations from the 10 m Keck telescope.

    NRAO/VLA, on the Plains of San Agustin fifty miles west of Socorro, NM, USA
    NRAO/VLA, on the Plains of San Agustin fifty miles west of Socorro, NM, USA

    Caltech Palomar 200 inch Hale Telescope, at Mt Wilson, CA, USA
    Caltech Hale Telescope at Palomar interior
    Caltech Palomar 200 inch Hale Telescope, at Mt Wilson, CA, USA

    Keck Observatory, Mauna Kea, Hawaii, USA
    Keck Observatory Interior
    Keck Observatory, Mauna Kea, Hawaii, USA

    The results of the observations are shown in Figure 1, where the light curve from the optical measurements (Fig 1a) shows a clear periodicity of 2.84 h. Observations of the radio emission (Fig 1b) show the same periodicity, with a slight offset in phase causing it to lag slightly behind the optical emission. The authors attribute their findings to auroras which are driven by strong electric currents flowing in the magnetosphere of the dwarf.

    2
    Figure 1: (a) Optical measurements of Balmer line emission of LSR J1835 made using the Hale telescope. (b) Corresponding radio observations of the same object made using the VLA radio telescope. [Figure 1 from Hallinan et al. 2015]

    With this discovery many open questions are presented. What is the mechanism driving the auroras? It may be interaction with the interstellar medium, analogous to the process of the Earth’s magnetosphere interacting with the solar wind. Or it could be due to a continuously replenishing source of plasma mass outflow from within a closed magnetosphere, analogous to the mechanism producing Jupiter’s main auroral oval. Additionally, the source of the required plasma population is unknown, with the cool temperatures (∼2000 K) of brown dwarfs being unable to support significant ionisation of their atmospheres, and the lack of nearby stars restricting the possibility ionisation by stellar irradiation.

    Ultimately it is an exciting prospect that this discovery, along with the arrival of even more sensitive radio telescopes (e.g. the Square Kilometre Array), may pave the way towards detecting auroras at exoplanets.

    SKA Square Kilometer Array

    This which would add a novel technique to the exoplanet-detectors toolkit, and enable us to learn about the magnetic fields and plasma populations around those objects.

    See the full article here .

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    What do we do?

    Astrobites is a daily astrophysical literature journal written by graduate students in astronomy. Our goal is to present one interesting paper per day in a brief format that is accessible to undergraduate students in the physical sciences who are interested in active research.
    Why read Astrobites?

    Reading a technical paper from an unfamiliar subfield is intimidating. It may not be obvious how the techniques used by the researchers really work or what role the new research plays in answering the bigger questions motivating that field, not to mention the obscure jargon! For most people, it takes years for scientific papers to become meaningful.
    Our goal is to solve this problem, one paper at a time. In 5 minutes a day reading Astrobites, you should not only learn about one interesting piece of current work, but also get a peek at the broader picture of research in a new area of astronomy.

     
  • richardmitnick 9:34 pm on December 23, 2016 Permalink | Reply
    Tags: Aquaporin, Caltech, ,   

    From Caltech: “Visualizing Gene Expression with MRI” 

    Caltech Logo
    Caltech

    12/23/2016

    Lori Dajose
    (626) 395-1217
    ldajose@caltech.edu

    1
    An illustration of aquaporin’s effect on cells. Credit: M. Shapiro Laboratory/Caltech

    Genes tell cells what to do—for example, when to repair DNA mistakes or when to die—and can be turned on or off like a light switch. Knowing which genes are switched on, or expressed, is important for the treatment and monitoring of disease. Now, for the first time, Caltech scientists have developed a simple way to visualize gene expression in cells deep inside the body using a common imaging technology.

    Researchers in the laboratory of Mikhail Shapiro, assistant professor of chemical engineering and Heritage Medical Research Institute Investigator, have invented a new method to link magnetic resonance imaging (MRI) signals to gene expression in cells—including tumor cells—in living tissues. The technique, which eventually could be used in humans, would allow gene expression to be monitored non-invasively, requiring no surgical procedures such as biopsies.

    The work appears in the December 23 online edition of the journal Nature Communications.

    In MRI, hydrogen atoms in the body—atoms that are mostly contained in water molecules and fat—are excited using a magnetic field. The excited atoms, in turn, emit signals that can be used to create images of the brain, muscle, and other tissues, which can be distinguished based on the local physical and chemical environment of the water molecules. While this technique is widely used, it usually provides only anatomical snapshots of tissues or physiological functions such as blood flow rather than observations of the activity of specific cells.

    “We thought that if we could link signals from water molecules to the expression of genes of interest, we could change the way the cell looks under MRI,” says Arnab Mukherjee, a postdoctoral scholar in chemical engineering at Caltech and co-lead author on the paper.

    The group turned to a protein that naturally occurs in humans, called aquaporin. Aquaporin sits within the membrane that envelops cells and acts as a gatekeeper for water molecules, allowing them to move in and out of the cell. Shapiro’s team realized that increasing the number of aquaporins on a given cell made it stand out in MRI images acquired using a common clinical technique called diffusion-weighted imaging, which is sensitive to the movement of water molecules. They then linked aquaporin to genes of interest, making it what scientists call a reporter gene. This means that when a gene of interest is turned on, the cell will overexpress aquaporin, making the cell look darker under diffusion-weighted MRI.

    The researchers showed that this technique was successful in monitoring gene expression in a brain tumor in mice. After implanting the tumor, they gave the mice a drug to trigger the tumor cells to express the aquaporin reporter gene, which made the tumor look darker in MRI images.

    “Overexpression of aquaporin has no negative impact on cells because it is exclusive to water and simply allows the molecules to go back and forth across the cell membrane,” Shapiro says. Under normal physiological conditions the number of water molecules entering and exiting an aquaporin-expressing cell is the same, so that the total amount of water in each cell does not change. “Aquaporin is a very convenient way to genetically change the way that cells look under MRI.”

    Though the work was done in mice, it has the potential for clinical translation, according to Shapiro. Aquaporin is a naturally occurring gene and will not cause an immune reaction. Previously developed reporter genes for MRI have been much more limited in their capabilities, requiring the use of specific metals that are not always available in some tissues.

    “An effective reporter gene for MRI is a ‘holy grail’ in biomedical imaging because it would allow cellular function to be observed non-invasively,” says Shapiro. “Aquaporins are a new way to think about this problem. It is remarkable that simply allowing water molecules to more easily get into and out of cells in a tissue gives us the ability to remotely see those cells in the middle of the body.”

    The paper is titled Non-invasive imaging using reporter genes altering cellular water permeability. In addition to Shapiro and Mukherjee, other coauthors include Caltech graduate students Di Wu (MS ’16 and co-lead author) and Hunter Davis. The work was funded by the Dana Foundation, a Burroughs Wellcome Career Award at the Scientific Interface, the Heritage Medical Research Institute, and the National Institutes of Health.

    See the full article here .

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    Caltech campus
    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”

     
  • richardmitnick 12:14 pm on December 16, 2016 Permalink | Reply
    Tags: , , Caltech, , RIK-210   

    From Caltech via phys.org: “Astronomers observe mysterious dimming of a young nearby star” 

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    Caltech

    phys.org

    phys.org

    December 16, 2016
    Tomasz Nowakowski

    1
    Flattened and median filtered K2 light curve of RIK-210. The data are phase-wrapped on the dip period of 5.6685 days. A grouping of shallow dips preceding the main dip is prominent for the first four rotation periods of the campaign, then largely disappears. Variability fit B was used to make this figure. Credit: David et al., 2016.

    Astronomers have spotted transient, transit-like dimming events of a young star named RIK-210 located some 472 light years away in the Upper Scorpius OB association. However, what puzzles the scientists is the mystery behind this dimming as it can not be caused by an eclipsing stellar or brown dwarf companion. They describe their search for plausible explanations in a paper published Dec. 12 on the arXiv pre-print server.

    RIK-210 is around five to 10 million years old, about half as massive as the sun and has a radius of approximately 1.24 solar radii. The star has been recently observed by NASA’s prolonged Kepler mission, known as K2, during its Campaign 2, lasting from Aug. 22 to Nov. 11, 2014. A team of researchers led by Trevor David of the California Institute of Technology (Caltech) has analyzed the data provided by K2.

    “We find transient, transit-like dimming events within the K2 time series photometry of the young star RIK-210 in the Upper Scorpius OB association. These dimming events are variable in depth, duration, and morphology,” the scientists wrote in the paper.

    The team found that these dimming events occur approximately every 5.67 days, in phase with the stellar rotation, noting that they are deep (sometimes greater than 15 percent) and short in duration relative to the rotational period. Moreover, the morphology of the dimmings is variable throughout the whole observational campaign, while the starspot modulation pattern remains stable over this period of time.

    While such variable dimmings have been documented around mature stars and stellar remnants, it has not been previously observed around a young star lacking a protoplanetary disk, as in the case of RIK-210.

    In the search for possible explanations of the observed transient, transit-like dimming events, the researchers at first excluded the possibility that they can be caused by an eclipsing stellar or brown dwarf companion. This hypothesis was ruled out as it is inconsistent with radial velocity measurements as well as with archival and follow-up photometry data.

    The researchers emphasized that the dimmings cannot be due to a single spherical body because of the variable morphology of these events. They added that based on the observed depths and durations, it is also unlikely that the dimmings could be explained by features on the stellar surface.

    According to the team, the most plausible explanation of the nature of the obscuring material is that it could be a magnetospheric cloud. They assume that a cloud of plasma analogous to those observed in high-mass stars, or a dusty accretion column, could naturally explain the synchronicity between the rotation period and the dimming events.

    “Since the accretion timescale is … much shorter than the orbital period, this model might explain the variable depths and morphologies of dimming events,” the paper reads.

    Other explanations taken into account by the researchers are: an accretion flow from residual gas and dust, remnants of the late stages of planet formation, the product of a giant-impact type collision, an enshrouded protoplanet with an extended tail, or one or more eccentric bodies undergoing periodic tidal disruption upon each periastron passage.

    In order to finally confirm which of the proposed hypotheses is true, the team calls for continued photometric and spectroscopic monitoring.

    “Multi-band photometric monitoring can be used to test whether the dip depths are wavelength-dependent; solid-body transits are achromatic, while extinction by dust is less severe at redder wavelengths. Finally, spectroscopic monitoring while the star is known to be dimming can test whether there is enhanced absorption by a gaseous cloud transiting the star,” the scientists concluded.

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 6:50 pm on December 11, 2016 Permalink | Reply
    Tags: Caltech, , , The right way to simulate the Milky Way   

    From Science Node: “The right way to simulate the Milky Way” 

    Science Node bloc
    Science Node

    13 Sep, 2016 [Where oh where has this been?]
    Whitney Clavin

    Astronomers have created the most detailed computer simulation to date of our Milky Way galaxy’s formation, from its inception billions of years ago as a loose assemblage of matter to its present-day state as a massive, spiral disk of stars.

    The simulation solves a decades-old mystery surrounding the tiny galaxies that swarm around the outside of our much larger Milky Way. Previous simulations predicted that thousands of these satellite, or dwarf, galaxies should exist. However, only about 30 of the small galaxies have ever been observed. Astronomers have been tinkering with the simulations, trying to understand this ‘missing satellites’ problem to no avail.


    Access mp4 video here .
    Supercomputers and superstars. Caltech associate professor of theoretical astrophysics Phil Hopkins and Carnegie-Caltech research fellow Andrew Wetzel use XSEDE supercomputers to build the most detailed and realistic simulation of galaxy formation ever created. The results solve a decades-long mystery regarding dwarf galaxies around our Milky Way. Courtesy Caltech.

    Now, with the new simulation — which used resources from the Extreme Science and Engineering Discovery Environment (XSEDE) running in parallel for 700,000 central processing unit (CPU) hours — astronomers at the California Institute of Technology (Caltech) have created a galaxy that looks like the one we live in today, with the correct, smaller number of dwarf galaxies.

    “That was the aha moment, when I saw that the simulation can finally produce a population of dwarf galaxies like the ones we observe around the Milky Way,” says Andrew Wetzel, postdoctoral fellow at Caltech and Carnegie Observatories in Pasadena, and lead author of a paper about the new research, published August 20 in Astrophysical Journal Letters.

    One of the main updates to the new simulation relates to how supernovae, explosions of massive stars, affect their surrounding environments. In particular, the simulation incorporated detailed formulas that describe the dramatic effects that winds from these explosions can have on star-forming material and dwarf galaxies. These winds, which reach speeds up to thousands of kilometers per second, “can blow gas and stars out of a small galaxy,” says Wetzel.

    Indeed, the new simulation showed the winds can blow apart young dwarf galaxies, preventing them from reaching maturity. Previous simulations that were producing thousands of dwarf galaxies weren’t taking the full effects of supernovae into account.

    “We had thought before that perhaps our understanding of dark matter was incorrect in these simulations, but these new results show we don’t have to tinker with dark matter,” says Wetzel. “When we more precisely model supernovae, we get the right answer.”

    Astronomers simulate our galaxy to understand how the Milky Way, and our solar system within it, came to be. To do this, the researchers tell a computer what our universe was like in the early cosmos. They write complex codes for the basic laws of physics and describe the ingredients of the universe, including everyday matter like hydrogen gas as well as dark matter, which, while invisible, exerts gravitational tugs on other matter. The computers then go to work, playing out all the possible interactions between particles, gas, and stars over billions of years.

    “In a galaxy, you have 100 billion stars, all pulling on each other, not to mention other components we don’t see, like dark matter,” says Caltech’s Phil Hopkins, associate professor of theoretical astrophysics and principal scientist for the new research. “To simulate this, we give a supercomputer equations describing those interactions and then let it crank through those equations repeatedly and see what comes out at the end.”

    The researchers are not done simulating our Milky Way. They plan to use even more computing time, up to 20 million CPU hours, in their next rounds. This should lead to predictions about the very faintest and smallest of dwarf galaxies yet to be discovered. Not a lot of these faint galaxies are expected to exist, but the more advanced simulations should be able to predict how many are left to find.

    The study was funded by Caltech, a Sloan Research Fellowship, the US National Science Foundation (NSF), NASA, an Einstein Postdoctoral Fellowship, the Space Telescope Science Institute, UC San Diego, and the Simons Foundation.

    Other coauthors on the study are: Ji-Hoon Kim of Stanford University, Claude-André Faucher-Giguére of Northwestern University, Dušan Kereš of UC San Diego, and Eliot Quataert of UC Berkeley.

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

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  • richardmitnick 3:18 pm on December 9, 2016 Permalink | Reply
    Tags: , Biofilms, , Caltech, ,   

    From Caltech: “Protein Disrupts Infectious Biofilms” 

    Caltech Logo

    Caltech

    12/08/2016

    Lori Dajose
    (626) 395-1217
    ldajose@caltech.edu

    Many infectious pathogens are difficult to treat because they develop into biofilms, layers of metabolically active but slowly growing bacteria embedded in a protective layer of slime, which are inherently more resistant to antibiotics. Now, a group of researchers at Caltech and the University of Oxford have made progress in the fight against biofilms. Led by Dianne Newman, the Gordon M. Binder/Amgen Professor of Biology and Geobiology, the group identified a protein that degrades and inhibits biofilms of Pseudomonas aeruginosa, the primary pathogen in cystic fibrosis (CF) infections.

    The work is described in a paper in the journal Science that will appear online December 8.

    1
    Crystal structure of the PodA protein complex with three molecules of 1-hydroxyphenazine, the reaction product, bound in the active sites.
    Credit: Kyle Costa/Caltech

    “Pseudomonas aeruginosa causes chronic infections that are difficult to treat, such as those that inhabit burn wounds, diabetic ulcers, and the lungs of individuals living with cystic fibrosis,” Newman says. “In part, the reason these infections are hard to treat is because P. aeruginosa enters a biofilm mode of growth in these contexts; biofilms tolerate conventional antibiotics much better than other modes of bacterial growth. Our research suggests a new approach to inhibiting P. aeruginosa biofilms.”

    The group targeted pyocyanin, a small molecule produced by P. aeruginosa that produces a blue pigment. Pyocyanin has been used in the clinical identification of this strain for over a century, but several years ago the Newman group demonstrated that the molecule also supports biofilm growth, raising the possibility that its degradation might offer a new route to inhibit biofilm development.

    To identify a factor that would selectively degrade pyocyanin, Kyle Costa, a postdoctoral scholar in biology and biological engineering, turned to a milligram of soil collected in the courtyard of the Beckman Institute on the Caltech campus. From the soil, he isolated another bacterium, Mycobacterium fortuitum, that produces a previously uncharacterized small protein called pyocyanin demethylase (PodA).

    Adding PodA to growing cultures of P. aeruginosa, the team discovered, inhibits biofilm development.

    “While there is precedent for the use of enzymes to treat bacterial infections, the novelty of this study lies in our observation that selectively degrading a small pigment that supports the biofilm lifestyle can inhibit biofilm expansion,” says Costa, the first author on the study. The work, Costa says, is relevant to anyone interested in manipulating microbial biofilms, which are common in natural, clinical, and industrial settings. “There are many more pigment-producing bacteria out there in a wide variety of contexts, and our results pave the way for future studies to explore whether the targeted manipulation of analogous molecules made by different bacteria will have similar effects on other microbial populations.”

    While it will take several years of experimentation to determine whether the laboratory findings can be translated to a clinical context, the work has promise for the utilization of proteins like PodA to treat antibiotic-resistant biofilm infections, the researchers say.

    “What is interesting about this result from an ecological perspective is that a potential new therapeutic approach comes from leveraging reactions catalyzed by soil bacteria,” says Newman. “These organisms likely co-evolved with the pathogen, and we may simply be harnessing strategies other microbes use to keep it in check in nature. The chemical dynamics between microorganisms are fascinating, and we have so much more to learn before we can best exploit them.”

    The paper is titled Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. In addition to Costa and Newman, other co-authors include Caltech graduate student Nathaniel Glasser and Professor Stuart Conway of the University of Oxford. The work was funded by the National Institutes of Health’s National Institute of Allergy and Infectious Diseases, the National Science Foundation, the Howard Hughes Medical Institute, the Molecular Observatory at the Beckman Institute at Caltech, the Gordon and Betty Moore Foundation, and the Sanofi-Aventis Bioengineering Research Program at Caltech.

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 6:53 am on November 26, 2016 Permalink | Reply
    Tags: A distinct state of matter, , , Caltech, New Clues Emerge in 30-Year-Old Superconductor Mystery, Nonlinear optical rotational anisotropy, Pseudogap,   

    From Caltech: “New Clues Emerge in 30-Year-Old Superconductor Mystery” 

    Caltech Logo

    Caltech

    11/21/2016

    Whitney Clavin
    (626) 395-1856
    wclavin@caltech.edu

    1
    An artistic representation of the data showing the breaking of spatial inversion and rotational symmetries in the pseudogap region of superconducting materials—evidence that the pseudogap is a distinct phase of matter. Rings of light reflected from a superconductor reveal the broken symmetries. Credit: Hsieh Lab/Caltech

    One of the greatest mysteries of experimental physics is how so-called high-temperature superconducting materials work. Despite their name, high-temperature superconductors—materials that carry electrical current with no resistance—operate at chilly temperatures less than minus 135 degrees Celsius. They can be used to make superefficient power cables, medical MRIs, particle accelerators, and other devices. Cracking the mystery of how these materials work could lead to superconducting devices that operate at room temperatures—and could revolutionize electrical devices, including laptops and phones.

    In a new paper in the journal Nature Physics, researchers with the Institute for Quantum Information and Matter at Caltech have at last solved one piece of this enduring puzzle. They have confirmed that a transitional phase of matter called the pseudogap—one that occurs before these materials are cooled down to become superconducting—represents a distinct state of matter, with properties very different from those of the superconducting state itself.

    When matter transitions from one state, or phase, to another—say, water freezing into ice—there is a change in the ordering pattern of the materials’ particles. Physicists previously had detected hints of some type of ordering of electrons inside the pseudogap state. But exactly how they were ordering—and whether that ordering constituted a new state of matter—was unclear until now.

    “A peculiar property of all these high-temperature superconductors is that just before they enter the superconducting state, they invariably first enter the pseudogap state, whose origins are equally if not more mysterious than the superconducting state itself,” says David Hsieh, professor of physics at Caltech and principal investigator of the new research. “We have discovered that in the pseudogap state, electrons form a highly unusual pattern that breaks nearly all of the symmetries of space. This provides a very compelling clue to the actual origin of the pseudogap state and could lead to a new understanding of how high-temperature superconductors work.”

    The phenomenon of superconductivity was first discovered in 1911. When certain materials are chilled to super-cold temperatures, as low as a few degrees above absolute zero (a few degrees Kelvin), they carry electrical current with no resistance, so that no heat or energy is lost. In contrast, our laptops are not made of superconducting materials and therefore experience electrical resistance and heat up.

    Chilling materials to such extremely low temperatures requires liquid helium. However, because liquid helium is rare and expensive, physicists have been searching for materials that can function as superconductors at ever-higher temperatures. The so-called high-temperature superconductors, discovered in 1986, are now known to operate at temperatures up to 138 Kelvin (minus 135 degrees Celsius) and thus can be cooled with liquid nitrogen, which is more affordable than liquid helium. The question that has eluded physicists, however—despite three Nobel Prizes to date awarded in the field of superconductivity—is exactly how high-temperatures superconductors work.

    The dance of superconducting electrons

    Materials become superconducting when electrons overcome their natural repulsion and form pairs. This pairing can occur under extremely cold temperatures, allowing the electrons, and the electrical currents they carry, to move unencumbered. In conventional superconductors, electron pairing is caused by natural vibrations in the crystal lattice of the superconducting material, which act like glue to hold the pairs together.

    But in high-temperature superconductors, this form of “glue” is not strong enough to bind the electron pairs. Researchers think that the pseudogap, and how electrons order themselves in this phase, holds clues about what this glue may constitute for high-temperature superconductors. To study electron ordering in the pseudogap, Hsieh and his team have invented a new laser-based method called nonlinear optical rotational anisotropy. In the method, a laser is pointed at the superconducting material; in this case, crystals of ytttrium barium copper oxide (YBa2Cu3Oy). An analysis of the light reflected back at half the wavelength compared to that going in reveals any symmetry in the arrangement of the electrons in the crystals.

    Broken symmetries point to new phase

    Different phases of matter have distinct symmetries. For example, when water turns into ice, physicists say the symmetry has been “broken.”

    “In water,” Hsieh explains, “the H2O molecules are pretty randomly oriented. If you were swimming in an infinite pool of water, your surroundings look the same no matter where you are. In ice, on the other hand, the H2O molecules form a regular periodic network, so if you imagine yourself submerged in an infinite block of ice, your surroundings appear different depending on whether you are sitting on an H or O atom. Therefore, we say that the translational symmetry of space is broken in going from water to ice.”

    With the new tool, Hsieh’s team was able to show that the electrons cooled to the pseudogap phase broke a specific set of spatial symmetries called inversion and rotational symmetry. “As soon as the system entered the pseudogap region, either as a function of temperature or the amount of oxygen in the compound, there was a loss of inversion and rotational symmetries, clearly indicating a transition into a new phase of matter,” says Liuyan Zhao, a postdoctoral scholar in the Hsieh lab and lead author of the new study. “It is exciting that we are using a new technology to solve an old problem.”

    “The discovery of broken inversion and rotational symmetries in the pseudogap drastically narrows down the set of possibilities for how the electrons are self-organizing in this phase,” says Hsieh. “In some ways, this unusual phase may turn out to be the most interesting aspect of these superconducting materials.”

    The Nature Physics study, entitled A global-inversion-symmetry-broken phase inside the pseudogap region of YBa2Cu3Oy, was funded by the Army Research Office, the National Science Foundation, the Gordon and Betty Moore Foundation, the Canadian Institute for Advanced Research, and the Natural Sciences and Engineering Research Council. Other authors are C. A. Belvin of Wellesley College, Massachusetts; R. Liang, D.A. Bonn, and W.N. Hardy of the University of British Columbia, Vancouver; and N.P. Armitage of The Johns Hopkins University, Baltimore.

    See the full article here .

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