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  • richardmitnick 5:31 pm on July 20, 2017 Permalink | Reply
    Tags: , Chemistry, If all the states in a group of bands are filled with electrons then the electrons cannot move and the material is an insulator, , , Princeton University, The approach combined tools from such disparate fields as chemistry and mathematics also physics and materials science, The nearly century-old band theory of solids considered one of the early landmark achievements of quantum mechanics, The research shows that symmetry and topology also chemistry and physics all have a fundamental role to play in our understanding of materials, The theory describes the electrons in crystals as residing in specific energy levels known as bands,   

    From Princeton: “Researchers find path to discovering new topological materials, holding promise for technological applications” 

    Princeton University
    Princeton University

    July 20, 2017
    No writer credit

    Researchers have discovered how to identify new examples of topological materials, which have unique and desirable electronic properties. The technique involves finding the connection between band theory, which describes the energy levels of electrons in a solid, with a material’s topological nature. The disconnected bands indicate the material is a topological insulator. Image courtesy of Nature.

    Researchers find path to discovering new topological materials, holding promise for technological applications.

    An international team of researchers has found a way to determine whether a crystal is a topological insulator — and to predict crystal structures and chemical compositions in which new ones can arise. The results, published July 20 in the journal Nature, show that topological insulators are much more common in nature than currently believed.

    Topological materials, which hold promise for a wide range of technological applications due to their exotic electronic properties, have attracted a great deal of theoretical and experimental interest over the past decade, culminating in the 2016 Nobel Prize in physics. The materials’ electronic properties include the ability of current to flow without resistance and to respond in unconventional ways to electric and magnetic fields.

    Until now, however, the discovery of new topological materials occurred mainly by trial and error. The new approach described this week [see above reference to the Nature article] allows researchers to identify a large series of potential new topological insulators. The research represents a fundamental advance in the physics of topological materials and changes the way topological properties are understood.

    The team included: at Princeton University, Barry Bradlyn and Jennifer Cano, both associate research scholars at the Princeton Center for Theoretical Science, Zhijun Wang, a postdoctoral research associate, and B. Andrei Bernevig, professor of physics; professors Luis Elcoro and Mois Aroyo at the University of the Basque Country in Bilbao; assistant professor Maia Garcia Vergniory of University of the Basque Country and Donostia International Physics Center (DIPC) in Spain; and Claudia Felser, professor at the Max Planck Institute for Chemical Physics of Solids in Germany.

    “Our approach allows for a much easier way to find topological materials, avoiding the need for detailed calculations,” Felser said. “For some special lattices, we can say that, regardless of whether a material is an insulator or a metal, something topological will be going on,” Bradlyn added.

    Until now, of the roughly 200,000 materials catalogued in materials databases, only around a few hundred are known to host topological behavior, according to the researchers. “This raised the question for the team: Are topological materials really that scarce, or does this merely reflect an incomplete understanding of solids?” Cano said.

    To find out, the researchers turned to the nearly century-old band theory of solids, considered one of the early landmark achievements of quantum mechanics. Pioneered by Swiss-born physicist Felix Bloch and others, the theory describes the electrons in crystals as residing in specific energy levels known as bands. If all the states in a group of bands are filled with electrons, then the electrons cannot move and the material is an insulator. If some of the states are unoccupied, then electrons can move from atom to atom and the material is capable of conducting an electrical current.

    Because of the symmetry properties of crystals, however, the quantum states of electrons in solids have special properties. These states can be described as a set of interconnected bands characterized by their momentum, energy and shape. The connections between these bands, which on a graph resemble tangled spaghetti strands, give rise to topological behaviors such as those of electrons that can travel on surfaces or edges without resistance.

    The team used a systematic search to identify many previously undiscovered families of candidate topological materials. The approach combined tools from such disparate fields as chemistry, mathematics, physics and materials science.

    First, the team characterized all the possible electronic band structures arising from electronic orbitals at all the possible atomic positions for all possible crystal patterns, or symmetry groups, that exist in nature, with the exception of magnetic crystals. To search for topological bands, the team first found a way to enumerate all allowed non-topological bands, with the understanding that anything left out of the list must be topological. Using tools from group theory, the team organized into classes all the possible non-topological band structures that can arise in nature.

    Next, by employing a branch of mathematics known as graph theory — the same approach used by search engines to determine links between websites — the team determined the allowed connectivity patterns for all of the band structures. The bands can either separate or connect together. The mathematical tools determine all the possible band structures in nature — both topological and non-topological. But having already enumerated the non-topological ones, the team was able to show which band structures are topological.

    By looking at the symmetry and connectivity properties of different crystals, the team identified several crystal structures that, by virtue of their band connectivity, must host topological bands. The team has made all of the data about non-topological bands and band connectivity available to the public through the Bilbao Crystallographic Server. “Using these tools, along with our results, researchers from around the world can quickly determine if a material of interest can potentially be topological,” Elcoro said.

    The research shows that symmetry, topology, chemistry and physics all have a fundamental role to play in our understanding of materials, Bernevig said. “The new theory embeds two previously missing ingredients, band topology and orbital hybridization, into Bloch’s theory and provides a prescriptive path for the discovery and characterization of metals and insulators with topological properties.”

    David Vanderbilt, a professor of physics and astronomy at Rutgers University who was not involved in the study, called the work remarkable. “Most of us thought it would be many years before the topological possibilities could be catalogued exhaustively in this enormous space of crystal classes,” Vanderbilt said. “This is why the work of Bradlyn and co-workers comes as such a surprise. They have developed a remarkable set of principles and algorithms that allow them to construct this catalogue at a single stroke. Moreover, they have combined their theoretical approach with materials database search methods to make concrete predictions of a wealth of new topological insulator materials.”

    The theoretical underpinnings for these materials, called “topological” because they are described by properties that remain intact when an object is stretched, twisted or deformed, led to the awarding of the Nobel Prize in physics in 2016 to F. Duncan M. Haldane, Princeton’s Sherman Fairchild University Professor of Physics; J. Michael Kosterlitz of Brown University; and David J. Thouless of the University of Washington.

    Chemistry and physics take different approaches to describing crystalline materials, in which atoms occur in regularly ordered patterns or symmetries. Chemists tend to focus on the atoms and their surrounding clouds of electrons, known as orbitals. Physicists tend to focus on the electrons themselves, which can carry electric current when they hop from atom to atom and are described by their momentum.

    “This simple fact — that the physics of electrons is usually described in terms of momentum, while the chemistry of electrons is usually described in terms of electronic orbitals — has left material discovery in this field at the mercy of chance,” Wang said.

    “We initially set out to better understand the chemistry of topological materials — to understand why some materials have to be topological,” Vergniory said.

    Aroyo added, “What came out was, however, much more interesting: a way to marry chemistry, physics and mathematics that adds the last missing ingredient in a century-old theory of electronics, and in the present-day search for topological materials.”

    Funding for the study was provided by the U.S. Department of Energy (DE-SC0016239), the U.S. National Science Foundation (EAGER DMR-1643312 and MRSEC DMR-1420541), and the U.S. Office of Naval Research (N00014-14-1-0330). Additional funding came from a Simons Investigator Award, the David & Lucile Packard Foundation, and Princeton University’s Eric and Wendy Schmidt Transformative Technology Fund. Funding was also provided by the Spanish Ministry of Economy and Competitiveness (FIS2016-75862-P and FIS2013-48286-C2-1-P), the Government of the Basque Country (project IT779-13), and the Spanish Ministry of Economy and Competitiveness and European Federation for Regional Development (MAT2015-66441-P).

    The study, Topological quantum chemistry, by Barry Bradlyn, Luis Elcoro, Jennifer Cano, Maia Garcia Vergniory, Zhijun Wang, Claudia Felser, Mois Aroyo and B. Andrei Bernevig, was published in the journal Nature on July 20, 2017.

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  • richardmitnick 1:42 pm on July 12, 2017 Permalink | Reply
    Tags: , Chemistry, , , Preventing severe blood loss on the battlefield or in the clinic, Reginald Avery   

    From MIT: “Preventing severe blood loss on the battlefield or in the clinic” Reginald Avery 

    MIT News

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    July 11, 2017
    Dara Farhadi

    At MIT graduate student Reginald Avery has been conducting research on a biomaterial that could stop wounded soldiers from dying from shock due to severe blood loss. “I wanted to do something related to the military because I grew up around that environment,” he says. “The people, the uniformed soldiers, and the well-controlled atmosphere created a good environment to grow up in, and I wanted to still contribute in some way to that community.” Photo: Ian MacLellan

    PhD student Reginald Avery is developing an injectable material that patches ruptured blood vessels.

    In a tiny room in the sub-basement of MIT’s Building 66 sits a customized, super-resolution microscope that makes it possible to see nanoscale features of a red blood cell. Here, Reginald Avery, a fifth-year graduate student in the Department of Biological Engineering, can be found conducting research with quiet discipline, occasionally fidgeting with his silver watch.

    He spends most of his days either at the microscope, taking high-resolution images of blood clots forming over time, or at the computer, reading literature about super-resolution microscopy. Without windows to approximate the time of day, Avery’s watch comes in handy. Not surprisingly for those who know him, it’s set to military time.

    Avery describes his father as a hard-working inspector general for the U.S. Army Test and Evaluation Command. Avery and his fraternal twin brother, Jeff, a graduate student in computer science at Purdue University, were born in Germany and lived for a portion of their childhoods on military bases in Hawaii and Alabama. Eventually the family moved to Maryland and entered civilian life, but Avery’s experiences on a military base never left him. At MIT he’s been conducting research on a biomaterial that could stop wounded soldiers from dying from shock due to severe blood loss.

    “I wanted to do something related to the military because I grew up around that environment,” he says. “The people, the uniformed soldiers, and the well-controlled atmosphere created a good environment to grow up in, and I wanted to still contribute in some way to that community.”

    Blocking blood loss

    Avery is one of the first graduate students to join the Program in Polymers and Soft Matter (PPSM) from the Department of Biological Engineering. When he first joined the lab of Associate Professor Bradley Olsen in the Department of Chemical Engineering, his focus was on optimizing and testing a material that could be topically applied to wounded soldiers.

    The biomaterial is a hydrogel — a material consisting largely of water — with a viscosity similar to toothpaste. Gelatin proteins and inorganic silica nanoparticles are incorporated into the material and function as a substrate that helps to accelerate coagulation rates and reduce clotting times.

    Co-advised by Ali Khademhosseini at Brigham and Women’s Hospital and in collaboration with others at Massachusetts General Hospital, Avery further developed the material so that it could be injected into ruptured blood vessels. Like a cork on a wine bottle, the biomaterial forms a plug in the leaky vessel and stops any blood loss. Avery’s research was published in Science Translational Medicine and featured on the front cover of the November 2016 issue.

    The current standard for patching blood vessels is imperfect. Surgeons typically use metallic coils, special plastic beads, or compounds also found in super glue. Each technology has limitations that the nanocomposite hydrogel attempts to address.

    “The old techniques don’t take advantage of tissue engineering. It can be difficult for a surgeon to deliver metallic coils and beads to the targeted site, and blood may sometimes still find a path through and result in re-bleeding. It’s also expensive, and some techniques have a finite time period to place the material where it needs to be,” Avery says. “We wanted to use a hydrogel that could completely fill a vessel and not allow any leakage to occur through that injury site.”

    The nanocomposite, which can be injected easily with a syringe or catheter, has been tested in animal models without causing inflammatory side-effects or the formation of clots elsewhere in the animal’s circulatory system. Some in vitro experiments also indicate that the material could be useful for treating aneurysms.

    For the past six months Avery has concentrated on uncovering the physical mechanism by which the nanocomposite material interacts with blood. A super-resolution microscope can achieve a resolution of 250 nanometers; a single red blood cell, for a comparison, is about 8,000 nanometers wide. Avery says the ability to visualize how the physiological molecules and proteins interact with the nanocomposite and other surgical tools may also help him design a better material. Obtaining a comprehensive view of the process, however, can be time-consuming.

    “It’s taking snapshots every 10 or 20 seconds for approximately 30 minutes, and putting all of those pictures together,” he says. “What I want to do is visualize these gels and clots forming over time.”

    Found in translation

    While he is eager to see his material put to use to save lives, Avery is glad to be contributing to the work at the basic and translational research stages. He says he’s driven to appropriately characterize a treatment or biomaterial, ask the right questions, and make sure it functions just as well as, or better than, what is currently used in the clinic.

    “I’m comfortable doing a thorough study in vitro to characterize materials or design some synthetic tests prior to in vivo testing,” he says. “You must be very confident in [the biomaterial] before getting to that step so that you’re effectively utilizing the animals, or even more important, you’re not putting a person at risk if something finally does get to that point.”

    Avery also finds meaning in collaborating and helping others with their research. He has worked on projects using neutron scattering to elucidate the network structure of a homo-polypeptide, performed cell culture on thermoresponsive hydrogels, and developed highly elastic polypeptides, projects that Avery says aren’t directly applicable to his thesis work of treating internal bleeding. However, he was happy to have simply had the experience of learning something new.

    “If I can help somebody with something then I’m going to try to do the best that I can. Whether it’s a homework assignment or something in lab, my goal is not to leave somebody worse off,” Avery says. “If there’s something I’ve done in the past that could help you now, I’m excited to show you and hopefully have it work out well for you. If it doesn’t, we can talk even longer to try to figure out what we could do to make it work better.”

    Of the seven papers that Avery has been involved in over the past three years, almost half were collaborative projects outside the area of his thesis work.

    Avery hopes to finish his PhD thesis by the summer of next year. Afterward, he envisions working for a research institute that is devoted to a single disease or condition, or perhaps for a research center associated with a hospital within the military health system so that he could continue developing biomaterials, diagnostics, or other approaches to help soldiers.

    “I’m usually excited to help somebody get something done or get something done for my project. It’s always exciting to get closer to determining the optimum concentration that you need, seeing that one data point that’s higher than the others, or getting that nice image that shows the effect that you have hypothesized,” Avery says. “That’s still a motivating aspect of coming to lab, to eventually get those results. It can take a long time to get there but once you do, you appreciate the journey.”

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  • richardmitnick 2:48 pm on July 10, 2017 Permalink | Reply
    Tags: , , Chemistry, How do you build a metal nanoparticle?, , , U Pittsburgh   

    From U Pittsburgh via phys.org: “How do you build a metal nanoparticle?” 

    University of Pittsburgh


    July 10, 2017

    A structure of a ligand-protected Au25 nanocluster. Credit: Computer-Aided Nano and Energy Lab (C.A.N.E.LA.)

    Although scientists have for decades been able to synthesize nanoparticles in the lab, the process is mostly trial and error, and how the formation actually takes place is obscure. However, a study recently published in Nature Communications by chemical engineers at the University of Pittsburgh’s Swanson School of Engineering explains how metal nanoparticles form.

    Thermodynamic Stability of Ligand-Protected Metal Nanoclusters (DOI: 10.1038/ncomms15988) was co-authored by Giannis Mpourmpakis, assistant professor of chemical and petroleum engineering, and PhD candidate Michael G. Taylor. The research, completed in Mpourmpakis’ Computer-Aided Nano and Energy Lab (C.A.N.E.LA.), is funded through a National Science Foundation CAREER award and bridges previous research focused on designing nanoparticles for catalytic applications.

    “Even though there is extensive research into metal nanoparticle synthesis, there really isn’t a rational explanation why a nanoparticle is formed,” Dr. Mpourmpakis said. “We wanted to investigate not just the catalytic applications of nanoparticles, but to make a step further and understand nanoparticle stability and formation. This new thermodynamic stability theory explains why ligand-protected metal nanoclusters are stabilized at specific sizes.”

    A ligand is a molecule that binds to metal atoms to form metal cores that are stabilized by a shell of ligands, and so understanding how they contribute to nanoparticle stabilization is essential to any process of nanoparticle application. Dr. Mpourmpakis explained that previous theories describing why nanoclusters stabilized at specific sizes were based on empirical electron counting rules – the number of electrons that form a closed shell electronic structure, but show limitations since there have been metal nanoclusters experimentally synthesized that do not necessarily follow these rules.

    “The novelty of our contribution is that we revealed that for experimentally synthesizable nanoclusters there has to be a fine balance between the average bond strength of the nanocluster’s metal core, and the binding strength of the ligands to the metal core,” he said. “We could then relate this to the structural and compositional characteristic of the nanoclusters, like size, number of metal atoms, and number of ligands.

    “Now that we have a more complete understanding of this stability, we can better tailor the nanoparticle morphologies and in turn properties, to applications from biolabeling of individual cells and targeted drug delivery to catalytic reactions, thereby creating more efficient and sustainable production processes.”

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  • richardmitnick 11:03 am on July 10, 2017 Permalink | Reply
    Tags: , Chemistry, , eGaIn a liquid alloy of indium and gallium, Magnetic Liquid Metals, The Earth's liquid outer core made of iron is crucial to creating Earth’s magnetic field, University of Maryland Three Meter dynamo experiment,   

    From Yale: “Study of the Center of the Earth” 

    Yale University bloc

    Yale University

    June 30, 2017
    Sonia Wang

    Study of the Center of the Earth | Yale Scientific

    What would you do with two million dollars? Chances are dim that your first answer would be to build and buy enough liquid sodium to fill a three-meter radius spherical tank. But for some scientists, this investment—the University of Maryland Three Meter dynamo experiment—paid off, serving as a key step to understanding the age-old question of how Earth’s magnetic field is generated.

    Earth’s magnetic field not only shields us from the sun’s damaging radiation, but also helps us navigate the Earth. Geophysicists have long studied the magnetic field created by Earth’s liquid core, but attempts to re-create them in the lab have previously been unsuccessful due to the prohibitively high costs of building equipment to do so.

    However, in a study published in January[Physical Review Fluids], a team of Yale researchers in Mechanical Engineering Professor Eric Brown’s lab developed a method for producing liquid metal with improved magnetic properties. The researchers created a protocol to create these Magnetic Liquid Metals (MLM) after studying a suspension of magnetic iron particles in eGaIn, a liquid alloy of indium and gallium. Such a technique could enable researchers to conduct dynamo experiments, which model the generation of Earth’s magnetic field, on a far smaller size scale.

    Magnetic Field’s Liquid Beginnings

    By studying earthquakes as they travel through the planet, seismologists know that the Earth has a fluid outer core surrounding a solid iron inner core. The liquid outer core, made of iron, is crucial to creating Earth’s magnetic field and is an example of a magnetohydrodynamic (MHD) phenomenon—magnetic properties resulting from an electrically conductive fluid. Movement of the outer core in the presence of Earth’s magnetic field induces electrical currents, which then create their own magnetic field aligning with Earth’s overall magnetic field. This process sustains itself and allows for the maintenance of Earth’s magnetic field over the years.

    The Earth’s magnetic field is responsible for phenomenon such as the Northern Lights, which occurs when the sun’s radiation is deflected by the magnetic field and collides with atmospheric particles. Image courtesy of Kristian Pikner, Wikimedia Commons.

    Magnetohydrodynamic phenomena only occur at a high magnetic Reynolds number, which describes the magnetohydrodynamic properties of an object; at a high Reynolds number, MHD phenomena are more likely. The magnetic Reynolds number depends on several properties, such as the system size, the fluid velocity, electrical conductivity, and magnetic susceptibility—the response of the fluid to a magnetic influence. Something as large as a planet would have an extremely high Reynolds number, making MHD phenomena more natural. However, re-creating such phenomena in a laboratory setting is extremely difficult, requiring materials with high magnetic and electrical properties.

    Traditional studies of MHD have used liquid metals and plasmas because they have the highest electric conductivities of any known materials. Liquid sodium has the highest conductivity and has been used to create a dynamo experiment in the past, but is both expensive and dangerous; sodium reacts explosively with water and needs to be heated above its high melting temperature. Looking for a safer and easier alternative, the researchers sought to use a different liquid metal base for the study.

    However, as noted before, other factors such as the magnetic susceptibility also affect the Reynolds number. Despite having a good electrical conductivity, pure eGaIn has a low magnetic susceptibility and therefore a low Reynolds number. To boost the Reynolds number, the researchers proposed creating a new material by suspending magnetic particles in liquid metals to increase their magnetic susceptibility and take advantage of the liquid metals natural high conductivity.

    Acid’s Key Role

    While scientists have previously attempted to suspend magnetic particles in liquid metals, they have not been very successful because of metallic oxidation. The oxidation of the metal causes a new “rusted” oxidation layer on the liquid metal, with its own set of properties. As this layer is more solid, it prevents some of the delicate suspension effects.

    eGaIn shows stronger magnetic properties than liquid sodium. Image courtesy of Florian Carle.

    Initially, stirring iron particles into the liquid eGaIn failed to create a successful suspension, since a solid oxide layer formed at the surface of the liquid upon exposure to air. Despite vigorous stirring to break the oxide skin, the particles clung to the oxide skin due to the strength of the interactions between the two layers.

    Seeking solutions to this problem, the scientists used hydrochloric acid (HCl), at a dangerously low pH of 0.69 capable of corroding skin, as a chemical cleaner or purifying agent; in eGaIn, hydrochloric acid removes the oxide layer on the liquid metal and iron particles, allowing for more liquid-like properties in the metal and increasing the conductivity of the iron particles. The suspension process was successful after the researchers added enough HCl to cover the metals and prevent further contact with air.

    Design Your Own Fluid

    The new material has increased magnetohydrodynamic properties compared to the original eGaIn. The resulting MLM had a Reynolds number over 5 times higher than that of pure liquid metal, or two times higher than liquid sodium. Thus, a dynamo experiment that would previously have required a three-meter radius tank might be possible on a much smaller size scale—10 square centimeters rather than three meters. “Until this study, no one thought about doing dynamo experiments with eGaIn because the quantity needed for these experiments make it cost prohibitive,” said Florian Carle, the lead author of the paper.

    Furthermore, certain properties of the MLM can be customized for different purposes and different applications. As long as the conductivity of the iron particles you would like to suspend is higher than that of the liquid metal base, nearly any material can be used for the liquid and suspended particles. “It’s basically Design Your Own Fluid…you can suspend silver, graphene, diamond…you can tune the size of the particles within this huge range,” Carle said. Changing the quantity of iron particles in eGaIn will modify the material viscosity—the more particles, the more viscous the fluid. Furthermore, changing the type of particle used can further affect the conductivity and magnetic properties of the material; using highly conductive particles will increase conductivity, and using magnetic particles like iron or steel can increase magnetic properties.

    The applications are myriad. Separately controlling the viscosity and the magnetic properties of the material will allow scientists to isolate the effects of magnetohydrodynamics, which is indicated by the Reynolds number, and turbulence, a measure affected by fluid viscosity and velocity that indicates how chaotic the flow of the material is.

    Carle designed the paper to be easily accessible, so that even a scientist without special training could re-create the material. He hopes that more scientists will apply the procedure to their research: “Now that we can tune the properties…hopefully people will start picking up on that and be able to use that. I hope in the near future we will see more and more experiments using MLMs,” Carle said.

    Of Sustainability and Superfluids

    Though Carle has moved on to work at the Yale Quantum Institute, research continues in the Brown lab on the material. One challenge the group is investigating is in keeping the magnetic liquid metals fresh during storage: after six months of storage, samples exhibited a loss in magnetic susceptibility as the hydrochloric acid slowly ate away at the iron particles.

    “It’s a bit of a conflict, since you need to protect the eGaIn with HCl, but then the HCl will eat the iron,” Carle said. Further research is being done to develop storage methods for eGaIn, including solidifying the samples or removing HCl to allow formation of a protective oxide layer on the surface of the fluid during storage.

    Carle further speculates that there are applications beyond MHD and dynamo experiments, since it is a customizable new material. And perhaps an MLM could eventually be created out of sodium, which has the highest electric conductivity of any known liquid metal. Adding magnetic particles to that suspension could allow scientists to attain a Reynolds number off the charts. “You would have a superfluid…maybe we would see phenomena we haven’t seen anywhere before,” Carle said.

    Featured Art by Isa del Toro Mijares

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  • richardmitnick 1:21 pm on July 8, 2017 Permalink | Reply
    Tags: , , Chemistry, , , , , , , UCSD Comet supercomputer   

    From Science Node: “Cracking the CRISPR clock” 

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    05 Jul, 2017
    Jan Zverina

    SDSC Dell Comet supercomputer

    Capturing the motion of gyrating proteins at time intervals up to one thousand times greater than previous efforts, a team led by University of California, San Diego (UCSD) researchers has identified the myriad structural changes that activate and drive CRISPR-Cas9, the innovative gene-splicing technology that’s transforming the field of genetic engineering.

    By shedding light on the biophysical details governing the mechanics of CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) activity, the study provides a fundamental framework for designing a more efficient and accurate genome-splicing technology that doesn’t yield ‘off-target’ DNA breaks currently frustrating the potential of the CRISPR-Cas9- system, particularly for clinical uses.

    Shake and bake. Gaussian accelerated molecular dynamics simulations and state-of-the-art supercomputing resources reveal the conformational change of the HNH domain (green) from its inactive to active state. Courtesy Giulia Palermo, McCammon Lab, UC San Diego.

    “Although the CRISPR-Cas9 system is rapidly revolutionizing life sciences toward a facile genome editing technology, structural and mechanistic details underlying its function have remained unknown,” says Giulia Palermo, a postdoctoral scholar with the UC San Diego Department of Pharmacology and lead author of the study [PNAS].

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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.)

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  • richardmitnick 8:42 am on July 7, 2017 Permalink | Reply
    Tags: A Duet of Firsts: Imaging Chemical Building Blocks, , , Chemistry,   

    From PNNL: “A Duet of Firsts: Imaging Chemical Building Blocks” 

    PNNL Lab

    July 2017

    The new metallic-organic framework, NU-1301, is made up of uranium oxide nodes and tricarboxylate organic linkers. Image courtesy of Northwestern University.

    Two firsts in science came about because of a near-dare. According to Nigel Browning at Pacific Northwest National Laboratory, “Omar Farha was giving a presentation on MOFs [metal-organic frameworks] and someone said ‘I bet you couldn’t make one out of uranium.’” Farha took the challenge and proved them wrong. In designing the uranium-laden frameworks, PNNL scientists Dr. Nigel Browning and Dr. Layla Mehdi helped Farha and his colleagues at Northwestern University overcome a troubling bottleneck in imaging the material. Before this study, scientists used x-ray analysis and modeling to map out MOF structures. The approaches come with sharp drawbacks. Browning and Mehdi showed that low-dose imaging is a viable option for MOF imaging, allowing for the structure to be resolved at the near-atomic level.

    This collaborative effort produced two notable milestones; it was first MOF made out of uranium, and the first time low-dose electron microscopy was used to map the MOF structure.

    Reference: Li P, NA Vermeulen, CD Malliakas, DA Gómez-Gualdrón, AJ Howarth, BL Mehdi, A Dohnalkova, ND Browning, M O’Keeffe, and OK Farha. 2017. Bottom-up construction of a superstructure in a porous uranium-organic crystal. Science 356(6338):624-627. DOI: 10.1126/science.aam7851

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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.


  • richardmitnick 8:17 am on July 7, 2017 Permalink | Reply
    Tags: , , Chemistry, , , Scientists Get First Direct Look at How Electrons ‘Dance’ with Vibrating Atoms,   

    From SLAC: “Scientists Get First Direct Look at How Electrons ‘Dance’ with Vibrating Atoms” 

    SLAC Lab

    July 6, 2017
    No writer credit

    A precise new way to study materials shows this ‘electron-phonon coupling’ can be far stronger than predicted, and could potentially play a role in unconventional superconductivity.

    In this illustration, an infrared laser beam (orange) triggers atomic vibrations in a thin layer of iron selenide, which are then recorded by ultrafast X-ray laser pulses (white) to create an ultrafast movie. The motion of the selenium atoms (red) changes the energy of the electron orbitals of the iron atoms (blue), and the resulting electron vibrations are recorded separately with a technique called ARPES (not shown). The coupling of atomic positions and electronic energies is much stronger than previously thought and may significantly impact the material’s superconductivity. (Greg Stewart/SLAC National Accelerator Laboratory)

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have made the first direct measurements, and by far the most precise ones, of how electrons move in sync with atomic vibrations rippling through an exotic material, as if they were dancing to the same beat.

    The vibrations are called phonons, and the electron-phonon coupling the researchers measured was 10 times stronger than theory had predicted – making it strong enough to potentially play a role in unconventional superconductivity, which allows materials to conduct electricity with no loss at unexpectedly high temperatures.

    What’s more, the approach they developed gives scientists a completely new and direct way to study a wide range of “emergent” materials whose surprising properties emerge from the collective behavior of fundamental particles, such as electrons. The new approach investigates these materials through experiments alone, rather than relying on assumptions based on theory.

    The experiments were carried out with SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser and with a technique called angle-resolved photoemission spectroscopy (ARPES) on the Stanford campus. The researchers described the study today in Science.


    See the full article here .

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    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.

  • richardmitnick 8:04 am on July 7, 2017 Permalink | Reply
    Tags: , , Chemistry,   

    From Rutgers: “Cutting the Cost of Ethanol, Other Biofuels and Gasoline” 

    Rutgers University
    Rutgers University

    July 5, 2017
    Todd B. Bates

    Enzymes, genetically engineered to avoid sticking to the surfaces of biomass such as corn stalks, may lower costs in the production of cellulose-based biofuels like ethanol. Shishir Chundawat/Rutgers University and U.S. Department of Energy

    Biofuels like the ethanol in U.S. gasoline could get cheaper thanks to experts at Rutgers University-New Brunswick and Michigan State University.

    They’ve demonstrated how to design and genetically engineer enzyme surfaces so they bind less to corn stalks and other cellulosic biomass, reducing enzyme costs in biofuels production, according to a study published this month on the cover of the journal ACS Sustainable Chemistry & Engineering.

    “The bottom line is we can cut down the cost of converting biomass into biofuels,” said Shishir P. S. Chundawat, senior author of the study and an assistant professor in the Department of Chemical and Biochemical Engineering at Rutgers University-New Brunswick.

    See the full article here .

    Follow Rutgers Research here .

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    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

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    Please give us back our original beautiful seal which the University stole away from us.

    As a ’67 graduate of University College, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society for non-tradional students.

  • richardmitnick 7:35 am on July 7, 2017 Permalink | Reply
    Tags: , , Chemistry, , ,   

    From BNL: “Electron Orbitals May Hold Key to Unifying Concept of High-Temperature Superconductivity” 

    Brookhaven Lab

    July 6, 2017
    Karen McNulty Walsh,
    (631) 344-8350

    Peter Genzer
    (631) 344-3174

    Iron-based superconductivity occurs in materials such as iron selenide (FeSe) that contain crystal planes made up of a square array of iron (Fe) atoms, depicted here. In these iron layers, each Fe atom has two active electron “clouds,” or orbitals—dxz (red) and dyz (blue)—each containing one electron. By directly visualizing the electron states in the iron planes of FeSe, the researchers revealed that that electrons in the dxz orbitals (red) do not form Cooper pairs or contribute to the superconductivity, but instead form an incoherent metallic state along the horizontal (x) axis. In contrast, all electrons in the dyz orbitals (blue) form strong Cooper pairs with neighboring atoms to generate superconductivity. Searching for other materials with this exotic “orbital-selective” pairing may lead to the discovery of new superconductors. No image credit.

    The custom-built Spectroscopic Imaging Scanning Tunneling Microscope used for these experiments stands one meter high, with cryogenic circuitry at the top for cooling samples to temperatures just above absolute zero (nearly -273 degrees Celsius). Inside, a needle with single atom on the end scans across the crystal surface in steps as small as 2 trillionths of a meter, measuring the electron tunneling current at each location. These measurements reveal the quantum wavefunctions of electrons in the material with exquisite precision. No image credit.

    A team of scientists has found evidence for a new type of electron pairing that may broaden the search for new high-temperature superconductors. The findings, described in the journal Science, provide the basis for a unifying description of how radically different “parent” materials—insulating copper-based compounds and metallic iron-based compounds—can develop the ability to carry electrical current with no resistance at strikingly high temperatures.

    According to the scientists, the materials’ dissimilar electronic characteristics actually hold the key to commonality.

    See the full article here .

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    BNL Campus

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

  • richardmitnick 11:57 am on July 4, 2017 Permalink | Reply
    Tags: , , Chemistry, , , , Tilting the sample gave a more complete dataset   

    From Salk: “Tilted microscopy technique better reveals protein structures” 

    Salk Institute bloc

    Salk Institute for Biological Studies

    July 3, 2017
    No writer credit found

    Cryo-Electron Microscope. No image credit.

    Salk Institute researcher describes new cryo-EM method to facilitate a better understanding of proteins involved in disease.

    The conventional way of placing protein samples under an electron microscope during cryo-EM experiments may fall flat when it comes to getting the best picture of a protein’s structure. In some cases, tilting a sheet of frozen proteins—by anywhere from 10 to 50 degrees—as it lies under the microscope, gives higher quality data and could lead to a better understanding of a variety of diseases, according to new research led by Salk scientist Dmitry Lyumkis.

    Dmitry Lyumkis. Credit: Salk Institute.

    “People have tried to implement tilting before, but there have been a lot of challenges,” says Lyumkis, a Helmsley-Salk Fellow at the Salk Institute and senior author of the new work, published July 3, 2017 in Nature Methods. “We’ve eliminated many of these problems with our new approach.”

    Cryo-EM, or cryo-electron microscopy, is a form of transmission electron microscopy in which samples are quickly cooled to below freezing before being imaged under the microscope. Unlike other methods commonly used to determine the structure of proteins, cryo-EM lets proteins remain in their natural conformations for imaging, which could reveal new information about the structures. Understanding proteins’ structures is a vital step to developing new therapies for disease, such as in the case of HIV.

    Researchers have long assumed that proteins adopt random conformations throughout the frozen grid that’s prepared for cryo-EM experiments, which means that by taking enough images, researchers can put together a full, 3D picture of the protein’s shape(s) from all imaging directions. But for many proteins, the approach seems to fall short, and parts of the proteins’ structures remain missing.

    “Researchers are starting to think that the proteins on a cryo-EM grid don’t adopt random conformations after all, but rather stick to the top or bottom of the sample grid in preferred orientations,” says Lyumkis. “Thus we may not be getting the full picture of proteins’ structures. More importantly, this behavior can prohibit structure determination altogether for select protein samples.”

    To understand the problem, imagine trying to look at the shadows of a dozen tin cans to figure out their shape but seeing only circles because all the cans are exactly upright. By making the light—or electron beam, in the case of cryo-EM—hit the samples at an angle, though, you’d be able to see the true shape better.

    When researchers have tried to tilt samples under a microscope in the past, they’ve been limited by poor resolution: an angle means that the electron beam has to travel through a thicker grid. Samples are also more likely to move within the frozen grid when they’re tilted, blurring out the data. And technically, analyzing data from a tilted sample is also more challenging, since cryo-EM methods were designed with the assumption that the grid containing proteins was always at the same distance from the microscope.

    To tackle these challenges, Lyumkis and his colleagues changed the materials used to create the cryo-EM grid, recorded movies of their data rather than still images, and developed new computational methods to analyze the information.

    When they tested the new approach on the influenza hemagglutinin protein, a notoriously hard protein to characterize using cryo-EM, the team found that tilting the sample gave a more complete dataset. When the protein sample was flat, typical algorithms introduced false positive shape to the protein that wasn’t backed up by experimental data. That wasn’t the case when it was tilted.

    “Due to the geometry of the data collection when we tilt, we fill up much more data characterizing the molecules, giving us a more complete picture of the protein’s shape” says Lyumkis.

    The algorithms that Lyumkis and his team developed—which include ways to analyze whether a cryo-EM experiment is introducing bad data, as well as the methods to interpret a tilted experiment—are now openly available. They hope other researchers will start using them and that it becomes a standard metric for cryo-EM structure validation (since most experimentally derived structures suffer from missing information to different extents).

    “One of the ideas we’re looking at now is whether data collection should always be performed at a tilt rather than in the conventional way,” says Lyumkis. “It won’t hurt and it should help.”

    Other researchers on the study were Yong Zi Tan, Philip Baldwin, Clinton Potter and Bridget Carragher of the New York Structural Biology Center, and Joseph David and James Williamson of The Scripps Research Institute.

    The work and the researchers involved were supported by grants from the Agency for Science, Technology, and Research Singapore, the Leona M. and Harry B. Helmsley Charitable Trust, the U.S. National Institutes of Health, the Jane Coffin Childs Foundation, the National Institute of Aging, the National Institute of General Medical Sciences and the Simons Foundation.

    See the full article here .

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    Salk Institute Campus

    Every cure has a starting point. Like Dr. Jonas Salk when he conquered polio, Salk scientists are dedicated to innovative biological research. Exploring the molecular basis of diseases makes curing them more likely. In an outstanding and unique environment we gather the foremost scientific minds in the world and give them the freedom to work collaboratively and think creatively. For over 50 years this wide-ranging scientific inquiry has yielded life-changing discoveries impacting human health. We are home to Nobel Laureates and members of the National Academy of Sciences who train and mentor the next generation of international scientists. We lead biological research. We prize discovery. Salk is where cures begin.

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