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  • richardmitnick 5:33 pm on October 27, 2014 Permalink | Reply
    Tags: , Chemistry   

    From Princeton: “What makes a tumor switch from dormant to malignant?” 

    Princeton University
    Princeton University

    October 27, 2014
    Tien Nguyen, Department of Chemistry

    Cancer constantly wages war on the human body. Battles are won, lost or sometimes end in a stalemate. This stalemate, known as tumor dormancy, is extremely difficult to study in both cellular and animal models.

    A new computational model developed in the laboratory of Salvatore Torquato, a professor of chemistry at Princeton University, offers a way to probe the conditions surrounding tumor dormancy and the switch to a malignant state. Published Oct. 16 in the journal “PLOS ONE,” the so-called cellular automaton model simulated various scenarios of tumor growth leading to tumor dormancy or proliferation.
    ph
    Researchers from Princeton University have developed a computer model that simulates the competition between tumor dormancy and proliferation under various conditions. Through a series of simulations, they generated a phase diagram, pictured here, that could be used by experimentalists to predict when the tumor will be in a proliferative or dormant state. (Image courtesy of Salvatore Torquato Lab)

    “The power of the model is that it lets people test medically realistic scenarios,” said Torquato, who is also affiliated with the Princeton Institute for the Science and Technology of Materials. In future collaborations, these scenarios could be engineered in laboratory experiments and the observed outcomes could be used to calibrate the model.

    For each scenario, a set of rules is imposed on the virtual cell population. Rules are possible interactions, such as neighboring cell death or immune system suppression, that dictate cell division through probabilities derived from past experimental data. Once the researchers programmed the rules, they watched as the simulated competition unfolded between the tumor and the environmental factors that may suppress its growth.

    “We were very surprised to observe this phenomena where the tumor all of a sudden began to rapidly divide,” said Duyu Chen, graduate student in the Torquato lab and lead author on the article. This was the first time that the emergent switch behavior, which has been observed clinically, occurred spontaneously in a model, Chen said.

    The researchers evaluated a number of factors that could affect tumor cell growth including spontaneous cell mutations, mechanical properties, and the rate and strength of suppression factors such as the immune system. One of the model’s findings was the likely suppression of tumors in harsh environments, characterized by high density and pressure.

    “The way [the researchers] built their model system is that the dormancy state is not one of cells simply sleeping, in fact it’s an active state, it’s just that the whole system is held in equilibrium or stalemate,” said Micheal Espey, program manager at the National Cancer Institute who was not involved in the research. “That’s a very interesting viewpoint.”

    The research team also predicted that if the number of actively dividing cells within the proliferative rim reached a certain critical level, the tumor was very likely to begin growing rapidly. This result could provide insight into early cancer treatment, Chen said.

    Through repeated simulations the research team constructed a phase diagram that revealed the boundary between a dormant and proliferative state. If experimental data was incorporated into the model, Espey said, researchers could predict when the tumor was in a dormant state and when it was heading toward a proliferative state. “That’s the value,” he said.

    The research was supported by the National Cancer Institute under Award No. U54CA143803.

    See the full article here.

    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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  • richardmitnick 1:45 pm on October 17, 2014 Permalink | Reply
    Tags: , , Chemistry   

    From AAAS: “Would-be drug mimics ‘good’ cholesterol” 

    AAAS

    AAAS

    16 October 2014
    Robert F. Service

    A new drug candidate designed to mimic the body’s “good” cholesterol shows a striking ability in mice to lower cholesterol levels in the blood and dissolve artery-clogging plaques. What’s more, the compound works when given orally, rather than as an injection. If the results hold true in humans—a big if, given past failures at transferring promising treatments from mice—it could provide a new way to combat atherosclerosis, the biggest killer in developed countries.

    Although doctors already have effective cholesterol-lowering agents, such as statins, at their disposal, there’s room for improvement. Statins have significant side effects in some people and don’t always reduce cholesterol enough in others. “There is still plenty of heart disease out there even among people who take statins,” says Godfrey Getz, an experimental pathologist at the University of Chicago in Illinois.

    For that reason, researchers around the globe are searching for novel drugs that affect cholesterol levels in one of two ways. The first has been to reduce levels of low-density lipoprotein (LDL), commonly known as bad cholesterol, which has been associated with higher heart disease risk. This is the goal of statins, which block an enzyme involved in cholesterol production. The second strategy is to increase levels of good cholesterol, or high-density lipoprotein (HDL), which seems to boost heart health in people who have a lot of it. But producing HDL-raising drugs that prevent heart disease has proven difficult. In the body, a large protein called apolipoprotein A-I (apoA-I) wraps around fatty lipid molecules to create HDL particles that sop up LDL and ferry it to the liver where it is eliminated. So for several decades researchers have been designing and testing small protein fragments called peptides to see if they could mimic the behavior of apoA-I. One such peptide, known as 4F, did not reduce serum cholesterol levels, but it did shrink arterial plaques in mice, rabbits, and monkeys. And in an early clinical trial by researchers at Bruin Pharma Inc. in Beverly Hills, California, that was designed only to measure its safety in people, 4F didn’t appear to show any beneficial effect.

    pro
    Multiple copies of a four-armed peptide wrap around lipids to create particles that mimic the behavior of HDL, the “good” cholesterol.
    Y.Zhao et al., J. Am. Chem. Soc

    M. Reza Ghadiri, a chemist at the Scripps Research Institute in San Diego, California, and his colleagues took a slightly different tack, creating a peptide that mimics another part of the apoA-I protein than 4F does. Initial in vitro studies suggested the peptide formed HDL-like particles and sopped up LDL, an encouraging result that prompted them to push it further. Ghadiri and his Scripps colleagues have now tested their compound in mice that develop artery clogging plaques when fed a Western-style high-fat diet. One group of animals received the peptide intravenously. For another group, the researchers simply added the compound to the animals’ water, a strategy they considered unlikely to work, because the gut contains high amounts of proteases designed to chop proteins apart. To their surprise, in both groups, serum cholesterol levels dropped 40% from their previous levels within 2 weeks of starting to take the drug. And by 10 weeks, the number of artery-clogging lesions had been reduced by half, the team reports in the October issue of the Journal of Lipid Research. What remains puzzling, however, is that Ghadiri and his colleagues did not detect their peptides in the blood of their test animal. Ghadiri says this suggests that the new peptide may work by removing cholesterol precursors in the gut before they enter the bloodstream.

    “It’s a very interesting result,” Getz says. But he cautions that the work has been tested only in animals, and many therapies—including the closely related 4F peptide—fail to transfer to humans. That said, Getz notes that some of the initial promising results with this peptide and other apoA-I mimics offer hope that researchers may soon come up with novel drugs capable of dissolving artery-clogging plaques before they can wreak their havoc.

    See the full article here.

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  • richardmitnick 9:02 am on October 17, 2014 Permalink | Reply
    Tags: , Chemistry, ,   

    From MIT: “Nanoparticles get a magnetic handle” 


    MIT News

    October 9, 2014
    David L. Chandler | MIT News Office

    A long-sought goal of creating particles that can emit a colorful fluorescent glow in a biological environment, and that could be precisely manipulated into position within living cells, has been achieved by a team of researchers at MIT and several other institutions. The finding is reported this week in the journal Nature Communications.

    4
    Elemental mapping of the location of iron atoms (blue) in the magnetic nanoparticles and cadmium (red) in the fluorescent quantum dots provide a clear visualization of the way the two kinds of particles naturally separate themselves into a core-and-shell structure. Image courtesy of the researchers

    The new technology could make it possible to track the position of the nanoparticles as they move within the body or inside a cell. At the same time, the nanoparticles could be manipulated precisely by applying a magnetic field to pull them along. And finally, the particles could have a coating of a bioreactive substance that could seek out and bind with particular molecules within the body, such as markers for tumor cells or other disease agents.

    “It’s been a dream of mine for many years to have a nanomaterial that incorporates both fluorescence and magnetism in a single compact object,” says Moungi Bawendi, the Lester Wolfe Professor of Chemistry at MIT and senior author of the new paper. While other groups have achieved some combination of these two properties, Bawendi says that he “was never very satisfied” with results previously achieved by his own team or others.

    For one thing, he says, such particles have been too large to make practical probes of living tissue: “They’ve tended to have a lot of wasted volume,” Bawendi says. “Compactness is critical for biological and a lot of other applications.”

    In addition, previous efforts were unable to produce particles of uniform and predictable size, which could also be an essential property for diagnostic or therapeutic applications.

    Moreover, Bawendi says, “We wanted to be able to manipulate these structures inside the cells with magnetic fields, but also know exactly what it is we’re moving.” All of these goals are achieved by the new nanoparticles, which can be identified with great precision by the wavelength of their fluorescent emissions.

    The new method produces the combination of desired properties “in as small a package as possible,” Bawendi says — which could help pave the way for particles with other useful properties, such as the ability to bind with a specific type of bioreceptor, or another molecule of interest.

    In the technique developed by Bawendi’s team, led by lead author and postdoc Ou Chen, the nanoparticles crystallize such that they self-assemble in exactly the way that leads to the most useful outcome: The magnetic particles cluster at the center, while fluorescent particles form a uniform coating around them. That puts the fluorescent molecules in the most visible location for allowing the nanoparticles to be tracked optically through a microscope.

    “These are beautiful structures, they’re so clean,” Bawendi says. That uniformity arises, in part, because the starting material, fluorescent nanoparticles that Bawendi and his group have been perfecting for years, are themselves perfectly uniform in size. “You have to use very uniform material to produce such a uniform construction,” Chen says.

    Initially, at least, the particles might be used to probe basic biological functions within cells, Bawendi suggests. As the work continues, later experiments may add additional materials to the particles’ coating so that they interact in specific ways with molecules or structures within the cell, either for diagnosis or treatment.

    The ability to manipulate the particles with electromagnets is key to using them in biological research, Bawendi explains: The tiny particles could otherwise get lost in the jumble of molecules circulating within a cell. “Without a magnetic ‘handle,’ it’s like a needle in a haystack,” he says. “But with the magnetism, you can find it easily.”

    A silica coating on the particles allows additional molecules to attach, causing the particles to bind with specific structures within the cell. “Silica makes it completely flexible; it’s a well developed material that can bind to almost anything,” Bawendi says.

    For example, the coating could have a molecule that binds to a specific type of tumor cells; then, “You could use them to enhance the contrast of an MRI, so you could see the spatial macroscopic outlines of a tumor,” he says.

    The next step for the team is to test the new nanoparticles in a variety of biological settings. “We’ve made the material,” Chen says. “Now we’ve got to use it, and we’re working with a number of groups around the world for a variety of applications.”

    Christopher Murray, a professor of chemistry and materials science and engineering at the University of Pennsylvania who was not connected with this research, says, “This work exemplifies the power of using nanocrystals as building blocks for multiscale and multifunctional structures. We often use the term ‘artificial atoms’ in the community to describe how we are exploiting a new periodic table of fundamental building blocks to design materials, and this is a very elegant example.”

    The study included researchers at MIT; Massachusetts General Hospital; Institut Curie in Paris; the Heinrich-Pette Institute and the Bernhard-Nocht Institute for Tropical Medicine in Hamburg, Germany; Children’s Hospital Boston; and Cornell University. The work was supported by the National Institutes of Health, the Army Research Office through MIT’s Institute for Soldier Nanotechnologies, and the Department of Energy.

    See the full article, with video, here.

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  • richardmitnick 9:08 am on October 15, 2014 Permalink | Reply
    Tags: , , Chemistry   

    From AAAS: “Storing greenhouse gas underground—for a million years” 

    AAAS

    AAAS

    14 October 2014
    Jia You

    When Canada switched on its Boundary Dam power plant earlier this month, it signaled a new front in the war against climate change. The commercial turbine burns coal, the dirtiest of fossil fuels, but it traps nearly all the resulting carbon dioxide underground before it reaches the atmosphere. Part of this greenhouse gas is pumped into porous, water-bearing underground rock layers. Now, a new study provides the first field evidence that CO2 can be stored safely for a million years in these saline aquifers, assuaging worries that the gas might escape back into the atmosphere.

    g
    Geologist Martin Cassidy, who co-authored the new study, samples a gas well at Bravo Dome, the world’s largest natural CO2 reservoir.

    “It’s a very comprehensive piece of work,” says geochemist Stuart Gilfillan of the University of Edinburgh in the United Kingdom, who was not involved in the study. “The approach is very novel.”

    There have been several attempts to capture the carbon dioxide released by the world’s 7000-plus coal-fired plants. Pilot projects in Algeria, Japan, and Norway indicate that CO2 can be stored in underground geologic formations such as depleted oil and gas reservoirs, deep coal seams, and saline aquifers. In the United States, saline aquifers are believed to have the largest capacity for CO2 storage, with potential sites spread out across the country, and several in western states such as Colorado also host large coal power plants. CO2 pumped into these formations are sealed under impermeable cap rocks, where it gradually dissolves into the salty water and mineralizes. Some researchers suggest the aquifers have enough capacity to store a century’s worth of emissions from America’s coal-fired plants, but others worry the gas can leak back into the air through fractures too small to detect.

    To resolve the dilemma, geoscientists need to know how long it takes for the trapped CO2 to dissolve. The faster the CO2 dissolves and mineralizes, the less risk that it would leak back into the atmosphere. But determining the rate of dissolution is no easy feat. Lab simulations suggest that the sealed gas could completely dissolve over 10,000 years, a process too slow to be tested empirically.

    So computational geoscientist Marc Hesse of the University of Texas, Austin, and colleagues turned to a natural lab: the Bravo Dome gas field in New Mexico, one of the world’s largest natural CO2 reservoirs. Ancient volcanic activities there have pumped the gas into a saline aquifer 700 meters underground. Since the 1980s, oil companies have drilled hundreds of wells there to extract the gas for enhanced oil recovery, leaving a wealth of data on the site’s geology and CO2 storage.

    To find out how fast CO2 dissolves in the aquifers, the researchers needed to know two things: the total amount of gas dissolved at the reservoir and how long it has been there. Because the gas is volcanic in origin, the researchers reasoned that it must have arrived at Bravo Dome steaming hot—enough to warm up the surrounding rocks. So they examined the buildup of radiogenic elements in the mineral apatite. These elements accumulate at low temperatures, but are released if the mineral is heated above 75°C, allowing the researchers to determine when the mineral was last heated above such a high temperature. The team estimated that the CO2 was pumped into the reservoir about 1.2 million years ago.

    Then the scientists calculated the amount of gas dissolved over the millennia, using the helium-3 isotope as a tracer. Like CO2, helium-3 is released during volcanic eruptions, and it is rather insoluble in saline water. By studying how the ratio of helium-3 to CO2 changes across the reservoir, the researchers found that out of the 1.6 gigatons of gas trapped underground at the reservoir, only a fifth has dissolved over 1.2 million years. That’s the equivalent of 75 years of emissions from a single 500-megawatt coal power plant, they report online this week in the Proceedings of the National Academy of Sciences.

    More intriguingly, the analysis also provided the first field evidence of how CO2 dissolves after it is pumped into the aquifers. In theory, the CO2 dissolves through diffusion, which takes place when the gas comes into contact with the water surface. But the process could move faster if convection—in which water saturated with CO2 sinks and fresh water flows into its place to absorb more gas—were also at work. Analysis revealed that at Bravo Dome, 10% of the total gas at the reservoir dissolved after the initial emplacement. Diffusion alone cannot account for that amount, the researchers argue, as the gas accumulating at the top of the reservoir would have quickly saturated still water. Instead, convection most likely occurred.

    Hesse says constraints on convection might explain why CO2 dissolves much more slowly in saline aquifers at Bravo Dome than previously estimated, at a rate of 0.1 gram per square meter per year. The culprit would be the relatively impermeable Brava Dome rocks, which limit water flow and thus the rate of convective CO2 dissolution. At storage sites with more porous rocks, the gas could dissolve much faster and mineralize earlier, he says.

    Even so, the fact that CO2 stayed locked up underground for so long at Bravo Dome despite ongoing industrial drilling should allay concerns about potential leakage, Hesse says. Carbon capture and storage “can work, if you do it in the right place,” he says. “[This is] an enormous amount of CO2 that has sat there, for all we can tell, very peacefully for more than a million years.”

    See the full article here.

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  • richardmitnick 3:11 pm on September 28, 2014 Permalink | Reply
    Tags: , Chemistry, ,   

    From Scientific American: “Weak Nuclear Force Shown to Give Asymmetry to Biochemistry of Life” 

    Scientific American

    Scientific American

    Sep 26, 2014
    Elizabeth Gibney and Nature magazine

    Physicists have found hints that the asymmetry of life — the fact that most biochemical molecules are ‘left-handed’ or ‘right-handed’ — could have been caused by electrons from nuclear decay in the early days of evolution. In an experiment that took 13 years to perfect, the researchers have found that these electrons tend to destroy certain organic molecules slightly more often than they destroy their mirror images.

    fish
    Life is made largely of molecules that are different than their mirror images.
    Credit: Brett Weinstein via Flickr

    Many organic molecules, including glucose and most biological amino acids, are ‘chiral’. This means that they are different than their mirror-image molecules, just like a left and a right glove are. Moreover, in such cases life tends to consistently use one of the possible versions — for example, the DNA double helix in its standard form always twists like a right-handed screw. But the reason for this preference has long remained a mystery.

    Many scientists think that the choice was simply down to chance. Perhaps, in one of the warm little ponds filled with organic chemicals where life arose, a statistical fluke generated a small imbalance in the relative amounts of the two versions of one chemical. This small imbalance could have then amplified over time.

    But an asymmetry in the laws of nature has led others to wonder whether some physical phenomenon could have tipped the balance during the early stages of life. The weak nuclear force, which is involved in nuclear decay, is the only force of nature known to have a handedness preference: electrons created in the subatomic process known as β decay are always ‘left-handed’. This means that their spin — a quantum property analogous to the magnetization of a bar magnet — is always opposite in direction to the electron’s motion.

    In 1967, biochemist Frederic Vester and environmental scientist Tilo Ulbricht proposed that photons generated by these so-called spin-polarized electrons — which are produced in the decay of radioactive materials or of cosmic-ray particles in the atmosphere — could have destroyed more of one kind of molecule than another, creating the imbalance. Some physicists have since suggested that the electrons themselves might be the source of the asymmetry.

    But the hunt to find chemical processes through which electrons or photons could preferentially destroy one version of a molecule over its mirror image has seen little success. Many claims have proven impossible to reproduce. The few experiments in which electron handedness produced a chiral imbalance could not identify the chemical process behind it, says Timothy Gay, a chemical physicist at the University of Nebraska–Lincoln and a co-author of the latest study. But pinpointing a chemical reaction would help scientists to rule out some candidate causes of the process and to better understand the physics that underlie it, he adds.

    Taking it slow

    Gay and Joan Dreiling, a physicist also at the University of Nebraska–Lincoln, fired low-energy, spin-polarized electrons at a gas of bromocamphor, an organic compound used in some parts of the world as a sedative. In the resulting reaction, some electrons were captured by the molecules, which then were kicked into an excited state. The molecules then fell apart, producing bromide ions and other highly reactive compounds. By measuring the flow of ions produced, the researchers could see how often the reaction occurred for each handedness of electron.

    The researchers found that left-handed bromocamphor was just slightly more likely to react with right-handed electrons than with left-handed ones. The converse was true when they used right-handed bromocamphor molecules. At the lowest energies, the direction of the preference flipped, causing an opposite asymmetry.

    In all cases the asymmetry was tiny, but consistent, like flipping a not-quite-fair coin. “The scale of the asymmetry is as though we flip 20,000 coins again and again, and on average, 10,003 of them land on heads while 9,997 land on tails,” says Dreiling.

    The low speed of the electrons was the key to why the experiment finally worked after so many years, Dreiling says. “The interaction takes longer, and it was that insight, I think, that led to our success,” she says.

    The test offers an explanation for how a chiral excess could — at least in principle — arise, Gay says. The research was published in Physical Review Letters on 12 September.

    The idea that spin-polarized electrons could transmit their asymmetry to organic molecules is attractive, says Uwe Meierhenrich, an analytical chemist at the University of Nice Sophia Antipolis in France. The tiny effect that Gay and Dreiling observed would have to be amplified to affect the chemistry of life as a whole — but there are known mechanisms for such amplification, he says. “From my point of view, the main question does not concern the amplification processes, but the first chiral-symmetry breaking,” he says.

    Meierhenrich says that he would like to see the experiment repeated with chiral molecules that are relevant to the origin of life, such as amino acids, to see whether the left-handed electrons produce the same effect.

    Primordial cause

    Even if spin-polarized electrons caused life to become chirally selective, it is still unclear what would have produced those electrons in the first place. Sources of β particles include phosphorus-32 decaying into sulphur-32, or the decay of muons, elementary particles produced at the end of a chain of decays that begin when cosmic ray particles hit the atmosphere. In both cases, the electrons would have been travelling much faster than in Gay’s reaction, but he says that it is possible for electrons to slow down without losing their chirality.

    Slower-moving, left-handed electrons are produced in other ways than via β decay, says Richard Rosenberg, a chemist at the Argonne National Laboratory in Illinois. In 2008 he and his team showed that irradiating a layer of magnetized iron with X-rays could also produce a chirality preference. Chirality could therefore also have been created in molecules stuck to magnetized particles in a dust cloud or comet, he says.

    Gay and his colleagues plan to look at similar reactions with other varieties of camphor molecules to understand how the spin of an electron dictates which of two chiral molecules it prefers.

    The interaction of left-handed electrons with organic molecules is not the only potential explanation for the chiral asymmetry of life.. Meierhenrich favors an alternative — the circularly polarized light that is produced by the scattering of light in the atmosphere and in neutron stars. In 2011, Meierhenrich and colleages showed that such light could transfer its handedness to amino acids.

    But even demonstrating how a common physical phenomenon would have favoured left-handed amino acids over right-handed ones would not tell us that this was how life evolved, adds Laurence Barron, a chemist at the University of Glasgow, UK. “There are no clinchers. We may never know.”

    See the full article here.

    Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years.

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  • richardmitnick 12:26 pm on September 14, 2014 Permalink | Reply
    Tags: , Chemistry, ,   

    From Rutgers: “Rutgers Physics Professors Find New Order in Quantum Electronic Material” 

    Rutgers University
    Rutgers University

    January 30, 2013
    Media Contact: Carl Blesch
    732-932-7084 x616
    E-mail: cblesch@ur.rutgers.edu

    May open door to new kinds of materials, magnets and superconductors

    Two Rutgers physics professors have proposed an explanation for a new type of order, or symmetry, in an exotic material made with uranium – a theory that may one day lead to enhanced computer displays and data storage systems and more powerful superconducting magnets for medical imaging and levitating high-speed trains.

    pc
    Piers Coleman

    Their discovery, published in this week’s issue of the journal Nature, has piqued the interest of scientists worldwide. It is one of the rare theory-only papers that this selective publication accepts. Typically the journal’s papers describe results of laboratory experimentation.

    Collaborating with the Rutgers professors was a postdoctoral researcher at Massachusetts Institute of Technology (MIT) who earned her doctorate at Rutgers.

    “Scientists have seen this behavior for 25 years, but it has eluded explanation.” said Piers Coleman, professor in the Department of Physics and Astronomy in the School of Arts and Sciences. When cooled to 17.5 degrees above absolute zero or lower (a bone-chilling minus 428 degrees Fahrenheit), the flow of electricity through this material changes subtly.

    The material essentially acts like an electronic version of polarized sunglasses, he explains. Electrons behave like tiny magnets, and normally these magnets can point in any direction. But when they flow through this cooled material, they come out with their magnetic fields aligned with the material’s main crystal axis.

    This effect, claims Coleman, comes from a new type of hidden order, or symmetry, in this material’s magnetic and electronic properties. Changes in order are what make liquid crystals, magnetic materials and superconductors work and perform useful functions.

    “Our quest to understand new types of order is a vital part of understanding how materials can be developed to benefit the world around us,” he said.

    Similar discoveries have led to technologies such as liquid crystal displays, which are now ubiquitous in flat-screen TVs, computers and smart phones, although the scientists are quick to acknowledge that their theoretical discovery won’t transform high-tech products overnight.

    pc
    Premala Chandra
    Nick Romanenko

    Coleman, along with Rutgers colleague Premala Chandra and MIT collaborator Rebecca Flint, describe what they call a “hidden order” in this compound of uranium, ruthenium and silicon. Uranium is commonly known for being nuclear reactor fuel or weapons material, but in this case physicists value it as a heavy metal with electrons that behave differently than those in common metals.

    Recent experiments on the material at the National High Magnetic Field Laboratory at Los Alamos National Laboratory in New Mexico provided the three physicists with data to refine their discovery.

    “We’ve dubbed our fundamental new order ‘hastatic’ order, named after the Greek word for spear,” said Chandra, also a professor in the Department of Physics and Astronomy. The name reflects the highly ordered properties of the material and its effect on aligning electrons that flow through it.

    “This new category of order may open the world to new kinds of materials, magnets, superconductors and states of matter with properties yet unknown,” she said. The scientists have predicted other instances where hastatic order may show up, and physicists are beginning to test for it.

    The scientists’ work was funded by the National Science Foundation and the Simons Foundation. Flint is a Simons Postdoctoral Fellow in physics at MIT.

    See the full article here.

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

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

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  • richardmitnick 1:49 pm on September 3, 2014 Permalink | Reply
    Tags: , , Chemistry, , , Peptoids   

    From LBL: “Peptoid Nanosheets at the Oil/Water Interface” 

    Berkeley Logo

    Berkeley Lab

    September 3, 2014
    Lynn Yarris (510) 486-5375

    From the people who brought us peptoid nanosheets that form at the interface between air and water, now come peptoid nanosheets that form at the interface between oil and water. Scientists at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed peptoid nanosheets – two-dimensional biomimetic materials with customizable properties – that self-assemble at an oil-water interface. This new development opens the door to designing peptoid nanosheets of increasing structural complexity and chemical functionality for a broad range of applications, including improved chemical sensors and separators, and safer, more effective drug delivery vehicles.

    Supramolecular assembly at an oil-water interface is an effective way to produce 2D nanomaterials from peptoids because that interface helps pre-organize the peptoid chains to facilitate their self-interaction,” says Ron Zuckermann, a senior scientist at the Molecular Foundry, a DOE nanoscience center hosted at Berkeley Lab. “This increased understanding of the peptoid assembly mechanism should enable us to scale-up to produce large quantities, or scale- down to screen many different nanosheets for novel functions.”

    nano
    Peptoid nanosheets are among the largest and thinnest free-floating organic crystals ever made, with an area-to-thickness equivalent of a plastic sheet covering a football field. Peptoid nanosheets can be engineered to carry out a wide variety of functions.
    two
    Ron Zuckerman and Geraldine Richmond led the development of peptoid nanosheets that form at the interface between oil and water, opening the door to increased structural complexity and chemical functionality for a broad range of applications.

    Zuckermann, who directs the Molecular Foundry’s Biological Nanostructures Facility, and Geraldine Richmond of the University of Oregon are the corresponding authors of a paper reporting these results in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled Assembly and molecular order of two-dimensional peptoid nanosheets at the oil-water interface. Co-authors are Ellen Robertson, Gloria Olivier, Menglu Qian and Caroline Proulx.

    Peptoids are synthetic versions of proteins. Like their natural counterparts, peptoids fold and twist into distinct conformations that enable them to carry out a wide variety of specific functions. In 2010, Zuckermann and his group at the Molecular Foundry discovered a technique to synthesize peptoids into sheets that were just a few nanometers thick but up to 100 micrometers in length. These were among the largest and thinnest free-floating organic crystals ever made, with an area-to-thickness equivalent of a plastic sheet covering a football field. Just as the properties of peptoids can be chemically customized through robotic synthesis, the properties of peptoid nanosheets can also be engineered for specific functions.

    “Peptoid nanosheet properties can be tailored with great precision,” Zuckermann says, “and since peptoids are less vulnerable to chemical or metabolic breakdown than proteins, they are a highly promising platform for self-assembling bio-inspired nanomaterials.”

    In this latest effort, Zuckermann, Richmond and their co-authors used vibrational sum frequency spectroscopy to probe the molecular interactions between the peptoids as they assembled at the oil-water interface. These measurements revealed that peptoid polymers adsorbed to the interface are highly ordered, and that this order is greatly influenced by interactions between neighboring molecules.

    “We can literally see the polymer chains become more organized the closer they get to one another,” Zuckermann says.

    ft
    Peptoid polymers adsorbed to the oil-water interface are highly ordered thanks to interactions between neighboring molecules.

    The substitution of oil in place of air creates a raft of new opportunities for the engineering and production of peptoid nanosheets. For example, the oil phase could contain chemical reagents, serve to minimize evaporation of the aqueous phase, or enable microfluidic production.

    “The production of peptoid nanosheets in microfluidic devices means that we should soon be able to make combinatorial libraries of different functionalized nanosheets and screen them on a very small scale,” Zuckermann says. “This would be advantageous in the search for peptoid nanosheets with the molecular recognition and catalytic functions of proteins.”

    Zuckermann and his group at the Molecular Foundry are now investigating the addition of chemical reagents or cargo to the oil phase, and exploring their interactions with the peptoid monolayers that form during the nanosheet assembly process.

    “In the future we may be able to produce nanosheets with drugs, dyes, nanoparticles or other solutes trapped in the interior,” he says. “These new nanosheets could have a host of interesting biomedical, mechanical and optical properties.”

    This work was primarily funded by the DOE Office of Science and the Defense Threat Reduction Agency. Part of the research was performed at the Molecular Foundry and the Advanced Light Source, which are DOE Office of Science User Facilities.

    See the full article here.

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

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  • richardmitnick 1:41 pm on August 29, 2014 Permalink | Reply
    Tags: , , , , Chemistry,   

    From LBL: “Going to Extremes for Enzymes” 

    Berkeley Logo

    Berkeley Lab

    August 29, 2014
    Lynn Yarris (510) 486-5375

    In the age-old nature versus nurture debate, Douglas Clark, a faculty scientist with Berkeley Lab and the University of California (UC) Berkeley, is not taking sides. In the search for enzymes that can break lignocellulose down into biofuel sugars under the extreme conditions of a refinery, he has prospected for extremophilic microbes and engineered his own cellulases.

    ext
    Extremophiles thriving in thermal springs where the water temperature can be close to boiling can be a rich source of enzymes for the deconstruction of lignocellulose.

    Speaking at the national meeting of the American Chemical Society (ACS) in San Francisco, Clark discussed research for the Energy Biosciences Institute (EBI) in which he and his collaborators are investigating ways to release plant sugars from lignin for the production of liquid transportation fuels. Sugars can be fermented into fuels once the woody matter comprised of cellulose, hemicellulose, and lignin is broken down, but lignocellulose is naturally recalcitrant.

    “Lignocellulose is designed by nature to stand tall and resist being broken down, and lignin in particular acts like a molecular glue to help hold it together” said Clark, who holds appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Chemical and Biomolecular Engineering Department where he currently serves as dean of the College of Chemistry. “Consequently, lignocellulosic biomass must undergo either chemical or enzymatic deconstruction to release the sugars that can be fermented to biofuels.”

    dc
    Douglas Clark holds joint appointments with Berkeley Lab and UC Berkeley and is a principal investigator with the Energy Biosciences Institute. (Photo by Roy Kaltschmidt)

    For various chemical reasons, all of which add up to cost-competitiveness, biorefineries could benefit if the production of biofuels from lignocellulosic biomass is carried out at temperatures between 65 and 70 degrees Celsius. The search by Clark and his EBI colleagues for cellulases that can tolerate these and even harsher conditions led them to thermal springs near Gerlach, Nevada, where the water temperature can be close to boiling. There they discovered a consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius.

    “This consortium represents the first instance of Archaea able to deconstruct lignocellulose optimally above 90°C,” Clark said.

    Following metagenomic studies on the consortium, the most active high-temperature cellulase was identified and named EBI-244.

    “The EBI-244 cellulase is active at temperatures as high as 108 degrees Celsius, the most extremely heat-tolerant enzyme ever found in any cellulose-digesting microbe,” Clark said.

    The most recent expedition of Clark and his colleagues was to thermal hot springs in Lassen Volcanic National Park, where they found an enzyme active on cellulose up to 100°C under highly acidic conditions – pH approximately 2.2.

    “The Lassen enzyme is the most acidothermophilic cellulase yet discovered,” Clark said. “The final products that it forms are similar to those produced by EBI244.”

    three
    A consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius yielded EBI-244, the most active high-temperature cellulase ever identified.

    In addition to bioprospecting for heat tolerant enzymes, Clark and his colleagues have developed a simple and effective mutagenesis method to enhance the properties of natural enzymes. Most recently they used this technique to increase the optimal temperature and enhance the thermostability of Ce17A, a fungal cellulase that is present in high concentrations in commercial cellulase cocktails. They engineered yeast to produce this enzyme with encouraging results.

    “The yeast Saccharomyces cerevisiae has often been used both in the engineering and basic study of Cel7A; however, Cel7A enzymes recombinantly expressed in yeast are often less active and less stable than their native counterparts,” Clark said. “We discovered that an important post-translational modification that was sometimes absent in the yeast-expressed enzyme was the underlying cause of this disparity and successfully carried out the post-translational modification in vitro. After this treatment, the properties of Cel7A recombinantly expressed in yeast were improved to match those of the native enzyme.”

    Collaborators in this research include Harvey Blanch, who also holds joint appointments with Berkeley Lab and UC Berkeley, and Frank Robb from the University of Maryland.

    EBI, which provided the funding for this research, is a collaborative partnership between BP, the funding agency, UC Berkeley, Berkeley Lab and the University of Illinois at Urbana-Champaign.

    See the full article here.

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  • richardmitnick 4:29 pm on August 28, 2014 Permalink | Reply
    Tags: , Chemistry,   

    From PNNL Lab: “Playing Twenty Questions with Molecules at Plasmonic Junctions” 


    PNNL Lab

    August 2014
    Toward engineering ultrasensitive probes of nanoscale physical and chemical processes

    Results: Sometimes, it seems as if molecules struggle to communicate with scientists. When it comes to junction plasmons, essentially light waves trapped at tiny gaps between noble metals, what the molecules have to say could radically change the design of detectors used for science and security. Single molecule detection sensitivity is feasible through Raman scattering from molecules coaxed into plasmonic junctions. Scientists at Pacific Northwest National Laboratory (PNNL) found that sequences of Raman spectra recorded at a plasmonic junction, formed by a gold tip and a silver surface, exhibit dramatic intensity fluctuations, accompanied by switching from familiar vibrational line spectra of a molecule to broad band spectra of the same origin. The fluctuations confirm the team’s earlier model that assigns enhanced band spectra in Raman scattering from plasmonic nanojunctions to shorting of the junction plasmon through intervening molecular bridges.

    “It’s all about asking it the right questions and listening to what it has to say,” said Dr. Patrick El-Khoury, who has been working on this project for 2 years.

    charts
    “This is a paradigm shift in molecular spectroscopy, as we are no longer after molecular properties. Rather, we use those properties — in this study the symmetry of the observable vibrational modes — to tell us about the rich environments in which molecules reside,” said Dr. Patrick El-Khoury. (A) Time evolution of contact mode spectra of DMS on a 15 nm silver film. (B) Cross-correlation map of the individually normalized spectra shown in the image on the top. Copyright 2014: American Chemical Society

    Why It Matters: A host of emerging state-of-the-art devices and instruments rely on molecule-plasmon interactions. Recent works demonstrated yoctomolar detection sensitivity in Raman scattering from plasmonic nanojunctions, or the ability to detect 1 molecule in 602,214,000,000,000,000,000,000. Plasmonic sensors operating at this detection limit are able to determine the chemical identity of minute quantities of radioactive and environmental hazards. The development of single molecule chemical nanoscopes could answer fundamental questions about physical and chemical processes taking place over nanometer length scales. The fundamentals gained from this study could impact the design of ultrasensitive plasmonic sensors and chemical nanoscopes used to understand the fundamental chemistry behind energy storage and production, as well as the blueprints of extremely tiny electronic devices.

    “Before you can engineer the devices you need, you need to know how molecules behave over length scales comparable to their characteristic dimensions. Our research is fundamental, providing novel insights into how molecules interact with junction plasmons,” said Dr. Wayne Hess, a chemical physicist at PNNL

    See the full article here.

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

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

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  • richardmitnick 2:39 pm on August 19, 2014 Permalink | Reply
    Tags: , Chemistry, , Nuclear magnetic resonance,   

    From Berkeley Lab: “News Center NMR Using Earth’s Magnetic Field” 

    Berkeley Logo

    Berkeley Lab

    August 19, 2014
    Rachel Berkowitz

    Earth’s magnetic field, a familiar directional indicator over long distances, is routinely probed in applications ranging from geology to archaeology. Now it has provided the basis for a technique which might, one day, be used to characterize the chemical composition of fluid mixtures in their native environments.

    Researchers from the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) conducted a proof-of-concept NMR experiment in which a mixture of hydrocarbons and water was analyzed using a high-sensitivity magnetometer and a magnetic field comparable to that of the Earth.

    The work was conducted in the NMR laboratory of Alexander Pines, one of the world’s foremost NMR authorities, as part of a long-standing collaboration with physicist Dmitry Budker at the University of California, Berkeley, along with colleagues at the National Institute of Standards and Technology (NIST). The work will be featured on the cover of Angewandte Chemie and is published in a paper titled Ultra-Low-Field NMR Relaxation and Diffusion Measurements Using an Optical Magnetometer. The corresponding author is Paul Ganssle, who was a PhD student in Pines’ lab at the time of the work.

    “This fundamental research program seeks to answer a broad question: how can we sense the interior chemical and physical attributes of an object at a distance, without sampling it or encapsulating it?” says Vikram Bajaj, a principal investigator in Pines’ group. “A particularly beautiful aspect of magnetic resonance is its ability to gently peer within intact objects, but it’s tough to do that from far away.”

    High-field and low-field NMR

    The exquisite sensitivity of NMR for detecting chemical composition, and the spatial resolution which it can provide in medical applications, requires large and precise superconducting magnets. These magnets are expensive and immobile. Further, the sample of interest must be placed inside the magnet, such that the entire sample is exposed to a homogeneous magnetic field. This well-developed method is called high-field NMR. The sensitivity of high-field NMR is proportional to magnetic field strength.

    three
    (From left) Alex Pines, Dimitry Budker and Scott Seltzer led a proof-of-concept NMR experiment using a high-sensitivity magnetometer and a magnetic field comparable to that of the Earth. (Photo by Roy Kaltschmidt)

    But chemical characterization of objects that cannot be placed inside a magnet requires a different approach. In ex situ NMR measurements, the geometry of a typical high-field experiment is reversed such that the detector probes the sample surface, and the magnetic field is projected into the object. A main challenge with this situation is generating a homogeneous magnetic field over a sufficiently large sample area: it is not feasible to generate field strengths necessary to make conventional high-resolution NMR measurements.

    Instead of a superconducting magnet, low-field NMR measurements may rely on Earth’s magnetic field, given a sufficiently sensitive magnetometer.

    “One nice thing about Earth’s magnetic field is that it’s very homogeneous,” explains Ganssle. “The problem with its use in inductively-detected MRI [MRI – magnetic resonance imaging – is NMR’s technological sibling] is that you need a magnetic field that’s both strong and homogeneous, so you need to surround the whole subject with superconducting coils, which is not something that’s possible in an application like oil-well logging.”

    “Sensitivity of magnetic resonance depends profoundly on the magnetic field, because the field causes the detected spins to align slightly,” adds Bajaj. “The stronger the applied field, the stronger the signal, and the higher its frequency, which also contributes to the detection sensitivity.”

    pg
    Paul Ganssle is the corresponding author of a paper in Angewandte Chemie describing the ultra-low-field NMR using an optical magnetometer. (Photo by Roy Kaltschmidt)

    Earth’s magnetic field is indeed very weak, but optical magnetometers can serve as detectors for ultra-low-field NMR measurements in the ambient field alone without any permanent magnets. This means that ex-situ measurements lose chemical sensitivity due to field strength alone. But this method offers other advantages.

    Relaxation and diffusion

    In high-field NMR, the chemical properties of a sample are determined from their resonance spectrum, but this is not possible without either extremely high fields or extremely long-lived coherent signals (neither of which are possible with permanent magnets). In contrast, relaxation and diffusion measurements in low-field NMR are more than sufficient to determine bulk materials properties.

    “The approach at low-field, which you can achieve using permanent magnets or Earth’s magnetic field, is to measure spin relaxation,” explains Ganssle. Relaxation refers to the rate at which polarized spin returns to equilibrium, based on chemical and physical characteristics of the system. Additionally, NMR experiments resolve chemical compounds based on their different diffusion coefficients, which depend on the size and shape of the molecule.

    A key difference between this and conventional experiments is that the relaxation and diffusion properties are resolved through optically-detected NMR, which operates sensitively even in low magnetic fields.

    “A previous achievement of our collaboration has been the development of magnetometers for the detection of NMR,” says Bajaj. “This experiment represents the first time magnetometers have been used to make combined relaxation and diffusion measurements of multicomponent mixtures.”

    Relaxation and/or diffusion measurements are already commonly used in the oil industry for underground NMR measurements, though conventional probes use a permanent magnet to increase the local magnetic field. There were attempts to perform oil well logging starting in the 1950s using the Earth’s ambient field, but insufficient detection sensitivity led to the introduction of magnets, which are now ubiquitous in logging tools.

    “What’s novel here is that using magnetometers, we finally have technology that might be sensitive enough for efficient detection in the Earth’s field, perhaps ultimately enabling detection at longer distances,” explains Scott Seltzer, a co-author on the study.

    The design was tested in the lab by measuring relaxation coefficients first for various hydrocarbons and water by themselves, then for a heterogeneous mixture, as well as in two-dimensional correlation experiments, using a magnetometer and an applied magnetic field representative of Earth’s.

    “This proof of concept might be productively applied in the oil industry,” says Ganssle. “We mixed hydrocarbons and water, pre-polarized them with a magnet, and applied a magnetic field the same as the Earth’s. Then we made measurements with our magnetometer and determined that we had easily enough sensitivity to separate components of oil and water based on their relaxation spectra.”

    This technology could help the oil industry to characterize fluids in rocks, because water relaxes at a different rate from oil. Other applications include measuring the content of water and oil flowing in a pipeline by measuring chemical composition with time, and inspecting the quality of foods and any kind of polymer curing process such as cement curing and drying.

    The next step involves understanding the depth in a geological formation that could be imaged with this technology.

    “Our next study will be tailored to that question,” says Bajaj. “We hope that this technology will eventually peer a meter or more into the formation and elucidate the chemistry within.”

    Eventually, probes could be used to characterize entire borehole environments in this way, while current devices can only image inches deep. The combination of terrestrial magnetism and versatile sensing technology again offers an elegant solution.

    Other authors on the Angewandte Chemie paper include Hyun Doug Shin, Micah Ledbetter, Dmitry Budker, Svenja Knappe, John Kitching, and Alexander Pines. The current publication presents some of the work for which Berkeley Lab won an R&D 100 award earlierthis year on optically-detected oil well logging by MRI.

    This research was supported by the U.S. Department of Energy’s Office of Science.

    See the full article here.

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

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