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  • richardmitnick 10:40 am on August 4, 2015 Permalink | Reply
    Tags: , Crystallography, ,   

    From U Washington: “Crystals form through a variety of paths, with implications for biological, materials and environmental research” 

    U Washington

    University of Washington

    August 3, 2015
    News and Information

    Crystals play an important role in the formation of substances from skeletons and shells to soils and semiconductor materials. But many aspects of their formation are shrouded in mystery. Scientists have long worked to understand how crystals grow into complex shapes. Now, an international group of researchers has shown how nature uses a variety of pathways to grow crystals beyond the classical, one-piece-at-a-time route.

    “Because crystallization is a ubiquitous phenomenon across a wide range of scientific disciplines, a shift in the picture of how this process occurs has far-reaching consequences,” said James De Yoreo, a materials scientist and physicist at the Department of Energy’s Pacific Northwest National Laboratory and affiliate UW professor of chemistry and materials science and engineering.

    These conclusions, published July 31 in Science with De Yoreo as lead author, have implications for decades-old questions in crystal formation, such as how animals and plants form minerals into shapes that have no relation to their original crystal symmetry or why some contaminants are so difficult to remove from stream sediments and groundwater.

    1
    An artist’s rendition of the early crystallization process of calcium carbonate. Adam F. Wallace/University of Delaware/David J. Carey

    Their findings crystalized during discussions among 15 scientists from diverse fields such as geochemistry, physics, biology and the earth and materials sciences. At their home institutions, these researchers conduct experiments, investigate animal skeletons, study soils and streams or use computer simulations to visualize how particles can form and attach. They met for a three-day workshop in Berkeley, California, that was sponsored by the Council on Geosciences from the Department of Energy’s Office of Basic Energy Sciences.

    “Researchers across all disciplines have made observations of skeletons and laboratory-grown crystals that cannot be explained by traditional theories,” said senior author Patricia Dove, a professor of geosciences at Virginia Tech. “We show how these crystals can be built up into complex structures by attaching particles — as nanocrystals, clusters, or droplets — that become organized into complex shapes. Many scientists have contributed to identifying these particles and pathways to becoming a crystal — our challenge was to put together a framework to understand them.”

    In animal and laboratory systems alike, the crystal formation process begins by constructing their constituent particles. These can be small molecules, clusters, droplets or nanocrystals. These particles are unstable and begin to combine with each other, nearby crystals and other surfaces. For example, nanocrystals prefer to orient themselves along the same direction as a larger crystal before attaching, much like adding Legos. In contrast, amorphous conglomerates can simply aggregate. Their atoms later become organized by “doing the wave” through the mass to rearrange into a single crystal.

    “Because we largely show a community consensus on this topic, the study has the potential to define the directions of future research on crystallization,” said De Yoreo.

    2
    Aragonite crystals forming on calcium carbonate.Pacific Northwest National Laboratory/James De Yoreo

    The authors say much work remains to understand the forces that cause these particles to move and combine. It is one of the driving forces behind new research.

    “Particle pathways are tricky because they can form what appear to be crystals with the traditional faceted surfaces or they can have completely unexpected shapes and chemical compositions,” said Dove. “Our group synthesized the evidence to show these pathways to growing a crystal become possible because of interplays between of thermodynamic and kinetic factors.”

    The implications of these discussions span diverse scientific fields. By understanding how animals form crystals into working structures such as shells, teeth and bones, scientists will have a bigger and better toolbox to interpret crystals formed in nature. These insights may also help design novel materials and explain unusual mineral patterns in rocks. In addition, knowledge of how pollutants are transported or trapped in the minerals of sediments has implications for environmental management of water and soil.

    “How we think about the ways to crystallization impacts how we interpret natural crystallization processes in geochemical and biological environments, as well as how we design and control synthetic crystal growth processes,” said De Yoreo. “I was surprised at how widespread a phenomenon particle-mediated crystallization is and how easily one can create a unified picture that captures its many styles.”

    The work was supported by the Council on Geosciences of the U.S. Department of Energy’s office of Science. All co-authors and their affiliations are listed on the paper.

    See the full article here.

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  • richardmitnick 2:58 pm on January 26, 2015 Permalink | Reply
    Tags: , Crystallography,   

    From PNNL: “How ionic: Scaffolding is in charge of calcium carbonate crystals” 


    PNNL Lab

    January 26, 2015
    Mary Beckman

    Using a powerful microscope that lets researchers see the formation of crystals in real time, a team led by the Department of Energy’s Pacific Northwest National Laboratory found that negatively charged molecules — such as carbohydrates found in the shells of mollusks — control where, when, and how calcium carbonate forms.

    These large macromolecules do so by directing where calcium ions bind in the scaffold. The negative charge on the macromolecules attract the positively charged calcium ions, placing them in the scaffold through so-called ion binding. Rather than these chemical interactions, researchers had previously thought the scaffold guides crystallization by providing the best energetic environment for the crystal.


    Watch crystals grow

    1
    Illustration of a polypeptide macromolecule

    “This whole story is different from what we had believed to be the case,” said lead researcher Jim De Yoreo at PNNL. “Ion binding defines a completely different mechanism for controlling crystallization than does making a perfect interface between the crystal and the scaffold. And it is one that should provide us with considerable control.”

    2
    Large charged molecules form a scaffold (red) that draw in calcium ions (blue) that guide carbonate (red and yellow) to form ACC (white spheres). No image credit.

    Missing Piece

    Previous work showed that calcium carbonate takes multiple routes to becoming a mineral. All of the common crystal forms, including calcite (found in limestone), aragonite (found in mother-of-pearl), and vaterite (found in gallstones), crystallized from solution, often at the same time. But in some cases, droplet-like particles of uncrystallized material known as amorphous calcium carbonate, or ACC, formed first and then transformed into either aragonite or vaterite.

    Those experiments, however, lacked a crucial element found in the biological world, where minerals form within an organic scaffold. For example, pearls develop in the presence of negatively charged carbohydrates and proteins from the oyster.

    In addition, biologically built minerals often start out as ACC. De Yoreo and his colleagues wondered what role macromolecules — carbs, proteins or other large molecules with a negative charge — play.

    To find out, De Yoreo and team allowed calcium carbonate to mineralize under a specialized transmission electron microscope at the Molecular Foundry, a DOE Office of Science User Facility at DOE’s Lawrence Berkeley National Laboratory. Collaborators also hailed from Eindhoven University of Technology in The Netherlands.

    But this time they added a negatively charged macromolecule, a polymer called polystyrene sulfonate. Without the polymer, they saw crystals of vaterite and a little calcite forming randomly under the microscope. With the polymer, however, ACC always appeared first and vaterite formed much later.

    Because the polymer interfered with vaterite formation, the team looked a little closer at what the polymer was doing. When they mixed the polymer with the calcium first before introducing carbonate, they found globules of the polymer forming in the solution. They determined that the polymer had soaked up more than half of the calcium to form the globules.

    When the researchers then added carbonate to the experimental chamber, ACC formed instead and it only appeared within these globules. The ACC grew in size until the supply of calcium ran out. The researchers concluded that calcium binding to the polymer is the key to forming the ACC and controlling where it forms.

    Mineral Motivation

    The team realized that controlling crystallization by attracting calcium ions to the macromolecules was not the way researchers had long thought it happened.

    There are two main ways that calcium carbonate molecules might be persuaded to come together to form a mineral. One is by providing an environment where the atoms assemble in the crystal in the least energetic way possible, sort of like organizing a classroom full of schoolchildren by having them sit in seats arranged neatly in rows side-by-side in the corner of the room.

    Another is via chemical binding — negatively or positively charged atoms or molecules called ions attract one another, sort of like waving popsicles in front of those kids to gather them in one spot.

    Researchers had long suspected that organic scaffolds caused calcium carbonate to mineralize and find its most stable form, calcite, by creating low energy surfaces where the ions could easily arrange themselves in rows side-by-side. In fact, scientists had seen this previously with highly organized films of organic molecules.

    But in this study, the polymer, like the popsicle, pulls in the calcium before minerals can form and turns it into ACC. This showed the researchers that ion binding can completely overwhelm any lower-energy advantage that crystallization on or outside of the polymer might confer.

    “This is definitely another means of controlling nucleation,” said De Yoreo. “Carbonate ions follow the calcium into the globules. They don’t crystallize outside the globules because there’s not enough calcium there to make a mineral. It’s like bank robbers out for a heist. They go where the money is.”

    “This work opens new avenues for the investigation of biomineralization. Can we extend these experiments beyond the simple polymers we used here? To what extent can we rebuild parts of the biological machinery inside the microscope?” said co-author Prof. Nico Sommerdijk of Eindhoven University of Technology. “Answering these questions may eventually allow us to understand the biological mineral formation and apply its principles to design green, sustainable routes for the production of advanced materials.”

    This work was supported by the U.S. Department of Energy Office of Science and the Dutch Science Foundation.

    See the full article here.

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    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 3:37 pm on July 14, 2014 Permalink | Reply
    Tags: , , Crystallography, ,   

    From PPPL: “PPPL’s dynamic diagnostic duo” 


    PPPL

    July 14, 2014
    John Greenwald

    Kenneth Hill and Manfred Bitter are scientific pioneers who have collaborated seamlessly for more than 35 years. Together they have revolutionized a key instrument in the quest to harness fusion energy — a device called an X-ray crystal spectrometer that is used around the world to reveal strikingly detailed information about the hot, charged plasma gas that fuels fusion reactions.

    two
    Kenneth Hill and Manfred Bitter inspect an X-ray crystal spectrometer to be used to study laser-produced plasmas. The vertically mounted silicon crystal has a thickness of 100 microns, about the average diameter of a human hair. (Photo by Elle Starkman/Princeton Office of Communications )

    sun
    The Sun is a natural fusion reactor.

    “Ken and Manfred are consummate diagnosticians,” said Michael Zarnstorff, deputy director for research at DOE’s Princeton Plasma Physics Laboratory(PPPL), where the duo has worked for nearly four decades. “Over the years they have developed highly innovative and uniquely capable tools for analyzing the results of fusion experiments.”

    These tools record key plasma parameters on fusion facilities in the United States, China, Japan and South Korea. They are being designed for a new German facility and will play a key role on ITER, the huge international experiment under construction in France to demonstrate the feasibility of fusion power.

    New applications for the spectrometers are rapidly expanding. Prospective new uses range from medical and industrial applications to the study of high energy-density physics. “An abundance of contexts is opening up,” Zarnstorff said.

    Low-key physicists

    Behind all these efforts are two low-key physicists. “I have known and worked with Ken and Manfred for over 30 years and have always admired their scientific work and polite demeanor,” said Philip Efthimion, who heads the Plasma Science and Technology Department at PPPL.

    The two divvy up tasks based on “whatever one of us is interested in and needs to do,” said Hill. “We have to try to check each other and make rational decisions instead of emotional ones.” Bitter puts it this way: “We are in this business together some 35 years. Everything that comes up is discussed between us.”

    The physicists first joined forces at PPPL in the late 1970s when the Princeton Large Torus, the Lab’s major experiment at the time, was reaching temperatures of more than 10 million degrees Celsius. That blistering heat stripped light-emitting electrons from the hydrogen atoms in the plasma, eliminating light as a source of information about the atomic nuclei, or ions, in the plasma and creating the need for a new diagnostic tool.

    Princeton Large Torus
    Princeton Large Torus

    Enter the X-ray crystal spectrometer, which gleans vital data from the X-rays that ions emit. At the heart of this tool is a hair-thin crystal that separates the X-rays into their wavelengths, or spectrum, and sends them to a detector. Shifts in the wavelengths reveal the temperature of the ions and other key data through a process called Doppler broadening — the same process that causes sirens to sound higher when speeding toward someone and lower when rushing away.

    Bitter and Hill worked on early X-ray spectrometers under Schweickhard von Goeler, who headed diagnostics and whom everyone called “Schwick.” Von Goeler and Hill introduced the first such device, whose lower resolution — or ability to distinguish between wavelengths in the spectra — was not yet sufficient to measure Doppler broadening. Responding to this challenge, von Goeler and Bitter built an improved spectrometer with higher resolution for Doppler measurements.

    Astonishing solar scientists

    The new PPPL device produced results that astonished solar scientists. The spectrometer revealed far more details of the X-ray spectrum for iron, an element used for diagnostic purposes in the plasma, than instruments aboard satellites that studied the spectra of iron in the sun had been able to show.

    But the new spectrometer, which PPPL also installed on the Tokamak Fusion Test Reactor (TFTR), the Laboratory’s key fusion experiment in the 1980s and 1990s, had a severe limitation. The cylindrically curved crystal provided only a single line of sight through the donut-shaped plasma and could record only the temperature of ions found at points along that line of sight. “What you really want to know is how hot it is at many points throughout the plasma,” said Hill.

    To increase the number of sightlines, PPPL put five X-ray spectrometers on TFTR. “They were large,” Hill said of the devices, “and you couldn’t imagine many more. So Manfred came up with the idea for a single crystal and a 2D [or two-dimensional] detector that would give you a continuous profile of the plasma.”

    Bitter’s concept, now a worldwide standard for fusion research, was simple and elegant. He envisioned a crystal whose spherically curved surface collected X-ray spectra from the entire plasma and imaged them onto a detector that recorded both the spectra and the location of the ions they came from. The revolutionary result: A complete picture of the plasma’s ion temperature, captured with just one X-ray spectrometer.

    Bitter and Hill first tested this design in 2003 on Alcator C-MOD, the fusion facility at MIT. While this trial showed that the concept worked, the 2D detector used at the time couldn’t record all the spectra that flowed in from the crystal. “The count-rate limit of this detector was very low,” recalled Hill. “You couldn’t see how the temperature evolved over time.”

    Like comparing an airplane to a bicycle

    This problem led to a search for a better detector, which Bitter found on a trip to Europe. While there in 2005, he learned of a device that the European Organization for Nuclear Research (CERN) had developed that could record spectral images in far greater detail than the detector he had been using. “It was like comparing an airplane to a bicycle,” Bitter said of the new detector, which made the spherically curved crystal spectrometer fully operational.

    MIT became the first to use the new spectrometer when the university’s Plasma Science and Fusion Center installed it on Alcator C-MOD in 2006 in a collaboration between MIT and PPPL. “It’s been a really great leap forward,” said John Rice, the principal research scientist at the MIT facility. “The original detector [on the 2003 spectrometer] had all sorts of problems and with this new system we can image the complete plasma.”

    Other fusion laboratories quickly followed. PPPL-designed spectrometers are now essential tools on the Korea Superconducting Tokamak Advanced Research (KSTAR) facility in Daejon, South Korea; the Experimental Advanced Superconducting Tokamak (EAST) in Hefei, China; and the Large Helical Device (LHD) in Toki, Japan.

    Still to come are spectrometers planned for ITER in Cadarache, France; Wendelstein 7-X (W7-X) in Greifswald, Germany; and the upgraded National Spherical Torus Experiment (NSTX-U) at PPPL. For these projects, Bitter and Hill are providing expert guidance.

    “The highlight of my time here has been working with Ken and Manfred,” said physicist Novimir Pablant, who led the design of the LHD spectrometer and is developing the devices to be installed on ITER and W7-X. Joining Pablant on the ITER project is physicist Luis Delgado-Aparicio, who is developing the NSTX-U spectrometer and has likewise been inspired by Bitter and Hill. “They are incredible to work with,” said Delgado-Aparicio. “The degree of certainty to which they want to test their ideas is acute.”

    Bitter and Hill are still collaborating on new spectrometers. Among them are devices to study laser-produced plasmas at the University of Rochester and the Lawrence Livermore National Laboratory. What keeps the two scientists going? “X-ray spectrometry is a field that I find fascinating,” said Bitter. “It has so many applications and it’s very interesting to design new diagnostics.” Hill fully seconds those sentiments. “There’s just a lot of interesting physics in this field,” he said. “And there are broad applications and interest for this technology.”

    See the full article here.

    Princeton Plasma Physics Laboratory is a U.S. Department of Energy national laboratory managed by Princeton University.


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  • richardmitnick 4:25 pm on December 19, 2013 Permalink | Reply
    Tags: , , Crystallography, ,   

    From SLAC: “X-ray Laser Maps Important Drug Target” 

    December 19, 2013
    Press Office Contact:
    Angela Anderson, SLAC National Accelerator Laboratory: angelaa@slac.stanford.edu, (650) 926-3505.

    Scientist Contacts:
    Vadim Cherezov, The Scripps Research Institute: vcherezo@scripps.edu, (858) 784-7307 or (857) 353-5584.

    Sébastien Boutet, SLAC National Accelerator Laboratory: sboutet@slac.stanford.edu.

    New Technology Allows Faster, More Accurate Imaging of Hard-to-study Membrane Proteins

    Researchers have used one of the brightest X-ray sources on the planet to map the 3-D structure of an important cellular gatekeeper known as a G protein-coupled receptor, or GPCR, in a more natural state than possible before. The new technique is a major advance in exploring GPCRs, a vast, hard-to-study family of proteins that plays a key role in human health and is targeted by an estimated 40 percent of modern medicines.

    The research, performed at the Linac Coherent Light Source (LCLS) X-ray laser at the Department of Energy’s (DOE’s) SLAC National Accelerator Laboratory, is also a leap forward for structural biology experiments at LCLS, which has opened up many new avenues for exploring the molecular world since its launch in 2009.

    “For the first time we have a room-temperature, high-resolution structure of one of the most difficult to study but medically important families of membrane proteins,” said Vadim Cherezov, a pioneer in GPCR research at The Scripps Research Institute who led the experiment. “And we have validated this new method so that it can be confidently used for solving new structures.”

    In the experiment, published in the Dec. 20 issue of Science, researchers examined the human serotonin receptor, which plays a role in learning, mood and sleep and is the target of drugs that combat obesity, depression and migraines. The scientists prepared crystallized samples of the receptor in a fatty gel that mimics its environment in the cell. With a newly designed injection system, they streamed the gel into the path of the LCLS X-ray pulses, which hit the crystals and produced patterns used to reconstruct a high-resolution, 3-D model of the receptor.

    The method eliminates one of the biggest hurdles in the study of GPCRs: They are notoriously difficult to crystallize in the large sizes needed for conventional X-ray studies at s. Because LCLS is millions of times brighter than the most powerful synchrotrons and produces ultrafast snapshots, it allows researchers to use tiny crystals and collect data in the instant before any damage sets in. As a bonus, the samples do not have to be frozen to protect them from X-ray damage, and can be examined in a more natural state.

    “This is one of the niches that LCLS is perfect for,” said SLAC Staff Scientist Sébastien Boutet, a co-author of the report. “With really challenging proteins like this you often need years to develop crystals that are large enough to study at synchrotron X-ray facilities.”


    X-ray Crystallography Explained: Narrated by structural biologist Stephen Curry, this animated film explores the extraordinary history of crystallography. Dozens of Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique for determining the structures of a huge range of complex molecules. (The Royal Institution/12foot6, Creative Commons/not for commercial use)

    See the full article here.

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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