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  • richardmitnick 10:40 am on May 8, 2015 Permalink | Reply
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    From AAAS: “Electron microscopes close to imaging individual atoms” 



    7 May 2015
    Robert F. Service

    This composite image of the protein β-galactosidase shows the progression of cryo-EM’s ability to resolve a protein’s features from mere blobs (left) a few years ago to the ultrafine 0.22-nanometer resolution today (right). Veronica Falconieri/ Subramaniam Lab/CCR/ NCI/ NIH

    Today’s digital photos are far more vivid than just a few years ago, thanks to a steady stream of advances in optics, detectors, and software. Similar advances have also improved the ability of machines called cryo-electron microscopes (cryo-EMs) to see the Lilliputian world of atoms and molecules. Now, researchers report that they’ve created the highest ever resolution cryo-EM image, revealing a druglike molecule bound to its protein target at near atomic resolution. The resolution is so sharp that it rivals images produced by x-ray crystallography, long the gold standard for mapping the atomic contours of proteins. This newfound success is likely to dramatically help drugmakers design novel medicines for a wide variety of conditions.

    “This represents a new era in imaging of proteins in humans with immense implications for drug design,” says Francis Collins, who heads the U.S. National Institutes of Health in Bethesda, Maryland. Collins may be partial. He’s the boss of the team of researchers from the National Cancer Institute (NCI) and the National Heart, Lung, and Blood Institute that carried out the work. Still, others agree that the new work represents an important milestone. “It’s a major advance in the technology,” says Wah Chiu, a cryo-EM structural biologist at Baylor College of Medicine in Houston, Texas. “It shows [cryo-EM] technology is here.”

    Cryo-EM has long seemed behind the times—an old hand tool compared with the modern power tools of structural biology. The two main power tools, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, enable researchers to pin down the position of protein features to less than 0.2 nanometers, good enough to see individual atoms. By contrast, cryo-EM has long been limited to a resolution of 0.5 nm or more.

    Cryo-EM works by firing a beam of electrons at a thin film containing myriad copies of a protein that have been instantly frozen in place by plunging them in liquid nitrogen. Detectors track the manner in which electrons scatter off different atoms in the protein. When an image is taken, the proteins are strewn about in random orientations. So researchers use imaging software to do two things; first, they align their images of individual proteins into a common orientation. Then, they use the electron scattering data to reconstruct the most likely position of all the protein’s amino acids and—if possible—its atoms.

    Cryo-EM has been around for decades. But until recently its resolution hasn’t even been close to crystallography and NMR. “We used to be called the field of blob-ology,” says Sriram Subramaniam, a cryo-EM structural biologist at NCI, who led the current project. But steady improvements to the electron beam generators, detectors, and imaging analysis software have slowly helped cryo-EM inch closer to the powerhouse techniques. Earlier this year, for example, two groups of researchers broke the 0.3-nm-resolution benchmark, enough to get a decent view of the side arms of two proteins’ individual amino acids. Still, plenty of detail in the images remained fuzzy.

    For their current study, Subramaniam and his colleagues sought to refine their images of β-galactosidase, a protein they imaged last year at a resolution of 0.33 nm. The protein serves as a good test case, Subramaniam says, because researchers can compare their images to existing x-ray structures to check their accuracy. Subramaniam adds that the current advance was more a product of painstaking refinements to a variety of techniques—including protein purification procedures that ensure each protein copy is identical and software improvements that allow researchers to better align their images. Subramaniam and his colleagues used some 40,000 separate images to piece together the final shape of their molecule. They report online today in Science that these refinements allowed them to produce a cryo-EM image of β-galactosidase at a resolution of 0.22 nm, not quite sharp enough to see individual atoms, but clear enough to see water molecules that bind to the protein in spots critical to the function of the molecule.

    That level of detail is equal to the resolution of many structures using x-ray crystallography, Chiu says. That’s vital, he adds, because for x-ray crystallography to work, researchers must produce millions of identical copies of a protein and then coax them to align in exactly the same orientation as they solidify into a crystal. But many proteins resist falling in line, making it impossible to determine their x-ray structure. NMR spectroscopy doesn’t require crystals, but it works only on small proteins. Cryo-EM represents the best of both worlds: It can work with massive proteins, but it doesn’t require crystals.

    As a result, the new advances could help structural biologists map vast numbers of new proteins they’ve never mapped before, Chiu says. That, in turn, could help drug developers design novel drugs for a multitude of conditions associated with different proteins. But one thing the technique has already shown is crystal clear, that in imaging, as well as biology, slow, evolutionary advances over time can produce big results.

    See the full article here.

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  • richardmitnick 8:25 am on April 22, 2015 Permalink | Reply
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    From Harvard: “A leap for ‘artificial leaf’” 

    Harvard University

    Harvard University

    April 21, 2015
    Peter Reuell

    New technique could open door to producing alternative-energy devices more cheaply

    With support from Harvard President Drew Faust’s Climate Change Solutions Fund, Patterson Rockwood Professor of Energy Daniel Nocera and colleagues created an efficient method to harness the power of light to generate two powerful fuels. File photo by Rose Lincoln/Harvard Staff Photographer

    As an idea, the notion of an “artificial leaf” was always meant to be simple: Could scientists, using a handful of relatively cheap materials, harness the power of light to generate two powerful fuels — hydrogen and oxygen — by breaking apart water molecules?

    In practice, however, the idea faced a number of hurdles, including how to pattern the catalysts on silicon that would power the reaction. But that could soon change, says Patterson Rockwood Professor of Energy Daniel Nocera.

    Using an electro-chemical process similar to etching, Nocera and colleagues have developed a system of patterning that works in just minutes, as opposed to the weeks other techniques need.

    Dubbed reactive interface patterning promoted by lithographic electrochemistry, or RIPPLE, the process can be so tightly controlled that researchers can build photonic structures that control the light hitting the device and greatly increase its efficiency. The new system is described in two papers that appeared in recent weeks in the Journal of the American Chemical Society and the Proceedings of the National Academy of Sciences.

    “This is what I call frugal innovation,” Nocera said. “We called it RIPPLE because you can think of it like dropping a pebble in water that makes a pattern of ripples. This is really the simplest patterning technique that I know of. We take silicon, coat it with our catalyst, and within minutes we can pattern it using a standard electro-chemical technique we use in the lab.”

    The project was one of seven research efforts supported in the inaugural year of Harvard President Drew Faust’s Climate Change Solutions Fund. The $20 million fund was created to spur the development of renewable energy solutions and speed the transition from fossil fuels.

    “It’s already working,” Nocera said of the project. “We already have a home run, and that makes me very happy, because the idea we proposed actually works.”

    The ability to pattern catalysts — using cobalt phosphate to spur the creation of oxygen and a nickel-zinc alloy for hydrogen — on the silicon substrate is particularly important, Nocera said.

    “In our current system, we just have flat silicon and the catalyst is covering it, so the light has to come through the catalyst, and we have some energy loss,” he explained. “Using this, we are able to pattern the catalyst, so we have bare silicon in one location and the catalyst in another, so the light doesn’t have to go though the catalyst, making the system more efficient.”

    Equally important, Nocera said, the system allows for fast patterning of relatively large areas — far larger than other systems that use nano-scale patterning techniques.

    Ironically, the discovery of the technique came about almost by accident.

    “What we were trying to do was generate intense electrical fields to deposit the catalyst selectively on silicon,” Nocera explained. “It was during what was basically a control experiment that we noticed we didn’t need an intense electric field and could pattern the silicon quite easily.”

    While the mechanism at work in the patterning isn’t fully understood, Nocera and colleagues can maintain precise control over the process and produce everything from patterns of lines to rings to squares on silicon substrates.

    “It’s phenomenological. We don’t understand the mechanism yet,” Nocera said. “But we do understand how to control it, so we can fine-tune the spacing of the patterns, and what we’ve already produced can work for energy applications — with the catalyst and the artificial leaf, it’s remarkable.”

    See the full article here.

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

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  • richardmitnick 7:29 am on April 6, 2015 Permalink | Reply
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    From AAAS: “U.S. takes possible first step toward regulating nanochemicals” 



    2 April 2015
    Puneet Kollipara

    Nanocubes, which researchers have explored as a possible way to store hydrogen for energy. BASF/Flickr

    The U.S. Environmental Protection Agency (EPA) is ratcheting up its scrutiny of nanoscale chemicals amid concerns that they could pose unique environmental and health risks. Late last month, the agency proposed requiring companies to submit data on industrial nanomaterials that they already make and sell. Observers say EPA’s move could be a prelude to tighter federal regulation of nanomaterials, which have begun to show up in consumer products.

    For years, EPA has grappled with whether and how to use the Toxic Substances Control Act (TSCA), the nation’s leading chemical regulation law, to handle nanomaterials. TSCA is silent on nanoproducts, generally defined as materials composed of structures between 1 and 100 billionths of a meter. But many environmental groups worry that they potentially carry unknown risks by virtue of their size. Other observers, however, have argued that size alone shouldn’t trigger new regulation and that existing rules are adequate to deal with the new products.

    EPA’s 25 March proposal actually walks back an earlier version—now scrapped—that would have let the agency more easily clamp down on any new uses of nanomaterials. Still, the weaker version being proposed now represents the first time EPA would use its powers under TSCA to request information specifically on nanomaterials. (The proposal comes as Congress is debating revamping TSCA, which has drawn extensive criticism.)

    Under the rule, manufacturers would have to submit a range of data regarding the nanoscale substances they now make and that fall under TSCA’s scope—such as substances used in industrial applications. EPA wants to know how much the company is producing, for example, as well as potential public exposures, and manufacturing and processing methods. It also wants see any existing health and safety data. In addition, the agency would require manufacturers of proposed new nanomaterials to submit existing data before they want to start making and selling those substances.

    The rule wouldn’t force companies to generate any new health and safety data. And by itself, the rule wouldn’t restrict any nanomaterials’ use, EPA notes in its draft proposal. The agency’s actions “do not conclude and are not intended to conclude that nanoscale materials as a class, or specific uses of nanoscale materials, necessarily give rise to or are likely to cause harm,” the notice states. Rather, EPA says the information would let it better assess nanomaterials’ risks.

    And the agency states that its approach would help protect human health and the environment “without prejudging new technologies or creating unnecessary barriers to trade or hampering innovation.” EPA argues that case-by-case approach would jibe with a set of nanotech regulation principles released in 2011 by the White House Office of Science and Technology Policy. Those principles advise agencies against making one-size-fits-all judgments.

    The American Chemistry Council (ACC), the largest chemical industry trade group, is still evaluating the proposal, it said in a statement. But it “is particularly interested in how EPA defines the materials to be covered by the proposed rule,” says Jay West, manager of ACC’s Nanotechnology Panel, says in the statement.

    The proposal is “logical” and “creatively written,” says Lynn Bergeson, a managing partner with the law firm Bergeson & Campbell, P.C. in Washington, D.C., which advises companies on EPA regulatory compliance. Some companies may argue the rule is too broad or burdensome, she says, or worry that EPA’s move could stigmatize their products. But the government effort to collect information could potentially help the industry by reassuring a skeptical public, she adds. “If there are no data on which EPA is able to rely to conclude that there is no risk, then the agency really is not doing its job,” she says.

    The proposal is a good first step for EPA, says Jaydee Hanson, policy director at the International Center for Technology Assessment, a group in Washington, D.C., that has raised concerns about nanotechnology’s potential risks. But he worries that many companies might simply not respond and that the cash-strapped EPA would struggle to crack down on violators. And he worries that the proposal would let companies keep too much information secret, by claiming it as confidential business information. (TSCA reforms that Congress is debating would limit the types of information that companies could claim as confidential, he notes.) But Hanson is looking on the bright side. “We wish [EPA was] doing more, but we’re excited that they are doing it,” he says.

    Still, even with all the new information in hand, it’s unclear how much action EPA could take to restrict nanomaterials under current law. In general, EPA has moved slowly to regulate new chemicals, and struggled to meet the burden that TSCA sets on it for removing, restricting, or preventing the sale of chemicals found to be unsafe. Congress says it wants to make that process easier, but it is unclear how any new rules would apply to nanotechnologies.

    See the full article here.

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

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  • richardmitnick 5:20 pm on February 23, 2015 Permalink | Reply
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    From DOE Pulse: “NETL invents improved oxygen carriers” 


    National Energy Technology Lab

    February 23, 2015
    Linda Morton, 304.285.4543,

    Oxygen carriers are similar in texture to
    sand. The oxygen carrier pictured here
    blends magnesium oxide and hematite.

    One of the keys to the successful deployment of chemical looping technologies is the development of affordable, high performance oxygen carriers. One potential solution is the naturally-occurring iron oxide, hematite. “Hematite is pretty cheap,” says Doug Straub, Technical Coordinator for the National Energy Technology Laboratory’s Chemical Looping Combustion (CLC) projects and the just-completed Industrial Carbon Management Initiative (ICMI). “You just dig it out of the ground and run it through a screen.” That affordability makes hematite attractive as an oxygen-carrier material, but high performance at the conditions imposed by the chemical looping process is also important. Researchers at the DOE lab are investigating how to enhance hematite-based oxygen carriers so they can stand up to high reactor temperatures. Oxygen carriers also need to be resilient in the face of frequent impacts with reactor walls, with each other, and (in coal-burning reactors) with coal particles. Researchers are also improving oxygen carriers so that they more completely combust the fuel.

    Their work has paid off. Dr. Ranjani Siriwardane (who leads the CLC oxygen carrier research) and Dr. Duane Miller (a chemical engineer at NETL) have invented an oxygen carrier that pairs magnesium oxide with hematite. During a pilot-scale run through NETL’s fluidized bed reactor last year, their carrier showed better performance than carriers that contained just natural hematite.

    What’s next? In the words of Dr. Siriwardane, “this is a big scale-up problem,” and that scale-up can be difficult. The quantities of carriers used at the laboratory scale are small, and techniques for preparing them are easier to control. But, as Dr. Siriwardane explains, “some of the techniques we use for lab-scale preparations are not practical for large-scale preparations, where different techniques and equipment are used. Finding the proper production techniques for our carriers that still deliver the required performance is a big challenge.” However NETL researchers are clearly up to the challenge: when Drs. Siriwardane and Miller applied for the patent for their magnesium-oxide-and-hematite carrier, they had about 100 grams of material, just enough for a lab-scale run. Since then, they have worked with NexTech Materials, a commercial materials vendor, to prepare a 400-pound batch of the carrier for the pilot-scale test.

    In addition to the hematite-based carrier, NETL is also exploring alternative carrier materials, with the goal of optimizing carrier performance and affordability for specific chemical looping applications. A second carrier developed by Drs. Siriwardane and Hanjing Tian (formerly of NETL but now a West Virginia University faculty member) relies on manmade materials instead of natural hematite. Made of copper oxide, iron oxide, and alumina, it too is ready for pilot-scale testing.

    The oxygen carriers that NETL invents to enable CLC could have applications beyond electricity generation. CLC is also useful in industrial steam production, says Dr. Miller, and can be used for the production of hydrogen or syngas from methane. NETL scientists continue research to discover and develop carriers for such real-world applications with the expectation that the energy technologies they enable will one day be very green and very, very affordable.

    See the full article here.

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    DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

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  • richardmitnick 3:41 am on February 18, 2015 Permalink | Reply
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    From New Scientist: “Half a dozen molecules cause vital acid break-up” 


    New Scientist

    12 February 2015
    Rachel Ehrenberg

    It sounds like a bad physics joke: how many water molecules does it take to change an acid? At some point the acid breaks apart, giving up a proton to the water. But exactly when enough water is present to cause the break-up has been hard to pin down. New experiments may not only tell us the answer, but also shed light on questions in fields from atmospheric science to biochemistry.

    Precisely how an acid molecule falls apart when surrounded by a handful of water molecules is a long-standing mystery, even though it’s a common and important interaction. “This is fundamental,” says chemist Ken Leopold of the University of Minnesota in Minneapolis. “Proton transfer is ubiquitous; it’s the simplest chemical reaction.”

    Previous work was largely theoretical and probed water-acid mixes only at exceedingly low temperatures. So physicist Vitaly Kresin of the University of Southern California in Los Angeles and colleagues decided to study the less unearthly temperature of 200 kelvin (-73.15 °C).

    The team blasted hot water vapour through a pinhole a mere 75 micrometres wide and added hydrochloric acid to the spray. The spray of water-acid clusters was then passed through an electric field, which deflected the clusters certain distances. Previous work suggested that the distribution of positive and electric charges in the clusters changes when the acid splits apart, and this knowledge, combined with the measured deflections, allowed the team to deduce how many water molecules it took to spur the acid into ditching its proton.

    Communal proton

    The simplest scenario is that just one water molecule in the cluster is the lucky recipient. But the team also did some modelling that hints at quantum effects kicking in once there are half a dozen or so water molecules. In this scenario, the proton is shared, bouncing freely around the cluster. “Protons are very small and mobile, they can bounce all over the place,” says Kresin, “and each water molecule can spin and very easily change shape.”

    There’s a third possibility: perhaps the experiment wasn’t seeing the acid splitting at all. In this scenario, the water molecules in the clusters redistribute their charges, leading to the deflections the team saw. If that’s the case, then more water is needed to make the acid break apart, and some other experiment will have to be devised to see it happening.

    Whatever the case, a better understanding of proton transfer will shed light on biochemical reactions, and on atmospheric processes in which acids and water form aerosols that affect the climate and human health.

    Journal reference: Physical Review Letters, DOI: 10.1103/PhysRevLett.114.043401

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  • richardmitnick 5:32 pm on February 13, 2015 Permalink | Reply
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    From SLAC: “Scientists Get First Glimpse of a Chemical Bond Being Born” 

    SLAC Lab

    February 12, 2015

    Scientists have used an X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory to get the first glimpse of the transition state where two atoms begin to form a weak bond on the way to becoming a molecule.

    This illustration shows atoms forming a tentative bond, a moment captured for the first time in experiments with an X-ray laser at SLAC National Accelerator Laboratory. The reactants are a carbon monoxide molecule, left, made of a carbon atom (black) and an oxygen atom (red), and a single atom of oxygen, just to the right of it. They are attached to the surface of a ruthenium catalyst, which holds them close to each other so they can react more easily. When hit with an optical laser pulse, the reactants vibrate and bump into each other, and the carbon atom forms a transitional bond with the lone oxygen, center. The resulting carbon dioxide molecule detaches and floats away, upper right. The Linac Coherent Light Source (LCLS) X-ray laser probed the reaction as it proceeded and allowed the movie to be created. (SLAC National Accelerator Laboratory)

    This fundamental advance, reported Feb. 12 in Science Express and long thought impossible, will have a profound impact on the understanding of how chemical reactions take place and on efforts to design reactions that generate energy, create new products and fertilize crops more efficiently.

    “This is the very core of all chemistry. It’s what we consider a Holy Grail, because it controls chemical reactivity,” said Anders Nilsson, a professor at the SLAC/Stanford SUNCAT Center for Interface Science and Catalysis and at Stockholm University who led the research. “But because so few molecules inhabit this transition state at any given moment, no one thought we’d ever be able to see it.”

    Anders Nilsson, a professor at SLAC and at Stockholm University, explains how scientists used an X-ray laser to watch atoms form a tentative bond, and why that’s important.

    The experiments took place at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. Its brilliant, strobe-like X-ray laser pulses are short enough to illuminate atoms and molecules and fast enough to watch chemical reactions unfold in a way never possible before.

    Researchers used LCLS to study the same reaction that neutralizes carbon monoxide (CO) from car exhaust in a catalytic converter. The reaction takes place on the surface of a catalyst, which grabs CO and oxygen atoms and holds them next to each other so they pair up more easily to form carbon dioxide.

    In the SLAC experiments, researchers attached CO and oxygen atoms to the surface of a ruthenium catalyst and got reactions going with a pulse from an optical laser. The pulse heated the catalyst to 2,000 kelvins – more than 3,000 degrees Fahrenheit – and set the attached chemicals vibrating, greatly increasing the chance that they would knock into each other and connect.

    The team was able to observe this process with X-ray laser pulses from LCLS, which detected changes in the arrangement of the atoms’ electrons – subtle signs of bond formation – that occurred in mere femtoseconds, or quadrillionths of a second.

    “First the oxygen atoms get activated, and a little later the carbon monoxide gets activated,” Nilsson said. “They start to vibrate, move around a little bit. Then, after about a trillionth of a second, they start to collide and form these transition states.”

    ‘Rolling Marbles Uphill’

    The researchers were surprised to see so many of the reactants enter the transition state – and equally surprised to discover that only a small fraction of them go on to form stable carbon dioxide. The rest break apart again.

    “It’s as if you are rolling marbles up a hill, and most of the marbles that make it to the top roll back down again,” Nilsson said. “What we are seeing is that many attempts are made, but very few reactions continue to the final product. We have a lot to do to understand in detail what we have seen here.”

    Theory played a key role in the experiments, allowing the team to predict what would happen and get a good idea of what to look for. “This is a super-interesting avenue for theoretical chemists. It’s going to open up a completely new field,” said report co-author Frank Abild-Pedersen of SLAC and SUNCAT.

    A team led by Associate Professor Henrik Öström at Stockholm University did initial studies of how to trigger the reactions with the optical laser. Theoretical spectra were computed under the leadership of Stockholm Professor Lars G.M. Pettersson, a longtime collaborator with Nilsson.

    Preliminary experiments at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), another DOE Office of Science User Facility, also proved crucial. Led by SSRL’s Hirohito Ogasawara and SUNCAT’s Jerry LaRue, they measured the characteristics of the chemical reactants with an intense X-ray beam so researchers would be sure to identify everything correctly at the LCLS, where beam time is much more scarce. “Without SSRL this would not have worked,” Nilsson said.

    The team is already starting to measure transition states in other catalytic reactions that generate chemicals important to industry.

    “This is extremely important, as it provides insight into the scientific basis for rules that allow us to design new catalysts,” said SUNCAT Director and co-author Jens Nørskov.

    Researchers from LCLS, Helmholtz-Zentrum Berlin for Materials and Energy, University of Hamburg, Center for Free Electron Laser Science, University of Potsdam, Fritz-Haber Institute of the Max Planck Society, DESY and University of Liverpool also contributed to the research. The research was funded by the DOE Office of Science, the Swedish National Research Council, the Knut and Alice Wallenberg Foundation, the Volkswagen Foundation and the German Research Foundation (DFG) Center for Ultrafast Imaging.

    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 2:25 pm on February 12, 2015 Permalink | Reply
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    From APS: “Viewpoint: Making Waves with DNA” 


    American Physical Society

    February 9, 2015
    Irving R. Epstein

    Strands of DNA can be used to generate waves of chemical reactions with programmable shape and velocity.

    Figure 1 Schematic view of the system studied by Zadorin et al. A single-stranded DNA (A) binds to one of the two complementary ends of the DNA template T. The resulting A:T complex uses the polymerase enzyme (pol) to generate another molecule of A on the template. A second enzyme (nick) facilitates the splitting of the two A molecules and their detachment from T. The net result is an “autocatalytic” reaction in which A catalyzes its own production: A+T+monomers→2A+T. By varying the concentration of DNA strands and enzymes, the authors were able to generate waves of chemical reactions with controllable shape and velocity.

    Research in chemistry can be roughly divided into two categories: analysis—the measurement of existing objects and phenomena—and synthesis—the construction of those objects and phenomena from simpler pieces. Typically, synthesis lags behind analysis: one first determines the formula of a molecule (and often its structure) before attempting to make it. However, as chemistry advances, investigators are increasingly attempting to synthesize first, designing chemical systems that realize desired phenomena. A team led by André Estevez-Torres at CNRS in France and co-workers has demonstrated an experimental toolkit that could be used for the rational engineering of nonlinear chemical effects in solution. Using DNA strands moving in a narrow channel and reacting under the action of enzymes, the authors are able to create chemical waves whose shapes and velocity can be finely controlled. Their setup could be programmed to yield a broad spectrum of other nonlinear phenomena in systems governed by a combination of chemical reactivity and molecular diffusion (“reaction-diffusion” systems).

    Nonlinear chemical dynamics characterizes many natural and industrial processes and is a quintessential feature of living organisms: most of their chemistry occurs far from equilibrium, has a nonlinear dependence on parameters like molecular concentrations, and may exhibit temporal oscillations (many biological functions are, for instance, synchronized to a 24-hour cycle). Researchers have applied a number of algorithms to design systems featuring such nonlinear behavior, engineering chemical oscillators (reactions in which the concentration of one or more components exhibits periodic changes), propagating reaction fronts or “Turing patterns” —spatial patterns of concentrations that, as Alan Turing proposed, might be related to biological morphogenesis (e.g., the formation of leopard spots or zebra stripes).

    But design algorithms are severely limited by the realities imposed by nature. One may write down a set of equations that generates a desired phenomenon, e.g., spatiotemporal chaos, for a set of reaction rates and diffusion coefficients. There is, however, no guarantee that an actual collection of molecules can be found that realizes the theorized behavior. For example, over the past several decades, researchers have successfully engineered, through systematic studies, new chemical oscillators with desired parameters for a variety of applications. These efforts have resulted in the discovery of several oscillators, but none of these oscillators “by design” has attained the importance of the Belousov-Zhabotinsky (BZ) reactions, a family of oscillating reactions (discovered serendipitously) that remains the most versatile and reliable chemical oscillator for most applications.

    Most efforts to design reaction-diffusion phenomena have utilized small inorganic molecules, largely because these substances are cheap, easy to work with, and produce visible color changes when they undergo reduction and oxidation (redox) reactions. Unfortunately, these reaction mixtures are typically not biocompatible, and they cannot be used in applications that place them in contact with components of living systems like proteins. The BZ reaction, for example, only works at acidity levels lethal to most biological cells.

    A solution may be offered by oligonucleotides (short single strands of DNA or RNA), which have been utilized as versatile building blocks for oscillators, computational elements, and structures with arbitrary shapes. In their new work, Estevez-Torres et al. have focused on dynamical aspects: They demonstrated that DNA strands can be used to realize an experimental model for reaction-diffusion systems whose spatiotemporal dynamics is fully controllable by programming three key elements of the system: the reaction rates, the diffusion coefficients, and the topology of the chemical reaction network (i.e., which reactions are linked to each other in ways that generate positive or negative feedback).

    Figure 1 shows a schematic of the authors’ setup: a linear channel in which they are able to generate traveling waves of chemical concentrations whose velocity can be precisely controlled. A single strand of DNA (A) can attach to either half of a complementary strand (T) to form a complex (A:T). In the presence of an enzyme (pol), the A:T complex serves as a template for growth of an additional A strand from monomeric precursors in the solution. A second “nicking” enzyme (nick) causes the two A molecules to detach from the T strand. The net result is an “autocatalytic” reaction in which A acts as a catalyst of its own production: A+T+monomers→2A+T

    It is known that autocatalytic reactions can generate chemical waves that travel with a characteristic velocity (ν) depending on the effective rate constant (k) for the reaction and the diffusion coefficient (D) of the autocatalyst (A in this case): ν=(kD)1/2. This idea has been exploited to generate a family of propagating acidity fronts in inorganic reactions, where the hydrogen ion (H+) was the autocatalyst. It was not possible, however, to control the velocity of those fronts, because the reaction rate depends on diffusion and the diffusion coefficient of H+ in water is fixed. Here, the authors are instead able to tune the effective rate constant k by varying the concentration of either the template or the enzyme. They can also control D, the effective diffusion rate of A (which depends on the diffusion rate of A relative to the A:T complex). By binding a heavy but chemically inert group C to T, they can reduce its diffusion rate and that of the complex without affecting its affinity to A. In other words, by choosing the concentrations of T, C, and pol, they can act on the two independent “control knobs” of the diffusion coefficient and the reaction rate constant. In this way, they can generate reaction waves with velocities that vary by as much as 3 orders of magnitude.

    What is exciting about this approach is that it is not limited to the generation of chemical waves. The scheme could be extended to generate any desired reaction-diffusion phenomenon for which one can write a set of elementary reactions. Turing patterns, for example, could be produced, as suggested by a previous study, by picking a slightly different reaction network, including an activator (like A in this case) but also an inhibitor that diffuses 1 order of magnitude faster than A. The “toolbox” employed by Estevez-Torres’ team, in which the activator species (A) can be slowed down by the massive inert group (C), already contains all elements needed to achieve the necessary range for diffusion coefficients.

    Approaches like the one explored by the authors, building on eons of evolution in the ability to control nucleic acids, suggest a bright future for this research line. The fact that DNA-based reactions are inherently biocompatible makes them attractive for potential applications, in particular if the system can be coupled to mechanical forces, as has been done for the BZ reaction. For example, one could envision inserting an anticancer drug into a DNA shell designed to undergo a mechanical deformation and release the drug when it encounters a molecule with a characteristic shape on the tumor surface.

    This research is published in Physical Review Letters.

    See the full article here.

    For those who are interested, the original article has a complete list of references and a numeric key for those references.

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    American Physical Society
    Physicists are drowning in a flood of research papers in their own fields and coping with an even larger deluge in other areas of physics. How can an active researcher stay informed about the most important developments in physics? Physics highlights a selection of papers from the Physical Review journals. In consultation with expert scientists, the editors choose these papers for their importance and/or intrinsic interest. To highlight these papers, Physics features three kinds of articles: Viewpoints are commentaries written by active researchers, who are asked to explain the results to physicists in other subfields. Focus stories are written by professional science writers in a journalistic style and are intended to be accessible to students and non-experts. Synopses are brief editor-written summaries.

  • richardmitnick 8:12 am on February 3, 2015 Permalink | Reply
    Tags: , Chemistry, ,   

    From PNNL: “Duets by Molecules and Plasmons” 

    PNNL Lab

    January 2015

    Scientists examine the information content in nanoscale chemical images

    Physical Sciences Division
    Research Highlights

    January 2015

    Frequency resolved TERS images of the laser-irradiated region, reconstructed using four different Raman-allowed vibrations of DMS. The representative images are obtained from the same pass of the AFM probe through the laser-illuminated region of the substrate. Namely, this is the same image, reconstructed at four different energies. The 2D contours have a color bar starting at white (brightest signals), passing through yellow to black (lowest signals). Copyright 2014: American Chemical Society. Enlarge/expand Image.

    Results: Light waves trapped on a metal’s surface can interrogate the nearby molecules about their chemical identity through the molecule’s characteristic vibrations, which act as fingerprints. Scientists at Pacific Northwest National Laboratory (PNNL) “saw” the interaction between the molecules and the trapped light waves or surface plasmons. Their fundamental endeavor could lead to breakthroughs in interpreting ultrasensitive chemical images for characterizing new materials with potential uses in catalysis and energy conversion.

    The article is featured in the American Chemical Society (ACS) Editors’ Choice collection. The decision was made by the journal editors, who select one article a day from across the 55 ACS journals to appear in this special collection. As such, it was made freely available to the public. The article was the editors’ choice for November 12, 2014.

    Why It Matters: To detect only a few molecules, researchers using ultrasensitive spectroscopic and microscopic techniques rely on localized surface plasmons. This is particularly the case when the molecular identity must be determined. These plasmons are essentially light waves trapped at the surface of nanoscale noble metal structures. In surface plasmon-enhanced vibrational spectroscopy, the recorded optical signals result from the interaction between molecular and plasmonic states. This was revealed by PNNL scientists, who set out to understand the information content encoded in nanoscale chemical images, recorded by taking advantage of the unique properties of localized surface plasmons. They found that each pixel in their recorded images reports on the distinct local environments in which each probed molecule resides.

    “This is really fundamental science that takes us a step closer to understanding what one actually measures with this type of spectroscopy,” said Dr. Patrick El-Khoury, a PNNL chemical physicist who carried out the measurements.

    User Facility: EMSL

    Research Team: Patrick Z. El-Khoury, Dehong Hu, and Wayne P. Hess, Pacific Northwest National Laboratory; Tyler W. Ueltschi and Amanda L. Mifflin, University of Puget Sound

    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.


  • richardmitnick 8:02 am on January 27, 2015 Permalink | Reply
    Tags: , , , Chemistry   

    From AAAS: “How Earth’s earliest life overcame a genetic paradox” 



    26 January 2015
    Tim Wogan

    The unique temperature conditions of hydrothermal vents like this one could have favored the evolution of complex life.

    On ancient Earth, the earliest life encountered a paradox. Chains of RNA—the ancestor of DNA—were floating around, haphazardly duplicating themselves. Scientists know that eventually, these RNA chains must have become longer and longer, setting the stage for the evolution of complex life forms like amoebas, worms, and eventually humans. But under all current models, shorter RNA molecules, having less material to copy, would have reproduced faster, favoring the evolution of primitive organisms over complex ones. Now, new research offers a potential solution: Longer RNA chains could have hidden out in porous rocks near volcanic sites such as hydrothermal ocean vents, where unique temperature conditions might have helped complex organisms evolve.

    Hydrothermal vents are fissures in Earth’s crust that pump out superheated water. They would have been common on early Earth, which was more tectonically active than the planet is today, says Dieter Braun, an experimental biophysicist at Ludwig Maximilian University in Munich, Germany. The water in hydrothermal vents is particularly rich in nutrients, making them promising sites for the origin of life.

    To figure out if hydrothermal vents could have given the evolution of complex life a boost, Braun and his colleagues examined the physics of a theoretical single pore in the rock surrounding a vent. The pore is open at the top and at the bottom and filled with a dilute solution of RNA molecules of various lengths. The solution on the hot side—the one closer to the stream of superheated water—would become less dense and rise up through the pore. Some of it would escape at the top, to be replenished by more nutrient-rich fluid entering at the bottom. The remainder would diffuse across to the cold side of the pore and drop back down. A complex physical effect called thermophoresis causes charged molecules in a solution to accumulate in colder water, and the longer chains, having more charge, would do this more often than shorter chains. Therefore, the shorter RNA chains would be more likely to escape out of the top of the pore, whereas the longer ones would stay trapped inside where, continually fed by nutrients, they could reproduce. Better still, Braun says, the continuous temperature cycling could actually help split the RNA double helix apart, making it easier for it to reproduce.

    To test this elaborate hypothesis, Braun and his colleagues constructed a simulated piece of porous rock from a network of tiny glass capillary tubes heated on one side. They allowed dissolved fragments of DNA to be washed into the tubes from the bottom. Ideally, they would have used RNA, but Braun explains that there’s no good way to reproduce RNA in a lab, whereas it’s easy to reproduce DNA with a standard laboratory process called PCR. “All the thermophoresis and the characteristics of the trapping mechanism are the same for DNA and RNA,” he says. Once they let the experiment run, the researchers found that longer chains of DNA were more likely to accumulate inside the tubes than shorter chains were. As a result, the longer strands reproduced much better inside the pores and their populations grew, whereas the shorter strands were diluted so much that they went extinct, the team reports online today in Nature Chemistry.

    It’s “nice chemistry,” says marine chemist Jeffrey Bada of the University of California (UC), San Diego, but he is not convinced that hydrothermal vents, or any other likely habitat on early Earth, could have provided the conditions created in the lab: “The processes outlined are not likely to take place on a significant scale on the Earth or elsewhere.” Biochemist Irene Chen of UC Santa Barbara disagrees and even thinks the research opens a door to studying environments beyond just volcanic ones. She suggests rock pores hotter on one side than the other could result from solar, as well as hydrothermal, heating, expanding the types of environments that could have favored the evolution of complex life. A physical environment that could plausibly have existed on the early Earth “actually selects for longer RNA sequences,” she says. “The extra length is basically room for biological creativity.”

    See the full article here.

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

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  • richardmitnick 12:59 pm on January 18, 2015 Permalink | Reply
    Tags: , , Chemistry, Institut d'Astrophysique Spatiale   

    From Institut d’Astrophysique Spatiale: “Detection of sugars in a laboratory simulation of interstellar and pre-cometary organic matter produced from the photo/thermos chemistry of ices” 

    Institut d'Astrophysique Spatiale bloc

    Institut d’Astrophysique Spatiale

    No Writer Credit

    Ten aldehydes, including two sugars potentially important for prebiotic chemistry, have for the first time been identified in organic residues issued from photochemistry of interstellar ice analogues, produced in the laboratory by the IAS MICMOC/SUGARS experiment.

    The MICMOC experiment (Matière Interstellaire et Cométaire: Molécules Organiques Complexes) has a variant (Chiral-MICMOC on the SOLEIL synchrotron) which investigates the spatial conformation (left, L, or right D) of the amino acids produced under the photochemical action of ultraviolet circularly polarized light. The aim of this experiment is to propose an astrophysical scenario for the origin of homochirality observed in biological molecules on the Earth. The MICMOC/SUGARS experiment is another variant of the initial set-up. This fully interdisciplinary approach assembles astrophysicists, molecular physicists, and chemists. It mixes an experimental approach including a strong astrophysical background with the simulation of the evolution of interstellar ice analogues in the laboratory and sophisticated analytical chemistry methods for the detection of molecules of prebiotic interest.

    The detection of numerous amino acids in the organic residues produced by the photo/thermo-chemistry of ices has been reported, in part thanks to our collaboration between IAS (Orsay) and INC (Nice). The overall quality of the samples produced by the IAS team « Astrochimie et Origines » has been attested by the use of 13C atoms markers in the original ice samples to avoid any confusion with possible contamination of the samples during manipulation.

    Recently, a change in the analytical procedure has allowed the detection of a new family of molecules: the aldehydes. Among them are the two sugars glycolaldehyde and glyceraldehyde, potentially important for prebiotic chemistry. According to a recent study, these molecules may be considered as possible precursors of ribonucleotides (constituents of RNA), in the same manner that amino acids (which are detected within the same experimental protocol) are key molecules for the early formation of proteins. The detection of these molecules in our samples strengthens the scenario of an exogenous delivery of organic molecules essential for starting prebiotic chemistry at the surface of the early Earth.

    Finally, if glycolaldehyde is indeed detected in the interstellar medium, that is not the case yet for glyceraldehyde, which can be seen now as a potential target for large modern radioastronomy instruments such as ALMA. Glyceraldehyde could also be proposed for detection in primitive carbonaceous meteorites.

    Research paper: P. de Marcellus et al. (2015). Aldehydes and sugars from evolved precometary ice analogues: Importance of ices in astrochemical and prebiotic evolution.
    PNAS. DOI : 10.1073/pnas.1418602112 10.1073/pnas.1418602112


    Left: UV source for astrochemistry experiments at IAS (picture : P. de Marcellus). Right: the “Pillars of Creation” (in the Eagle nebula) seen by the Hubble Space Telescope (HST, NASA).

    See the full article here.

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    Institut d'Astrophysique Spatiale campus

    The Institut d’Astrophysique Spatiale (IAS) is a laboratory of the National Center of Scientific Research (CNRS) and of the University of Paris-Sud 11. in addition to having the status of Observatory.The IAS comprises 140 scientists, engineers, technicians, administrators and graduate students.

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