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  • richardmitnick 12:41 pm on January 20, 2018 Permalink | Reply
    Tags: , , , , , Electron Microscopy, Meteoritic stardust unlocks timing of supernova dust formation, Type II supernovae   

    From Carnegie Institution for Science: “Meteoritic stardust unlocks timing of supernova dust formation” 

    Carnegie Institution for Science
    Carnegie Institution for Science

    January 18, 2018
    Conel Alexander
    Larry Nittler

    Dust is everywhere—not just in your attic or under your bed, but also in outer space. To astronomers, dust can be a nuisance by blocking the light of distant stars, or it can be a tool to study the history of our universe, galaxy, and Solar System.

    For example, astronomers have been trying to explain why some recently discovered distant, but young, galaxies contain massive amounts of dust. These observations indicate that type II supernovae—explosions of stars more than ten times as massive as the Sun—produce copious amounts of dust, but how and when they do so is not well understood.

    An electron microscope image of a micron-sized supernova silicon carbide, SiC, stardust grain (lower right) extracted from a primitive meteorite. Such grains originated more than 4.6 billion years ago in the ashes of Type II supernovae, typified here by a Hubble Space Telescope image of the Crab Nebula, the remnant of a supernova explosion in 1054. Laboratory analysis of such tiny dust grains provides unique information on these massive stellar explosions. (1 μm is one millionth of a meter.) Image credits: NASA and Larry Nittler.

    New work from a team of Carnegie cosmochemists published by Science Advances reports analyses of carbon-rich dust grains extracted from meteorites that show that these grains formed in the outflows from one or more type II supernovae more than two years after the progenitor stars exploded. This dust was then blown into space to be eventually incorporated into new stellar systems, including in this case, our own.

    The researchers—led by former-postdoctoral fellow Nan Liu, along with Larry Nittler, Conel Alexander, and Jianhua Wang of Carnegie’s Department of Terrestrial Magnetism—came to their conclusion not by studying supernovae with telescopes. Rather, they analyzed microscopic silicon carbide, SiC, dust grains that formed in supernovae more than 4.6 billion years ago and were trapped in meteorites as our Solar System formed from the ashes of the galaxy’s previous generations of stars.

    Some meteorites have been known for decades to contain a record of the original building blocks of the Solar System, including stardust grains that formed in prior generations of stars.

    “Because these presolar grains are literally stardust that can be studied in detail in the laboratory,” explained Nittler, “they are excellent probes of a range of astrophysical processes.”

    For this study, the team set out to investigate the timing of supernova dust formation by measuring isotopes—versions of elements with the same number of protons but different numbers of neutrons—in rare presolar silicon carbide grains with compositions indicating that they formed in type II supernovae.

    Certain isotopes enable scientists to establish a time frame for cosmic events because they are radioactive. In these instances, the number of neutrons present in the isotope make it unstable. To gain stability, it releases energetic particles in a way that alters the number of protons and neutrons, transmuting it into a different element.

    The Carnegie team focused on a rare isotope of titanium, titanium-49, because this isotope is the product of radioactive decay of vanadium-49 which is produced during supernova explosions and transmutes into titanium-49 with a half-life of 330 days. How much titanium-49 gets incorporated into a supernova dust grain thus depends on when the grain forms after the explosion.

    Using a state-of-the-art mass spectrometer to measure the titanium isotopes in supernova SiC grains with much better precision than could be accomplished by previous studies, the team found that the grains must have formed at least two years after their massive parent stars exploded.

    Because presolar supernova graphite grains are isotopically similar in many ways to the SiC grains, the team also argues that the delayed formation timing applies generally to carbon-rich supernova dust, in line with some recent theoretical calculations.

    “This dust-formation process can occur continuously for years, with the dust slowly building up over time, which aligns with astronomer’s observations of varying amounts of dust surrounding the sites of stellar explosions,” added lead author Liu. “As we learn more about the sources for dust, we can gain additional knowledge about the history of the universe and how various stellar objects within it evolve.”

    See the full article here .

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    Carnegie Institution of Washington Bldg

    Andrew Carnegie established a unique organization dedicated to scientific discovery “to encourage, in the broadest and most liberal manner, investigation, research, and discovery and the application of knowledge to the improvement of mankind…” The philosophy was and is to devote the institution’s resources to “exceptional” individuals so that they can explore the most intriguing scientific questions in an atmosphere of complete freedom. Carnegie and his trustees realized that flexibility and freedom were essential to the institution’s success and that tradition is the foundation of the institution today as it supports research in the Earth, space, and life sciences.

    6.5 meter Magellan Telescopes located at Carnegie’s Las Campanas Observatory, Chile.
    6.5 meter Magellan Telescopes located at Carnegie’s Las Campanas Observatory, Chile

  • richardmitnick 10:53 am on January 4, 2018 Permalink | Reply
    Tags: , , Electron Microscopy, MicroED=micro-electron diffraction, ,   

    From UCLA Newsroom: “Imaging technique could be ‘new ballgame’ in drug development” 

    UCLA Newsroom

    January 02, 2018
    Tami Dennis

    UCLA researcher Tamir Gonen explores the potential of MicroED in neurological diseases.

    Courtesy of Tamir Gonen
    Tamir Gonen published his proof of principle paper [eLIFE] on MicroED in 2013.

    Biochemistry and structural biology are surprisingly — at least to the uninitiated — visual fields. This is especially true in the study of proteins. Scientists like to see the structure of proteins within cells to help them truly understand how they work, how they don’t work or how they can be modified to work as they should. That is, how they can be targeted with drugs to cure disease.

    Current methods, however, have their downsides. Many widely used techniques require large amounts of protein for analysis, even though many diseases are caused by proteins that are far from abundant or that are difficult to amass in large quantities. A new method pioneered by a professor who recently joined UCLA overcomes this challenge, offering untold potential in the exploration of disease and treatment.

    Called “MicroED,” for micro-electron diffraction, the technique uses high-powered electron microscopy to determine the structure of proteins with atomic precision, using samples that are only one-billionth the size required by other imaging methods.

    Tamir Gonen, a new professor of physiology and biological chemistry at the David Geffen School of Medicine at UCLA, is the developer of MicroED. For the past five years, Gonen has been spearheading the exploration of MicroED in his lab at the Janelia Research Campus of the Howard Hughes Medical Institute near Washington D.C.

    Now, in joining UCLA’s faculty, Gonen’s goal is to set up a lab centered on this new imaging tool. Already the university is using the technique in the labs of Jose Rodriguez, assistant professor of biochemistry, and David Eisenberg, a professor of chemistry and biochemistry and of biological chemistry. Both use MicroED to view the structures of proteins involved in neurodegeneration.

    “With MicroED, the way we think about disease is going to be different,” Gonen said. “Because it uses minute samples and the resolution we get is very high, problems that were beyond our reach are suddenly attainable. We can see individual atoms and even peer deeper into subatomic space and see things that have not been seen before.”

    Samples used in MicroED resemble jewels with one exception, they are made out of biological material rather than precious mineral. Gonen lab.

    Gonen began working on the technique at the Howard Hughes Medical Institute Janelia Research Campus, where he was a group leader. Upon moving to UCLA Gonen is now an investigator of the Howard Hughes Medical Institute and professor of physiology and biological chemistry. Prior to that, he was an assistant professor, then a tenured associate professor, at the University of Washington School of Medicine, as well as a Howard Hughes Medical Institute Early Career Scientist.

    Since 2013, which marked his publication of a proof of principle paper on MicroED [eLIFE], Gonen has been an advocate for the technique. As other researchers have come to understand the long-sought imaging potential MicroED offers, about 20 institutions worldwide have begun setting up MicroED labs, many with Gonen’s help.

    “I have fantastic folks working in my lab, and they are extremely collegial and want to help others get their science done,” Gonen said.

    That focus on getting “science done” — and MicroED itself — has enormous ramifications for the treatment of HIV, Parkinson’s, Alzheimer’s and other neurodegenerative diseases. “When you’re talking about drug discovery, it’s a whole new ballgame,” Gonen said.

    Gonen’s development of MicroED stemmed from his study of cell membranes, specifically the protein gateways within those membranes.

    These gateways can help cells maintain healthy homeostasis in which everything works as it should — think of it as a biological “peace.” When things go wrong, however, as happens with disease, these gateways might allow too much of one substance, such as water or sugar, in or out.

    This illustration of a protein shows an example of a structure that could only be determined by the capabilities of micro-electron diffraction. Gonen lab.

    Gonen knew that targeting these gateways — or targeting their function — could lead to innovative ways to control disease and help patients. But he and other scientists needed good images to facilitate the design of better drugs.

    “More than 90 percent of all medicines sold these days target G-protein coupled receptors,” Gonen said. “When you feel pain, when you see light, when you taste, when you have any neurological sensation, all of this is occurring because of these receptors.”

    Another potential, and timely, target of this type: opioid receptors. “Opioids are an increasingly challenging problem, and not surprisingly there exists an opioid receptor,” Gonen said.

    MicroED makes it possible to image these G-protein coupled receptors, which move around a lot. This movement has made it difficult for traditional methods to capture images of them.

    MicroED’s potential goes far beyond such receptors, however.

    Larry Zipursky, a distinguished professor biological chemistry and the leader of the neuroscience research theme at the David Geffen School of Medicine at UCLA, called the approach “revolutionary.”

    “This technique uses a rational approach to disease,” Zipursky said. “It allows researchers to assess the structure of abnormal proteins that give rise to disease; from this structural determination, they can assess the disease in a more strategic way.”

    Gonen is enthusiastic about the larger potential as well. “For a medical school, this is going to be quite a resource for pushing research forward. I’m hoping to collaborate with a lot of people.”

    In fact, he’s already working on several projects, including one that points to a way to make more efficient HIV medicines. This is in addition to the projects with Eisenberg and Rodriguez, who’s studying the conversion of proteins from a normal state into an abnormal, clumped — or aggregated — state, as seen in Alzheimer’s and other diseases of the brain and nervous system.

    “We need new and better treatments for neurodegenerative diseases, one way to achieve this is to understand how atomic scale changes in the brain lead to disease. What do the structures look like before and after, and, quite simply, how are they so toxic?” Rodriguez said. “MicroED may finally open the door to that understanding.”

    The potential of such collaborations is what brought Gonen — and his emphasis on MicroED — to UCLA.

    “What I like about UCLA is it’s a top-rate institution — you can find some expert in every field,” Gonen said. “They’re a world leader, but they come without the ego you may find at other institutions.”

    That collaboration, he’s convinced, will lead to new approaches, new discoveries and new cures.

    Further papers:
    >Structure of catalase determined by MicroED
    Taking the measure of MicroED
    Protein structure determination by MicroED

    See the full article here .

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    UC LA Campus

    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

  • richardmitnick 1:34 pm on December 21, 2017 Permalink | Reply
    Tags: , , Electron Microscopy, Magnetic fields of bacterial cells and magnetic nano-objects in liquid can be studied at high resolution using electron microscopy,   

    From Ames National Lab: “Ames Laboratory-led research team maps magnetic fields of bacterial cells and nano-objects for the first time” 

    Ames Laboratory

    Dec. 21, 2017
    Tanya Prozorov, Division of Materials Sciences and Engineering
    (515) 294-3376

    Laura Millsaps, Ames Laboratory Public Affairs
    (515) 294-3474

    A research team led by a scientist from the U.S. Department of Energy’s Ames Laboratory has demonstrated for the first time that the magnetic fields of bacterial cells and magnetic nano-objects in liquid can be studied at high resolution using electron microscopy. This proof-of-principle capability allows first-hand observation of liquid environment phenomena, and has the potential to vastly increase knowledge in a number of scientific fields, including many areas of physics, nanotechnology, biofuels conversion, biomedical engineering, catalysis, batteries and pharmacology.

    Left: Schematic of the off-axis electron holography using a fluid cell. Right: (A)
    Hologram of a magnetite nanocrystal chain released from a magnetotactic
    bacterium, and (B) corresponding magnetic induction map.

    “It is much like being able to travel to a Jurassic Park and witness dinosaurs walking around, instead of trying to guess how they walked by examining a fossilized skeleton,” said Tanya Prozorov, an associate scientist in Ames Laboratory’s Division of Materials Sciences and Engineering.

    Prozorov works with biological and bioinspired magnetic nanomaterials, and faced what initially seemed to be an insurmountable challenge of observing them in their native liquid environment. She studies a model system, magnetotactic bacteria, which form perfect nanocrystals of magnetite. In order to best learn how bacteria do this, she needed an alternative to the typical electron microscopy process of handling solid samples in vacuum, where soft matter is studied in prepared, dried, or vitrified form.

    For this work, Prozorov received DOE recognition through an Office of Science Early Career Research Program grant to use cutting-edge electron microscopy techniques with a liquid cell insert to learn how the individual magnetic nanocrystals form and grow with the help of biological molecules, which is critical for making artificial magnetic nanomaterials with useful properties.

    To study magnetism in bacteria, she applied off-axis electron holography, a specialized technique that is used for the characterization of magnetic nanostructures in the transmission electron microscope, in combination with the liquid cell.

    “When we look at samples prepared in the conventional way, we have to make many assumptions about their properties based on their final state, but with the new technique, we can now observe these processes first-hand,” said Prozorov. “It can help us understand the dynamics of macromolecule aggregation, nanoparticle self-assembly, and the effects of electric and magnetic fields on that process.”

    “This method allows us to obtain large amounts of new information,” said Prozorov. “It is a first step, proving that the mapping of magnetic fields in liquid at the nanometer scale with electron microscopy could be done; I am eager to see the discoveries it could foster in other areas of science.”

    The work was done in collaboration with the Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Germany.

    The research is detailed in the paper, Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid, by T. Prozorov, T.P. Almeida, A. Kovács, and R.E. Dunin-Borkowski: and published in the Journal of the Royal Society Interface.

    See the full article here .

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    Ames Laboratory is a government-owned, contractor-operated research facility of the U.S. Department of Energy that is run by Iowa State University.

    For more than 60 years, the Ames Laboratory has sought solutions to energy-related problems through the exploration of chemical, engineering, materials, mathematical and physical sciences. Established in the 1940s with the successful development of the most efficient process to produce high-quality uranium metal for atomic energy, the Lab now pursues a broad range of scientific priorities.

    Ames Laboratory is a U.S. Department of Energy Office of Science national laboratory operated by Iowa State University. Ames Laboratory creates innovative materials, technologies and energy solutions. We use our expertise, unique capabilities and interdisciplinary collaborations to solve global problems.

    Ames Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
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  • richardmitnick 6:02 pm on November 21, 2017 Permalink | Reply
    Tags: , , , , Electron Microscopy, , , , Plasma-facing material   

    From BNL: “Designing New Metal Alloys Using Engineered Nanostructures” 

    Brookhaven Lab

    Stony Brook University assistant professor Jason Trelewicz brings his research to design and stabilize nanostructures in metals to Brookhaven Lab’s Center for Functional Nanomaterials.

    Materials scientist Jason Trelewicz in an electron microscopy laboratory at Brookhaven’s Center for Functional Nanomaterials, where he characterizes nanoscale structures in metals mixed with other elements.

    Materials science is a field that Jason Trelewicz has been interested in since he was a young child, when his father—an engineer—would bring him to work. In the materials lab at his father’s workplace, Trelewicz would use optical microscopes to zoom in on material surfaces, intrigued by all the distinct features he would see as light interacted with different samples.

    Now, Trelewicz—an assistant professor in the College of Engineering and Applied Sciences’ Department of Materials Science and Chemical Engineering with a joint appointment in the Institute for Advanced Computational Science at Stony Brook University and principal investigator of the Engineered Metallic Nanostructures Laboratory—takes advantage of the much higher magnifications of electron microscopes to see tiny nanostructures in fine detail and learn what happens when they are exposed to heat, radiation, and mechanical forces. In particular, Trelewicz is interested in nanostructured metal alloys (metals mixed with other elements) that incorporate nanometer-sized features into classical materials to enhance their performance. The information collected from electron microscopy studies helps him understand interactions between structural and chemical features at the nanoscale. This understanding can then be employed to tune the properties of materials for use in everything from aerospace and automotive components to consumer electronics and nuclear reactors.

    Since 2012, when he arrived at Stony Brook University, Trelewicz has been using the electron microscopes and the high-performance computing (HPC) cluster at the Center for Functional Nanomaterials (CFN)—a U.S. Department of Energy (DOE) Office of Science User Facility at Brookhaven National Laboratory—to perform his research.

    “At the time, I was looking for ways to apply my idea of stabilizing nanostructures in metals to an application-oriented problem,” said Trelewicz. “I’ve long been interested in nuclear energy technologies, initially reading about fusion in grade school. The idea of recreating the processes responsible for the energy we receive from the sun here on earth was captivating, and fueled my interest in nuclear energy throughout my entire academic career. Though we are still very far away from a fusion reactor that generates power, a large international team on a project under construction in France called ITER is working to demonstrate a prolonged fusion reaction at a large scale.”

    Plasma-facing materials for fusion reactors

    Nuclear fusion—the reaction in which atomic nuclei collide—could provide a nearly unlimited supply of safe, clean energy, like that naturally produced by the sun through fusing hydrogen nuclei into helium atoms. Harnessing this carbon-free energy in reactors requires generating and sustaining a plasma, an ionized gas, at the very high temperatures at which fusion occurs (about six times hotter than the sun’s core) while confining it using magnetic fields. Of the many challenges currently facing fusion reactor demonstrations, one of particular interest to Trelewicz is creating viable materials to build a reactor.

    A model of the ITER tokamak, an experimental machine designed to harness the energy of fusion. A powerful magnetic field is used to confine the plasma, which is held in a doughnut-shaped vessel. Credit: ITER Organization.

    “The formidable materials challenges for fusion are where I saw an opportunity for my research—developing materials that can survive inside the fusion reactor, where the plasma will generate high heat fluxes, high thermal stresses, and high particle and neutron fluxes,” said Trelewicz. “The operational conditions in this environment are among the harshest in which one could expect a material to function.”

    A primary candidate for such “plasma-facing material” is tungsten, because of its high melting point—the highest one among metals in pure form—and low sputtering yield (number of atoms ejected by energetic ions from the plasma). However, tungsten’s stability against recrystallization, oxidation resistance, long-term radiation tolerance, and mechanical performance are problematic.

    Trelewicz thinks that designing tungsten alloys with precisely tailored nanostructures could be a way to overcome these problems. In August, he received a $750,000 five-year award from the DOE’s Early Career Research Program to develop stable nanocrystalline tungsten alloys that can withstand the demanding environment of a fusion reactor. His research is combining simulations that model atomic interactions and experiments involving real-time ion irradiation exposure and mechanical testing to understand the fundamental mechanisms responsible for the alloys’ thermal stability, radiation tolerance and mechanical performance. The insights from this research will inform the design of more resilient alloys for fusion applications.

    In addition to the computational resources they use at their home institution, Trelewicz and his lab group are using the HPC cluster at the CFN—and those at other DOE facilities, such as Titan at Oak Ridge Leadership Computing Facility (a DOE Office of Science User Facility at Oak Ridge National Laboratory)—to conduct large-scale atomistic simulations as part of the project.

    ORNL Cray Titan XK7 Supercomputer

    “The length scales of the structures we want to design into our materials are on the order of a few nanometers to 100 nanometers, and a single simulation can involve up to 10 million atoms,” said Trelewicz. “Using HPC clusters, we can build a system atom-by-atom, representative of the structure we would like to explore experimentally, and run simulations to study the response of that system under various external stimuli. For example, we can fire a high-energy atom into the system and watch what happens to the material and how it evolves, hundreds or thousands of times. Once damage has accumulated in the structure, we can simulate thermal and mechanical forces to understand how defect structure impacts other behavior.”

    These simulations inform the structures and chemistries of experimental alloys, which Trelewicz and his students fabricate at Stony Brook University through high-energy milling. To characterize the nanoscale structure and chemical distribution of the engineered alloys, they extensively use the microscopy facilities at the CFN—including scanning electron microscopes, transmission electron microscopes, and scanning transmission electron microscopes. Imaging is conducted at high resolution and often combined with heating within the microscope to examine in real time how the structures evolve with temperature. Experiments are also conducted at other DOE national labs, such as Sandia through collaboration with materials scientist Khalid Hattar of the Ion Beam Laboratory. Here, students in Trelewicz’s research group simultaneously irradiate the engineered alloys with an ion beam and image them with an electron microscope over the course of many days.

    Trelewicz and his students irradiated a nanostructured tungsten-titanium alloy with high-energy gold ions to explore the radiation tolerance of this novel material.

    “Though this damage does not compare to what the material would experience in a reactor, it provides a starting point to evaluate whether or not the engineered material could indeed address some of the limitations of tungsten for fusion applications,” said Trelewicz.

    Electron microscopy at the CFN has played a key role in an exciting discovery that Trelewicz’s students recently made: an unexpected metastable-to-stable phase transition in thin films of nanostructured tungsten. This phase transition drives an abnormal “grain” growth process in which some crystalline nanostructure features grow very dramatically at the expense of others. When the students added chromium and titanium to tungsten, this metastable phase was completely eliminated, in turn enhancing the thermal stability of the material.

    “One of the great aspects of having both experimental and computational components to our research is that when we learn new things from our experiments, we can go back and tailor the simulations to more accurately reflect the actual materials,” said Trelewicz.

    Other projects in Trelewicz’s research group.

    The research with tungsten is only one of many projects ongoing in the Engineered Metallic Nanostructures Laboratory.

    “All of our projects fall under the umbrella of developing new metal alloys with enhanced and/or multifunctional properties,” said Trelewicz. “We are looking at different strategies to optimize material performance by collectively tailoring chemistry and microstructure in our materials. Much of the science lies in understanding the nanoscale mechanisms that govern the properties we measure at the macroscale.”

    Jason Trelewicz (left) with Olivia Donaldson, who recently graduated with her PhD from Trelewicz’s group, and Jonathan Gentile, a current doctoral student, in front of the scanning electron microscope/focused-ion beam at Stony Brook University’s Advanced Energy Center. Credit: Stony Brook University.

    Through a National Science Foundation CAREER (Faculty Early Career Development Program) award, Trelewicz and his research group are exploring another class of high-strength alloys—amorphous metals, or “metallic glasses,” which are metals that have a disordered atomic structure akin to glass. Compared to everyday metals, metallic glasses are often inherently higher strength but usually very brittle, and it is difficult to make them in large parts such as bulk sheets. Trelewicz’s team is designing interfaces and engineering them into the metallic glasses—initially iron-based and later zirconium-based ones—to enhance the toughness of the materials, and exploring additive manufacturing processes to enable sheet-metal production. They will use the Nanofabrication Facility at the CFN to fabricate thin films of these interface-engineered metallic glasses for in situ analysis using electron microscopy techniques.

    In a similar project, they are seeking to understand how introducing a crystalline phase into a zirconium-based amorphous alloy to form a metallic glass matrix composite (composed of both amorphous and crystalline phases) augments the deformation process relative to that of regular metallic glasses. Metallic glasses usually fail catastrophically because strain becomes localized into shear bands. Introducing crystalline regions in the metallic glasses could inhibit the process by which strain localizes in the material. They have already demonstrated that the presence of the crystalline phase fundamentally alters the mechanism through which the shear bands form.

    Trelewicz and his group are also exploring the deformation behavior of metallic “nanolaminates” that consist of alternating crystalline and amorphous layers, and are trying to approach the theoretical limit of strength in lightweight aluminum alloys through synergistic chemical doping strategies (adding other elements to a material to change its properties).

    Trelewicz and his students perform large-scale atomistic simulations to explore the segregation of solute species to grain boundaries (GBs)—interfaces between grains—in nanostructured alloys, as shown here for an aluminum-magnesium (Al-Mg) system, and its implications for the governing deformation mechanisms. They are using the insights gained through these simulations to design lightweight alloys with theoretical strengths.

    “We leverage resources of the CFN for every project ongoing in my research group,” said Trelewicz. “We extensively use the electron microscopy facilities to look at material micro- and nanostructure, very often at how interfaces are coupled with compositional inhomogeneities—information that helps us stabilize and design interfacial networks in nanostructured metal alloys. Computational modeling and simulation enabled by the HPC clusters at the CFN informs what we do in our experiments.”

    Beyond his work at CFN, Trelewicz collaborates with his departmental colleagues to characterize materials at the National Synchrotron Light Source II—another DOE Office of Science User Facility at Brookhaven.



    “There are various ways to characterize structural and chemical inhomogeneities,” said Trelewicz. “We look at small amounts of material through the electron microscopes at CFN and on more of a bulk level at NSLS-II through techniques such as x-ray diffraction and the micro/nano probe. We combine this local and global information to thoroughly characterize a material and use this information to optimize its properties.”

    Future of next-generation materials

    When he is not doing research, Trelewicz is typically busy with student outreach. He connects with the technology departments at various schools, providing them with materials engineering design projects. The students not only participate in the engineering aspects of materials design but are also trained on how to use 3D printers and other tools that are critical in today’s society to manufacture products more cost effectively and with better performance.

    Going forward, Trelewicz would like to expand his collaborations at the CFN and help establish his research in metallic nanostructures as a core area supported by CFN and, ultimately, DOE, to achieve unprecedented properties in classical materials.

    “Being able to learn something new every day, using that knowledge to have an impact on society, and seeing my students fill gaps in our current understanding are what make my career as a professor so rewarding,” said Trelewicz. “With the resources of Stony Brook University, nearby CFN, and other DOE labs, I have an amazing platform to make contributions to the field of materials science and metallurgy.”

    Trelewicz holds a bachelor’s degree in engineering science from Stony Brook University and a doctorate in materials science and engineering with a concentration in technology innovation from MIT. Before returning to academia in 2012, Trelewicz spent four years in industry managing technology development and transition of harsh-environment sensors produced by additive manufacturing processes. He is the recipient of a 2017 Department of Energy Early Career Research Award, 2016 National Science Foundation CAREER award, and 2015 Young Leaders Professional Development Award from The Minerals, Metals & Materials Society (TMS), and is an active member of several professional organizations, including TMS, the Materials Research Society, and ASM International (the Materials Information Society).

    See the full article here .

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

  • richardmitnick 11:53 am on July 29, 2017 Permalink | Reply
    Tags: 3D structure of human chromatin, , ChromEMT, , Electron Microscopy, , , ,   

    From Salk: “Salk scientists solve longstanding biological mystery of DNA organization” 

    Salk Institute bloc

    Salk Institute for Biological Studies

    July 27, 2017

    Stretched out, the DNA from all the cells in our body would reach Pluto. So how does each tiny cell pack a two-meter length of DNA into its nucleus, which is just one-thousandth of a millimeter across?

    The answer to this daunting biological riddle is central to understanding how the three-dimensional organization of DNA in the nucleus influences our biology, from how our genome orchestrates our cellular activity to how genes are passed from parents to children.

    Now, scientists at the Salk Institute and the University of California, San Diego, have for the first time provided an unprecedented view of the 3D structure of human chromatin—the combination of DNA and proteins—in the nucleus of living human cells.

    In the tour de force study, described in Science on July 27, 2017, the Salk researchers identified a novel DNA dye that, when paired with advanced microscopy in a combined technology called ChromEMT, allows highly detailed visualization of chromatin structure in cells in the resting and mitotic (dividing) stages. By revealing nuclear chromatin structure in living cells, the work may help rewrite the textbook model of DNA organization and even change how we approach treatments for disease.

    “One of the most intractable challenges in biology is to discover the higher-order structure of DNA in the nucleus and how is this linked to its functions in the genome,” says Salk Associate Professor Clodagh O’Shea, a Howard Hughes Medical Institute Faculty Scholar and senior author of the paper. “It is of eminent importance, for this is the biologically relevant structure of DNA that determines both gene function and activity.”

    A new technique enables 3D visualization of chromatin (DNA plus associated proteins) structure and organization within a cell nucleus (purple, bottom left) by painting the chromatin with a metal cast and imaging it with electron microscopy (EM). The middle block shows the captured EM image data, the front block illustrates the chromatin organization from the EM data, and the rear block shows the contour lines of chromatin density from sparse (cyan and green) to dense (orange and red). Credit: Salk Institute.

    Ever since Francis Crick and James Watson determined the primary structure of DNA to be a double helix, scientists have wondered how DNA is further organized to allow its entire length to pack into the nucleus such that the cell’s copying machinery can access it at different points in the cell’s cycle of activity. X-rays and microscopy showed that the primary level of chromatin organization involves 147 bases of DNA spooling around proteins to form particles approximately 11 nanometers (nm) in diameter called nucleosomes. These nucleosome “beads on a string” are then thought to fold into discrete fibers of increasing diameter (30, 120, 320 nm etc.), until they form chromosomes. The problem is, no one has seen chromatin in these discrete intermediate sizes in cells that have not been broken apart and had their DNA harshly processed, so the textbook model of chromatin’s hierarchical higher-order organization in intact cells has remained unverified.

    To overcome the problem of visualizing chromatin in an intact nucleus, O’Shea’s team screened a number of candidate dyes, eventually finding one that could be precisely manipulated with light to undergo a complex series of chemical reactions that would essentially “paint” the surface of DNA with a metal so that its local structure and 3D polymer organization could be imaged in a living cell. The team partnered with UC San Diego professor and microscopy expert Mark Ellisman, one of the paper’s coauthors, to exploit an advanced form of electron microscopy that tilts samples in an electron beam enabling their 3D structure to be reconstructed. By combining their chromatin dye with electron-microscope tomography, they created ChromEMT.

    The team used ChromEMT to image and measure chromatin in resting human cells and during cell division when DNA is compacted into its most dense form—the 23 pairs of mitotic chromosomes that are the iconic image of the human genome. Surprisingly, they did not see any of the higher-order structures of the textbook model anywhere.

    From left: Horng Ou and Clodagh O’Shea. Credit: Salk Institute.

    “The textbook model is a cartoon illustration for a reason,” says Horng Ou, a Salk research associate and the paper’s first author. “Chromatin that has been extracted from the nucleus and subjected to processing in vitro—in test tubes—may not look like chromatin in an intact cell, so it is tremendously important to be able to see it in vivo.”

    What O’Shea’s team saw, in both resting and dividing cells, was chromatin whose “beads on a string” did not form any higher-order structure like the theorized 30 or 120 or 320 nanometers. Instead, it formed a semi-flexible chain, which they painstakingly measured as varying continuously along its length between just 5 and 24 nanometers, bending and flexing to achieve different levels of compaction. This suggests that it is chromatin’s packing density, and not some higher-order structure, that determines which areas of the genome are active and which are suppressed.

    With their 3D microscopy reconstructions, the team was able to move through a 250 nm x 1000 nm x 1000 nm volume of chromatin’s twists and turns, and envision how a large molecule like RNA polymerase, which transcribes (copies) DNA, might be directed by chromatin’s variable packing density, like a video game aircraft flying through a series of canyons, to a particular spot in the genome. Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.

    “We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”

    Future work will examine whether chromatin’s structure is universal among cell types or even among organisms.

    Other authors included Sébastien Phan, Thomas Deerinck and Andrea Thor of the UC San Diego.

    The work was largely funded by the W. M. Keck Foundation, the NIH 4D Nucleome Roadmap Initiative and the Howard Hughes Medical Institute, with additional support from the William Scandling Trust, the Price Family Foundation and the Leona M. and Harry B. Helmsley Charitable Trust.

    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.

  • richardmitnick 9:28 am on July 24, 2017 Permalink | Reply
    Tags: , , Electron Microscopy, , Native mass spectrometry, Signaling islands in cells: targets for precision drug design,   

    From U Washington: “Signaling islands in cells: targets for precision drug design” 

    U Washington

    University of Washington

    Leila Gray

    A critical component of the cell signaling system, anchored protein kinase A, has some flexible molecular parts, allowing it to both contract and stretch, with floppy arms that can reach out to find appropriate targets. John Scott Lab.

    Research results reported in the journal Science overturn long-held views on a basic messaging system within living cells.

    The findings suggest new approaches to designing precisely targeted drugs for cancer and other serious diseases.

    Dr. John D. Scott, professor and chair of pharmacology at the University of Washington School of Medicine and a Howard Hughes Medical Institute Investigator, along with Dr. F. Donelson Smith of the UW and HHMI, led this study, which also involved Drs. Claire and Patrick Eyers and their group at the University of Liverpool. Visit the Scott lab web site, Cell Signaling in Space and Time.

    The researchers explained that key cellular communication machinery is more regionally constrained inside the cell than was previously thought. Communication via this vital system is akin to social networking on your Snapchat account.

    Within a cell, the precise positioning of such messaging components allows hormones, the body’s chief chemical communicators, to transmit information to exact places inside the cell. Accurate and very local activation of the enzyme that Scott and his group study helps assure a correct response occurs in the right place and at the right time.

    “The inside of a cell is like a crowded city,” said Scott, “It is a place of construction and tearing down, goods being transported and trash being recycled, countless messages, (such as the ones we have discovered), assembly lines flowing, and packages moving. Strategically switching on signaling enzyme islands allows these biochemical activities to keep the cell alive and is important to protect against the onset of chronic diseases such as diabetes, heart disease and certain cancers.”

    Advances in electron microscopy and native mass spectrometry enabled the researchers to determine that a critical component of the signaling system, anchored protein kinase A, remains intact during activation. Parts of the molecule are flexible, allowing it to both contract and stretch, with floppy arms that can reach out to find appropriate targets.

    Still, where the molecule performs its act, space is tight. The distance is, in fact, about the width of two proteins inside the cell.

    Green, circled area show where the enzyme in the signalling study is active in mitochondria, the powerhouses of living cells. John D. Scott.

    “We realize that in designing drugs to reach such targets that they will have to work within very narrow confines, ” Scott said.

    One of his group’s collective goals is figuring out how to deliver precision drugs to the right address within this teeming cytoplasmic metropolis.

    “Insulating the signal so that the drug effect can’t happen elsewhere in the cell is an equally important aspect of drug development because it could greatly reduce side effects,” Scott said.

    An effort to take this idea of precision medicine a step further is part of the Institute for Targeted Therapeutics at UW Medicine in Seattle. The institute is being set up by Scott and his colleagues in the UW Department of Pharmacology.

    The scientists are collaborating with cancer researchers to better understand the molecular causes — and possible future treatments — for a certain liver malignancy. This particular liver cancer arises from a mutation that produces an abnormal form of the enzyme that is the topic of this current work, protein kinase A, and alters the enzyme’s role in cell signaling.

    Other advances that gave the researchers a clearer view of the signaling mechanisms reported in Science include CRISPR gene editing, live-cell imaging techniques, and more powerful ways to look at all components of a protein complex.

    See the full article here .

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

  • richardmitnick 2:52 pm on April 3, 2017 Permalink | Reply
    Tags: , , Electron Microscopy   

    From Cornell: “New electron microscope sees more than an image” 

    Cornell Bloc

    Cornell University

    March 30, 2017
    Bill Steele

    Sol Gruner, left, professor of physics, and David Muller, professor of applied and engineering physics. Chris Kitchen/University Photography

    . Their electron microscope pixel array detector (EMPAD) yields not just an image, but a wealth of information about the electrons that create the image and, from that, more about the structure of the sample.

    “We can extract local strains, tilts, rotations, polarity and even electric and magnetic fields,” explained David Muller, professor of applied and engineering physics, who developed the new device with Sol Gruner, professor of physics, and members of their research groups.

    Cornell’s Center for Technology Licensing (CTL) has licensed the invention to FEI, a leading manufacturer of electron microscopes (a division of Thermo Fisher Scientific, which supplies products and services for the life sciences through several brands). FEI expects to complete the commercialization of the design and offer the detector for new and retrofitted electron microscopes this year.

    “It’s mind-boggling to contemplate what researchers around the world will discover through this match of Cornell’s deep expertise in detector science with market leader Thermo Fisher Scientific,” said Patrick Govang, technology licensing officer at CTL.

    The scientists described their work in the February 2016 issue of the journal Microscopy and Microanalysis.

    In the usual scanning transmission electron microscope (STEM), a narrow beam of electrons is fired down through a sample, scanning back and forth to produce an image. A detector underneath reads the varying intensity of electrons coming through and sends a signal that draws an image on a computer screen.

    The EMPAD that replaces the usual detector is made up of a 128×128 array of electron-sensitive pixels, each 150 microns (millionths of a meter) square, bonded to an integrated circuit that reads out the signals – somewhat like the array of light-sensitive pixels in the sensor in a digital camera, but not to form an image. Its purpose is to detect the angles at which electrons emerge, as each electron hits a different pixel. The EMPAD is a spinoff of X-ray detectors the physicists have built for X-ray crystallography work at the Cornell High Energy Synchrotron Source (CHESS), and it can work in a similar way to reveal the atomic structure of a sample.

    Combined with the focused beam of the electron microscope, the detector allows researchers to build up a “four-dimensional” map of both position and momentum of the electrons as they pass through a sample to reveal the atomic structure and forces inside. The EMPAD is unusual in its speed, sensitivity and wide range of intensities it can record – from detecting a single electron to intense beams containing hundreds of thousands or even a million electrons.

    “It would be like taking a photograph of a sunset that showed both details on the surface of the sun and the details of darkest shadows,” Muller explained.

    See the full article here .

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    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

  • richardmitnick 9:22 am on July 18, 2016 Permalink | Reply
    Tags: A glimpse inside the atom, Electron Microscopy, Electron orbitals, TU Wein   

    From TU Wein: “A glimpse inside the atom” 

    Techniche Universitat Wein (Vienna)

    Techniche Universität Wein (Vienna)

    Florian Aigner

    Further information:
    Dr. Stefan Löffler
    Service-Einrichtung für Transmissions-Elektronenmikroskopie (USTEM)
    TU Wien (Vienna)
    Wiedner Hauptstraße 8, 1040 Vienna

    Prof. Peter Schattschneider
    Institute of Solid State Physics
    TU Wien (Vienna)
    Wiedner Hauptstraße 8, 1040 Vienna

    Using electron microscopes, it is possible to image individual atoms. Scientists at TU Wien have calculated how it is possible to look inside the atom to image individual electron orbitals.

    Atomic orbitals of carbon atoms in graphene

    Peter Schattschneider, Johannes Bernardi, Stefan Löffler

    An electron microscope can’t just snap a photo like a mobile phone camera can. The ability of an electron microscope to image a structure – and how successful this imaging will be – depends on how well you understand the structure. Complex physics calculations are often needed to make full use of the potential of electron microscopy. An international research team led by TU Wien’s Prof. Peter Schattschneider set out to analyse the opportunities offered by EFTEM, that is energy-filtered transmission electron microscopy. The team demonstrated numerically that under certain conditions, it is possible to obtain clear images of the orbital of each individual electron within an atom. Electron microscopy can therefore be used to penetrate down to the subatomic level – experiments in this area are already planned. The study has now been published in the physics journal Physical Review Letters.

    In search of the electron orbital

    We often think of atomic electrons as little spheres that circle around the nucleus of the atom like tiny planets around a sun. This image is barely reflected in reality, however. The laws of quantum physics state that the position of an electron cannot be clearly defined at any given point in time. The electron is effectively smeared across an area close to the nucleus. The area that could contain the electron is called the orbital. Although it has been possible to calculate the shape of these orbitals for a long time, efforts to image them with electron microscopes have been unsuccessful to date.

    “We have calculated how we might have a chance of visualising orbitals with an electron microscope”, says Stefan Löffler from the University Service Centre for Transmission Electron Microscopy (USTEM) at TU Wien. “Graphene, which is made of just one single layer of carbon atoms, is an excellent candidate for this task. The electron ray is able to pass easily through the graphene with hardly any elastic scattering. An image of the graphene structure can be created with these electrons.”

    Researchers have been aware of the principle of “energy-filtered transmission electron microscopy” (EFTEM) for some time. EFTEM can be used to create quite specific visualisations of certain kinds of atoms whilst blocking out the others. For this reason, it is often used today to analyse the chemical composition of microscopic samples. “The electrons shot through the sample can excite the sample’s atoms”, explains Stefan Löffler. “This costs energy, so when the electrons emerging emerge from the sample, they are slower than when they entered it. This velocity and energy change is characteristic for certain excitations of electron orbitals within the sample.”

    After the electrons have passed through the sample, a magnetic field sorts the electrons by energy. “A filter is used to block out electrons that aren’t of interest: the recorded image contains only those electrons that carry the desired information.”

    Defects can be helpful

    The team used simulations to investigate how this technique could help reach a turning point in the study of electron orbitals. While doing so, they discovered something that actually facilitated the imaging of individual orbitals: “The symmetry of the graphene has to be broken”, says Stefan. “If, for instance, there is a hole in the graphene structure, the atoms right beside this hole have a slightly different electronic structure, making it possible to image the orbitals of these atoms. The same thing can happen if a nitrogen atom rather than a carbon atom is found somewhere in the graphene. When doing this, it’s important to focus on the electrons found within a narrow and precise energy window, minimise certain aberrations of the electromagnetic lens and, last but not least, use a first-rate electron microscope.” All of these issues can be overcome, however, as the research group’s calculations show.

    The Humboldt-Universität zu Berlin, the Universität Ulm, and McMaster University in Canada also worked alongside the TU Wien on the study in a joint FWF-DFG project (“Towards orbital mapping”, I543-N20) and a FWF Erwin-Schrödinger project (“EELS at interfaces”, J3732-N27). Ulm is currently developing a new, high-performance transmission electron microscope that will be used to put these ideas into practice in the near future. Initial results have already exceeded expectations.

    Science paper:
    Mapping Atomic Orbitals with the Transmission Electron Microscope: Images of Defective Graphene Predicted from First-Principles Theory

    See the full article here .

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    Techniche Universitat Wein (Vienna) campus

    Our mission is “technology for people”. Through our research we “develop scientific excellence”,
    through our teaching we “enhance comprehensive competence”.

    TU Wien (TUW) is located in the heart of Europe, in a cosmopolitan city of great cultural diversity. For nearly 200 years, TU Wien has been a place of research, teaching and learning in the service of progress. TU Wien is among the most successful technical universities in Europe and is Austria’s largest scientific-technical research and educational institution.

  • richardmitnick 4:24 pm on February 29, 2016 Permalink | Reply
    Tags: , Electron Microscopy,   

    From LBL: “New Form of Electron-beam Imaging Can See Elements that are ‘Invisible’ to Common Methods” 

    Berkeley Logo

    Berkeley Lab

    February 29, 2016
    Glenn Roberts Jr. 510-486-5582

    Electrons can extend our view of microscopic objects well beyond what’s possible with visible light—all the way to the atomic scale. A popular method in electron microscopy for looking at tough, resilient materials in atomic detail is called STEM, or scanning transmission electron microscopy, but the highly focused beam of electrons used in STEM can also easily destroy delicate samples.

    This is why using electrons to image biological or other organic compounds, such as chemical mixes that include lithium—a light metal that is a popular element in next-generation battery research—requires a very low electron dose.

    Scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a new imaging technique, tested on samples of nanoscale gold and carbon, that greatly improves images of light elements using fewer electrons.

    The newly demonstrated technique, dubbed MIDI-STEM, for matched illumination and detector interferometry STEM, combines STEM with an optical device called a phase plate that modifies the alternating peak-to-trough, wave-like properties (called the phase) of the electron beam.

    In MIDI-STEM (right), developed at Berkeley Lab, an electron beam travels through a ringed “phase plate,” producing a high-resolution image (bottom right) that provides details about a sample containing a heavy element (gold) and light element (carbon). Details about the carbon are missing in an image (bottom left) of the sample using a conventional electron imaging technique (ADF-STEM). (Colin Ophus/Berkeley Lab, Nature Communications: 10.1038/ncomms10719)

    This phase plate modifies the electron beam in a way that allows subtle changes in a material to be measured, even revealing materials that would be invisible in traditional STEM imaging.

    Another electron-based method, which researchers use to determine the detailed structure of delicate, frozen biological samples, is called cryo-electron microscopy, or cryo-EM. While single-particle cryo-EM is a powerful tool—it was named as science journal Nature’s 2015 Method of the Year—it typically requires taking an average over many identical samples to be effective. Cryo-EM is generally not useful for studying samples with a mixture of heavy elements (for example, most types of metals) and light elements like oxygen and carbon.

    “The MIDI-STEM method provides hope for seeing structures with a mixture of heavy and light elements, even when they are bunched closely together,” said Colin Ophus, a project scientist at Berkeley Lab’s Molecular Foundry and lead author of a study, published Feb. 29 in Nature Communications, that details this method.

    If you take a heavy-element nanoparticle and add molecules to give it a specific function, conventional techniques don’t provide an easy, clear way to see the areas where the nanoparticle and added molecules meet.

    “How are they aligned? How are they oriented?” Ophus asked. “There are so many questions about these systems, and because there wasn’t a way to see them, we couldn’t directly answer them.”

    While traditional STEM is effective for “hard” samples that can stand up to intense electron beams, and cryo-EM can image biological samples, “We can do both at once” with the MIDI-STEM technique, said Peter Ercius, a Berkeley Lab staff scientist at the Molecular Foundry and co-author of the study.

    The phase plate in the MIDI-STEM technique allows a direct measure of the phase of electrons that are weakly scattered as they interact with light elements in the sample. These measurements are then used to construct so-called phase-contrast images of the elements. Without this phase information, the high-resolution images of these elements would not be possible.

    This animated representation shows a Berkeley Lab-developed technique called MIDI-STEM (at right) and conventional STEM (at left) that does not use a ringed object called a phase plate. In MIDI-STEM, an interference pattern (bottom right) introduced by the phase plate (top right) interacts with the electron beam before it travels through a sample (the blue wave in the center). As the phase of the sample (the distance between the peaks and valleys of the blue wave) changes, the electrons passing through the sample are affected and can be measured as a pattern (bottom right). (Colin Ophus/Berkeley Lab)

    In this study, the researchers combined phase plate technology with one of the world’s highest resolution STEMs, at Berkeley Lab’s Molecular Foundry, and a high-speed electron detector.

    They produced images of samples of crystalline gold nanoparticles, which measured several nanometers across, and the superthin film of amorphous carbon that the particles sat on. They also performed computer simulations that validated what they saw in the experiment.

    The phase plate technology was developed as part of a Berkeley Lab Laboratory Directed Research and Development grant in collaboration with Ben McMorran at University of Oregon.

    The MIDI-STEM technique could prove particularly useful for directly viewing nanoscale objects with a mixture of heavy and light materials, such as some battery and energy-harvesting materials, that are otherwise difficult to view together at atomic resolution.

    It also might be useful in revealing new details about important two-dimensional proteins, called S-layer proteins, that could serve as foundations for engineered nanostructures but are challenging to study in atomic detail using other techniques.

    In the future, a faster, more sensitive electron detector could allow researchers to study even more delicate samples at improved resolution by exposing them to fewer electrons per image.

    “If you can lower the electron dose you can tilt beam-sensitive samples into many orientations and reconstruct the sample in 3-D, like a medical CT scan. There are also data issues that need to be addressed,” Ercius said, as faster detectors will generate huge amounts of data. Another goal is to make the technique more “plug-and-play,” so it is broadly accessible to other scientists.

    Berkeley Lab’s Molecular Foundry is a DOE Office of Science User Facility. Researchers from the University of Oregon, Gatan Inc. and Ulm University in Germany also participated in the study.

    See the full article here .

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  • richardmitnick 2:23 pm on May 14, 2015 Permalink | Reply
    Tags: , Electron Microscopy,   

    From LBL: “CLAIRE Brings Electron Microscopy to Soft Materials” 

    Berkeley Logo

    Berkeley Lab

    May 14, 2015
    Lynn Yarris (510) 486-5375

    Berkeley Researchers Develop Breakthrough Technique for Non-invasive Nano-scale Imaging

    CLAIRE image of Al nanostructures with an inset that shows a cluster of six Al nanostructures.

    Soft matter encompasses a broad swath of materials, including liquids, polymers, gels, foam and – most importantly – biomolecules. At the heart of soft materials, governing their overall properties and capabilities, are the interactions of nano-sized components. Observing the dynamics behind these interactions is critical to understanding key biological processes, such as protein crystallization and metabolism, and could help accelerate the development of important new technologies, such as artificial photosynthesis or high-efficiency photovoltaic cells. Observing these dynamics at sufficient resolution has been a major challenge, but this challenge is now being met with a new non-invasive nanoscale imaging technique that goes by the acronym of CLAIRE.

    CLAIRE stands for “cathodoluminescence activated imaging by resonant energy transfer.” Invented by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley, CLAIRE extends the incredible resolution of electron microscopy to the dynamic imaging of soft matter.

    “Traditional electron microscopy damages soft materials and has therefore mainly been used to provide topographical or compositional information about robust inorganic solids or fixed sections of biological specimens,” says chemist Naomi Ginsberg, who leads CLAIRE’s development. “CLAIRE allows us to convert electron microscopy into a new non-invasive imaging modality for studying soft materials and providing spectrally specific information about them on the nanoscale.”

    Naomi Ginsberg

    Ginsberg holds appointments with Berkeley Lab’s Physical Biosciences Division and its Materials Sciences Division, as well as UC Berkeley’s departments of chemistry and physics. She is also a member of the Kavli Energy NanoScience Institute (Kavli-ENSI) at Berkeley. She and her research group recently demonstrated CLAIRE’s imaging capabilities by applying the technique to aluminum nanostructures and polymer films that could not have been directly imaged with electron microscopy.

    “What microscopic defects in molecular solids give rise to their functional optical and electronic properties? By what potentially controllable process do such solids form from their individual microscopic components, initially in the solution phase? The answers require observing the dynamics of electronic excitations or of molecules themselves as they explore spatially heterogeneous landscapes in condensed phase systems,” Ginsberg says. “In our demonstration, we obtained optical images of aluminum nanostructures with 46 nanometer resolution, then validated the non-invasiveness of CLAIRE by imaging a conjugated polymer film. The high resolution, speed and non-invasiveness we demonstrated with CLAIRE positions us to transform our current understanding of key biomolecular interactions.”

    CLAIRE imaging chip consists of a YAlO3:Ce scintillator film supported by LaAlO3 and SrTiO3 buffer layers and a Si frame. Al nanostructures embedded in SiO2 are positioned below and directly against the scintillator film. ProTEK B3 serves as a protective layer for etching.

    CLAIRE works by essentially combining the best attributes of optical and scanning electron microscopy into a single imaging platform. Scanning electron microscopes use beams of electrons rather than light for illumination and magnification. With much shorter wavelengths than photons of visible light, electron beams can be used to observe objects hundreds of times smaller than those that can be resolved with an optical microscope. However, these electron beams destroy most forms of soft matter and are incapable of spectrally specific molecular excitation.

    Ginsberg and her colleagues get around these problems by employing a process called “cathodoluminescence,” in which an ultrathin scintillating film, about 20 nanometers thick, composed of cerium-doped yttrium aluminum perovskite, is inserted between the electron beam and the sample. When the scintillating film is excited by a low-energy electron beam (about 1 KeV), it emits energy that is transferred to the sample, causing the sample to radiate. This luminescence is recorded and correlated to the electron beam position to form an image that is not restricted by the optical diffraction limit.

    Developing the scintillating film and integrating it into a microchip imaging device was an enormous undertaking, Ginsberg says, and she credits the “talent and dedication” of her research group for the success. She also gives much credit to the staff and capabilities of the Molecular Foundry, a DOE Office of Science User Facility, where the CLAIRE imaging demonstration was carried out.

    “The Molecular Foundry truly enabled CLAIRE imaging to come to life,” she says. “We collaborated with staff scientists there to design and install a high efficiency light collection apparatus in one of the Foundry’s scanning electron microscopes and their advice and input were fantastic. That we can work with Foundry scientists to modify the instrumentation and enhance its capabilities not only for our own experiments but also for other users is unique.”

    While there is still more work to do to make CLAIRE widely accessible, Ginsberg and her group are moving forward with further refinements for several specific applications.

    “We’re interested in non-invasively imaging soft functional materials like the active layers in solar cells and light-emitting devices,” she says. “It is especially true in organics and organic/inorganic hybrids that the morphology of these materials is complex and requires nanoscale resolution to correlate morphological features to functions.”

    Ginsberg and her group are also working on the creation of liquid cells for observing biomolecular interactions under physiological conditions. Since electron microscopes can only operate in a high vacuum, as molecules in the air disrupt the electron beam, and since liquids evaporate in high vacuum, aqueous samples must either be freeze-dried or hermetically sealed in special cells.

    “We need liquid cells for CLAIRE to study the dynamic organization of light-harvesting proteins in photosynthetic membranes,” Ginsberg says. “We should also be able to perform other studies in membrane biophysics to see how molecules diffuse in complex environments, and we’d like to be able to study molecular recognition at the single molecule level.”

    In addition, Ginsberg and her group will be using CLAIRE to study the dynamics of nanoscale systems for soft materials in general.

    “We would love to be able to observe crystallization processes or to watch a material made of nanoscale components anneal or undergo a phase transition,” she says. “We would also love to be able to watch the electric double layer at a charged surface as it evolves, as this phenomenon is crucial to battery science.”

    A paper describing the most recent work on CLAIRE has been published in the journal Nano Letters. The paper is titled Cathodoluminescence-Activated Nanoimaging: Noninvasive Near-Field Optical Microscopy in an Electron Microscope. Ginsberg is the corresponding author. Other authors are Connor Bischak, Craig Hetherington, Zhe Wang, Jake Precht, David Kaz and Darrell Schlom.

    This research was primarily supported by the DOE Office of Science and by the National Science Foundation.

    See the full article here.

    Please help promote STEM in your local schools.

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