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Young S.M.,Center for Computational Materials Science | Kane C.L.,University of Pennsylvania
Physical Review Letters | Year: 2015

Graphene is famous for being a host of 2D Dirac fermions. However, spin-orbit coupling introduces a small gap, so that graphene is formally a quantum spin Hall insulator. Here we present symmetry-protected 2D Dirac semimetals, which feature Dirac cones at high-symmetry points that are not gapped by spin-orbit interactions and exhibit behavior distinct from both graphene and 3D Dirac semimetals. Using a two-site tight-binding model, we construct representatives of three possible distinct Dirac semimetal phases and show that single symmetry-protected Dirac points are impossible in two dimensions. An essential role is played by the presence of nonsymmorphic space group symmetries. We argue that these symmetries tune the system to the boundary between a 2D topological and trivial insulator. By breaking the symmetries we are able to access trivial and topological insulators as well as Weyl semimetal phases. © 2015 American Physical Society.


News Article | April 11, 2016
Site: www.nrl.navy.mil

An international team of physicists has used a scanning tunneling microscope to create a minute transistor consisting of a single molecule and a small number of atoms. The observed transistor action is markedly different from the conventionally expected behavior and could be important for future device technologies as well as for fundamental studies of electron transport in molecular nanostructures. The physicists represent the Paul-Drude-Institut für Festkörperelektronik (PDI) and the Freie Universität Berlin (FUB), Germany, the NTT Basic Research Laboratories (NTT-BRL), Japan, and the U.S. Naval Research Laboratory (NRL). Their complete findings are published in the 13 July 2015 issue of the journal Nature Physics. Transistors have a channel region between two external contacts and an electrical gate electrode to modulate the current flow through the channel. In atomic-scale transistors, this current is extremely sensitive to single electrons hopping via discrete energy levels. In earlier studies, researchers have examined single-electron transport in molecular transistors using top-down approaches, such as lithography and break junctions. But atomically precise control of the gate—which is crucial to transistor action at the smallest size scales—is not possible with these approaches. The team used a highly stable scanning tunneling microscope (STM) to create a transistor consisting of a single organic molecule and positively charged metal atoms, positioning them with the STM tip on the surface of an indium arsenide (InAs) crystal. Dr. Kiyoshi Kanisawa, a physicist at NTT-BRL, used the growth technique of molecular beam epitaxy to prepare this surface. Subsequently, the STM approach allowed the researchers to assemble electrical gates from the +1 charged atoms with atomic precision and then to place the molecule at various desired positions close to the gates. Dr. Stefan Fölsch, a physicist at the PDI who led the team, explained that "the molecule is only weakly bound to the InAs template. So, when we bring the STM tip very close to the molecule and apply a bias voltage to the tip-sample junction, single electrons can tunnel between template and tip by hopping via nearly unperturbed molecular orbitals, similar to the working principle of a quantum dot gated by an external electrode. In our case, the charged atoms nearby provide the electrostatic gate potential that regulates the electron flow and the charge state of the molecule." But there is a substantial difference between a conventional semiconductor quantum dot—comprising typically hundreds or thousands of atoms—and the present case of a surface-bound molecule. Dr. Steven Erwin, a physicist in the Center for Computational Materials Science at NRL and expert in density-functional theory, pointed out that, "the molecule adopts different rotational orientations, depending on its charge state. We predicted this based on first-principles calculations and confirmed it by imaging the molecule with the STM." This coupling between charge and orientation has a dramatic effect on the electron flow across the molecule, manifested by a large conductance gap at low bias voltages. Dr. Piet Brouwer, a physicist at FUB and expert in quantum transport theory, said, "This intriguing behavior goes beyond the established picture of charge transport through a gated quantum dot. Instead, we developed a generic model that accounts for the coupled electronic and orientational dynamics of the molecule." This simple and physically transparent model entirely reproduces the experimentally observed single-molecule transistor characteristics. The perfection and reproducibility offered by these STM-generated transistors will enable researchers to explore elementary processes involving current flow through single molecules at a fundamental level. Understanding and controlling these processes—and the new kinds of behavior to which they can lead—will be important for integrating molecule-based devices with existing semiconductor technologies. This research is funded by the German Research Foundation, Collaborative Research Network 658. About the U.S. Naval Research Laboratory The U.S. Naval Research Laboratory provides the advanced scientific capabilities required to bolster our country's position of global naval leadership. The Laboratory, with a total complement of approximately 2,500 personnel, is located in southwest Washington, D.C., with other major sites at the Stennis Space Center, Miss., and Monterey, Calif. NRL has served the Navy and the nation for over 90 years and continues to advance research further than you can imagine. For more information, visit the NRL website or join the conversation on Twitter, Facebook, and YouTube.


Kim Y.C.,Center for Computational Materials Science | Mittal J.,Lehigh University
Physical Review Letters | Year: 2013

A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules. Predicted binding free energies are in excellent agreement with simulation data over a wide range of crowder sizes and packing fractions. It is shown that attractive interactions between proteins and crowding agents counteract the stabilizing effects of excluded volume interactions. A critical attraction strength, for which there is no net effect of crowding, is approximately independent of the crowder packing fraction. © 2013 American Physical Society.


News Article | April 11, 2016
Site: www.nrl.navy.mil

U.S. Naval Research Laboratory (NRL) research physicist, Dr. Alexander Efros, is bestowed the honor of Fellow by the Materials Research Society (MRS), recognizing a record of success in research in the field of optical science materials and technology. Most notably, Efros is recognized for his pioneering and fundamental contributions to the theory of low dimensional semiconductor structures, which have established the basic theoretical concepts that today are used by everyone for describing the electronic and optical properties of nanocrystal quantum dots, nanowires and nanoplatelets. These concepts are also commonly used in the development of novel nanocrystal-based optical devices, which are smaller, cheaper, more efficient, and consume less energy than the traditional devices. "Dr. Efros' rooted commitment to materials science theory and his profound knowledge of solid-state physics are notably recognized and respected by the scientific community worldwide," said Dr. Michael Mehl, head, NRL Center for Computational Materials Science. "His work has given us the ability to understand and control the behavior of semiconductor nanostructures, leading to new and exciting applications in lasers, light emitting diodes, and photovoltaics." In the early 1980s Efros and his colleagues, A. I. Ekimov and A. A. Onuschenko, discovered semiconductor nanocrystals while studying doped glasses. They also explained the origin of the size-dependent optical properties of nanocrystals, and established that nanocrystals act as 'artificial atoms' that opened the door to a new class of optical materials. Like atoms, nanocrystals have discrete optical energy spectra that are tunable over a wide spectral range by varying their size. At the same time these atoms can be manipulated with nanometer precision to form nanocrystal molecules and solids. Nanocrystals also can serve as dopants in nanocrystalline solids. As a result, researchers now have an unlimited number of new atomic elements available to create new materials. Based on size controlled tunable emission spectra and great structural and chemical flexibility, the nanocrystals have potential in the creation of a new class of tunable quantum dot lasers and light emitting diodes that function from the far infrared to deep ultraviolet wavelength ranges. An additional application is the labeling of biological molecules by nanocrystals, which are being developed as ultra-sensitive detectors and sensors for use in neuron and drug transport imaging, and the detection of dangerous chemical agents. The high optical stability of the nanocrystals allow for higher efficiency in quantum dot displays. In very recent developments of this area, researchers from Samsung Electronics demonstrated in 2012 a full-color quantum-dot display monitor that is brighter than liquid-crystal displays and consumes less than a fifth of the power. Receiving a Master of Science degree in physical engineering in 1973 and a Ph.D. in physics in 1978, both from the Technical University in Leningrad, USSR, Efros became senior researcher at the Ioffe Institute in Leningrad. From 1990 to 1992 he was senior researcher at the Technical University of Munich and a visiting scientist at Massachusetts Institute of Technology (MIT). In 1993 Efros came to NRL as a consultant and in 1999 become senior researcher in NRL's Materials Science and Technology Division. Efros has authored and co-authored more than 190 articles in refereed journals and holds two patents. He has given more than 80 invited talks at international meetings and more than 190 at various universities and laboratories. He is co-editor of two books on nanoscale semiconductors and co-organizer of many conferences on this topic and is a Fellow of the American Physical Society. Efros has received five Alan Berman publication awards, an NRL Patent Award (2003), the NRL Sigma Xi Award for Pure Science (2006), the E. F. Gross Medal of the D. S. Rozhdestvensky Optical Society of Russia (2013 with A. I. Ekimov and A. A. Onuschenko) the R.W. Wood Prize of the Optical Society of America (2006, with L. E. Brus and A. I. Ekimov), the Humboldt Research Award for Senior U.S. Scientists (2008), and the Dolores M. Etter Top Navy Scientists and Engineers of the Year Award (2009). About the U.S. Naval Research Laboratory The U.S. Naval Research Laboratory provides the advanced scientific capabilities required to bolster our country's position of global naval leadership. The Laboratory, with a total complement of approximately 2,500 personnel, is located in southwest Washington, D.C., with other major sites at the Stennis Space Center, Miss., and Monterey, Calif. NRL has served the Navy and the nation for over 90 years and continues to advance research further than you can imagine. For more information, visit the NRL website or join the conversation on Twitter, Facebook, and YouTube.


Kim Y.C.,Center for Computational Materials Science | Hummer G.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases
Biochimica et Biophysica Acta - Bioenergetics | Year: 2012

Cytochrome c oxidase is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, cytochrome c oxidase translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in cytochrome c oxidase. Basic principles of the cytochrome c oxidase proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the active-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for cytochrome c oxidase provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. This article is part of a Special Issue entitled: Respiratory Oxidases. © 2011 Elsevier B.V. All rights reserved.


Roycki B.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases | Kim Y.C.,Center for Computational Materials Science | Hummer G.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases
Structure | Year: 2011

We developed and implemented an ensemble-refinement method to study dynamic biomolecular assemblies with intrinsically disordered segments. Data from small angle X-ray scattering (SAXS) experiments and from coarse-grained molecular simulations were combined by using a maximum-entropy approach. The method was applied to CHMP3 of ESCRT-III, a protein with multiple helical domains separated by flexible linkers. Based on recent SAXS data by Lata et al. (J. Mol. Biol. 378, 818, 2008), we constructed ensembles of CHMP3 at low- and high-salt concentration to characterize its closed autoinhibited state and open active state. At low salt, helix α5 is bound to the tip of helices α1 and α2, in excellent agreement with a recent crystal structure. Helix α6 remains free in solution and does not appear to be part of the autoinhibitory complex. The simulation-based ensemble refinement is general and effectively increases the resolution of SAXS beyond shape information to atomically detailed structures. © 2011 Elsevier Ltd All rights reserved.


News Article | January 28, 2016
Site: phys.org

At the macro-scale, the conversion of ethylene has long been considered among the reactions insensitive to the structure of the catalyst used. However, by examining reactions catalyzed by platinum clusters containing between 9 and 15 atoms, researchers in Germany and the United States found that at the nanoscale, that's no longer true. The shape of nanoscale clusters, they found, can dramatically affect reaction efficiency. While the study investigated only platinum nanoclusters and the ethylene reaction, the fundamental principles may apply to other catalysts and reactions, demonstrating how materials at the very smallest size scales can provide different properties than the same material in bulk quantities. Supported by the Air Force Office of Scientific Research and the Department of Energy, the research will be reported January 28 in the journal Nature Communications. "We have re-examined the validity of a very fundamental concept on a very fundamental reaction," said Uzi Landman, a Regents' Professor and F.E. Callaway Chair in the School of Physics at the Georgia Institute of Technology. "We found that in the ultra-small catalyst range, on the order of a nanometer in size, old concepts don't hold. New types of reactivity can occur because of changes in one or two atoms of a cluster at the nanoscale." The widely-used conversion process actually involves two separate reactions: (1) dissociation of H2 molecules into single hydrogen atoms, and (2) their addition to the ethylene, which involves conversion of a double bond into a single bond. In addition to producing ethane, the reaction can also take an alternative route that leads to the production of ethylidene, which poisons the catalyst and prevents further reaction. The project began with Professor Ueli Heiz and researchers in his group at the Technical University of Munich experimentally examining reaction rates for clusters containing 9, 10, 11, 12 or 13 platinum atoms that had been placed atop a magnesium oxide substrate. The 9-atom nanoclusters failed to produce a significant reaction, while larger clusters catalyzed the ethylene hydrogenation reaction with increasingly better efficiency. The best reaction occurred with 13-atom clusters. Bokwon Yoon, a research scientist in Georgia Tech's Center for Computational Materials Science, and Landman, the center's director, then used large-scale first-principles quantum mechanical simulations to understand how the size of the clusters - and their shape - affected the reactivity. Using their simulations, they discovered that the 9-atom cluster resembled a symmetrical "hut," while the larger clusters had bulges that served to concentrate electrical charges from the substrate. "That one atom changes the whole activity of the catalyst," Landman said. "We found that the extra atom operates like a lightning rod. The distribution of the excess charge from the substrate helps facilitate the reaction. Platinum 9 has a compact shape that doesn't facilitate the reaction, but adding just one atom changes everything." Nanoclusters with 13 atoms provided the maximum reactivity because the additional atoms shift the structure in a phenomena Landman calls "fluxionality." This structural adjustment has also been noted in earlier work of these two research groups, in studies of clusters of gold which are used in other catalytic reactions. "Dynamic fluxionality is the ability of the cluster to distort its structure to accommodate the reactants to actually enhance reactivity," he explained. "Only very small aggregates of metal can show such behavior, which mimics a biochemical enzyme." The simulations showed that catalyst poisoning also varies with cluster size - and temperature. The 10-atom clusters can be poisoned at room temperature, while the 13-atom clusters are poisoned only at higher temperatures, helping to account for their improved reactivity. "Small really is different," said Landman. "Once you get into this size regime, the old rules of structure sensitivity and structure insensitivity must be assessed for their continued validity. It's not a question anymore of surface-to-volume ratio because everything is on the surface in these very small clusters." While the project examined only one reaction and one type of catalyst, the principles governing nanoscale catalysis - and the importance of re-examining traditional expectations - likely apply to a broad range of reactions catalyzed by nanoclusters at the smallest size scale. Such nanocatalysts are becoming more attractive as a means of conserving supplies of costly platinum. "It's a much richer world at the nanoscale than at the macroscopic scale," added Landman. "These are very important messages for materials scientists and chemists who wish to design catalysts for new purposes, because the capabilities can be very different." Along with the experimental surface characterization and reactivity measurements, the first-principles theoretical simulations provide a unique practical means for examining these structural and electronic issues because the clusters are too small to be seen with sufficient resolution using most electron microscopy techniques or traditional crystallography. "We have looked at how the number of atoms dictates the geometrical structure of the cluster catalysts on the surface and how this geometrical structure is associated with electronic properties that bring about chemical bonding characteristics that enhance the reactions," Landman added. Explore further: Scientists finely control methane combustion to get different products More information: Andrew S. Crampton et al. Structure sensitivity in the nonscalable regime explored via catalysed ethylene hydrogenation on supported platinum nanoclusters, Nature Communications (2016). DOI: 10.1038/ncomms10389


Hoang K.,North Dakota State University | Johannes M.D.,Center for Computational Materials Science
Journal of Materials Chemistry A | Year: 2014

We report a comprehensive first-principles study of the thermodynamics and transport of intrinsic point defects in layered oxide cathode materials LiMO2 (M = Co, Ni), using density-functional theory and the Heyd-Scuseria-Ernzerhof screened hybrid functional. We find that LiCoO 2 has a complex defect chemistry; different electronic and ionic defects can exist under different synthesis conditions, and LiCoO2 samples free of cobalt antisite defects can be made under Li-excess (Co-deficient) environments. A defect model for lithium over-stoichiometric LiCoO2 is also proposed, which involves negatively charged lithium antisites and positively charged small (hole) polarons. In LiNiO2, a certain amount of Ni3+ ions undergo charge disproportionation and the concentration of nickel ions in the lithium layers is high. Tuning the synthesis conditions may reduce the nickel antisites but would not remove the charge disproportionation. In addition, we find that LiMO2 cannot be doped n- or p-type; the electronic conduction occurs via hopping of small polarons and the ionic conduction occurs via migration of lithium vacancies, either through a monovacancy or divacancy mechanism, depending on the vacancy concentration. © 2014 the Partner Organisations.


Erwin S.C.,Center for Computational Materials Science
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

We recently proposed that impurity doping in colloidally grown semiconductor nanocrystals is often controlled primarily by kinetics rather than by thermodynamics. In this "trapped-dopant" model the diffusion of an impurity through a nanocrystal is negligible at colloidal growth temperatures. Consequently, an impurity can only be incorporated as a dopant into a growing nanocrystal if it first adsorbs on the surface and is then overgrown. This surface adsorption can be complicated by a competing process: the binding of the impurity by surfactant molecules and other agents added to the growth solution to passivate the nanocrystal and control its growth. Here we use density-functional theory to study the interplay and outcome of these processes for the doping of PbSe nanocrystals by a number of candidate dopants (Mn, Co, Cl, In, Cd, Tl, etc.) in the presence of two widely used growth additives (oleic acid and hexadecylamine). The results suggest that successful doping requires making a trade-off between surface adsorption (which favors small dopants) and interior trapping (which favors large dopants). Moreover, the widely used growth agent oleic acid binds strongly to almost all dopants, suggesting that the standard growth procedure may require modification for successful doping to be realized. © 2010 The American Physical Society.


Bernstein N.,Center for Computational Materials Science
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2012

Frette and Hemmer recently showed that for a simple model for the boarding of an airplane, the mean time to board scales as a power law with the number of passengers N and the exponent is less than 1. They note that this scaling leads to the prediction that the "back-to-front" strategy, where passengers are divided into groups from contiguous ranges of rows and each group is allowed to board in turn from back to front once the previous group has found their seats, has a longer boarding time than would a single group. Here I extend their results to a larger number of passengers using a sampling approach and explore a scenario where the queue is presorted into groups from back to front, but allowed to enter the plane as soon as they can. I show that the power law dependence on passenger numbers is different for large N and that there is a boarding time reduction for presorted groups, with a power law dependence on the number of presorted groups. © 2011 Published by the American Physical Society.

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