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  • richardmitnick 8:07 am on February 21, 2017 Permalink | Reply
    Tags: , , , Chemistry, , , The thread of star birth   

    From ESA: “The thread of star birth” 

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    European Space Agency

    1
    Title Star formation on filaments in RCW106
    Released 20/02/2017 9:30 am
    Copyright ESA/Herschel/PACS, SPIRE/Hi-GAL Project. Acknowledgement: UNIMAP / L. Piazzo, La Sapienza – Università di Roma; E. Schisano / G. Li Causi, IAPS/INAF, Italy
    Description

    ESA/Herschel spacecraft
    “ESA/Herschel spacecraft

    Stars are bursting into life all over this image from ESA’s Herschel space observatory. It depicts the giant molecular cloud RCW106, a massive billow of gas and dust almost 12 000 light-years away in the southern constellation of Norma, the Carpenter’s Square.

    Cosmic dust, a minor but crucial ingredient in the interstellar material that pervades our Milky Way galaxy, shines brightly at infrared wavelengths. By tracing the glow of dust with the infrared eye of Herschel, astronomers can explore stellar nurseries in great detail.

    Sprinkled across the image are dense concentrations of the interstellar mixture of gas and dust where stars are being born. The brightest portions, with a blue hue, are being heated by the powerful light from newborn stars within them, while the redder regions are cooler.

    The delicate shapes visible throughout the image are the result of radiation and mighty winds from the young stars carving bubbles and other cavities in the surrounding interstellar material.

    Out of the various bright, blue regions, the one furthest to the left is known as G333.6-0.2 and is one of the most luminous portions of the infrared sky. It owes its brightness to a stellar cluster, home to at least a dozen young and very bright stars that are heating up the gas and dust around them.

    Elongated and thin structures, or filaments, stand out in the tangle of gas and dust, tracing the densest portions of this star-forming cloud. It is largely along these filaments, dotted with many bright, compact cores, that new stars are taking shape.

    Launched in 2009, Herschel observed the sky at far-infrared and submillimetre wavelengths for almost four years. Scanning the Milky Way with its infrared eye, Herschel has revealed an enormous number of filamentary structures, highlighting their universal presence throughout the Galaxy and their role as preferred locations for stellar birth.

    This three-colour image combines Herschel observations at 70 microns (blue), 160 microns (green) and 250 microns (red), and spans over 1º on the long side; north is up and east to the left. The image was obtained as part of Herschel’s Hi-GAL key-project, which imaged the entire plane of the Milky Way in five different infrared bands. A video panorama compiling all Hi-GAL observations was published in April 2016.

    See the full article here .

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    The European Space Agency (ESA), established in 1975, is an intergovernmental organization dedicated to the exploration of space, currently with 19 member states. Headquartered in Paris, ESA has a staff of more than 2,000. ESA’s space flight program includes human spaceflight, mainly through the participation in the International Space Station program, the launch and operations of unmanned exploration missions to other planets and the Moon, Earth observation, science, telecommunication as well as maintaining a major spaceport, the Guiana Space Centre at Kourou, French Guiana, and designing launch vehicles. ESA science missions are based at ESTEC in Noordwijk, Netherlands, Earth Observation missions at ESRIN in Frascati, Italy, ESA Mission Control (ESOC) is in Darmstadt, Germany, the European Astronaut Centre (EAC) that trains astronauts for future missions is situated in Cologne, Germany, and the European Space Astronomy Centre is located in Villanueva de la Cañada, Spain.

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  • richardmitnick 1:31 pm on February 16, 2017 Permalink | Reply
    Tags: , Chemistry, , , Triangulene   

    From Futurism: “Scientists Have Finally Created a Molecule That Was 70 Years in the Making” 

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    Futurism

    2.16.17
    Neil C. Bhavsar

    Creating the Impossible

    Move over graphene, it’s 2017 and we have a new carbon structure to rave about: Triangulene. It’s one atom thick, six carbon hexagons in size, and in the shape of – you guessed it – a triangle.

    1

    Development of the molecule has eluded chemists for a period of nearly seventy years. It was first predicted mathematically in the 1950s by Czech scientist, Eric Clar. He noted that the molecule would be unstable electronically due to two unpaired electrons in the six benzene structure. Since then, the mysterious molecule has ushered generations of scientists in a pursuit for the unstable molecule – all resulting in failure due to the oxidizing properties of two lone electron pairs.

    Now, IBM researchers in Zurich, Switzerland seem to have done the impossible: they created the molecule. While most scientists build molecules from the ground up, Leo Gross and his team decided to take the opposite approach. They worked with a larger precursor model and removed two hydrogens substituents from the molecule to conjure up the apparition molecule that is triangulene.

    On top of this, they were able to successfully image the structure with a scanning probe microscope and note the molecule’s unexpected stability in the presence of copper. Their published work is available at Nature Nanotechnology.

    This new material is already proving to be impressive. The two unpaired electrons of the triangulene molecules were discovered to have aligned spins, granting the molecule magnetic properties. Meaning triangulene has a lot of potential in electronics, specifically by allowing us to encode and process information by manipulating the electron spin – a field known as spintronics.

    The IBM researchers still have a lot to learn about triangulene. Moving forward, other teams will attempt to verify whether the researchers actually created the triangle-shaped molecule or not. Until then, the technique the team developed could be used for making other elusive structures. Although, it still isn’t ideal, as it is a slow and expensive process. Even so, this could push us closer to the age of quantum computers.

    References: ScienceAlert – Latest, Nature

    See the full article here .

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    Futurism covers the breakthrough technologies and scientific discoveries that will shape humanity’s future. Our mission is to empower our readers and drive the development of these transformative technologies towards maximizing human potential.

     
  • richardmitnick 1:57 pm on February 15, 2017 Permalink | Reply
    Tags: , , , Chemistry, Fixing the Big Bang Theory’s Lithium Problem,   

    From AAS NOVA: “Fixing the Big Bang Theory’s Lithium Problem” 

    AASNOVA

    American Astronomical Society

    15 February 2017
    Susanna Kohler

    Inflationary Universe. NASA/WMAP
    Inflationary Universe. NASA/WMAP
    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey
    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey

    “The Big Bang theory is the most widely accepted cosmological model of the universe, but it still contains a few puzzles.”

    How did our universe come into being? The Big Bang theory is a widely accepted and highly successful cosmological model of the universe, but it does introduce one puzzle: the “cosmological lithium problem.” Have scientists now found a solution?

    Too Much Lithium

    In the Big Bang theory, the universe expanded rapidly from a very high-density and high-temperature state dominated by radiation. This theory has been validated again and again: the discovery of the cosmic microwave background radiation and observations of the large-scale structure of the universe both beautifully support the Big Bang theory, for instance. But one pesky trouble-spot remains: the abundance of lithium.

    2
    The arrows show the primary reactions involved in Big Bang nucleosynthesis, and their flux ratios, as predicted by the authors’ model, are given on the right. Synthesizing primordial elements is complicated! [Hou et al. 2017]

    According to Big Bang nucleosynthesis theory, primordial nucleosynthesis ran wild during the first half hour of the universe’s existence. This produced most of the universe’s helium and small amounts of other light nuclides, including deuterium and lithium.

    But while predictions match the observed primordial deuterium and helium abundances, Big Bang nucleosynthesis theory overpredicts the abundance of primordial lithium by about a factor of three. This inconsistency is known as the “cosmological lithium problem” — and attempts to resolve it using conventional astrophysics and nuclear physics over the past few decades have not been successful.

    In a recent study led by Suqing Hou (Institute of Modern Physics, Chinese Academy of Sciences), however, a team of scientists has proposed an elegant solution to this problem.

    3

    4
    Time and temperature evolution of the abundances of primordial light elements during the beginning of the universe. The authors’ model (dotted lines) successfully predicts a lower abundance of the beryllium isotope — which eventually decays into lithium — relative to the classical Maxwell-Boltzmann distribution (solid lines), without changing the predicted abundances of deuterium or helium. [Hou et al. 2017]

    Questioning Statistics

    Hou and collaborators questioned a key assumption in Big Bang nucleosynthesis theory: that the nuclei involved in the process are all in thermodynamic equilibrium, and their velocities — which determine the thermonuclear reaction rates — are described by the classical Maxwell-Boltzmann distribution.

    But do nuclei still obey this classical distribution in the extremely complex, fast-expanding Big Bang hot plasma? Hou and collaborators propose that the lithium nuclei don’t, and that they must instead be described by a slightly modified version of the classical distribution, accounted for using what’s known as “non-extensive statistics”.

    The authors show that using the modified velocity distributions described by these statistics, they can successfully predict the observed primordial abundances of deuterium, helium, and lithium simultaneously. If this solution to the cosmological lithium problem is correct, the Big Bang theory is now one step closer to fully describing the formation of our universe.

    Citation

    S. Q. Hou et al 2017 ApJ 834 165. doi:10.3847/1538-4357/834/2/165

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  • richardmitnick 9:17 am on February 10, 2017 Permalink | Reply
    Tags: (ReACT) - redox activated chemical tagging, , Chemistry,   

    From LBNL: Chemicals Hitch a Ride onto New Protein for Better Compounds” 

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    Berkeley Lab

    February 9, 2017
    Sarah Yang
    (510) 486-4575
    scyang@lbl.gov

    Chemists have developed a powerful new method of selectively linking chemicals to proteins, a major advance in the manipulation of biomolecules that could transform the way drugs are developed, proteins are probed, and molecules are tracked and imaged.

    1
    Researchers have developed a new method of protein ligation, the joining of molecules with proteins. The technique, called Redox Activated Chemical Tagging (ReACT), involves the modification of proteins by attaching chemical cargos to the amino acid methionine. ReACT functions as a new type of chemical Swiss army knife that supports a wide variety of fields, spanning fundamental studies of protein function to applications in cancer treatment and drug discovery. (Credit: Shixian Lin/Berkeley Lab)

    The new technique, called redox activated chemical tagging (ReACT), is described in the Feb. 10 issue of the journal Science. Developed at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), it could fundamentally change the process of bioconjugation, the process by which chemicals and tags are attached to biomolecules, particularly proteins.

    “We’ve essentially invented a new type of chemical Swiss army knife for proteins, the first that can be used for the essential and naturally occurring amino acid methionine,” said study principal investigator Christopher Chang. “This ReACT method can be incorporated into a variety of different tools depending on what you need it to do. You can mix-and-match different reagents for a variety of applications.”

    Chang and fellow Berkeley Lab faculty scientist F. Dean Toste led this work as part of the Catalysis Program at Berkeley Lab’s Chemical Sciences Division. Chang is also a Howard Hughes Medical Institute Investigator.

    Hitching a ride onto a new protein

    Toste compared the process of bioconjugation to hitching cargo onto the back of a pickup truck.

    “That cargo can be used for many purposes,” he said. “It can deliver drugs to cancerous cells, or it can be used as a tracking device to monitor the truck’s movements. We can even modify the truck and change it to an ambulance. This change can be done in a number of ways, like rebuilding a truck or putting on a new hitch.”

    Bioconjugation traditionally relies upon the amino acid cysteine, which is highly reactive. Cysteine is often used as an attachment point for tags and chemical groups because it is one of two amino acids that contain sulfur, providing an anchor for acid-base chemistry and making it easy to modify.

    But cysteine is often involved in the actual function of proteins, so “hitching cargo” to it creates instability and disrupts its natural function.

    For this reason, people have been looking for ways to circumvent cysteine, and they naturally turned to methionine, the only other sulfur amino acid available. However, methionine has an extra carbon atom attached to its sulfur, which blocks most hitches. The researchers developed a new hitch using a process called oxidation-reduction chemistry that allows cargo to be attached to the methionine sulfur with this extra carbon still attached.

    The potential of a chemical Swiss army knife

    A key benefit to methionine is that it is a relatively rare amino acid, which allows researchers to selectively target it with fewer side effects and less impact on the biomolecule.

    They put ReACT to the test by synthesizing an antibody-drug conjugate to highlight its applicability to biological therapeutics. They also identified the metabolic enzyme enolase as a potential therapeutic target for cancer, showing that the tool could help home in on new targets for drug discovery.

    In the long term, the researchers say, this new bioconjugation tool could be used in:

    Nanotechnology, where protein conjugation can help make nanomaterials compatible with air and water, reducing toxicity.
    The creation of artificial enzymes that can be recycled, have better stability, and have improved activity and selectivity through chemical protein modification.
    Synthetic biology, where it can be used to selectively make new proteins or augment the function of existing ones.

    “This method could also add to the functionality of living organisms by directly modifying natural proteins to improve their stability and activity without making a genetically modified organism that relies on gene editing,” said Chang. “It could have implications for the sustainable production of fuels, food, or medicines, as well as in bioremediation.”

    Co-lead authors of the study are Shixian Lin and Xiaoyu Yang, postdoctoral researchers at UC Berkeley. Both Chang and Toste are also professors of chemistry at UC Berkeley.

    This work was supported DOE’s Office of Science. The National Institutes of Health also supported some of the pilot protein labeling studies that contributed to this work.

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    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 1:34 pm on February 7, 2017 Permalink | Reply
    Tags: , Biomathematics, Chemistry, , New study is an advance toward preventing a ‘post-antibiotic era’,   

    From UCLA: “New study is an advance toward preventing a ‘post-antibiotic era’ “ 

    UCLA bloc

    UCLA

    February 07, 2017
    Stuart Wolpert

    UCLA biologists identify drug combinations that may be highly effective at reducing growth of deadly bacteria

    1
    UCLA’s Elif Tekin, Casey Beppler, Pamela Yeh and Van Savage are gaining insights into why certain groups of three antibiotics interact well together and others don’t.

    A landmark report by the World Health Organization in 2014 observed that antibiotic resistance — long thought to be a health threat of the future — had finally become a serious threat to public health around the world. A top WHO official called for an immediate and aggressive response to prevent what he called a “post-antibiotic era, in which common infections and minor injuries which have been treatable for decades can once again kill.”

    A team of UCLA biologists has been responding to the challenge, exploring possible ways to defeat life-threatening antibiotic-resistant bacteria. In 2016, they reported that combinations of three different antibiotics can often overcome bacteria’s resistance to antibiotics, even when none of the three antibiotics on its own — or even two of the three together — is effective.

    Their latest work, which is published online and appears in the current print edition of the Journal of the Royal Society Interface, extends their understanding of that phenomenon and identifies two combinations of drugs that are unexpectedly successful in reducing the growth of E. coli bacteria.

    A key to the study is an understanding that using two, three or more antibiotics in combination does not necessarily make the drugs more effective in combating bacteria — in fact, in many cases, their effectiveness is actually reduced when drugs are used together — so the combinations must be chosen carefully and systematically. The new paper also provides the first detailed explanation of how the scientists created a mathematical formula that can help predict which combinations of drugs will be most effective.

    The scientists tested every possible combination of a group of six antibiotics, including 20 different combinations of three antibiotics at a time.

    Among the three-drug combinations, the researchers found two that were noticeably more effective than they had expected. Those groupings used treatments from three different classes of antibiotics, so the combinations used a wide range of mechanisms to fight the bacteria. (Five of the three-drug combinations were less effective than they expected, and the other 13 groupings performed as they predicted.)

    2
    Pamela Yeh. Reed Hutchinson/UCLA

    “So many bacteria are now so resistant to antibiotics,” said Pamela Yeh, the study’s senior author and a UCLA assistant professor of ecology and evolutionary biology. “We have a logical, methodical way to identify three-drug combinations to pursue. We think it’s vital to have this framework for identifying the best possible combinations of antibiotics.”

    The researchers have identified cases where the effects of the interactions are larger than the sum of the parts.

    “Doctors may want to super-efficiently kill the bacteria, and that is what these enhanced interactions make possible,” said lead author Casey Beppler, who was an undergraduate in Yeh’s laboratory and is now a graduate student at UC San Francisco.

    For the current study, the scientists evaluated the drug combinations on plates in a lab. Beppler said a next step will be to test the most effective combinations in mice.

    In addition to reporting on how well various combinations of antibiotics worked, the paper also presents a mathematical formula the biologists developed for analyzing how three or more factors interact and of explaining complex, unexpected interactions. The framework would be useful for solving other questions in the sciences and social sciences in which researchers analyze how three or more components might interact — for example, how climate is affected by the interplay among temperature, rainfall, humidity and ocean acidity.

    The biologists are gaining a deep understanding of why certain groups of three antibiotics interact well together, and others don’t, said Van Savage, a co-author of the paper and a UCLA professor of ecology and evolutionary biology and of biomathematics.

    Beppler said more research is needed to determine which combinations are optimal for specific diseases and for specific parts of the body. And the researchers now are using the mathematical formula to test combinations of four antibiotics.

    Co-authors of the new research are Elif Tekin, a UCLA graduate student in Savage’s laboratory; Zhiyuan Mao, Cynthia White, Cassandra McDiarmid and Emily Vargas, who were undergraduates in Yeh’s laboratory; and Jeffrey H. Miller, a UCLA distinguished professor of microbiology, immunology and molecular genetics.

    Yeh’s research was funded by the Hellman Foundation. Savage’s research was funded by a James S. McDonnell Foundation Complex Systems Scholar Award and from the National Science Foundation. Beppler received funding from the National Institutes of Health Initiative to Maximize Student Development.

    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 12:20 pm on February 7, 2017 Permalink | Reply
    Tags: , Chemistry, , First-principles evolutionary algorithm called USPEX, Na2He electride, , Scientists discover helium chemistry   

    From EurekaAlert: “Scientists discover helium chemistry” 

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    EurekaAlert

    1
    Crystal structure of Na2He, resembling a three-dimensional checkerboard. The purple spheres represent sodium atoms, which are inside the green cubes that represent helium atoms. The red regions inside voids of the structure show areas where localized electron pairs reside. Credit: Illustration is provided courtesy of Artem R. Oganov.

    6-Feb-2017
    Media Contact
    Asya Shepunova
    shepunova@phystech.edu
    7-916-813-0267

    Although helium is the second most-abundant element (after hydrogen) in the universe, it doesn’t play well with others. It is a member of a family of seven elements called the noble gases, which are called that because of their chemical aloofness — they don’t easily form compounds with other elements. Helium, widely believed to be the most inert element, has no stable compounds under normal conditions.

    Now, an international team of researchers led by Skoltech’s Prof. Artem R. Oganov (also a professor at Stony Brook University and head of Computational Materials Discovery laboratory at Moscow Institute of Physics and Technology) has predicted two stable helium compounds — Na2He and Na2HeO. The scientists experimentally confirmed and theoretically explained the stability of Na2He. This work could hold clues about the chemistry occurring inside gas giant planets and possibly even stars, where helium is a major component. The work is published by Nature Chemistry.

    The authors of the study used a crystal structure-predicting tool, the first-principles evolutionary algorithm called USPEX, to conduct a systematic search for stable helium compounds. They predicted the existence of Na2He, which was then successfully synthesized in a diamond anvil cell (DAC) experiment performed at the Carnegie Institution for Science in Washington by Prof. Alexander F. Goncharov and his colleagues. The compound appeared at pressures of about 1.1 million times Earth’s atmospheric pressure and is predicted to be stable at least up to 10 million times that.

    “The compound that we discovered is very peculiar: helium atoms do not actually form any chemical bonds, yet their presence fundamentally changes chemical interactions between sodium atoms, forces electrons to localize inside cubic voids of the structure and makes this material insulating,” says Xiao Dong, the first author of this work, who was a long-term visiting student in Oganov’s laboratory at the time when this work was done.

    Na2He is what’s called an electride, which is a special type of an ionic salt-like crystal. It has a positively charged sublattice of sodium ions and another negatively charged sublattice formed of localized electron pairs. Because electrons are strongly localized, this material is an insulator, meaning that it cannot conduct the free-flowing electrons that make up an electric current.

    The other predicted helium compound, Na2HeO, was found to be stable in the pressure range from 0.15 to 1.1 million atmospheres. It is also an ionic crystal with a structure similar to that of Na2He. However, in place of electron pairs, it has negatively charged oxygen in the form of O²?.

    “This study shows how new surprising phenomena can be discovered by combination of powerful theoretical methods and state-of-the-art experiments. It shows that very weird chemical phenomena and compounds can emerge at extreme conditions, and the role of such phenomena inside planets needs to be explored,” says Oganov.

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    EurekAlert!, the premier online news source focusing on science, health, medicine and technology, is a free service for reporters worldwide.

    Since 1996, EurekAlert! has served as the leading destination for scientific organizations seeking to disseminate news to reporters and the public. Today, thousands of reporters around the globe rely on EurekAlert! as a source of ideas, background information, and advance word on breaking news stories.

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  • richardmitnick 3:41 pm on February 4, 2017 Permalink | Reply
    Tags: , “Giant acceleration of diffusion” or GAD, , , Brownian motion, Chemistry, ,   

    From Brown: “Research pushes concept of entropy out of kilter” 

    Brown University
    Brown University

    [THIS POST IS DEDICATED TO EBM, READY TO ROCK THE CAMPUS]

    February 2, 2017
    Kevin Stacey
    kevin_stacey@brown.edu
    401-863-3766

    Entropy, the measure of disorder in a physical system, is something that physicists understand well when systems are at equilibrium, meaning there’s no external force throwing things out of kilter. But new research by Brown University physicists takes the idea of entropy out of its equilibrium comfort zone.

    The research, published in Physical Review Letters, describes an experiment in which the emergence of a non-equilibrium phenomenon actually requires an entropic assist.

    1
    DNA drag race. Fluorescent stained DNA molecules make their way across of fluid channel pocked with tiny pits. The pits act as “entropic barriers.”
    Stein Lab / Brown University

    “It’s not clear what entropy even means when you’re moving away from equilibrium, so to have this interplay between a non-equilibrium phenomenon and an entropic state is surprising,” said Derek Stein, a Brown University physicist and co-author of the work. “It’s the tension between these two fundamental things that is so interesting.”

    The phenomenon the research investigated is known as “giant acceleration of diffusion,” or GAD. Diffusion is the term used to describe the extent to which small, jiggling particles spread out. The jiggling refers to Brownian motion, which describes the random movement of small particles as a result of collisions with surrounding particles. In 2001, a group of researchers developed a theory of how Brownian particles would diffuse in a system that was pushed out of equilibrium.

    Imagine jiggling particles arranged on a surface with undulating bumps like a washboard. Their jiggle isn’t quite big enough to enable the particles to jump over the bumps in the board, so they don’t diffuse much at all. However, if the board were tilted to some degree (in other words, moved out of equilibrium) the bumps would become easier to jump over in the downward-facing direction. As tilt begins to increase, some particles will jiggle free of the washboard barriers and run down the board, while others will stay put. In physics terms, the particles have become more diffusive — more spread-out — as the system is moved out of equilibrium. The GAD theory quantifies this diffusivity effect and predicts that as tilt starts to increase, diffusivity accelerates. When the tilt passes the point where all the particles are able to jiggle free and move down the washboard, then diffusivity decreases again.

    The theory is important, Stein says, because it’s one of only a few attempts to make solid predictions about how systems behave away from equilibrium. It’s been tested in a few other settings and has been found to make accurate predictions.

    But Stein and his team wanted to test the theory in an unfamiliar setting — one that introduces entropy into the mix.

    For the experiment, Stein and his colleagues placed DNA strands into nanofluidic channels — essentially, tiny fluid-filled hallways through which the molecules could travel. The channels were lined however with nanopits — tiny rectangular depressions that create deep spots within the relatively narrower channels. At equilibrium, DNA molecules tend to arrange themselves in disordered, spaghetti-like balls. As a result, when a molecule finds its way into a nanopit where it has more room to form a disordered ball, it tends to stay stuck there. The pits can be seen as being somewhat like the dips between bumps on the theoretical GAD washboard, but with a critical difference: The only thing actually holding the molecule in the pit is entropy.

    “This molecule is randomly jiggling around in the pit — randomly selecting different configurations to be in — and the number of possible configurations is a measure of the molecule’s entropy,” Stein explained. “It could, at some point, land on a configuration that’s thin enough to fit into the channel outside the pit, which would allow it to move from one pit to another. But that’s unlikely because there are so many more shapes that don’t go through than shapes that do. So the pit becomes an ‘entropic barrier.’”

    Stein and his colleagues wanted to see if the non-equilibrium GAD dynamic would still emerge in a system where the barriers were entropic. They used a pump to apply pressure to the nanofluidic channels, pushing them out of equilibrium. They then measured the speeds of each molecule to see if GAD emerged. What they saw was largely in keeping with the GAD theory. As the pressure increased toward a critical point, the diffusivity of the molecules increased — meaning some molecules zipped across the channel while others stayed stuck in their pits.

    “It wasn’t at all clear how this experiment would come out,” Stein said. “This is a non-equilibrium phenomenon that requires barriers, but our barriers are entropic and we don’t understand entropy away from equilibrium.”


    Anastasios Matzavinos, a professor of applied math at Brown, developed computer simulations of the experiment to help understand the forces at play.

    The fact that the barriers remained raises interesting questions about the nature of entropy, Stein says.

    “Non-equilibrium and entropy are two concepts that are kind of at odds, but we show a situation in which one depends on the other,” he said. “So what’s the guiding principle that tells what the tradeoff is between the two? The answer is: We don’t have one, but maybe experiments like this can start to give us a window into that.”

    In addition to the more profound implications, there may also be practical applications for the findings, Stein says. The researchers showed that they could estimate the tiny piconewton forces pushing the DNA forward just by analyzing the molecules’ motion. For reference, one newton of force is roughly the weight of an average apple. A piconewton is one trillionth of that.

    The experiment also showed that, with the right amount of pressure, the diffusivity of the DNA molecules was increased by factor of 15. So a similar technique could be useful in quickly making mixtures. If such a technique were developed to take advantage of GAD, it would be a first, Stein says.

    “No one has ever harnessed a non-equilibrium phenomenon for anything like that,” he said. “So that would certainly be an interesting possibility.”

    The work was led by Stein’s graduate student Daniel Kim. Co-authors were Clark Bowman, Jackson T. Del Bonis-O’Donnell and Anastasios Matzavinos, all from Brown. The work was supported by the National Science Foundation.

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    Welcome to Brown

    Brown U Robinson Hall
    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

     
  • richardmitnick 9:24 am on February 2, 2017 Permalink | Reply
    Tags: Advanced electron microscopy, , Chemistry, GENFIRE (GENeralized Fourier Iterative Reconstruction), , Mapping out the three-dimensional atomic positions at the grain boundaries for the first time, , ,   

    From UCLA: “UCLA physicists map the atomic structure of an alloy” 

    UCLA bloc

    UCLA

    February 01, 2017
    Katherine Kornei

    1
    Identification of the precise 3-D coordinates of iron, shown in red, and platinum atoms in an iron-platinum nanoparticle. Courtesy of Colin Ophus and Florian Nickel

    In the world of the very tiny, perfection is rare: virtually all materials have defects on the atomic level. These imperfections — missing atoms, atoms of one type swapped for another, and misaligned atoms — can uniquely determine a material’s properties and function. Now, UCLA physicists and collaborators have mapped the coordinates of more than 23,000 individual atoms in a tiny iron-platinum nanoparticle to reveal the material’s defects.

    The results demonstrate that the positions of tens of thousands of atoms can be precisely identified and then fed into quantum mechanics calculations to correlate imperfections and defects with material properties at the single-atom level. This research will be published Feb. 2 in the journal Nature.

    Jianwei “John” Miao, a UCLA professor of physics and astronomy and a member of UCLA’s California NanoSystems Institute, led the international team in mapping the atomic-level details of the bimetallic nanoparticle, more than a trillion of which could fit within a grain of sand.

    “No one has seen this kind of three-dimensional structural complexity with such detail before,” said Miao, who is also a deputy director of the Science and Technology Center on Real-Time Functional Imaging. This new National Science Foundation-funded consortium consists of scientists at UCLA and five other colleges and universities who are using high-resolution imaging to address questions in the physical sciences, life sciences and engineering.

    Miao and his team focused on an iron-platinum alloy, a very promising material for next-generation magnetic storage media and permanent magnet applications.

    By taking multiple images of the iron-platinum nanoparticle with an advanced electron microscope at Lawrence Berkeley National Laboratory and using powerful reconstruction algorithms developed at UCLA, the researchers determined the precise three-dimensional arrangement of atoms in the nanoparticle.

    “For the first time, we can see individual atoms and chemical composition in three dimensions. Everything we look at, it’s new,” Miao said.

    The team identified and located more than 6,500 iron and 16,600 platinum atoms and showed how the atoms are arranged in nine grains, each of which contains different ratios of iron and platinum atoms. Miao and his colleagues showed that atoms closer to the interior of the grains are more regularly arranged than those near the surfaces. They also observed that the interfaces between grains, called grain boundaries, are more disordered.

    “Understanding the three-dimensional structures of grain boundaries is a major challenge in materials science because they strongly influence the properties of materials,” Miao said. “Now we are able to address this challenge by precisely mapping out the three-dimensional atomic positions at the grain boundaries for the first time.”

    The researchers then used the three-dimensional coordinates of the atoms as inputs into quantum mechanics calculations to determine the magnetic properties of the iron-platinum nanoparticle. They observed abrupt changes in magnetic properties at the grain boundaries.

    “This work makes significant advances in characterization capabilities and expands our fundamental understanding of structure-property relationships, which is expected to find broad applications in physics, chemistry, materials science, nanoscience and nanotechnology,” Miao said.

    In the future, as the researchers continue to determine the three-dimensional atomic coordinates of more materials, they plan to establish an online databank for the physical sciences, analogous to protein databanks for the biological and life sciences. “Researchers can use this databank to study material properties truly on the single-atom level,” Miao said.

    Miao and his team also look forward to applying their method called GENFIRE (GENeralized Fourier Iterative Reconstruction) to biological and medical applications. “Our three-dimensional reconstruction algorithm might be useful for imaging like CT scans,” Miao said. Compared with conventional reconstruction methods, GENFIRE requires fewer images to compile an accurate three-dimensional structure.

    That means that radiation-sensitive objects can be imaged with lower doses of radiation.

    The study’s co-authors include Yongsoo Yang, Rui Xu, AJ Pryor, Li Wu and Jihan Zhou, all at UCLA; Mary Scott, Colin Ophus, and Peter Ercius of Lawrence Berkeley National Laboratory; Chien-Chun Chen of the National Sun Yat-sen University; Fan Sun and Hao Zeng of the University at Buffalo; Markus Eisenbach and Paul Kent of Oak Ridge National Laboratory; Wolfgang Theis of the University of Birmingham; and Renat Sabirianov of the University of Nebraska Omaha.

    This work was supported by the U.S. Department of Energy’s Office of Basic Energy Sciences (grants DE-SC0010378, DE-AC02—05CH11231 and DE-AC05-00OR22725) as well as the U.S. National Science Foundation’s Division of Materials Research (grants DMR-1548924 and DMR-1437263).

    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 2:48 pm on January 30, 2017 Permalink | Reply
    Tags: , Chemistry, , Dr. Miriam Eisenstein, GSK-3, Modeling of molecules on the computer, , ,   

    From Weizmann: Women in STEM – “Staff Scientist: Dr. Miriam Eisenstein” 

    Weizmann Institute of Science logo

    Weizmann Institute of Science

    30.01.2017
    No writer credit found

    1
    Name: Dr. Miriam Eisenstein
    Department: Chemical Research Support

    “The modeling of molecules on the computer,” says Dr. Miriam Eisenstein, Head of the Macromolecular Modeling Unit of the Weizmann Institute of Science’s Chemical Research Support Department, “is sometimes the only way to understand exactly how such complex molecules as proteins interact.”

    Eisenstein was one of the first to develop molecular docking methods while working with Prof. Ephraim Katzir – over two decades ago – and she has worked in collaboration with many groups at the Weizmann Institute.

    But even with all her experience, protein interactions can still surprise her. This was the case in a recent collaboration with the lab group of Prof. Hagit Eldar-Finkelman of Tel Aviv University, in research that was hailed as a promising new direction for finding treatments for Alzheimer’s disease. Eldar-Finkelman and her group were investigating an enzyme known as GSK-3, which affects the activity of various proteins by clipping a particular type of chemical tag, known as a phosphate group, onto them. GSK-3 thus performs quite a few crucial functions in the body, but it can also become overactive, and this extra activity has been implicated in a number of diseases, including diabetes and Alzheimer’s.

    The Tel Aviv group, explains Eisenstein, was exploring a new way of blocking, or at least damping down, the activity of this enzyme. GSK-3 uses ATP — a small, phosphate-containing molecule — in the chemical tagging process, transferring one of the ATP phosphate groups to a substrate. The ATP binding site on the enzyme is often targeted with ATP-like drug compounds that by themselves binding prevent the ATP from binding, thus blocking the enzyme’s activity. But such compounds are not discriminating enough, often blocking related enzymes in the process, which is an undesired side effect. This is why Eldar-Finkelman and her team looked for molecules that would compete with the substrate and occupy its binding cavity, so that the enzyme’s normal substrates cannot attach to GSK-3 and clip onto the phosphate groups.

    After identifying one molecule – a short piece of protein, or peptide – that substituted for GSK-3’s substrates in experiments, Eldar-Finkelman turned to Eisenstein to design peptides that would be better at competing with the substrate. At first Eisenstein computed model structures of the enzyme with an attached protein substrate and the enzyme with an attached peptide; she then characterized the way in which the enzyme binds either the substrate or the competing peptide. The model structures pinpointed the contacts, and these were verified experimentally by Eldar-Finkelman.

    This led to the next phase, a collaborative effort to introduce alterations to the peptide so as to improve its binding capabilities. One of the new peptides was predicted by Eisenstein to be a good substrate, and Eldar-Finkelman’s experiments showed that it indeed was. Once chemically tagged, the new peptide proved to be excellent at binding to GSK-3 – many times better than the original – and this was the surprise, because normally, once they are tagged, such substrates are repelled from the substrate-binding cavity and end up dissociating from the enzyme. Molecular modeling explained what was happening. After initially binding as a substrate and attaining a phosphate group, the peptide slid within the substrate-binding cavity, changing its conformation in the process, and attached tightly to a position normally occupied by the protein substrate.

    Experiments in Eldar-Finkelman’s group showed that this peptide is also active in vivo and, moreover, was able to reduce the symptoms of an Alzheimer-like condition in mice. The results of this research appeared in Science Signaling.

    “This experiment is a great example of the synergy between biologists and computer modelers,” says Eisenstein. “Hagit understands the function of this enzyme in the body, and she had this great insight on a possible way to control its actions. I am interested in the way that two proteins fit together and influence one another at the molecular and atomic levels, so I can provide the complementary insight.”

    “Molecular modeling is such a useful tool, it has enabled me to work with a great many groups and take part in a lot of interesting, exciting work, over the years,” she adds. “Computers have become much stronger in that time, but the basic, chemical principles of attraction and binding between complex molecules remain the same, and our work is as relevant as ever.”

    See the full article here .

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    Weizmann Institute Campus

    The Weizmann Institute of Science is one of the world’s leading multidisciplinary research institutions. Hundreds of scientists, laboratory technicians and research students working on its lushly landscaped campus embark daily on fascinating journeys into the unknown, seeking to improve our understanding of nature and our place within it.

    Guiding these scientists is the spirit of inquiry so characteristic of the human race. It is this spirit that propelled humans upward along the evolutionary ladder, helping them reach their utmost heights. It prompted humankind to pursue agriculture, learn to build lodgings, invent writing, harness electricity to power emerging technologies, observe distant galaxies, design drugs to combat various diseases, develop new materials and decipher the genetic code embedded in all the plants and animals on Earth.

    The quest to maintain this increasing momentum compels Weizmann Institute scientists to seek out places that have not yet been reached by the human mind. What awaits us in these places? No one has the answer to this question. But one thing is certain – the journey fired by curiosity will lead onward to a better future.

     
  • richardmitnick 12:39 pm on January 30, 2017 Permalink | Reply
    Tags: , Chemistry, , , , Symmetry in patterns, symmorphic and nonsymmorphic patterns of atoms, Theorists propose new class of topological metals with exotic electronic properties, tungsten telluride (WTe2)   

    From Princeton: “Theorists propose new class of topological metals with exotic electronic properties (Physics Review X)” 

    Princeton University
    Princeton University

    January 30, 2017
    Tien Nguyen, Department of Chemistry

    1
    A new theory explains the behavior of a class of metals with exotic electronic properties. Credit: Muechler et al., Physics Review X

    Researchers at Princeton, Yale, and the University of Zurich have proposed a theory-based approach to characterize a class of metals that possess exotic electronic properties that could help scientists find other, similarly-endowed materials.

    Published in the journal Physical Review X, the study described a new class of metals based on their symmetry and a mathematical classification known as a topological number, which is predictive of special electronic properties. Topological materials have drawn intense research interest since the early 2000s culminating in last year’s Nobel Prize in Physics awarded to three physicists, including F. Duncan Haldane, Princeton’s Eugene Higgins Professor of Physics, for theoretical discoveries in this area.

    “Topological classification is a very general way of looking at the properties of materials,” said Lukas Muechler, a Princeton graduate student in the laboratory of Roberto Car, Princeton’s Ralph W. *31 Dornte Professor in Chemistry and lead author on the article.

    A popular way of explaining this abstract mathematical classification involves breakfast items. In topological classification, donuts and coffee cups are equivalent because they both have one hole and can be smoothly deformed into one another. Meanwhile donuts cannot deform into muffins which makes them inequivalent. The number of holes is an example of a topological invariant that is equal for the donut and coffee cup, but distinguishes between the donut and the muffin.

    “The idea is that you don’t really care about the details. As long as two materials have the same topological invariants, we can say they are topologically equivalent,” he said.

    Muechler and his colleagues’ interest in the topological classification of this new class of metals was sparked by a peculiar discovery in the neighboring laboratory of Robert Cava, Princeton’s Russell Wellman Moore Professor of Chemistry. While searching for superconductivity in a crystal called tungsten telluride (WTe2), the Cava lab instead found that the material could continually increase its resistance in response to ever stronger magnetic fields – a property that might be used to build a sensor of magnetic fields.

    The origin of this property was, however, mysterious. “This material has very interesting properties, but there had been no theory around it,” Muechler said.

    The researchers first considered the arrangement of the atoms in the WTe2 crystal. Patterns in the arrangement of atoms are known as symmetries, and they fall into two fundamentally different classes – symmorphic and nonsymmorphic – which lead to profound differences in electronic properties, such as the transport of current in an electromagnetic field.

    2
    a) Symmorphic symmetry b) Nonsymmorphic symmetry Credit: Lukas Muechler

    While WTe2 is composed of many layers of atoms stacked upon each other, Car’s team found that a single layer of atoms has a particular nonsymmorphic symmetry, where the atomic arrangement is unchanged overall if it is first rotated and then translated by a fraction of the lattice period (see figure).

    Having established the symmetry, the researchers mathematically characterized all possible electronic states having this symmetry, and classified those states that can be smoothly deformed into each other as topologically equivalent, just as a donut can be deformed into a cup. From this classification, they found WTe2 belongs to a new class of metals which they coined nonsymmorphic topological metals. These metals are characterized by a different electron number than the nonsymmorphic metals that have previously been studied.

    In nonsymmorphic topological metals, the current-carrying electrons behave like relativistic particles, in other words, as particles traveling at nearly the speed of light. This property is not as susceptible to impurities and defects as ordinary metals, making them attractive candidates for electronic devices.

    The abstract topological classification also led the researchers to suggest some explanations for some of the outstanding electronic properties of bulk WTe2, most importantly its perfect compensation, meaning that it has an equal number of holes and electrons. Through theoretical simulations, the researchers found that this property could be achieved in the three-dimensional crystalline stacking of the WTe2 monolayers, which was a surprising result, Muechler said.

    “Usually in theory research there isn’t much that’s unexpected, but this just popped out,” he said. “This abstract classification directly led us to explaining this property. In this sense, it’s a very elegant way of looking at this compound and now you can actually understand or design new compounds with similar properties.”

    Recent photoemission experiments have also shown that the electrons in WTe2 absorb right-handed photons differently than they would left-handed photons. The theory formulated by the researchers showed that these photoemission experiments on WTe2 can be understood based on the topological properties of this new class of metals.

    In future studies, the theorists want to test whether these topological properties are also present in atomically-thin layers of these metals, which could be exfoliated from a larger crystal to make electronic devices. “The study of this phenomena has big implications for the electronics industry, but it’s still in its infant years,” Muechler said.

    This work was supported by the U.S. Department of Energy (DE-FG02-05ER46201), the Yale Postdoctoral Prize Fellowship, the National Science Foundation (NSF CAREER DMR-095242 and NSF-MRSEC DMR-0819860), the Office of Naval Research (ONR-N00014-11-1- 0635), the U.S. Department of Defense (MURI-130-6082), the David and Lucile Packard Foundation, the W. M. Keck Foundation, and the Eric and Wendy Schmidt Transformative Technology Fund.

    See the full article here .

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    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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