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Sample records for dialkylimidazolium chloroaluminates ab

  1. Dialkylimidazolium chloroaluminates: Ab initio calculations, Raman and neutron scattering measurements

    SciTech Connect

    Takahasi, S. ); Curtiss, L.A.; Gosztola, D.; Koura, N. ); Loong, C.K.; Saboungi, M.L. . Materials Science Div.)

    1993-04-01

    The Raman and neutron scattering spectra of 46 mol% AlCl[sub 3] -54 mol% 1-ethyl-3-methyl imidazolium chloride (EMIC) and 67 mol% AlCl[sub 3] - 33 mol% EMIC melts are presented. Ab initio molecular orbital calculations have been carried out on structures of chloroaluminate anion and EMI cation and the interaction between anion and cation.

  2. Wetting behavior of dialkylimidazolium chloroaluminate, a room-temperature molten salt. Interim report, May-September 1984

    SciTech Connect

    Eberhart, J.G.

    1985-08-01

    The wetting behavior of a battery electrolyte can have a dramatic effect on the internal resistance of the battery as well as its cycle life. Good wetting of battery separators by electrolyte is essential for easy passage of ions through the separator pores during charge and discharge. Porous, gas-diffusion electrodes require, on the other hand, a lesser degree of electrolyte wetting, so that the line of contact of three phases (reactive gas/liquid electrolyte/porous-electrode or current collector) can be maintained within the porous electrode through a balance of capillary and hydrostatic pressures. Advancing and receding contact angles were determined for diakylimidazolium chloroaluminate, room-temperature molten salts on various candidate battery separator and porous electrode materials. The wetting angles were determined for the binary 1-methyl-3-ethylimidazolium chloride/aluminum chloride melt as a function of such variables as composition, chlorination of the imidazolium ion, replacement of AlCl3 by LiCl, solid porosity, and solid surface cleaning procedure. In nearly all cases involving AlCl3 as a second component, the melt easily wets the substrate.

  3. Ab initio MO Calculations on the Structure and Raman and Infrared Spectra of [Al4O2Cl10]2- Oxide in Chloroaluminate Melts

    NASA Astrophysics Data System (ADS)

    Berg, Rolf W.

    2007-04-01

    The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio molecular orbital calculations are carried out on these various aluminium chloride and oxochloride ions, in assumed isolated gaseous free ionic state, by use of the Gaussian 03W program at the restricted Hartree-Fock (HF) level and with the 6-31+G(d,p) basis set.Without any pre-assumed symmetries and with tight optimization convergence criteria and by using the modified GDIIS algorithm, the model calculations generally converge. The structures and their binding energies are presented. The expected geometries are supported, with one exception perhaps being the [Al2OCl6]2- ion, that gave a linear Al-O-Al bonding system of staggered AlCl3-groups (approximate D3d symmetry), in analogy to the linear Al-O-Al geometry of the analogous [Al2OF6]2- ion, found previously. The calculations include determination of the vibrational harmonic normal modes and the infrared and Raman spectra (vibrational band wavenumbers and intensities), without any empiric adjustments of the harmonic force constants, using constants directly predicted from the Gaussian 03W program. Previously obtained IR absorption and Raman scattering spectra of melts are assigned, by comparing to the ab initio quantum mechanical vibrational analysis results. It is concluded that the small oxide content commonly found in basic and neutral tetrachloroaluminate melts, most probably consists of [Al4O2Cl10]2- ions, and the vibrational spectra are given.

  4. Sodium-tetravalent sulfur molten chloroaluminate cell

    DOEpatents

    Mamantov, Gleb

    1985-04-02

    A sodium-tetravalent sulfur molten chloroaluminate cell with a .beta."-alumina sodium ion conductor having a S-Al mole ratio of above about 0.15 in an acidic molten chloroaluminate cathode composition is disclosed. The cathode composition has an AlCl.sub.3 -NaCl mole percent ratio of above about 70-30 at theoretical full charge. The cell provides high energy densities at low temperatures and provides high energy densities and high power densities at moderate temperatures.

  5. Functional dialkylimidazolium-mediated synthesis of silver nanocrystals with sensitive Hg(2+)-sensing and efficient catalysis.

    PubMed

    Zhang, Hucheng; Ye, Lu; Wang, Xingang; Li, Fangfang; Wang, Jianji

    2014-03-11

    Thiol-functionalized dialkylimidazolium bromide was synthesized, and used as a stabilizer to prepare monodisperse silver nanocrystals through a facile one-pot aqueous approach. It is shown that the multipurpose ligands play a vital role in improving the performance of nanocrystals. The mechanisms of dialkylimidazolium-mediated promotion were analyzed on the basis of the physicochemical properties of the specifically designed ligand. PMID:24430653

  6. A Refined Ionic Model for Clusters Relevant to Molten Chloroaluminates

    NASA Astrophysics Data System (ADS)

    Akdeniz, Z.; Tosi, M. P.

    1999-04-01

    A model of ionic interactions in neutral and ionized aluminium trichloride clusters, which accounts for ionic deformability through (i) effective valences and (ii) electrostatic and overlap polarizabilities, is evaluated for applications to classical simulation studies of the pure melt and of molten alkali chloroaluminates. The disposable parameters in the model are determined from the measured values of the bond length in the (AlCl4)- molecular ion and of an Al-Cl bond length and a vibrational frequency in the Al2Cl6 molecular dimer. The model is tested against the remaining available data from experiment and from quantum chemical calculations on molecular bond lengths, bond angles and vibrational frequencies for Al2Cl6 , (AlCl4)- and (Al 2Cl7)-clusters. Structural and dynamical properties are also evaluated for the (Al2Cl5)+ , AlCl3 and (AlCl2)+ clusters. The results for the energetics of dissociation, ion transfer and isomer excitation reactions are compared with as yet unpublished data obtained by P. Ballone in first-principles calculations by a density functional method. The overall quality of the tests supports the approximate validity and transferability of the model.

  7. From diphosphino-functionalized 1,3-dialkylimidazolium cations to imidazolones through dehydrogenative C-N coupling.

    PubMed

    Ruiz, Javier; Mesa, Alejandro F

    2014-01-01

    Diphosphino-functionalized 1,3-dialkylimidazolium salts react with KOH affording amine/formamide open-chain products, which fully revert to the imidazolium cation by treatment with a variety of acids or are converted to 2-imidazolones by noncatalyzed intramolecular dehydrogenative C-N coupling, a process that is modulated by coordination of the phosphino functionalities to transition metals. PMID:24285356

  8. Lignin dissolution in dialkylimidazolium-based ionic liquid-water mixtures.

    PubMed

    Wang, Yantao; Wei, Ligang; Li, Kunlan; Ma, Yingchong; Ma, Ningning; Ding, Shan; Wang, Linlin; Zhao, Deyang; Yan, Bing; Wan, Wenying; Zhang, Qian; Wang, Xin; Wang, Junmei; Li, Hui

    2014-10-01

    Lignin dissolution in dialkylimidazolium-based ionic liquid (IL)-water mixtures (40wt%-100wt% IL content) at 60°C was investigated. The IL content and type are found to considerably affect lignin solubility. For the IL-water mixtures except 1-butyl-3-methylimidazolium tetrafluoroborate ([C4C1im]BF4), the maximum lignin solubility can be achieved at 70wt% IL content. Lignin solubility in IL-water mixtures with different cations follows the order 1-butyl-3-methylimidazolium ([C4C1im](+))>1-hexyl-3-methylimidazolium ([C6C1im](+))>1-ethyl-3-methylimidazolium ([C2C1im](+))>1-octyl-3-methylimidazolium ([C8C1im](+))>1-butyl-3-ethylimidazolium ([C4C2im](+))>1-butyl-3-propylimidazolium ([C4C3im](+)). For IL mixtures with different anions, lignin solubility decreases in the following order: methanesulfonate (MeSO3(-))>acetate (MeCO2(-))>bromide (Br(-))>dibutylphosphate (DBP(-)). Evaluation using the theory of Hansen solubility parameter (HSP) is consistent with the experimental results, suggesting that HSP can aid in finding the appropriate range of IL content for IL-water mixtures. However, HSP cannot be used to evaluate the effect of IL type on lignin solubility. PMID:25164342

  9. Studies in molten chloroaluminates: I. Multipass spectroelectrochemistry; II. Spectroscopic and electrochemical investigations of iridium carbonyls

    SciTech Connect

    Harward, B.L.

    1985-12-01

    The multipass technique is introduced as an optical enhancement method for thin-layer spectroelectrochemistry. In this approach, the light beam is redirected through an optically transparent electrode (OTE) several times by an external mirror assembly. This arrangement is achieved using a low power continuum source which allows simultaneous multiwavelength measurements. The gain in optical sensitivity is directly related to the number of passes through the cell and has a practical limit of three to five. Initial evaluation with an aqueous test system yielded results which agree well with theory. The enhancement is not dependent upon electrode reflectivity and, therefore, the method may be applied to studies in highly corrosive media. Studies of the oxidation of sulfur and the reduction of niobium pentachloride in molten chloroaluminates are presented to demonstrate the utility of ths technique for investigations in such media. 203 refs., 51 figs., 15 tabs.

  10. Chloroaluminate ionic liquids as reagents for isolating soluble hexanuclear zirconium halide cluster compounds.

    PubMed

    Sun, D; Hughbanks, T

    2000-05-01

    Ambient-temperature chloroaluminate molten salts, mixtures of aluminum trichloride (AlCl3) and 1-ethyl-3-methylimidazolium chloride (ImCl), have been used as solvents to excise and isolate centered hexanuclear zirconium halide clusters from their solid-state precursors. Cluster compounds synthesized via high-temperature reactions, KZr6CCl15 and Li2Zr6MnCl15, were dissolved into basic molten salts at 100-110 degrees C. The C-centered cluster compound, Im4Zr6CCl18, was isolated in 70% yield, and the Mn-centered cluster compound, Im5Zr6MnCl18.C7H(8).2CH3CN, was isolated in 54% yield. Im5Zr6BCl18 is efficiently oxidized by ferrocenium tetrafluoroborate, and one-electron-oxidized B-centered cluster, [(Zr6B)Cl18]4-, was isolated in 90% yield as the salt Im4Zr6BCl18. PMID:11428116

  11. The electrochemistry of metals in room-temperature chloroaluminate molten salts

    SciTech Connect

    Xu, Xiao-Hong.

    1992-01-01

    The room-temperature chloroaluminate molten salt, aluminum chloride-1-methyl-3-ethylimidazolium chloride has proven to be useful electrolyte for the electrodeposition and electrodissolution of metals. The electrodeposition of lead, tin, silver, gold, and mercury was studied in this melt. Evidence for the underpotential deposition of lead and silver in acidic (66.7-33.3 mol%) melt and tin in acidic and basic (44.4-55.6 mol%) melt was found at polycrystalline gold. Nucleation overpotentials were observed for the deposition of mercury on gold in basic melt. The deposition of lead and silver from acidic melt and the deposition of gold from basic melt on glassy carbon involves progressive 3-D nucleation on a large number of active sites with hemispherical diffusion-controlled growth of the nuclei. The deposition of tin and and mercury from acidic melt exhibits progressive 3-D nucleation on a finite number of active sites. The deposition of tin and mercury from basic melt on glassy carbon involves instantaneous 3-D nucleation. The electrode-position of lead and silver from acidic melt on tungsten involves instantaneous 3-D nucleation, whereas the electrodeposition of gold and mercury from basic melt exhibits 3-D progressive nucleation. The deposition of lead and silver from acidic melt and the deposition of tin from both acidic and basic melt on platinum does not exhibit obvious evidence for either UPD or nucleation. The electrodeposition of gold and mercury on platinum from basic melt involves progressive 3-D nucleation. The voltammetric oxidation of Sn(II) to Sn(IV) is hindered by the weak adsorption of Sn(II). Sn(IV) is complexed as [SnCl[sub 6

  12. Vapor pressures of 1,3-dialkylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids with long alkyl chains

    SciTech Connect

    Rocha, Marisa A. A. E-mail: marisa.alexandra.rocha@gmail.com; Coutinho, João A. P.; Santos, Luís M. N. B. F. E-mail: marisa.alexandra.rocha@gmail.com

    2014-10-07

    This work presents the vapor pressure at several temperatures for the 1,3-dialkylimidazolium bis(trifluoromethylsulfonyl)imide series, [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (N = 14, 16, 18, and 20), measured by a Knudsen effusion method combined with a quartz crystal microbalance. The thermodynamic properties of vaporization of the ionic liquids under study are analysed together with the results obtained previously for the shorter alkyl chain length [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (N = 2, 4, 6, 8, 10, and 12), in order to evaluate the effect of the alkyl side chains of the cation and to get additional insights concerning the nanostructuration of ionic liquids. The symmetry effect is explored, based on the comparison with the asymmetric imidazolium based ionic liquids, [C{sub N-1}C{sub 1}im][NTf{sub 2}]. A trend shift on the thermodynamic properties of vaporization along the alkyl side chains of the extended symmetric ionic liquids, around [C{sub 6}C{sub 6}im][NTf{sub 2}], was detected. An intensification of the odd-even effect was observed starting from [C{sub 6}C{sub 6}im][NTf{sub 2}], with higher enthalpies and entropies of vaporization for the odd numbered ionic liquids, [C{sub 7}C{sub 7}im][NTf{sub 2}] and [C{sub 9}C{sub 9}im][NTf{sub 2}]. Similar, but less pronounced, odd-even effect was found for the symmetric ionic liquids with lower alkyl side chains length, [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (with N = 4, 6, 8, 10, and 12). This effect is related with the predominant orientation of the terminal methyl group of the alkyl chain to the imidazolium ring and their influence in the cation-anion interaction. The same Critical Alkyl length at the hexyl, (C{sub 6}C{sub 1}and C{sub 6}C{sub 6}) was found for both asymmetric and symmetric series indicating that the nanostructuration of the ionic liquids is related with alkyl chain length.

  13. Structure and aggregation in the 1,3-dialkyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquid family: 2. From single to double long alkyl side chains.

    PubMed

    Bernardes, Carlos E S; Shimizu, Karina; Lobo Ferreira, Ana I M C; Santos, Luís M N B F; Canongia Lopes, José N

    2014-06-19

    A systematic molecular dynamics study using large simulation boxes has been performed in order to extend the analysis of the mesoscopic segregation behavior observed in ionic liquids of the 1,3-dialkyl-imidazolium bis(trifluoromethylsulfonyl)imide homologous series, [C(n)C(mim)][Ntf2] (2 ≤ n ≤ 10, 2 ≤ m ≤ n). The analyses include the discussion of the structure factors, S(q), in the low-q range (1.6 ≤ q/nm(-1) ≤ 20); the confirmation of the periodicity of the polar network of the ionic liquid and its relation to the so-called intermediate peaks; and the characterization of the polar network and the nonpolar regions that are formed along the series using aggregate analyses by means of five different statistical tools. The analyses confirmed that the percolation of the nonpolar regions into a continuous domain occurs when the total number of carbon atoms in the alkyl chains exceeds six but that this is not a sufficient condition for the emergence of a distinct and intense prepeak. The existence of such a peak also requires that the longer alkyl chain contains more than a critical alkyl length (CAL) of five carbon atoms. PMID:24873822

  14. Remembering AB

    NASA Astrophysics Data System (ADS)

    Belyayev, S. T.

    2013-06-01

    In 1947 I became a second-year student at Moscow State University's Physics and Engineering Department, where a part of the week's classes were taught at base organizations. Our group's base was the future Kurchatov Institute, at that time known as the mysterious "Laboratory N^circ 2," and later as LIPAN. . Besides group lectures and practical work at the experimental laboratories, we also had access to the general seminars which Igor Vasilyevich Kurchatov tried to hold, with Leonid Vasilyevich Groshev filling in when he was absent. At the seminar, theorists spoke as welcome co-presenters and commentators. In 1949 I felt ready to approach A. B. Migdal to ask if I could transfer to his theoretical sector. In response, he suggested a number of simple qualitative problems, which I then successfully solved. (Incidentally, AB used the very same "introductory problems" for screening many generations of students.) So I wound up among AB's students. From 1952 on (for 10 years) I also served as an employee of the Migdal Sector. My memoirs here are mainly inspired by these years of constant communication with AB. After my departure for Novosibirsk in 1962, although our meetings still took place, they became occasional....

  15. Memories of AB

    NASA Astrophysics Data System (ADS)

    Vaks, V. G.

    2013-06-01

    I had the good fortune to be a student of A. B. Migdal - AB, as we called him in person or in his absence - and to work in the sector he headed at the Kurchatov Institute, along with his other students and my friends, including Vitya Galitsky, Spartak Belyayev and Tolya Larkin. I was especially close with AB in the second half of the 1950s, the years most important for my formation, and AB's contribution to this formation was very great. To this day, I've often quoted AB on various occasions, as it's hard to put things better or more precisely than he did; I tell friends stories heard from AB, because these stories enhance life as AB himself enhanced it; my daughter is named Tanya after AB's wife Tatyana Lvovna, and so on. In what follows, I'll recount a few episodes in my life in which AB played an important or decisive role, and then will share some other memories of AB...

  16. NMR measurements in solutions of dialkylimidazolium haloaluminates

    SciTech Connect

    Takahashi, S.; Saboungi, M.L.; Klingler, R.J.; Chen, M.J.; Rathke, J.W.

    1992-06-01

    {sup 27}Al and {sup 35}Cl NMR spectra of AlCl{sub 3}-1-ethyl-3-methyl imidazolium chloride (EMIC) melts were measured for initial compositions ranging from 50 to 67 mol % AlCl{sub 3} at various temperatures. It was shown by changing the preaquisition delay time (DE value) that the dominant aluminum species are AlCl{sub 4}{sup {minus}} in the melt formed by mixing 50 mol % with EMIC and Al{sub 2}Cl{sub 7}{sup {minus}} in the 67 mol % AlCl{sub 3} melt. In the equimolar mixture, the chemical shift of {sup 27}Al NMR spectrum is 103.28 ppm and the line width is 22.83Hz. In the 67 mol % AlCl{sub 3} mixture, the chemical shift is 103.41 ppm and the line width is 2624Hz. A third species observed at 97 ppm in the {sup 27}Al spectra for the 55 and 60 mol % AlCl{sub 3} mixtures is identified to be a product of the reaction with residual water. The relaxation rates for each species in the melts were determined.

  17. Omega-AB

    Energy Science and Technology Software Center (ESTSC)

    2007-05-01

    A hierarchical, modular modeling environment for hybrid simulations of sequential-modular, systems dynamics, discrete-event, and agent-based paradigms Omega-AB models contain a hierarchically-defined module tree that specifies the execution logic for the simulation, and a multi-network graph that defines the environment within which the simulation occurs. Modules are the fundamental buildinig blocks of an Omega-AB model and can define anything from a basic mathematical operation to a complex behavioral response model. Modules rely on the "plug-in" conceptmore » which allows developers to build independent module libraries that are gathered, linked, and instantiated by the Omega-AB engine at run time. Inter-module communication occurs through two complimentary systems: pull-based "ports" for general computation patterns and push-based "plugs" for event processing. The simulation environment is an abstract graph of nodes and links. Agents (module sub-trees headed up by an Agent module) reside at nodes and relate to their neighbors through typed links. To facilitate the construction and visualization of complex, interacting networks with dramatically different structure, Omega-AB provides a system for organizing the nodes into hierarchica trees that describe "slices" of the overall network.« less

  18. Ordered ionic liquids: chloroaluminates and silicates

    SciTech Connect

    Blander, M.; Tumidajski, P.; Bloom, I.; Newman, D.

    1990-01-01

    Ordering in NaCl--AlCl{sub 3} melts leads to sharp minima in the solubility of divalent chlorides MCl{sub 2} (e.g., CoCl{sub 2}, and NiCl{sub 2}) near the 50-50 mole % composition. The composition dependence of these solubilities in acids melts can be described by using either the coordination cluster theory or the solubility product principle. The magnitudes of the solubility products are largely related to the fact the standard free energy of formation of 2NaNlCl{sub 4} form 2NaCl and 2AlCl{sub 3} is considerably more negative that the corresponding free energy for N (AlCl{sub 4}){sub 2}. In basic melts solubilities are largely related to the formation of the associated species MCI{sup +}, MCI{sup 2}, MCI {sup {minus}3} and MCI {sub 4}{sup {minus}2}, which appear to have very large formation constants. 15 refs., 3 figs.

  19. ABS plastic RPCs

    SciTech Connect

    Ables, E.; Bionta, R.; Olson, H.; Ott, L.; Parker, E.; Wright, D.; Wuest, C

    1996-02-01

    After investigating a number of materials, we discovered that an ABS plastic doped with a conducting polymer performs well as the resistive electrode in a narrow gap RPC (resistive plate chamber). Operating in the streamer mode, we find efficiencies of 90-96% with low noise and low strip multiplicities. We have also studied a variety of operating gases and found that a mixture containing SF{sub 6}, a non-ozone depleting gas, argon and isobutane gives good streamer mode performance, even with isobutane concentrations of 20% or less.

  20. AB 1725: A Comprehensive Analysis.

    ERIC Educational Resources Information Center

    California Community Colleges, Sacramento. Board of Governors.

    A summary and analysis is provided of California Assembly Bill (AB) 1725, a reform bill that provides new direction and support for the state's community colleges. The analysis addresses each of the eight sections of the bill: (1) mission, highlighting reforms related to mission statements, transfer core curriculum, remedial limits, articulation…

  1. Vaporisation and thermal decomposition of dialkylimidazolium halide ion ionic liquids.

    PubMed

    Lovelock, Kevin R J; Armstrong, James P; Licence, Peter; Jones, Robert G

    2014-01-28

    Vaporisation and liquid phase thermal decomposition, TD, of two halide ion ionic liquids, 1-octyl-3-methylimidazolium chloride, [C8C1Im]Cl, and 1-octyl-3-methylimidazolium iodide, [C8C1Im]I, are investigated using temperature programmed desorption (TPD) line of sight mass spectrometry (LOSMS) at ultra-high vacuum (UHV). The ability to use MS to distinguish between vaporisation and TD allows the thermodynamics/kinetics of both vaporisation and TD to be investigated within the same experiments. Vaporisation of both halide ion ionic liquids is demonstrated. For both [C8C1Im]Cl and [C8C1Im]I the vapour is shown to be composed of neutral ion pairs (NIPs). The enthalpy of vaporisation at temperature T, ΔvapHT, was experimentally determined as ΔvapH455 = 151 ± 10 kJ mol(-1) for [C8C1Im]Cl and ΔvapH480 = 149 ± 8 kJ mol(-1) for [C8C1Im]I. Extrapolation of ΔvapHT to the reference temperature, 298 K, gave ΔvapH298 = 166 ± 10 kJ mol(-1) for [C8C1Im]Cl and ΔvapH298 = 167 ± 8 kJ mol(-1) for [C8C1Im]I, higher than most ΔvapH298 values measured to date for other [C8C1Im](+)-containing ionic liquids. In addition, predictions of ΔvapH298 for other halide ion ionic liquids are made. Liquid phase TD is shown to proceed via nucleophilic substitution to give two sets of products: 1-octylimidazole and methylhalide, and 1-methylimidazole and 1-octylhalide. The activation energy of TD at a temperature T, Ea,TD,T, is measured for the nucleophilic substitution of [C8C1Im]I to give methyliodide; Ea,TD,480 = 136 ± 15 kJ mol(-1). Ea,TD,T is measured for the nucleophilic substitution of [C8C1Im]Cl to give methylchloride; Ea,TD,455 = 132 ± 10 kJ mol(-1). The fact that ΔvapHT and Ea,TD,T are the same (within error) for both ionic liquids is commented upon, and conclusions are drawn as to the thermal stability of these ionic liquids. PMID:24105256

  2. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

    Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

  3. Ultrasound Biomicroscopy Comparison of Ab Interno and Ab Externo Intraocular Lens Scleral Fixation.

    PubMed

    Horiguchi, Lie; Garcia, Patricia Novita; Malavazzi, Gustavo Ricci; Allemann, Norma; Gomes, Rachel L R

    2016-01-01

    Purpose. To compare ab interno and ab externo scleral fixation of posterior chamber intraocular lenses (PCIOL) using ultrasound biomicroscopy (UBM). Methods. Randomized patients underwent ab externo or ab interno scleral fixation of a PCIOL. Ultrasound biomicroscopy was performed 3 to 6 months postoperatively, to determine PCIOL centration, IOL distance to the iris at 12, 3, 6, and 9 hours, and haptics placement in relation to the ciliary sulcus. Results. Fifteen patients were enrolled in the study. The ab externo technique was used in 7 eyes (46.6%) and the ab interno in 8 eyes (53.3%). In the ab externo technique, 14 haptics were located: 4 (28.57%) in the ciliary sulcus; 2 (14.28%) anterior to the sulcus; and 8 (57.14%) posterior to the sulcus, 6 in the ciliary body and 2 posterior to the ciliary body. In the ab interno group, 4 haptics (25.0%) were in the ciliary sulcus, 2 (12.50%) anterior to the sulcus, and 10 (75.0%) posterior to the sulcus, 4 in the ciliary body and 6 posterior to the ciliary body. Conclusions. Ab externo and ab interno scleral fixation techniques presented similar results in haptic placement. Ab externo technique presented higher vertical tilt when compared to the ab interno. PMID:27293878

  4. Ultrasound Biomicroscopy Comparison of Ab Interno and Ab Externo Intraocular Lens Scleral Fixation

    PubMed Central

    Horiguchi, Lie; Garcia, Patricia Novita; Malavazzi, Gustavo Ricci; Allemann, Norma

    2016-01-01

    Purpose. To compare ab interno and ab externo scleral fixation of posterior chamber intraocular lenses (PCIOL) using ultrasound biomicroscopy (UBM). Methods. Randomized patients underwent ab externo or ab interno scleral fixation of a PCIOL. Ultrasound biomicroscopy was performed 3 to 6 months postoperatively, to determine PCIOL centration, IOL distance to the iris at 12, 3, 6, and 9 hours, and haptics placement in relation to the ciliary sulcus. Results. Fifteen patients were enrolled in the study. The ab externo technique was used in 7 eyes (46.6%) and the ab interno in 8 eyes (53.3%). In the ab externo technique, 14 haptics were located: 4 (28.57%) in the ciliary sulcus; 2 (14.28%) anterior to the sulcus; and 8 (57.14%) posterior to the sulcus, 6 in the ciliary body and 2 posterior to the ciliary body. In the ab interno group, 4 haptics (25.0%) were in the ciliary sulcus, 2 (12.50%) anterior to the sulcus, and 10 (75.0%) posterior to the sulcus, 4 in the ciliary body and 6 posterior to the ciliary body. Conclusions. Ab externo and ab interno scleral fixation techniques presented similar results in haptic placement. Ab externo technique presented higher vertical tilt when compared to the ab interno. PMID:27293878

  5. Ab initio nuclear structure theory

    NASA Astrophysics Data System (ADS)

    Negoita, Gianina Alina

    Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous

  6. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  7. A spinor boson AB chain

    NASA Astrophysics Data System (ADS)

    Cruz Reyes, Greis Julieth; Franco, Roberto; Silva Valencia, Jereson; Universidad Santo Tomas Collaboration; Universidad Nacional de Colombia Collaboration

    Recent research is focused on superlattices arising from optical lattices, which allow a tunable environment. Experimentally bosons present transitions from superfluid to Mott insulator by changing the energy offset in the unit cell [Nat. Commun. 5:5735 (2014)]. Many studies displayed that ground state of spinless boson systems on superlattices present superfluid, Mott insulator and an additional CDW phase created by the energy shift between the sites into the unit cell [Phys. Rev. A 83, 053621 (2011)]. The first confinement methods were magnetic traps, which freezes the spin; with optical lattices the grade of freedom of spin plays an important role. We consider bosons with spin S =1 on a superlattice made by two sites with energy offset per unit cell (AB chain). The Hamiltonian that describes the system is the Bose-Hubbard model with the superlattice potential (W) and the exchange interaction (V) parameters. This model supports CDW, Mott insulator and superfluid phases. For W near to U, with V =0, Mott phase disappears, but for V increasing, a new CDW appears due to the spin interaction, while the half-integer CDW decrease. These results are widely different from spinless boson, where the CDW phases are stables.

  8. Ab inito investigation of hydrodesulferization

    SciTech Connect

    Tilson, J.L.; Marshall, C.L.; Brenner, J.R.

    1997-12-31

    We utilize MPP and vector computers to model the interaction of large sulfur-containing species bonded with hydrodesulfurization (HDS) catalysts. This work is made possible by the availability large aggregate memory, parallel computers. The ability of modern non-traditional computers to solve large-scale scientific problems has been demonstrated. This success is accomplished, in part, by access to portable low- and user-level software tools which exhibit good control over NUMA. ab initio SCF methods are used to characterize the energies of adsorption of poly-aromatic, sulfur-containing hydrocarbons onto a series of molecular-based models of MoS2. These hydrocarbon include thiophene (TP), benzothiophene (BT) and dibenzothiophene (DBT) which are representative of heavy crude feedstocks. Our work attempts to ascertain if a consistent model of adsorption onto a MoS2 surface exists and to determine how the electronic and steric configuration of each species affect their energies of interaction with the metal surface.

  9. GINGA Observations of AB Doradus

    NASA Astrophysics Data System (ADS)

    Vilhu, O.; Tsuru, T.; Collier Cameron, A.

    We report GINGA observations of the pre main sequence star AB Doradus (HD 36705), performed during 8 - 12 January, 1990. Some rotational modulation might be present. four X-ray flares were detected. Three of these events were similar to the EINSTEIN HRI-flare (Vilhu and Linsky, 1987), with decay times around 25 min. The last flare had long rise and decay times (100 min), resembling the EXOSAT flares observed by Collier Cameron et.al. (1988). The mean flare spectrum can be fitted by a thermal bremstrahlung with temperature 5.0 keV, or by a power-law model with photon index 2.2. The 3 upper limit of the Iron line equivalent width in the flare spectrum is 1 keV, weaker than predicted by thermal models. This Iron line anomaly was first discussed in the case of UX Ari by Tsuru et. al. (1989). However, normal equivalent widths can be derived from several EXOSAT spectra of active cool stars (Pallavicini and Tagliaferri, 1990). We discuss the possibility that the continuum from non-thermal electrons (producing also the microwave emission) could occasionally lower the apparent equivalent width. The mechanism works for reasonably low magnetic field strengths and electon power-law indexes. However, a large population of non-thermal electrons is needed (comparable to the thermal one). Stronger magnetic fields could explain the radio emission with less electrons, but then the non-thermal X-ray continuum remains small.

  10. The B AB AR detector

    NASA Astrophysics Data System (ADS)

    Aubert, B.; Bazan, A.; Boucham, A.; Boutigny, D.; De Bonis, I.; Favier, J.; Gaillard, J.-M.; Jeremie, A.; Karyotakis, Y.; Le Flour, T.; Lees, J. P.; Lieunard, S.; Petitpas, P.; Robbe, P.; Tisserand, V.; Zachariadou, K.; Palano, A.; Chen, G. P.; Chen, J. C.; Qi, N. D.; Rong, G.; Wang, P.; Zhu, Y. S.; Eigen, G.; Reinertsen, P. L.; Stugu, B.; Abbott, B.; Abrams, G. S.; Amerman, L.; Borgland, A. W.; Breon, A. B.; Brown, D. N.; Button-Shafer, J.; Clark, A. R.; Dardin, S.; Day, C.; Dow, S. F.; Fan, Q.; Gaponenko, I.; Gill, M. S.; Goozen, F. R.; Gowdy, S. J.; Gritsan, A.; Groysman, Y.; Hernikl, C.; Jacobsen, R. G.; Jared, R. C.; Kadel, R. W.; Kadyk, J.; Karcher, A.; Kerth, L. T.; Kipnis, I.; Kluth, S.; Kral, J. F.; Lafever, R.; LeClerc, C.; Levi, M. E.; Lewis, S. A.; Lionberger, C.; Liu, T.; Long, M.; Luo, L.; Lynch, G.; Luft, P.; Mandelli, E.; Marino, M.; Marks, K.; Matuk, C.; Meyer, A. B.; Minor, R.; Mokhtarani, A.; Momayezi, M.; Nyman, M.; Oddone, P. J.; Ohnemus, J.; Oshatz, D.; Patton, S.; Pedrali-Noy, M.; Perazzo, A.; Peters, C.; Pope, W.; Pripstein, M.; Quarrie, D. R.; Rasson, J. E.; Roe, N. A.; Romosan, A.; Ronan, M. T.; Shelkov, V. G.; Stone, R.; Strother, P. D.; Telnov, A. V.; von der Lippe, H.; Weber, T. F.; Wenzel, W. A.; Zizka, G.; Bright-Thomas, P. G.; Hawkes, C. M.; Kirk, A.; Knowles, D. J.; O'Neale, S. W.; Watson, A. T.; Watson, N. K.; Deppermann, T.; Koch, H.; Krug, J.; Kunze, M.; Lewandowski, B.; Peters, K.; Schmuecker, H.; Steinke, M.; Andress, J. C.; Barlow, N. R.; Bhimji, W.; Chevalier, N.; Clark, P. J.; Cottingham, W. N.; De Groot, N.; Dyce, N.; Foster, B.; Mass, A.; McFall, J. D.; Wallom, D.; Wilson, F. F.; Abe, K.; Hearty, C.; McKenna, J. A.; Thiessen, D.; Camanzi, B.; Harrison, T. J.; McKemey, A. K.; Tinslay, J.; Antohin, E. I.; Blinov, V. E.; Bukin, A. D.; Bukin, D. A.; Buzykaev, A. R.; Dubrovin, M. S.; Golubev, V. B.; Ivanchenko, V. N.; Kolachev, G. M.; Korol, A. A.; Kravchenko, E. A.; Mikhailov, S. F.; Onuchin, A. P.; Salnikov, A. A.; Serednyakov, S. I.; Skovpen, Yu. I.; Telnov, V. I.; Yushkov, A. N.; Booth, J.; Lankford, A. J.; Mandelkern, M.; Pier, S.; Stoker, D. P.; Zioulas, G.; Ahsan, A.; Arisaka, K.; Buchanan, C.; Chun, S.; Faccini, R.; MacFarlane, D. B.; Prell, S. A.; Rahatlou, Sh.; Raven, G.; Sharma, V.; Burke, S.; Callahan, D.; Campagnari, C.; Dahmes, B.; Hale, D.; Hart, P. A.; Kuznetsova, N.; Kyre, S.; Levy, S. L.; Long, O.; Lu, A.; May, J.; Richman, J. D.; Verkerke, W.; Witherell, M.; Yellin, S.; Beringer, J.; DeWitt, J.; Dorfan, D. E.; Eisner, A. M.; Frey, A.; Grillo, A. A.; Grothe, M.; Heusch, C. A.; Johnson, R. P.; Kroeger, W.; Lockman, W. S.; Pulliam, T.; Rowe, W.; Sadrozinski, H.; Schalk, T.; Schmitz, R. E.; Schumm, B. A.; Seiden, A.; Spencer, E. N.; Turri, M.; Walkowiak, W.; Wilder, M.; Williams, D. C.; Chen, E.; Dubois-Felsmann, G. P.; Dvoretskii, A.; Hanson, J. E.; Hitlin, D. G.; Kolomensky, Yu. G.; Metzler, S.; Oyang, J.; Porter, F. C.; Ryd, A.; Samuel, A.; Weaver, M.; Yang, S.; Zhu, R. Y.; Devmal, S.; Geld, T. L.; Jayatilleke, S.; Jayatilleke, S. M.; Mancinelli, G.; Meadows, B. T.; Sokoloff, M. D.; Bloom, P.; Broomer, B.; Erdos, E.; Fahey, S.; Ford, W. T.; Gaede, F.; van Hoek, W. C.; Johnson, D. R.; Michael, A. K.; Nauenberg, U.; Olivas, A.; Park, H.; Rankin, P.; Roy, J.; Sen, S.; Smith, J. G.; Wagner, D. L.; Blouw, J.; Harton, J. L.; Krishnamurthy, M.; Soffer, A.; Toki, W. H.; Warner, D. W.; Wilson, R. J.; Zhang, J.; Brandt, T.; Brose, J.; Dahlinger, G.; Dickopp, M.; Dubitzky, R. S.; Eckstein, P.; Futterschneider, H.; Kocian, M. L.; Krause, R.; Müller-Pfefferkorn, R.; Schubert, K. R.; Schwierz, R.; Spaan, B.; Wilden, L.; Behr, L.; Bernard, D.; Bonneaud, G. R.; Brochard, F.; Cohen-Tanugi, J.; Ferrag, S.; Fouque, G.; Gastaldi, F.; Matricon, P.; Mora de Freitas, P.; Renard, C.; Roussot, E.; T'Jampens, S.; Thiebaux, C.; Vasileiadis, G.; Verderi, M.; Anjomshoaa, A.; Bernet, R.; Di Lodovico, F.; Muheim, F.; Playfer, S.; Swain, J. E.; Falbo, M.; Bozzi, C.; Dittongo, S.; Folegani, M.; Piemontese, L.; Ramusino, A. C.; Treadwell, E.; Anulli, F.; Baldini-Ferroli, R.; Calcaterra, A.; de Sangro, R.; Falciai, D.; Finocchiaro, G.; Patteri, P.; Peruzzi, I. M.; Piccolo, M.; Xie, Y.; Zallo, A.; Bagnasco, S.; Buzzo, A.; Contri, R.; Crosetti, G.; Fabbricatore, P.; Farinon, S.; Lo Vetere, M.; Macri, M.; Minutoli, S.; Monge, M. R.; Musenich, R.; Pallavicini, M.; Parodi, R.; Passaggio, S.; Pastore, F. C.; Patrignani, C.; Pia, M. G.; Priano, C.; Robutti, E.; Santroni, A.; Bartoldus, R.; Dignan, T.; Hamilton, R.; Mallik, U.; Cochran, J.; Crawley, H. B.; Fischer, P. A.; Lamsa, J.; McKay, R.; Meyer, W. T.; Rosenberg, E. I.; Albert, J. N.; Beigbeder, C.; Benkebil, M.; Breton, D.; Cizeron, R.; Du, S.; Grosdidier, G.; Hast, C.; Höcker, A.; Lacker, H. M.; LePeltier, V.; Lutz, A. M.

    2002-02-01

    B AB AR, the detector for the SLAC PEP-II asymmetric e +e - B Factory operating at the ϒ(4 S) resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagnetic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by d E/d x measurements in the tracking detectors and by a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

  11. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, M. A.; Maris, P.; Vary, J. P.; Smith, R.

    2015-08-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.

  12. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

  13. The use of tetravalent sulfur in molten chloroaluminate secondary batteries

    NASA Astrophysics Data System (ADS)

    Mamantov, G.; Marassi, R.; Matsunaga, M.; Ogata, Y.; Wiaux, J. P.; Frazer, E. J.

    1980-11-01

    A new rechargeable Na/Na(+) ion conductor/SCl3(+) in molten AlCl3-NaCl cell is described. This cell operates at temperatures in the range of 180-250 C and has an open-circuit voltage of 4.2 V. The discharge process involves the reduction of tetravalent sulfur to the elemental state; sulfur can be further reduced to sulfide. The preferred sodium ion conductor is beta double prime alumina. High energy density values, large percent utilization of the active material, and good energy efficiency have been demonstrated. The performances of cells prepared in the discharged and charged states were found to be the same. The number of deep charge/discharge cycles has exceeded 400.

  14. Ab interno trabeculectomy: patient selection and perspectives.

    PubMed

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm's canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

  15. MELCOR 1.8.2 assessment: Aerosol experiments ABCOVE AB5, AB6, AB7, and LACE LA2

    SciTech Connect

    Souto, F.J.; Haskin, F.E.; Kmetyk, L.N.

    1994-10-01

    The MELCOR computer code has been used to model four of the large-scale aerosol behavior experiments conducted in the Containment System Test Facility (CSTF) vessel. Tests AB5, AB6 and AB7 of the ABCOVE program simulate the dry aerosol conditions during a hypothetical severe accident in an LMFBR. Test LA2 of the LACE program simulates aerosol behavior in a condensing steam environment during a postulated severe accident in an LWR with failure to isolate the containment. The comparison of code results to experimental data show that MELCOR is able to correctly predict most of the thermal-hydraulic results in the four tests. MELCOR predicts reasonably well the dry aerosol behavior of the ABCOVE tests, but significant disagreements are found in the aerosol behavior modelling for the LA2 experiment. These results tend to support some of the concerns about the MELCOR modelling of steam condensation onto aerosols expressed in previous works. During these analyses, a limitation in the MELCOR input was detected for the specification of the aerosol parameters for more than one component. A Latin Hypercube Sampling (LHS) sensitivity study of the aerosol dynamic constants is presented for test AB6. The study shows the importance of the aerosol shape factors in the aerosol deposition behavior, and reveals that MELCOR input/output processing is highly labor intensive for uncertainty and sensitivity analyses based on LHS.

  16. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs.

    PubMed

    Plath, Friederike; Ringler, Philippe; Graff-Meyer, Alexandra; Stahlberg, Henning; Lauer, Matthias E; Rufer, Arne C; Graewert, Melissa A; Svergun, Dmitri; Gellermann, Gerald; Finkler, Christof; Stracke, Jan O; Koulov, Atanas; Schnaible, Volker

    2016-07-01

    The formation of undesired high molecular weight species such as dimers is an important quality attribute for therapeutic monoclonal antibody formulations. Therefore, the thorough understanding of mAb dimerization and the detailed characterization mAb dimers is of great interest for future pharmaceutical development of therapeutic antibodies. In this work, we focused on the analyses of different mAb dimers regarding size, surface properties, chemical identity, overall structure and localization of possible dimerization sites. Dimer fractions of different mAbs were isolated to a satisfactory purity from bulk material and revealed 2 predominant overall structures, namely elongated and compact dimer forms. The elongated dimers displayed one dimerization site involving the tip of the Fab domain. Depending on the stress applied, these elongated dimers are connected either covalently or non-covalently. In contrast, the compact dimers exhibited non-covalent association. Several interaction points were detected for the compact dimers involving the hinge region or the base of the Fab domain. These results indicate that mAb dimer fractions are rather complex and may contain more than one kind of dimer. Nevertheless, the overall appearance of mAb dimers suggests the existence of 2 predominant dimeric structures, elongated and compact, which are commonly present in preparations of therapeutic mAbs. PMID:27031922

  17. On the Strain Rate Sensitivity of Abs and Abs Plus Fused Deposition Modeling Parts

    NASA Astrophysics Data System (ADS)

    Vairis, A.; Petousis, M.; Vidakis, N.; Savvakis, K.

    2016-06-01

    In this work the effect of strain rate on the tensile strength of fused deposition modeling parts built with Acrylonitrile-butadiene-styrene (ABS) and ABS plus material is presented. ASTM D638-02a specimens were built with ABS and ABS plus and they were tested on a Schenck Trebel Co. tensile test machine at three different test speeds, equal, lower, and higher to the test speed required by the ASTM D638-02a standard. The experimental tensile strength results were compared and evaluated. The fracture surfaces of selected specimens were examined with a scanning electron microscope, to determine failure mode of the filament strands. It was found that, as the test speed increases, specimens develop higher tensile strength and have higher elastic modulus. Specimens tested in the highest speed of the experiment had on average about 10% higher elastic modulus and developed on average about 11% higher tensile strength.

  18. Rapid digestion of Cry34Ab1 and Cry35Ab1 in simulated gastric fluid.

    PubMed

    Herman, Rod A; Schafer, Barry W; Korjagin, Valerie A; Ernest, April D

    2003-11-01

    Two genes were identified in Bacillus thuringiensis Berliner (Bt) that code for the proteins that comprise a Cry34Ab1/Cry35Ab1 binary insecticidal crystal protein. Maize, Zea mays L., plants have been transformed to express the Cry34Ab1/Cry35Ab1 proteins, and as a result, these plants are resistant to attack by western corn rootworm, Diabrotica virgifera virgifera LeConte, a major pest in the Midwestern corn-growing area of the U.S.A. As part of the safety assessment for the proteins, digestibility studies were conducted. Digestion experiments with both proteins demonstrated rapid degradation in simulated gastric fluid, comparable to other registered plant-incorporated protectants. Quantitative and qualitative approaches for determining digestibility are illustrated. PMID:14582981

  19. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  20. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, Mark A.; Maris, Pieter; Vary, James P.

    2015-10-01

    The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).

  1. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  2. Interaction of vermiculite with Katamin AB

    SciTech Connect

    Veksler, V.I.; Makashev, Yu.A.; Mikhailova, V.N.; Aleksandrova, E.M.; Vinogradova, I.A.

    1986-12-10

    Vermiculite can interact with quaternary ammonium salts to form organmineral compounds in the ion-exchange adsorption of these salts from waste water. This paper investigates this interaction between vermiculite and Katamin AB, a commercial cationic surfactant consisting of an aqueous solution of alkylbenyldimethylammonium chloride homologs. It is shown that ion exchange and molecular sorption occur simultaneously during the interaction and that vermiculite is a highly effective adsorbent in process water purification.

  3. Ab initio vel ex eventu. II

    NASA Astrophysics Data System (ADS)

    Thiessen, P. A.; Treder, H.-J.

    Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.

  4. Ab initio Bogoliubov coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

    Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.

  5. Ab interno trabeculectomy: patient selection and perspectives

    PubMed Central

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

  6. Ab-inition melting curve of titanium

    NASA Astrophysics Data System (ADS)

    Stutzmann, Vincent; Bouchet, Johann; Bottin, Francois

    2014-03-01

    Thermodynamical properties of titanium are of great interest for aerospace and aviation industries and many studies are done in order to understand its behaviour under pressure (P) and temperature (T) : phase transitions at low T, melting curve at high T and P. In this work we compute the first ab-initio melting curve of titanium. This one is obtained with the Abinit package using DFT, in the GGA approximation, and in the framework of the projector augmented wave method (PAW). At first, we perform ground state calculations and study the five allotropic phases of titanium. Two PAW atomic data are generated with two different cutoff radius. The larger one gives results near previews ab-initio calculations, whereas the smaller one gives results near all electron calculation. Using the second PAW atomic data and performing ab-initio molecular dynamic simulations, we then compute the melting curve of titanium with three different methods. Results show relevance of our calculations, but also discrepencies with experimental data.

  7. Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

    NASA Astrophysics Data System (ADS)

    Knotts, Greg

    2009-11-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

  8. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of...

  9. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of...

  10. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of...

  11. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of...

  12. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Preston, D. L.

    2015-11-01

    The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.

  13. New challenges to medicare beneficiary access to mAbs

    PubMed Central

    Wilson, Andrew

    2009-01-01

    Precision binding of monoclonal antibodies (mAbs) to biological targets, their relative clinical success, and expansion of indications following initial approval, are distinctive clinical features. The relatively high cost of mAbs, together with the absence of a regulatory pathway to generics, stand out as distinctive economic features. Based on both literature review and primary data collection we enumerated mAb original approvals, supplemental indications and off-label uses, assessed payer formulary management of mAbs, and determined new challenges to Medicare beneficiary access to mAbs. We found that the FDA has approved 22 mAbs and 30 supplemental indications pertaining to the originally approved mAbs. In addition, there are 46 off-label use citations in officially recognized pharmaceutical compendia. Across Part B carriers and Part D plans, we found considerable variation in terms of coverage and conditions of reimbursement related to on- and off-label uses of mAbs. Our results point to four major challenges facing mAb developers, health care providers, Medicare beneficiaries, payers and policymakers. These include administrative price controls, coverage variation, projected shift from physician- to self-administered mAbs, and comparative effectiveness. We suggest more systematic use of “coverage with evidence development” as a means of optimally addressing these challenges. PMID:20046575

  14. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  15. Testing Distributed ABS System with Fault Injection

    NASA Astrophysics Data System (ADS)

    Trawczyński, Dawid; Sosnowski, Janusz; Gawkowski, Piotr

    The paper deals with the problem of adapting software implemented fault injection technique (SWIFI) to evaluate dependability of reactive microcontroller systems. We present an original methodology of disturbing controller operation and analyzing fault effects taking into account reactions of the controlled object and the impact of the system environment. Faults can be injected randomly (in space and time) or targeted at the most sensitive elements of the controller to check it at high stresses. This approach allows identifying rarely encountered problems, usually missed in classical approaches. The developed methodology has been used successfully to verify dependability of ABS system. Experimental results are commented in the paper.

  16. Ab initio non-relativistic spin dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  17. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Frisch, Michael J.; Li, Xiaosong

    2014-12-01

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  18. Quantum phases of AB 2 fermionic chains

    NASA Astrophysics Data System (ADS)

    Murcia-Correa, L. S.; Franco, R.; Silva-Valencia, J.

    2016-02-01

    A fermionic chain is a one-dimensional system with fermions that interact locally and can jump between sites in the lattice, in particular an AB n chain type, where A and B are sites that exhibit a difference in energy level of Δ and site B is repeated n-times, such that the unit cell has n +1 sites. A limit case of this model, called the ionic Hubbard model (n = 1), has been widely studied due to its interesting physics and applications. In this paper, we study the ground state of an AB 2 chain, which describes the material R 4[Pt 2(P 2O5H2)4X] · nH 2 O. Specifically, we consider a filling with two electrons per unit cell, and using the density matrix renormalization group method we found that the system exhibits the band insulator and Mott correlated insulator phases, as well as an intermediate phase between them. For couplings of Δ = 2,10 and 20, we estimate the critical points that separate these phases through the structure factor and the energy gap in the sector of charge and spin, finding that the position of the critical point rises as a function of Δ.

  19. Longitudinal wheel slip during ABS braking

    NASA Astrophysics Data System (ADS)

    Hartikainen, Lassi; Petry, Frank; Westermann, Stephan

    2015-02-01

    Anti-lock braking system (ABS) braking tests with two subcompact passenger cars were performed on dry and wet asphalt, as well as on snow and ice surfaces. The operating conditions of the tyres in terms of wheel slip were evaluated using histograms of the wheel slip data. The results showed different average slip levels for different road surfaces. It was also found that changes in the tyre tread stiffness affected the slip operating range through a modification of the slip value at which the maximum longitudinal force is achieved. Variation of the tyre footprint length through modifications in the inflation pressure affected the slip operating range as well. Differences in the slip distribution between vehicles with different brake controllers were also observed. The changes in slip operating range in turn modified the relative local sliding speeds between the tyre and the road. The results highlight the importance of the ABS controller's ability to adapt to changing slip-force characteristics of tyres and provide estimates of the magnitude of the effects of different tyre and road operating conditions.

  20. Ab Initio Neutron Drops with Chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, Hugh; Maris, Pieter; Vary, James

    2015-04-01

    Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Supported by DOE Grants DESC0008485 (SciDAC/NUCLEI), DE-FG02-87ER40371, and NSF Grant 0904782; computational resources provided by the Oak Ridge Leadership Computing Facility (DOE Office of Science Contract DE-AC05-00OR22725) under an INCITE award.

  1. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2014-07-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  2. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2015-10-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  3. Guiding ab initio calculations by alchemical derivatives.

    PubMed

    to Baben, M; Achenbach, J O; von Lilienfeld, O A

    2016-03-14

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects. PMID:26979677

  4. Ab initio determination of light hadron masses.

    PubMed

    Dürr, S; Fodor, Z; Frison, J; Hoelbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabo, K K; Vulvert, G

    2008-11-21

    More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties. PMID:19023076

  5. Discovering chemistry with an ab initio nanoreactor

    DOE PAGESBeta

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

  6. Ab initio molar volumes and Gaussian radii.

    PubMed

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

    Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766

  7. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  8. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  9. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  10. Discovering chemistry with an ab initio nanoreactor.

    PubMed

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings. PMID:25411881

  11. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  12. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

    Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

  13. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

  14. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

    The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

  15. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  16. Ab initio alpha-alpha scattering.

    PubMed

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-01

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  17. Ablation dynamics in laser sclerotomy ab externo

    NASA Astrophysics Data System (ADS)

    Brinkmann, Ralf; Droege, Gerit; Mohrenstecher, Dirk; Scheu, M.; Birngruber, Reginald

    1996-01-01

    Laser sclerostomy ab externo with flashlamp excited mid-IR laser systems emitting in the 2-3 micrometer spectral range is in phase II clinical trials. Although acutely high success rates were achieved, the restenosis rate after several months is about 40%. Laser pulses of several hundreds of microseconds, known to induce thermo-mechanical explosive evaporation were used for this procedure. We investigated the ablation dynamics in tissue and the cavitation bubble dynamics in water by means of an Er:YAG laser system to estimate the extent of mechanical damage zones in the sclera and in the anterior chamber, which may contribute to the clinical failure. We found substantial mechanical tissue deformation during the ablation process caused by the cavitation effects. Stress waves up to several bar generated by explosive evaporization were measured. The fast mechanical stretching and collapsing of the scleral tissue induced by cavitation resulted in tissue dissection as could be proved by flash photography and histology. The observed high restenosis might be a result of a subsequent enhanced wound healing process. Early fistula occlusions due to iris adherences, observed in about 20% of the clinical cases may be attributed to intraocular trauma induced by vapor bubble expansion through the anterior chamber after scleral perforation. An automatic feedback system minimizing adverse effects by steering and terminating the laser process during scleral fistulization is demonstrated. Moreover, a new approach in laser sclerostomy ab externo is presented using a cw-IR laser diode system emitting at the 1.94 micrometer mid-IR water absorption peak. This system was used in vitro and showed smaller damage zones compared to the pulsed laser radiation.

  18. 12 CFR Appendixes A-B to Part 334 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false A Appendixes A-B to Part 334 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL POLICY FAIR CREDIT REPORTING Appendixes A-B to Part 334...

  19. AB1402: Design-Build Project Guidelines. 2002 Edition.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Sacramento. Div. of School Facilities Planning.

    Assembly Bill (AB) 1402 authorized California's school districts to enter into design-build contracts for projects with design and construction costs exceeding $10 million. These guidelines are intended to accomplish the following purposes: (1) inform school districts of the design-build process under AB 1402; (2) help school districts to…

  20. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 3 2014-01-01 2014-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part...

  1. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 3 2012-01-01 2012-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part 430...

  2. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 3 2013-01-01 2013-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part 430...

  3. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  4. History of California's AB 1725 and Its Major Provisions.

    ERIC Educational Resources Information Center

    Livingston, Tab

    This paper addresses the history of California's Assembly Bill 1725 (AB 1725) legislation and describes its major provisions. Signed in 1988 by Governor George Deukmejian, AB 1725's focus is to emphasize the new role of California community colleges as postsecondary institutions committed to transferring students, offering remedial courses, and…

  5. 7 CFR Exhibits A-B to Subpart G... - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 12 2013-01-01 2013-01-01 false A Exhibits A-B to Subpart G to Part 1822 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE..., Procedures, and Authorizations Exhibits A-B to Subpart G to Part 1822...

  6. Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

    ERIC Educational Resources Information Center

    Knotts, Greg

    2009-01-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

  7. Effects of Cry1F and Cry34Ab1/35Ab1 on storage pests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two crystalline protoxins from Bacillus thuringiensis (Bt), Cry1Fa1 and Cry34Ab1/Cry35Ab1 (Cry1F, Cry34/35), were evaluated for efficacy against lepidopteran and coleopteran storage pests. Cry1F was tested against the lepidopterans Sitotroga cerealella (Angoumois grain moth) and colonies of the lep...

  8. Structural and biophysical characterization of Bacillus thuringiensis insecticidal proteins Cry34Ab1 and Cry35Ab1.

    PubMed

    Kelker, Matthew S; Berry, Colin; Evans, Steven L; Pai, Reetal; McCaskill, David G; Wang, Nick X; Russell, Joshua C; Baker, Matthew D; Yang, Cheng; Pflugrath, J W; Wade, Matthew; Wess, Tim J; Narva, Kenneth E

    2014-01-01

    Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins. PMID:25390338

  9. Structural and Biophysical Characterization of Bacillus thuringiensis Insecticidal Proteins Cry34Ab1 and Cry35Ab1

    PubMed Central

    Kelker, Matthew S.; Berry, Colin; Evans, Steven L.; Pai, Reetal; McCaskill, David G.; Wang, Nick X.; Russell, Joshua C.; Baker, Matthew D.; Yang, Cheng; Pflugrath, J. W.; Wade, Matthew; Wess, Tim J.; Narva, Kenneth E.

    2014-01-01

    Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins. PMID:25390338

  10. ABS_PDv14.0 beta

    Energy Science and Technology Software Center (ESTSC)

    2008-07-30

    ABS_PD stands for Adaptive Background Suppression and Peak Detection algorithm. This algorithm uses an iterative process to simultaneously estimate the background and identify peaks in signals where the bakground is slowly varying relative to the peaks to be detected. This is sone on an automated manner. The algorithm can be applied to many physical processes where the desired signal is superimposed on a background. The main advantage of this algorithm is that the background canmore » be variable and doesn't have to be known. All that is required is that a set of basis function,s capa ble of representing the background, needs to be defined. Depending on the signals to be processed, the basis functions can be as simple as low order polynomials. The current algorithm has polynomials built-in and allows for additional basis functions to be defined by the user. An additional advantage is that the algorithm does not use any derivatives in detection of peaks and thus allows for analysis of noisy data. The noise level in the data is automatically taken into account when setting thresholds for peak detection.« less

  11. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  12. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-01

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H2 and O2. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  13. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

    Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M

    2015-11-25

    Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205

  14. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-21

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  15. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  16. Skutterudites under pressure: An ab initio study

    SciTech Connect

    Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.

    2014-03-07

    Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.

  17. Ab Initio: And a New Era of Airline Pilot Training.

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

    Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

  18. Tensile deformation mechanisms of ABS/PMMA/EMA blends

    NASA Astrophysics Data System (ADS)

    Wang, S. H.; Gao, J.; Lin, S. X.; Zhang, P.; Huang, J.; Xu, L. L.

    2014-08-01

    The tensile deformation mechanisms of acrylonitrile - butadiene - styrene (ABS) / polymethyl methacrylate (PMMA) blends toughened by ethylene methacrylate (EMA) copolymer was investigated by analysing the fracture morphology. ABS/PMMA was blended with EMA copolymer by melt mixing technique using co-rotating twin extruder. Tensile tests show that the elongation at break of ABS/PMMA blends can be efficiently improved with the increase in EMA content. Fracture morphology of ABS/PMMA/EMA blends reveals that the material yield induced by hollowing-out of EMA particles and its propagation into yield zone is the main toughening mechanism. Moreover, the appearance that EMA particles in the central area are given priority to hollowing-out may be related to the skin-core structure of the injection moulded parts caused by the different cooling rate between surface and inside in the process of injection moulding.

  19. Effect of electric field on the mechanical properties of bilayer boron nitride with AB stacking order: An ab initio study

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Faghihnasiri, M.; Malakpour, S.; Sahmani, S.

    2015-07-01

    In the current investigation, ab initio calculations are performed to explore the influence of electric field on the mechanical properties of bilayer boron nitride with AB stacking order (AB-2LBN). To accomplish this, density functional theory (DFT) within the framework of generalized gradient approximation (GGA) is implemented. It is demonstrated that the electric field has significant effects on Young's modulus and Poisson's ratio of AB-2LBN when its magnitude is small. With increasing the magnitude of electric field, these effects diminish so that the mechanical properties with and without considering the electric field become approximately identical. Also, it is shown that the equilibrium strain energy decreases linearly by increasing the magnitude of applied electric field.

  20. Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

    NASA Astrophysics Data System (ADS)

    Behzad, Somayeh

    2016-09-01

    Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

  1. Ab Initio No-Core Shell Model

    SciTech Connect

    Barrett, B R; Navratil, P; Vary, J P

    2011-04-11

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  2. Concentrations of AB-CHMINACA and AB-PINACA and Driving Behavior in Suspected Impaired Driving Cases.

    PubMed

    Peterson, Brianna L; Couper, Fiona J

    2015-10-01

    This article reviews case reports for 58 suspected impaired driving cases that were positive for the synthetic cannabinoids AB-CHMINACA or AB-PINACA. All cases were submitted to the Washington State Patrol Toxicology Laboratory in 2014 from either Washington State or State of Alaska law enforcement agencies. The population of drivers was predominantly male (95%), with a mean age of 28 years (range, 18-61 years). The range of blood concentrations was 0.6->10 ng/mL for AB-CHMINACA (N = 33) and 0.6-41.3 ng/mL for AB-PINACA (N = 25). Drug Recognition Expert exams were performed in 10 cases for each AB-CHMINACA and AB-PINACA. Horizontal gaze nystagmus was observed in 50 and 60% of the cases, respectively. Overall, several physiological indicators varied from those typically observed with marijuana use. The majority of these cases had very poor driving; subjects were involved in an accident, found passed out in a vehicle or were called in as a suspected impaired driver. Slurred speech, confusion, lack of coordination/dexterity and lethargy were commonly observed. PMID:26378139

  3. The AB Dor Moving Group: A Chemically Heterogeneous Kinematic Stream?

    NASA Astrophysics Data System (ADS)

    Barenfeld, Scott A.; Bubar, E. J.; Mamajek, E. E.; Young, P. A.

    2012-01-01

    The AB Dor Moving Group is the nearest kinematic group to the Sun. It consists of a "nucleus" of 10 comoving stars at distance 20 pc (Zuckerman et al. 2004), along with dozens of purported "stream" members spread out across the sky, with distances up to 140 pc away (Torres et al. 2008). We perform a kinematic and chemical analysis of a sample of 10 AB Dor "stream" members to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution, high S/N spectra taken with the MIKE spectrograph on the Magellan Clay 6.5-m telescope. Using a chi-squared test with the measured abundances for 10 different elements (Fe, Na, Mg, Si, Al, Ca, Cr, Mn, Ni, and Ba), we find that only a few of the ten purported AB Dor stream members appear to constitute a statistically chemically homogeneous sample. Our orbit simulations show that some of the "stream" members were hundreds of pc from AB Dor 100 Myr ago, and hence were unlikely to have formed near the eponymous star. The lack of kinematic and chemical coherence among the stream sample suggests that the published lists of AB Dor moving group members are unlikely to represent the dispersed remnant of a single star formation episode. Our study does not rule out the physicality of the AB Dor "nucleus" identified by Zuckerman et al., which appears to be coeval with the Pleiades ( 120 Myr). We conclude that the AB Dor stream is dynamical in nature, likely containing stars from many different birth sites. This research was supported by NSF grant AST-1008908, an REU supplement, and funds from the School of Arts and Sciences at the University of Rochester.

  4. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  5. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

    Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.

  6. The Over-Expression of Two Transcription Factors, ABS5/bHLH30 and ABS7/MYB101, Leads to Upwardly Curly Leaves

    PubMed Central

    Wang, Rui; Wu, Haicui; Liang, Shuang; Shao, Jingxia; Qi, Yafei; An, Lijun; Yu, Fei

    2014-01-01

    Proper leaf development is essential for plant growth and development, and leaf morphogenesis is under the control of intricate networks of genetic and environmental cues. We are interested in dissecting these regulatory circuits genetically and report here the isolation of two Arabidopsis dominant mutants, abnormal shoot5-1D (abs5-1D) and abs7-1D identified through activation tagging screens. Both abs5-1D and abs7-1D display an intriguing upwardly curly leaf phenotype. Molecular cloning showed that the elevated expression of a bHLH transcription factor ABS5/T5L1/bHLH30 or a MYB transcription factor ABS7/MYB101 is the cause for the abnormal leaf phenotypes found in abs5-1D or abs7-1D, respectively. Protoplast transient expression assays confirmed that both ABS5/T5L1 and ABS7/MYB101 are targeted to the nucleus. Interestingly, the expression domains of auxin response reporter DR5::GUS were abnormal in leaves of abs5-1D and ABS5/T5L1 over-expression lines. Moreover, cotyledon venation analysis showed that more areoles and free-ending veins are formed in abs5-1D. We found that the epidermis-specific expressions of ABS5/T5L1 or ABS7/MYB101 driven by the Arabidopsis Meristem Layer 1 promoter (PAtML1) were sufficient to recapitulate the curly leaf phenotype of abs5-1D or abs7-1D. In addition, PAtML1::ABS5 lines exhibited similar changes in DR5::GUS expression patterns as those found in 35S-driven ABS5/T5L1 over-expression lines. Our work demonstrated that enhanced expressions of two transcription factors, ABS5/T5L1 and ABS7/MYB101, are able to alter leaf lamina development and reinforce the notion that leaf epidermis plays critical roles in regulating plant organ morphogenesis. PMID:25268707

  7. Ab initio simulation of transport phenomena in rarefied gases.

    PubMed

    Sharipov, Felix; Strapasson, José L

    2012-09-01

    Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889

  8. Stimulation of UvrD helicase by UvrAB.

    PubMed

    Atkinson, John; Guy, Colin P; Cadman, Chris J; Moolenaar, Geri F; Goosen, Nora; McGlynn, Peter

    2009-04-01

    Helicases play critical roles in all aspects of nucleic acid metabolism by catalyzing the remodeling of DNA and RNA structures. UvrD is an abundant helicase in Escherichia coli with well characterized functions in mismatch and nucleotide excision repair and a possible role in displacement of proteins such as RecA from single-stranded DNA. The mismatch repair protein MutL is known to stimulate UvrD. Here we show that the nucleotide excision repair proteins UvrA and UvrB can together stimulate UvrD-catalyzed unwinding of a range of DNA substrates containing strand discontinuities, including forked DNA substrates. The stimulation is specific for UvrD, as UvrAB failed to stimulate Rep helicase, a UvrD homologue. Moreover, although UvrAB can promote limited strand displacement, stimulation of UvrD did not require the strand displacement function of UvrAB. We conclude that UvrAB, like MutL, modulate UvrD helicase activity. This stimulation likely plays a role in DNA strand and protein displacement by UvrD in nucleotide excision repair. Promotion of UvrD-catalyzed unwinding of nicked duplexes by UvrAB may also explain the need for UvrAB and UvrD in Okazaki fragment processing in cells lacking DNA polymerase I. More generally, these data support the idea that helicase activity is regulated in vivo, with helicases acting as part of multisubunit complexes rather than in isolation. PMID:19208629

  9. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

    Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

  10. An ABS control logic based on wheel force measurement

    NASA Astrophysics Data System (ADS)

    Capra, D.; Galvagno, E.; Ondrak, V.; van Leeuwen, B.; Vigliani, A.

    2012-12-01

    The paper presents an anti-lock braking system (ABS) control logic based on the measurement of the longitudinal forces at the hub bearings. The availability of force information allows to design a logic that does not rely on the estimation of the tyre-road friction coefficient, since it continuously tries to exploit the maximum longitudinal tyre force. The logic is designed by means of computer simulation and then tested on a specific hardware in the loop test bench: the experimental results confirm that measured wheel force can lead to a significant improvement of the ABS performances in terms of stopping distance also in the presence of road with variable friction coefficient.

  11. Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Sasaki, Akito

    Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.

  12. GJ 282 AB (WDS 07400-0336 AB = BGH 3 AB) and GICLAS 112-29: A Very Wide System in Process of Dissociation

    NASA Astrophysics Data System (ADS)

    Rica, F. M.; Benavides, R.

    2016-04-01

    Very wide binaries are interesting objects that shed light on the binary formation process and their dynamical evolution. Poveda et al. (2009) studied the possible physical relation of the near (14.2 pc) and wide (~58") binary star GJ 282 AB and the extremely wide (1.09º; ~55,000 AU) companion, NLTT 18149, and they concluded that this very wide system is in the process of dynamical disintegration. In this work, we confirm the same conclusion but using a different method. We first study dynamically GJ 282 AB, confirmed that it is a bound system and then we determine possible orbital solutions. Later, we calculate the relative velocity of NLTT 18149 with respect to the GJ 282 AB's center mass using their (U, V, W) galactocentric velocity. The relative velocity, Vrel = 1.98 ± 0.16 km s-1, is much larger than the escape velocity (0.25 ± 0.01 km s-1). Therefore, with a significance level of 11s, we also conclude that this very wide system is in a process of dynamical disintegration.

  13. A-B Distinction in a Sample of Prominent Psychotherapists

    ERIC Educational Resources Information Center

    Geller, Jesse D.; Berzins, Juris I.

    1976-01-01

    A sample of prominent psychotherapists were asked to fill out the A-B therapist "type" scale and comment on their possible differential effectiveness in treating schizoid/schizophrenic versus neurotic patients. The data suggest that B therapists desire and seek more complex and exciting sensory-cognitive inputs during therapy hours than A…

  14. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

    Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  15. Environmentally friendly process for nickel electroplating of ABS

    NASA Astrophysics Data System (ADS)

    Bazzaoui, M.; Martins, J. I.; Bazzaoui, E. A.; Albourine, A.

    2012-08-01

    Nickel electroplating of acrylonitrile butadiene styrene (ABS) plastic has been achieved successfully without any chromium or palladium pretreatment. Once the ABS is coated with polypyrrole (PPy), the sample may be electroplated. The process is fast, economic and involves three stages. Firstly, chemical deposition of PPy on ABS, secondly, copper deposition and finally nickel electroplating. A homogenous and adherent PPy has been synthesized chemically on ABS plate by using pyrrole as monomer and iron (III) chloride as oxidant. Copper and nickel were deposited galvanostatically from industrial plating baths. The metallic coatings were homogeneous and the adherence was estimated at 100%. The thickness of copper and nickel depend on the electrolysis time. As the current density increases, the Cu and Ni thickness raises. This result was confirmed from SEM characterization and RX map. The Ni coating is characterized by a globular structure with globules of different sizes. Energy dispersive X-ray spectroscopy (EDS) analysis shows the presence of Ni with some amount of carbon and oxygen due to the nickel oxides and contaminant from the bath solution.

  16. Nonreactive Measuring: Its Time Has Arrived with AB 65.

    ERIC Educational Resources Information Center

    Freda, James A.

    1978-01-01

    This article includes school improvement variables to be considered in the evaluation of school improvement under the provisions of California's AB 65. The variables are categorized as pupil and teacher attitudes, instructional methods involving pupils and teachers, and school plant data. (Author)

  17. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

    We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.

  18. Inhibited fragmentation of mAbs in buffered ionic liquids.

    PubMed

    Mazid, Romiza R; Vijayaraghavan, R; MacFarlane, Douglas R; Cortez-Jugo, Christina; Cheng, Wenlong

    2015-05-11

    We thoroughly investigated the biological, structural and chemical stability of epidermal growth factor receptor monoclonal antibody (EGFR mAb) using choline-based buffered ionic liquids (BILs). The results demonstrated substantially enhanced stabilities in our BILs, indicating their huge promise as real-world green biological buffers for antibody storage and transportation. PMID:25869239

  19. Ab initio pseudopotential band calculation of organic conductors

    SciTech Connect

    Ishibashi, Shoji; Kohyama, Masanori

    1999-12-01

    The authors have calculated the band structures of organic conductors TTF-TCNQ and {beta}-(BEDT-TTF){sub 2}I{sub 3} using the ab initio plane-wave pseudopotential method within the local-density approximation (LDA). The Fermi-surface shape and the origin of bands near the Fermi level are investigated for each compound.

  20. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  1. Discovery of New Substrates for LuxAB Bacterial Bioluminescence.

    PubMed

    Jiang, Tianyu; Wang, Weishan; Wu, Xingkang; Wu, Wenxiao; Bai, Haixiu; Ma, Zhao; Shen, Yuemao; Yang, Keqian; Li, Minyong

    2016-08-01

    In this article, four novel substrates with long halftime have been designed and synthesized successfully for luxAB bacterial bioluminescence. After in vitro and in vivo biological evaluation, these molecules can emit obvious bioluminescence emission with known bacterial luciferase, thus indicating a new promising approach to developing the bacterial bioluminescent system. PMID:26896339

  2. Environmental Study: Science and Engineering Buildings. ABS Publication No. 1.

    ERIC Educational Resources Information Center

    California Univ., Berkeley.

    This report is the first of a series which present the results of a systems analysis of the problem of providing science and engineering buildings at the university level conducted by the Academic Building Systems (ABS) program. The document includes (1) a user survey (data and conclusions from a series of studies involving a spectrum of…

  3. AB 1725 Model Accountability System. California Community Colleges. Revised.

    ERIC Educational Resources Information Center

    California Community Colleges, Sacramento. Board of Governors.

    This report proposes a model accountability system for the California community colleges to comply with the directives of Assembly Bill 1725 (AB 1725). The purpose of the accountability system is to provide colleges and districts, the board of governors, and the California legislature with information that will allow for the continued improvement…

  4. Information Manual: Procedures, Planning Concepts, Subsystems. ABS Publication No. 3.

    ERIC Educational Resources Information Center

    California Univ., Berkeley.

    This report, the third in a series which presents the results of a systems analysis of the problem of providing science and engineering buildings at the university level, is a technical manual for using the Academic Building Systems (ABS) approach in programing, designing, and constructing such facilities. The document presents (1) planning…

  5. Modeling and simulation research on automobile ABS bench detection

    NASA Astrophysics Data System (ADS)

    Hao, Ruru; Zhao, Xiangmo; Hao, Dingkun; Zhou, Zhou

    2014-10-01

    Modeling and simulation research on automobile ABS bench detection is conducted in this paper. First, the vehicle model, wheel model, braking force model, and tire-road model on the bench are established according to the ABS bench detection scheme. Then, the Matlab/Simulink simulation model of a single wheel vehicle is built through combining the sub-models described above. Finally, simulation experiments on a variety of simulated road conditions are carried out. And the comparative analysis between the ABS bench detection and ABS road experiments is accomplished. The contrast results show that the simulation curves of bench detection and those of road experiment have high similarity, which verified the correctness and feasibility of the proposed bench detection scheme. At the request of the authors this article is being retracted. It was inadvertently published in AIP Conf. Proc. 1618: The authors intended to publish a different article, but the wrong one was submitted for publication. The article is retracted from the scientific record with effect from 8 July 2015.

  6. Magnetic topology and prominence patterns on AB Doradus

    NASA Astrophysics Data System (ADS)

    Donati, J.-F.; Collier Cameron, A.; Hussain, G. A. J.; Semel, M.

    1999-01-01

    We report new Zeeman--Doppler imaging observations of the rapidly rotating young K0 dwarf AB Doradus, obtained with the Anglo-Australian Telescope in 1996 December. From such observations, simultaneous brightness and magnetic images of the stellar photosphere of AB Dor were reconstructed at three different epochs. The magnetic topology of AB Dor is found to be very complex, with at least 12 different radial field regions of opposite polarities located all around the star. Significant azimuthal field fluxes are also detected in the form of one negative polarity region close to the equator, a series of positive polarity patches at intermediate latitudes and an almost complete ring of negative polarity encircling the rotational pole at high latitudes. In particular, the azimuthal polarities we reconstruct are in very good agreement with those obtained by Donati & Cameron, confirming that this field component is directly related to the dynamo-generated large-scale toroidal magnetic structure. The triple polarity latitudinal pattern observed for this structure in the upper hemisphere of AB Dor indicates that the degree of the underlying large-scale poloidal structure in an axisymmetric spherical harmonics expansion is equal to or greater than five. It also strengthens the idea that the dynamo processes operating in AB Dor feature a non-solar component distributed throughout the convective zone. From the subtle distortion of successive brightness images, we can also confirm the surface differential rotation first measured on this star by Donati & Cameron in both sense and magnitude, with a pole rotating more slowly than the equator by about one part in 220. Finally, the rotation periods we measure for four prominences (from the recurrence rate of their spectral signatures in Balmer lines) confirm the presumption that such clouds are anchored at intermediate to high latitudes. The intrinsic variability of these prominences is not associated with any abrupt changes in the

  7. Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

    PubMed Central

    Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas; Pester, Michael; Loy, Alexander

    2015-01-01

    The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. PMID:25343514

  8. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  9. Ab initio molecular dynamics: concepts, recent developments, and future trends.

    PubMed

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E

    2005-05-10

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  10. Recent progress in ab initio density matrix renormalization group methodology

    NASA Astrophysics Data System (ADS)

    Hachmann, Johannes; Dorando, Jonathan J.; Kin-Lic Chan, Garnet

    2008-03-01

    We present some recent developments in the ab initio density matrix renormalization group (DMRG) method for quantum chemical problems, in particular our local, quadratic scaling algorithm [1] for low dimensional systems. This method is particularly suited for the description of strong nondynamic correlation, and allows us to compute numerically exact (FCI) correlated energies for large active spaces, up to one order of magnitude larger then can be done by conventional CASCI techniques. Other features of this method are its inherent multireference nature, compactness, variational results, size-consistency and size-extensivity. In addition we will review the problems (predominantly organic electronic materials) on which we applied the ab initio DMRG: 1) metal-insulator transition in hydrogen chains [1] 2) all-trans polyacetylene [1] 3) acenes [2] 4) polydiacetylenes [3]. References [1] Hachmann, Cardoen, Chan, JCP 125 (2006), 144101. [2] Hachmann, Dorando, Avil'es, Chan, JCP 127 (2007), 134309. [3] unpublished.

  11. Understanding phonon transport in thermoelectric materials using ab initio approaches

    NASA Astrophysics Data System (ADS)

    Broido, David

    Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.

  12. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

    Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

    2012-03-12

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  13. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  14. Exploring complex chemical reactions by ab-initio simulation

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    1998-03-01

    Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.

  15. Ab Initio Electronic Relaxation Times and Transport in Noble Metals

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Bernardi, Marco; Neaton, Jeffrey B.; Louie, Steven G.

    Relaxation times employed to study electron transport in metals are typically assumed to be constants and obtained empirically using the Drude model. Here, we employ ab initio calculations to compute the electron-phonon relaxation times of Cu, Ag, and Au, and find that they vary significantly on the Fermi surface, spanning ~15 -45 fs. We compute room temperature resistivities in excellent agreement with experiment by combining GW bandstructures, Wannier-interpolated band velocities, and ab initio relaxation times. Our calculations are compared to other approximations used for the relaxation times. Additionally, an importance sampling scheme is introduced to speed up the convergence of resistivity and transport calculations by sampling directly points on the Fermi surface. This work was supported by NSF Grant No. DMR15-1508412 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.

  16. Ab initio Monte Carlo investigation of small lithium clusters.

    SciTech Connect

    Srinivas, S.

    1999-06-16

    Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.

  17. Towards AB Initio Calculation of the Circular Dichroism of Peptides

    NASA Astrophysics Data System (ADS)

    Molteni, E.; Onida, G.; Tiana, G.

    2012-08-01

    In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.

  18. Erythema Ab Igne in Three Girls with Anorexia Nervosa.

    PubMed

    Dessinioti, Clio; Katsambas, Andreas; Tzavela, Eleni; Karountzos, Vasileios; Tsitsika, Artemis K

    2016-03-01

    We present three girls with the eating disorder anorexia nervosa (AN) presenting with erythema ab igne (EAI), a benign, reticular, erythematous dermatosis caused by repeated prolonged skin exposure to mild heat. AN has been associated with abnormal peripheral vascular response to cold, vasoconstriction of the limbs, low hand blood flow, exaggerated response to cold stimuli, subnormal core temperature, and a general feeling of cold that may encourage prolonged heat exposure and induce EAI. PMID:26822102

  19. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  20. 77 FR 73279 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-10

    ...We are adopting a new airworthiness directive (AD) for certain Saab AB, Saab Aerosystems Model 340A (SAAB/SF340A) and SAAB 340B airplanes. This AD was prompted by reports of stall events during icing conditions where the natural stall warning (buffet) was not identified. This AD requires replacing the stall warning computer (SWC) with a new SWC, which provides an artificial stall warning in......

  1. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  2. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  3. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    SciTech Connect

    Draayer, Jerry P.

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  4. Pressure tracking control of vehicle ABS using piezo valve modulator

    NASA Astrophysics Data System (ADS)

    Jeon, Juncheol; Choi, Seung-Bok

    2011-03-01

    This paper presents a wheel slip control for the ABS(anti-lock brake system) of a passenger vehicle using a controllable piezo valve modulator. The ABS is designed to optimize for braking effectiveness and good steerability. As a first step, the principal design parameters of the piezo valve and pressure modulator are appropriately determined by considering the braking pressure variation during the ABS operation. The proposed piezo valve consists of a flapper, pneumatic circuit and a piezostack actuator. In order to get wide control range of the pressure, the pressure modulator is desired. The modulator consists of a dual-type cylinder filled with different substances (fluid and gas) and a piston rod moving vertical axis to transmit the force. Subsequently, a quarter car wheel slip model is formulated and integrated with the governing equation of the piezo valve modulator. A sliding mode controller to achieve the desired slip rate is then designed and implemented. Braking control performances such as brake pressure and slip rate are evaluated via computer simulations.

  5. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  6. Ab Initio Study of Defect Properties in YPO4

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Zhou, Yungang; Devanathan, Ramaswami; Hu, Shenyang Y.; Li, Yulan; Sun, Xin; Khaleel, Mohammad A.

    2012-03-01

    Ab initio methods based on density functional theory have been used to calculate the formation energies of intrinsic defects, including vacancies, interstitials, antisites and Frenkel pairs in YPO4 under the O-rich and Y2O3-rich, and the O-rich and Y-rich conditions. The larger size of the yttrium atom may give rise to higher formation energy of the phosphorus antisite defect. In general, the formation energies of anion interstitials are much smaller than those of cation interstitials for both conditions considered. It is of greatly interest to find that the relative stabilities among the same types of interstitials are independent of the reference states. The most stable configuration for oxygen interstitials is an O-O split interstitial near the Ta site, while the most stable configuration for cation interstitials is a tetrahedral interstitial near the Ta site. The cation split interstitials are unfavorable in YPO4, with much higher formation energies. Furthermore, the properties of Frenkel pairs are compared with those calculated using empirical potentials. The results reveal that both ab initio and empirical potential calculations show a similar trend in the formation energies of Frenkel pairs, but the formation energies obtained by empirical potentials are much larger than those calculated by ab initio method.

  7. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  8. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573

  9. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

  10. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

  11. Probing Inflationary Cosmology: The Atacama B-Mode Search (ABS)

    NASA Astrophysics Data System (ADS)

    Essinger-Hileman, Thomas

    Observations of the Cosmic Microwave Background (CMB) have provided compelling evidence for the Standard Model of Cosmology and have led to the most precise estimates of cosmological parameters to date. Through its sensitivity to gravitational waves, the CMB provides a glimpse into the state of the universe just 10-35 seconds after the Big Bang and of physics on grand-unification-theory (GUT) energy scales around 1016 GeV, some 13 orders of magnitude above the energies achievable by current terrestrial particle accelerators. A gravitational-wave background (GWB) in the early universe would leave a unique, odd-parity pattern of polarization in the CMB called B modes, the magnitude of which is characterized by the tensor-to-scalar ratio, r. A GWB is generically predicted to exist by inflationary theories, and the current generation of CMB polarization experiments will probe the interesting parameter space of r < 0.05 corresponding to single-field inflationary models at GUT scales. I detail the design and construction of the Atacama B-Mode Search (ABS), which aims to measure the polarization of the CMB at degree angular scales where the primordial B-mode signal is expected to peak. ABS is a 145-GHz polarimeter that will operate from a high-altitude site in the Atacama Desert of Chile, consisting of a 60-cm crossed-Dragone telescope with cryogenic primary and secondary reflectors; an array of 240 feedhorn-coupled, transition-edge-sensor, bolometric polarimeters; and, a continuously-rotating, warm, sapphire half-wave plate (HWP) that will provide modulation of the incoming polarization of light. In this thesis, I describe the optical, mechanical, and cryogenic design of the receiver, including the reflector design, focal-plane layout, HWP design, and free-space lowpass filters. I describe physical-optics modeling of the reflector and feedhorn to validate the optical design. A matrix model that allows the calculation of the Mueller matrix of the anti

  12. Staphylococcus aureus Leukocidin A/B (LukAB) Kills Human Monocytes via Host NLRP3 and ASC when Extracellular, but Not Intracellular

    PubMed Central

    DuMont, Ashley L.; Torres, Victor J.; Duncan, Joseph A.

    2015-01-01

    Staphylococcus aureus infections are a growing health burden worldwide, and paramount to this bacterium’s pathogenesis is the production of virulence factors, including pore-forming leukotoxins. Leukocidin A/B (LukAB) is a recently discovered toxin that kills primary human phagocytes, though the underlying mechanism of cell death is not understood. We demonstrate here that LukAB is a major contributor to the death of human monocytes. Using a variety of in vitro and ex vivo intoxication and infection models, we found that LukAB activates Caspase 1, promotes IL-1β secretion and induces necrosis in human monocytes. Using THP1 cells as a model for human monocytes, we found that the inflammasome components NLRP3 and ASC are required for LukAB-mediated IL-1β secretion and necrotic cell death. S. aureus was shown to kill human monocytes in a LukAB dependent manner under both extracellular and intracellular ex vivo infection models. Although LukAB-mediated killing of THP1 monocytes from extracellular S. aureus requires ASC, NLRP3 and the LukAB-receptor CD11b, LukAB-mediated killing from phagocytosed S. aureus is independent of ASC or NLRP3, but dependent on CD11b. Altogether, this study provides insight into the nature of LukAB-mediated killing of human monocytes. The discovery that S. aureus LukAB provokes differential host responses in a manner dependent on the cellular contact site is critical for the development of anti-infective/anti-inflammatory therapies that target the NLRP3 inflammasome. PMID:26069969

  13. Chloroaluminate molten salt electrolytes and vanadium pentoxide xerogel cathodes for high energy density batteries

    NASA Astrophysics Data System (ADS)

    Xie, Jian

    The work presented here is part of an effort to develop a new type of battery which uses an alkali metal such as lithium or sodium or the alkaline earth magnesium, as the anode, a V2O5 xerogel as cathode, and a 1-ethyl-3-methylimidazolium chloride/aluminum chloride room temperature molten salt as electrolyte. First, the stability of the electrolyte was studied. The electrochemistry of 1-ethyl-3-methylimidazolium chloride (EMIC), the organic component of the 1-ethyl-3-methylimidazolium chloride/aluminum chloride molten salt, was examined in acetonitrile. Cyclic voltammetry and differential pulse voltammetry were used to study the reduction of EMI+, the cation of EMIC. Controlled potential coulometry was used to determine the number of electrons involved in the EMI+ reduction process. EMI+ reduction was found to be a one-electron, diffusion controlled process occurring at -2.35V (vs. a reference electrode consisting of a Ag wire in 0.1 M tetra-n-butylammonium perchlorate (TBAP)/acetonitrile solution) in 0.1M TBAP/acetonitrile solution. Two products were generated from the reduction, which are oxidized at about -0.45 and -0.65V. Mass spectroscopy data for these two products suggest that they are degradation products of EMI+. The major products of EMI+ reduction are not electrochemically active within the available potential window. Thus, small amounts of these species should not have a serious effect on the operation of a cell using an EMIC/AlCl3 electrolyte. The second project was to develop a method for buffering a melt which contains free Mg2+ ion for insertion into a V2O 5 xerogel cathode. The buffering of melts with MgCl2 and Mg metal was investigated starting with both acidic and basic melts. The following reaction is proposed for the Mg ribbon in acidic melt: 8Al2Cl - 7+3Mg→2Al+3Mg2++14AlCl -4 This was verified by electrochemical and atomic emission spectroscopy inductively coupled plasma (AES/ICP) data. Finally, the intercalation of Li+, Na+, and Mg2+ ions into V2O5 xerogels in this room temperature molten salt system was investigated. Characterization of spin coated V2O5 xerogel electrodes was also carried out by atomic force microscopy (AFM), scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). Electrochemical data showed that Li + insertion is quite feasible in the melts. Preliminary studies of Na+, and Mg2+ insertion in melts show some evidence for insertion but need to be studied further.

  14. A silane-based electroactive film prepared in an imidazolium chloroaluminate molten salt

    SciTech Connect

    Carlin, R.T. . Frank J. Seiler Research Lab.); Osteryoung, R.A. . Dept. of Chemistry)

    1994-07-01

    Electrochemical oxidation of Ph[sub 3]SiCl (Ph = phenyl) in the room-temperature molten salt AlCl[sub 3]:EMICl (EMICl = 1-ethyl-3-methylimidazolium chloride) results in the formation of an adherent electroactive film on the surface of solid electrodes. The film is reversibly oxidized and reduced in the molten salt and is conducting when in the oxidized state. Based on x-ray photoelectron spectroscopy analysis, the film consists of both a silane and an imidazole component, and the charge storage properties of the film are localized on the heterocyclic rings. This electroactive film compares favorably to other conducting polymers currently being investigated as positive electrodes in room-temperature molten salt batteries.

  15. A rechargeable cadmium-bromine battery using room temperature chloroaluminate molten salts

    SciTech Connect

    Dymek, C.J. Jr.; Reynolds, G.F.; Wilkes, J.S.

    1987-07-01

    Galvanic cells were tested using as electrolytes room temperature molten salts formed by mixing AlCl/sub 3/ with 1-methyl-3-ethylimidazolium chloride (MEICl). Zn and Cd, each with basic melt (containing Cl/sup -/ and AlCl/sub 4//sup -/) were the anodes. Br/sub 2/ dissolved in basic melt with a reticulated vitreous carbon current collector was the cathode in each case. MEI/sup +/-selective Nafion was used as a separator. The Zn electrode was found to be irreversible, while the Cd/Br/sub 2/ cell is rechargeable with an open-circuit voltage of 2.0V, an extended temperature range of operation, and potential for high specific energy.

  16. Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

    NASA Technical Reports Server (NTRS)

    Hargittai, M.

    1980-01-01

    The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

  17. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PROCEDURES AND REQUIREMENTS FOR PLANT-INCORPORATED...

  18. Non Target Effect of Cry1 Ab and Cry Ab x Cry3 Bb1 Bt Transgenic Maize on Orius Insidiosus (Hemiptera: Anthocoridae) Abundance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Non-target effects of Cry1Ab x CP4 EPSPS and Cry1Ab + Cry3Bb1 x CP4 EPSPS Bt transgenic new maize hybrids on insidious flower bugs [Orius insidiosus (Say)] was studied in Nebraska (Mead, C lay Center, and Concord) during 2007 and 2008. The Bt effect was compared to CP4 EPSPS maize (isoline), convent...

  19. Pharmacology of Indole and Indazole Synthetic Cannabinoid Designer Drugs AB-FUBINACA, ADB-FUBINACA, AB-PINACA, ADB-PINACA, 5F-AB-PINACA, 5F-ADB-PINACA, ADBICA, and 5F-ADBICA.

    PubMed

    Banister, Samuel D; Moir, Michael; Stuart, Jordyn; Kevin, Richard C; Wood, Katie E; Longworth, Mitchell; Wilkinson, Shane M; Beinat, Corinne; Buchanan, Alexandra S; Glass, Michelle; Connor, Mark; McGregor, Iain S; Kassiou, Michael

    2015-09-16

    Synthetic cannabinoid (SC) designer drugs based on indole and indazole scaffolds and featuring l-valinamide or l-tert-leucinamide side chains are encountered with increasing frequency by forensic researchers and law enforcement agencies and are associated with serious adverse health effects. However, many of these novel SCs are unprecedented in the scientific literature at the time of their discovery, and little is known of their pharmacology. Here, we report the synthesis and pharmacological characterization of AB-FUBINACA, ADB-FUBINACA, AB-PINACA, ADB-PINACA, 5F-AB-PINACA, 5F-ADB-PINACA, ADBICA, 5F-ADBICA, and several analogues. All synthesized SCs acted as high potency agonists of CB1 (EC50 = 0.24-21 nM) and CB2 (EC50 = 0.88-15 nM) receptors in a fluorometric assay of membrane potential, with 5F-ADB-PINACA showing the greatest potency at CB1 receptors. The cannabimimetic activities of AB-FUBINACA and AB-PINACA in vivo were evaluated in rats using biotelemetry. AB-FUBINACA and AB-PINACA dose-dependently induced hypothermia and bradycardia at doses of 0.3-3 mg/kg, and hypothermia was reversed by pretreatment with a CB1 (but not CB2) antagonist, indicating that these SCs are cannabimimetic in vivo, consistent with anecdotal reports of psychoactivity in humans. PMID:26134475

  20. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  1. GQ Lup Ab Visible & Near-Infrared Photometric Analysis

    SciTech Connect

    Marois, C; Macintosh, B; Barman, T

    2006-08-07

    We have re-analyzed archival HST R and I band images and Subaru CH{sub 4}, H, Ks and L{prime} data of the recently discovered planetary mass companion (PMC) GQ Lup Ab. With these we produce the first R and I band photometry of the companion and fit a radius and effective temperature using detailed model atmospheres. We find an effective temperature of 2338 {+-} 100K, and a radius of 0.37 {+-} 0.05R{sub {circle_dot}} and luminosity of log(L/L{sub {circle_dot}}) = -2.43 {+-} 0.07 (at 140pc). Since we fit wavelengths that span most of the emitted radiation from GQ Lup this luminosity estimate is robust, with uncertainty dominated by the distance uncertainty. The radius obtained for 140pc (0.37R{sub {circle_dot}}) is significantly larger than the one originally derived. The mass of the object is much more model-dependent than the radiative properties, but for the GAIA dusty models we find a mass between 9-20 M{sub Jup}, in the range of the brown dwarf and PMC deuterium burning boundary. Assuming a distance of 140pc, observations fit to 1{sigma} the Baraffe evolution model for a {approx} 15 M{sub Jup} brown dwarf. Additionally, the F606W photometric band is significantly overluminous compared to model predictions. Such overluminosity could be explained by a bright H{alpha} emission from chromospheric activity, interaction with another undetected companion, or accretion. Assuming that GQ Lup Ab has a bright H{alpha} emission line, its H{alpha} emission strength is 10{sup -1.71 {+-} 0.10} L{sub bol}, significantly larger than field late-type dwarfs. GQ Lup Ab might be strongly accreting and still be in its formation phase.

  2. Functional Analysis of DNA Replication Fork Reversal Catalyzed by Mycobacterium tuberculosis RuvAB Proteins*

    PubMed Central

    Khanduja, Jasbeer Singh; Muniyappa, K.

    2012-01-01

    Initially discovered in Escherichia coli, RuvAB proteins are ubiquitous in bacteria and play a dual role as molecular motor proteins responsible for branch migration of the Holliday junction(s) and reversal of stalled replication forks. Despite mounting genetic evidence for a crucial role of RuvA and RuvB proteins in reversal of stalled replication forks, the mechanistic aspects of this process are still not fully understood. Here, we elucidate the ability of Mycobacterium tuberculosis RuvAB (MtRuvAB) complex to catalyze the reversal of replication forks using a range of DNA replication fork substrates. Our studies show that MtRuvAB, unlike E. coli RuvAB, is able to drive replication fork reversal via the formation of Holliday junction intermediates, suggesting that RuvAB-catalyzed fork reversal involves concerted unwinding and annealing of nascent leading and lagging strands. We also demonstrate the reversal of replication forks carrying hemi-replicated DNA, indicating that MtRuvAB complex-catalyzed fork reversal is independent of symmetry at the fork junction. The fork reversal reaction catalyzed by MtRuvAB is coupled to ATP hydrolysis, is processive, and culminates in the formation of an extended reverse DNA arm. Notably, we found that sequence heterology failed to impede the fork reversal activity of MtRuvAB. We discuss the implications of these results in the context of recognition and processing of varied types of replication fork structures by RuvAB proteins. PMID:22094465

  3. Ab Initio Computation of the Energies of Circular Quantum Dots

    SciTech Connect

    Lohne, M. Pedersen; Hagen, Gaute; Hjorth-Jensen, M.; Kvaal, S.; Pederiva, F.

    2011-01-01

    We perform coupled-cluster and diffusion Monte Carlo calculations of the energies of circular quantum dots up to 20 electrons. The coupled-cluster calculations include triples corrections and a renormalized Coulomb interaction defined for a given number of low-lying oscillator shells. Using such a renormalized Coulomb interaction brings the coupled-cluster calculations with triples correlations in excellent agreement with the diffusion Monte Carlo calculations. This opens up perspectives for doing ab initio calculations for much larger systems of electrons.

  4. The implementation of ab initio quantum chemistry calculations on transporters.

    PubMed

    Cooper, M D; Hillier, I H

    1991-06-01

    The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets. The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory. PMID:1919615

  5. Ab initio electronic properties of dual phosphorus monolayers in silicon

    PubMed Central

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated. PMID:25246862

  6. Ab initio vibrational and dielectric properties of Y V O

    NASA Astrophysics Data System (ADS)

    Vali, R.

    2009-10-01

    For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.

  7. AB 1007 Full Fuel Cycle Analysis (FFCA) Peer Review

    SciTech Connect

    Rice, D; Armstrong, D; Campbell, C; Lamont, A; Gallegos, G; Stewart, J; Upadhye, R

    2007-01-19

    LLNL is a participant of California's Advanced Energy Pathways (AEP) team funded by DOE (NETL). At the AEP technical review meeting on November 9, 2006. The AB 1007 FFCA team (Appendix A) requested LLNL participate in a peer review of the FFCA reports. The primary contact at the CEC was McKinley Addy. The following reports/presentations were received by LLNL: (1) Full Fuel Cycle Energy and Emissions Assumptions dated September 2006, TIAX; (2) Full Fuel cycle Assessment-Well to Tank Energy Inputs, Emissions, and Water Impacts dated December 2006, TIAX; and (3) Full Fuel Cycle Analysis Assessment dated October 12, 2006, TIAX.

  8. Potential Dependence of Electrochemical Barriers from ab Initio Calculations.

    PubMed

    Chan, Karen; Nørskov, Jens K

    2016-05-01

    We present a simple and computationally efficient method to determine the potential dependence of the activation energies for proton-electron transfer from a single ab initio barrier calculation. We show that the potential dependence of the activation energy is given by the partial charge transferred at the transition state. The method is evaluated against the potential dependence determined explicitly through multiple calculations at varying potential. We show that the transfer coefficient is given by the charge transferred from the initial to transition state, which has significant implications for electrochemical kinetics. PMID:27088442

  9. Ab-Initio Shell Model with a Core

    SciTech Connect

    Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

    2008-06-04

    We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

  10. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

    Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

    2010-12-20

    The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

  11. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

  12. Ab initio study of hydrogen on beryllium surfaces

    NASA Astrophysics Data System (ADS)

    Bachurin, D. V.; Vladimirov, P. V.

    2015-11-01

    Static ab initio calculations were performed for five principal hexagonal close-packed beryllium surfaces: basal, prismatic (type I and II) and pyramidal (type I and II). The basal plane was found to be the most energetically favorable, while the energies of the prismatic (type I) and pyramidal (type I) planes were slightly higher followed by the type II planes. Beryllium is known to show extreme interlayer distance relaxation near the surface. Up to five outermost atomic layers were involved in surface relaxation. The presence of hydrogen on the beryllium surfaces led to a noticeable reduction of the surface energy.

  13. An improved ab initio structure for fluorine peroxide (FOOF)

    NASA Astrophysics Data System (ADS)

    Mack, Hans-Georg; Oberhammer, Heinz

    1988-03-01

    Ab initio calculations with the 6-31G* and Dunning (9s5p/4s2p) basis sets augmented with p and d functions at various levels of theory (RHF, MP2, MP3, and MP4) were carried out on F 2O 2. The best result was obtained at the MP2 level with the Dunning basis plus one set of d functions on fluorine and two sets of d functions on oxygen. These calculations reproduce the experimental bond lengths to within 0.01 Å and the angles to within the experimental uncertainties.

  14. Ab initio study of neutron drops with chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, H. D.; Fischer, S.; Maris, P.; Vary, J. P.; Binder, S.; Calci, A.; Langhammer, J.; Roth, R.

    2014-12-01

    We report ab initio calculations for neutron drops in a 10 MeV external harmonic-oscillator trap using chiral nucleon-nucleon plus three-nucleon interactions. We present total binding energies, internal energies, radii and odd-even energy differences for neutron numbers N = 2- 18 using the no-core shell model with and without importance truncation. Furthermore, we present total binding energies for N = 8 , 16 , 20 , 28 , 40 , 50 obtained in a coupled-cluster approach. Comparisons with quantum Monte Carlo results, where available, using Argonne v8‧ with three-nucleon interactions reveal important dependences on the chosen Hamiltonian.

  15. Ab-initio study of transition metal hydrides

    SciTech Connect

    Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini

    2014-04-24

    We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

  16. Antigen identification and characterization of lung cancer specific monoclonal antibodies produced by mAb proteomics.

    PubMed

    Wang, Dongdong; Hincapie, Marina; Guergova-Kuras, Mariana; Kadas, Janos; Takacs, Laszlo; Karger, Barry L

    2010-04-01

    A mass spectrometric (MS)-based strategy for antigen (Ag) identification and characterization of globally produced monoclonal antibodies (mAbs) is described. Mice were immunized with a mixture of native glycoproteins, isolated from the pooled plasma of patients with nonsmall cell lung cancer (NSCLC), to generate a library of IgG-secreting hybridomas. Prior to immunization, the pooled NSCLC plasma was subjected to 3-sequential steps of affinity fractionation, including high abundant plasma protein depletion, glycoprotein enrichment, and polyclonal antibody affinity chromatography normalization. In this paper, to demonstrate the high quality of the globally produced mAbs, we selected 3 mAbs of high differentiating power against a matched, pooled normal plasma sample. After production of large quantities of the mAbs from ascites fluids, Ag identification was achieved by immunoaffinity purification, SDS-PAGE, Western blotting, and MS analysis of in-gel digest products. One antigen was found to be complement factor H, and the other two were mapped to different subunits of haptoglobin (Hpt). The 2 Hpt mAbs were characterized in detail to assess the quality of the mAbs produced by the global strategy. The affinity of one of the mAbs to the Hpt native tetramer form was found to have a K(D) of roughly 10(-9) M and to be 2 orders of magnitude lower than the reduced form, demonstrating the power of the mAb proteomics technology in generating mAbs to the natural form of the proteins in blood. The binding of this mAb to the beta-chain of haptoglobin was also dependent on glycosylation on this chain. The characterization of mAbs in this work reveals that the global mAb proteomics process can generate high-quality lung cancer specific mAbs capable of recognizing proteins in their native state. PMID:20146545

  17. Antigen Identification and Characterization of Lung Cancer Specific Monoclonal Antibodies Produced by mAb Proteomics

    PubMed Central

    Wang, Dongdong; Hincapie, Marina; Guergova-Kuras, Mariana; Kadas, Janos; Takacs, Laszlo; Karger, Barry L.

    2010-01-01

    A mass spectrometric (MS)-based strategy for antigen (Ag) identification and characterization of globally produced monoclonal antibodies (mAbs) is described. Mice were immunized with a mixture of native glycoproteins, isolated from the pooled plasma of patients with non-small cell lung cancer (NSCLC), to generate a library of IgG-secreting hybridomas. Prior to immunization, the pooled NSCLC plasma was subjected to 3-sequential steps of affinity fractionation, including high abundant plasma protein depletion, glycoprotein enrichment and polyclonal antibody affinity chromatography normalization. In this paper, in order to demonstrate the high quality of the globally produced mAbs, we selected 3 mAbs of high differentiating power against a matched, pooled normal plasma sample. After production of large quantities of the mAbs from ascites fluids, Ag identification was achieved by immunoaffinity purification, SDS-PAGE, Western blotting and MS analysis of in-gel digest products. One antigen was found to be complement factor H, and the other two were mapped to different subunits of haptoglobin (Hpt). The 2 Hpt mAbs were characterized in detail in order to assess the quality of the mAbs produced by the global strategy. The affinity of one of the mAbs to the Hpt native tetramer form was found to have a KD of roughly 10−9 M and to be 2 orders of magnitude lower than the reduced form, demonstrating the power of the mAb proteomics technology in generating mAbs to the natural form of the proteins in blood. The binding of this mAb to the β-chain of haptoglobin was also dependent on glycosylation on this chain. The characterization of mAbs in this work reveals that the global mAb proteomics process can generate high-quality lung cancer specific mAbs capable of recognizing proteins in their native state. PMID:20146545

  18. Ab initio study of hot electrons in GaAs.

    PubMed

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G

    2015-04-28

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287

  19. Electrocatalytic reduction of nitrate and selenate by NapAB.

    PubMed

    Gates, Andrew J; Butler, Clive S; Richardson, David J; Butt, Julea N

    2011-01-01

    Bacterial cellular metabolism is renowned for its metabolic diversity and adaptability. However, certain environments present particular challenges. Aerobic metabolism of highly reduced carbon substrates by soil bacteria such as Paracoccus pantotrophus presents one such challenge since it may result in excessive electron delivery to the respiratory redox chain when compared with the availability of terminal oxidant, O2. The level of a periplasmic ubiquinol-dependent nitrate reductase, NAP, is up-regulated in the presence of highly reduced carbon substrates. NAP oxidizes ubiquinol at the periplasmic face of the cytoplasmic membrane and reduces nitrate in the periplasm. Thus its activity counteracts the accumulation of excess reducing equivalents in ubiquinol, thereby maintaining the redox poise of the ubiquinone/ubiquinol pool without contributing to the protonmotive force across the cytoplasmic membrane. Although P. pantotrophus NapAB shows a high level of substrate specificity towards nitrate, the enzyme has also been reported to reduce selenate in spectrophotometric solution assays. This transaction draws on our current knowledge concerning the bacterial respiratory nitrate reductases and extends the application of PFE (protein film electrochemistry) to resolve and quantify the selenate reductase activity of NapAB. PMID:21265780

  20. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    PubMed Central

    Elenewski, Justin E.; Hackett, John C

    2015-01-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906

  1. Three-cluster dynamics within an ab initio framework

    DOE PAGESBeta

    Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

    2013-09-26

    In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less

  2. Oxidation of GaN: An ab initio thermodynamic approach

    NASA Astrophysics Data System (ADS)

    Jackson, Adam J.; Walsh, Aron

    2013-10-01

    GaN is a wide-band-gap semiconductor used in high-efficiency light-emitting diodes and solar cells. The solid is produced industrially at high chemical purities by deposition from a vapor phase, and oxygen may be included at this stage. Oxidation represents a potential path for tuning its properties without introducing more exotic elements or extreme processing conditions. In this work, ab initio computational methods are used to examine the energy potentials and electronic properties of different extents of oxidation in GaN. Solid-state vibrational properties of Ga, GaN, Ga2O3, and a single substitutional oxygen defect have been studied using the harmonic approximation with supercells. A thermodynamic model is outlined which combines the results of ab initio calculations with data from experimental literature. This model allows free energies to be predicted for arbitrary reaction conditions within a wide process envelope. It is shown that complete oxidation is favorable for all industrially relevant conditions, while the formation of defects can be opposed by the use of high temperatures and a high N2:O2 ratio.

  3. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-01

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation. PMID:24679248

  4. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  5. 4He Thermophysical Properties: New Ab Initio Calculations

    PubMed Central

    Hurly, John J.; Mehl, James B.

    2007-01-01

    Since 2000, atomic physicists have reduced the uncertainty of the helium-helium “ab initio” potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of 4He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties. PMID:27110456

  6. Ab initio prediction of the critical thickness of a precipitate

    NASA Astrophysics Data System (ADS)

    Sampath, S.; Janisch, R.

    2013-09-01

    Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface. Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations.

  7. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin E.; Hackett, John C.

    2015-02-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  8. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    2015-02-14

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  9. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

    SciTech Connect

    French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes

    2012-09-15

    We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.

  10. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  11. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

    Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-05-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.

  12. Ab initio tight-binding Hamiltonian for transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kuate Defo, Rodrick; Shirodkar, Sharmila N.; Lieu, Simon; Tritsaris, Georgios A.; Kaxiras, Efthimios

    2015-11-01

    We present an accurate ab initio tight-binding Hamiltonian for the transition metal dichalcogenides, MoS2, MoSe2, WS2, WSe2, with a minimal basis (the d orbitals for the metal atoms and p orbitals for the chalcogen atoms) based on a transformation of the Kohn-Sham density functional theory Hamiltonian to a basis of maximally localized Wannier functions. The truncated tight-binding Hamiltonian, with only on-site, first, and partial second neighbor interactions, including spin-orbit coupling, provides a simple physical picture and the symmetry of the main band-structure features. Interlayer interactions between adjacent layers are modeled by transferable hopping terms between the chalcogen p orbitals. The full-range tight-binding Hamiltonian can be reduced to hybrid-orbital k .p effective Hamiltonians near the band extrema that capture important low-energy excitations. These ab initio Hamiltonians can serve as the starting point for applications to interacting many-body physics including optical transitions and Berry curvature of bands, of which we give some examples.

  13. Improved radioimaging and tumor localization with monoclonal F(ab')2

    SciTech Connect

    Wahl, R.L.; Parker, C.W.; Philpott, G.W.

    1983-04-01

    Monoclonal anti-tumor antibodies have great promise for radioimmunodetection and localization of tumors. Fab and F(ab')2 fragments, which lack the Fc fragment of antibody (Ab), are cleared more rapidly from the circulation and may have less nonspecific tissue binding than intact Ab. In radioimaging studies using a murine monoclonal antibody to carcinoembryonic antigen in a human colon carcinoma xenografted into hamsters, F(ab')2 fragments were shown superior to Fab fragments and intact antibody for scintiscanning. In double-label experiments with anti-CEA antibody and control monoclonal IgG, F(ab')2 fragments were found to give better and more rapid specific tumor localization than intact antibody or Fab fragments. F(ab')2 fragments offer significant promise for tumor imaging and possibly therapy.

  14. ABS polymer electroless plating through a one-step poly(acrylic acid) covalent grafting.

    PubMed

    Garcia, Alexandre; Berthelot, Thomas; Viel, Pascal; Mesnage, Alice; Jégou, Pascale; Nekelson, Fabien; Roussel, Sébastien; Palacin, Serge

    2010-04-01

    A new, efficient, palladium- and chromium-free process for the electroless plating of acrylonitrile-butadiene-styrene (ABS) polymers has been developed. The process is based on the ion-exchange properties of poly(acrylic acid) (PAA) chemically grafted onto ABS via a simple and one-step method that prevents using classical surface conditioning. Hence, ABS electroless plating can be obtained in three steps, namely: (i) the grafting of PAA onto ABS, (ii) the copper Cu(0) seeding of the ABS surface, and (iii) the nickel or copper metallization using commercial-like electroless plating bath. IR, XPS, and SEM were used to characterize each step of the process, and the Cu loading was quantified by atomic absorption spectroscopy. This process successfully compares with the commercial one based on chromic acid etching and palladium-based seed layer, because the final metallic layer showed excellent adhesion with the ABS substrate. PMID:20361751

  15. Millimeter observations and modeling of the AB Aur system

    NASA Astrophysics Data System (ADS)

    Semenov, Dmitry A.; Pavlyuchenkov, Yaroslav N.; Schreyer, Katharina; Henning, Thomas K.; Dullemond, Cornelius; Bacmann, Aurore

    We present the results of millimeter observations and first comprehensive physical, chemical and radiative transfer model of the AB Aur circumstellar disk and surrounding envelope. This system is studied at low (~ 10") resolution by observing CO, C18O, CS, HCO+, DCO+, H2CO, HCN, HNC, and SiO rotational lines with the IRAM 30-m antenna. At higher ≈ 5" resolution, the AB Aur disk is resolved in the HCO+(1-0) transition with the Plateau de Bure interferometer. The AB Aur system is modeled as a 2D flared disk with a vertical temperature gradient, surrounded by an isothermal spherical envelope with a shadowed midplane and two unshielded cones. Using this model together with a gas-grain chemical network including surface reactions, time-dependent molecular abundances are calculated. Finally, a 2D non-LTE line radiative transfer code is applied to compute level populations (Fig. 1) and beam-convolved interferometric map and single-dish spectra of the HCO+(1-0), HCO+(3-2), CO(2-1), C18O(2-1), CS(2-1), and CS(5-4) lines. Our disk model successfully reproduces observed interferometric HCO+(1-0) data (see Fig. 2), thus constraining the following disk properties: (1) the inclination angle ι = 17+6-3◦, (2) the position angle φ = 80 x 30◦, (3) the size Rout = 400 x 200 AU, (4) the mass Mdisk = 1.3 × 10-2 Msol (with a factor of ~ 7 uncertainty), and (5) that the disk is rotating. Indirect evidence for a local clumpiness of the AB Aur disk at ~ 600 AU is found. We synthesize the single-dish spectra for three different cases, namely, for the disk model, for the envelope model, and for their combination. An overall agreement between all modeled and acquired line intensities, widths, and profiles is achieved for the latter model, with the exception of the CS(5-4) data that require presence of dense clumpy structures in the model. It allows to constrain the physical structure of the inner envelope: (1) its average temperature is 35±14 K, (2) the density decreases with the

  16. Cry1Ab protein from Bacillus thuringiensis and MON810 cry1Ab-transgenic maize exerts no adjuvant effect after airway exposure.

    PubMed

    Andreassen, M; Bøhn, T; Wikmark, O-G; Van den Berg, J; Løvik, M; Traavik, T; Nygaard, U C

    2015-03-01

    The genetically modified (GM) maize event MON810 has been inserted with a processed version of the transgene, cry1Ab, derived from the soil bacterium Bacillus thuringiensis (Bt) to express proteins with insecticidal properties. Such proteins may introduce new allergens and also act as adjuvants that promote allergic responses. While focus has been on safe consumption and hence the oral exposure to GM food and feed, little is known regarding inhalation of pollen and desiccated airborne plant material from GM crops. The aim of this study was to investigate whether plant material from the Cry1Ab-expressing maize variety MON810, or trypsin-activated Cry1Ab (trypCry1Ab) protein produced in recombinant bacteria, may act as adjuvants against the allergen ovalbumin (OVA) in a mouse model of airway allergy. A clear proallergic adjuvant effect of the mucosal adjuvant cholera toxin (CT) was demonstrated, determined as increased specific IgE, eosinophils and Th2 cytokines in MLN cell supernates, while no elevation in OVA-specific antibodies or cytokine release from MLN cells after stimulation with OVA were observed in mice receiving Cry1Ab-containing plant materials or the trypCry1Ab protein. Our data suggest that Cry1Ab proteins had no detectable systemic adjuvant effect in mice after airway exposure. Further experiments with purified plant proteins, as well as long-term exposures needs be conducted to further evaluate exposures experienced in real-life situations. PMID:25564738

  17. Comparative Study of Electroless Copper Film on Different Self-Assembled Monolayers Modified ABS Substrate

    PubMed Central

    Xu, Jiushuai; Fan, Ruibin; Wang, Jiaolong; Jia, Mengke; Xiong, Xuanrui; Wang, Fang

    2014-01-01

    Copper films were grown on (3-Mercaptopropyl)trimethoxysilane (MPTMS), (3-Aminopropyl)triethoxysilane (APTES) and 6-(3-(triethoxysilyl)propylamino)-1,3,5- triazine-2,4-dithiol monosodium (TES) self-assembled monolayers (SAMs) modified acrylonitrile-butadiene-styrene (ABS) substrate via electroless copper plating. The copper films were examined using scanning electron microscopy (SEM) and X-ray diffraction (XRD). Their individual deposition rate and contact angle were also investigated to compare the properties of SAMs and electroless copper films. The results indicated that the formation of copper nuclei on the TES-SAMs modified ABS substrate was faster than those on the MPTMS-SAMs and APTES-SAMs modified ABS substrate. SEM images revealed that the copper film on TES-SAM modified ABS substrate was smooth and uniform, and the density of copper nuclei was much higher. Compared with that of TES-SAMs modified resin, the coverage of copper nuclei on MPTMS and APTES modified ABS substrate was very limited and the copper particle size was too big. The adhesion property test demonstrated that all the SAMs enhanced the interfacial interaction between copper plating and ABS substrate. XRD analysis showed that the copper film deposited on SAM-modified ABS substrate had a structure with Cu(111) preferred orientation, and the copper film deposited on TES-SAMs modified ABS substrate is better than that deposited on MPTMS-SAMs or APTES-SAMs modified ABS resins in electromigrtion resistance. PMID:24739812

  18. Adsorption of insecticidal Cry1Ab protein to humic substances. 1. Experimental approach and mechanistic aspects.

    PubMed

    Sander, Michael; Tomaszewski, Jeanne E; Madliger, Michael; Schwarzenbach, René P

    2012-09-18

    Adsorption is a key process affecting the fate of insecticidal Cry proteins (Bt toxins), produced by genetically modified Bt crops, in soils. However, the mechanisms of adsorption to soil organic matter (SOM) remain poorly understood. This work assesses the forces driving the adsorption of Cry1Ab to Leonardite humic acid (LHA), used as a model for SOM. We studied the effects of solution pH and ionic strength (I) on adsorption using a quartz crystal microbalance with dissipation monitoring and optical waveguide lightmode spectroscopy. Initial Cry1Ab adsorption rates were close to diffusion-limited and resulted in extensive adsorption, even at pH >6, at which LHA and Cry1Ab carry negative net charges. Adsorption increased with decreasing I at pH >6, indicating Cry1Ab-LHA patch-controlled electrostatic attraction via positively charged domains of Cry1Ab. Upon rinsing, only a fraction of Cry1Ab desorbed, suggesting a range of interaction energies of Cry1Ab with LHA. Different interaction energies likely resulted from nonuniformity in the LHA surface polarity, with higher Cry1Ab affinities to more apolar LHA regions due to the hydrophobic effect. Contributions from the hydrophobic effect were substantiated by comparison of the adsorption of Cry1Ab and the reference proteins albumin and lysozyme to LHA and to apolar and polar model surfaces. PMID:22862304

  19. Operator evolution for ab initio theory of light nuclei

    NASA Astrophysics Data System (ADS)

    Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navrátil, Petr

    2014-09-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range; short ranges have the largest absolute renormalization when including two- and three-body induced terms, while at long ranges the induced three-body contribution takes on increased relative importance. The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores

  20. The ab-initio density matrix renormalization group in practice

    SciTech Connect

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  1. Ab initio engineering of materials with stacked hexagonal tin frameworks.

    PubMed

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  2. Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

    Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.

  3. Highly anisotropic thermal conductivity of arsenene: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zeraati, Majid; Vaez Allaei, S. Mehdi; Abdolhosseini Sarsari, I.; Pourfath, Mahdi; Donadio, Davide

    2016-02-01

    Elemental two-dimensional (2D) materials exhibit intriguing heat transport and phononic properties. Here we have investigated the lattice thermal conductivity of newly proposed arsenene, the 2D honeycomb structure of arsenic, using ab initio calculations. Solving the Boltzmann transport equation for phonons, we predict a highly anisotropic thermal conductivity of 30.4 and 7.8 W/mK along the zigzag and armchair directions, respectively, at room temperature. Our calculations reveal that phonons with mean free paths between 20 nm and 1 μ m provide the main contribution to the large thermal conductivity in the zigzag direction; mean free paths of phonons contributing to heat transport in the armchair directions range between 20 and 100 nm. The obtained anisotropic thermal conductivity and feasibility of synthesis, in addition to high electron mobility reported elsewhere, make arsenene a promising material for nanoelectronic applications and thermal management.

  4. Ab initio study of II-(VI)2 dichalcogenides.

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783

  5. Ab initio study of guanine damage by hydroxyl radical.

    PubMed

    Chaban, Galina M; Wang, Dunyou; Huo, Winifred M

    2015-01-15

    Multiconfigurational ab initio methods are used in this study to examine two initial reactions that take place during the OH radical attack of the DNA base guanine: a ring opening reaction and a hydrogen transfer reaction. The same reactions are also studied in the presence of a single water molecule. The ring opening reaction has a moderate barrier height of ∼20-25 kcal/mol that is relatively insensitive to the presence of water. The barrier of the H-transfer reaction, on the other hand, is lowered from ∼50 to ∼22 kcal/mol when one water molecule is added, thus becoming comparable to the barrier height of the ring opening reaction. PMID:25517252

  6. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

  7. SEEDS Polarimetric Imagery of the AB Aur Protoplanetary Disk

    NASA Astrophysics Data System (ADS)

    Wisniewski, John P.; Fukagawa, M.; Grady, C.; Hashimoto, J.; Hodapp, K.; Kudo, T.; Munetake, M.; Okamoto, Y.; Tamura, M.; SEEDS Team

    2011-01-01

    The Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS) is a large survey which will be observing roughly 200 protoplanetary and debris disk systems over the next five years using the HiCIAO coronagraph + AO188 system on the Subaru telescope. We present new J-band polarimetric differential imagery of the proto-type Herbig Ae star, AB Aurigae, which diagnoses scattered light from the system between 20 - 540 AU at a resolution of roughly 8 AU. We discuss the morphology we observe in the outer disk region in the context of previous observations of the system, and compare/contrast the morphology in the inner disk region with recent H-band imagery of the system made with HiCIAO (Hashimoto et al 2010). This work was supported in part by NSF grants AST 0802230 and AST 1009314 and the AAS' Chretien International Research Grant.

  8. Pseudosymmetric features of non-centrosymmetric AB type crystals

    NASA Astrophysics Data System (ADS)

    Gazhulina, A. P.; Marychev, M. O.

    2016-07-01

    This work is supplement to our previous investigation (Gazhulina and Marychev, 2015) [1]. We have considered pseudosymmetric features with respect to the operation of inversion (pseudoinversion) for 340 non-centrosymmetric AB type crystals. Analysis of the features of particular structure types allowed us to determine the positions of pseudoinversion centers, subdivide them into separate types, and classify the entire set of crystals studied with respect to the types of pseudoinversion centers and peculiarities of the behavior of the degree of pseudoinversion depending on the ratio of atomic numbers of A and B components. For each group of crystals, average values and lower boundaries of the maximum pseudoinversion are determined and distribution with respect to the degree of pseudoinversion is constructed.

  9. Ab initio water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects. PMID:25687650

  10. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

    We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.

  11. Efficient Ab initio Modeling of Random Multicomponent Alloys

    NASA Astrophysics Data System (ADS)

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-01

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  12. Ab initio H2O in realistic hydrophilic confinement.

    PubMed

    Allolio, Christoph; Klameth, Felix; Vogel, Michael; Sebastiani, Daniel

    2014-12-15

    A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized. PMID:25208765

  13. [Erythema ab igne in a patient with bulimia nervosa].

    PubMed

    Beneke, Johannes; Koerner, Michael; de Zwaan, Martina

    2014-05-01

    Erythema ab igne (EAI) is a skin lesion, which is characterized by a localized netlike erythema. For the occurrence of the dermatosis a continuous or regular heat exposure and infrared radiation to a skin area is necessary. The reticulated maculae could fade after stopping the heat exposure, persist as hyperpigmentation and in single cases a malignant transformation is possible. We present a patient with bulimia nervosa (BN), who developed an EAI after consequent use of a hot-water bottle. In the context of the eating disorder the patient reported a general feeling of cold. She avoided the contact with the abdomen to prevent a stimulation of the digestion. Therefore the EAI was located predominantly on the medial thighs. After stopping the heat application the EAI faded slightly in the periphery und turned browner. PMID:24504523

  14. Monte Carlo simulation of the abBA experiment

    NASA Astrophysics Data System (ADS)

    Frlež, Emil

    2004-10-01

    The abBA collaboration proposes to conduct a program of precise measurements of neutron beta decay correlation coefficients a, b, A, and B at a cold neutron beam facility. We have performed studies of the energy and timing response of a pair of silicon detectors. To this end we have compared (i) the industry-standard SIMION 3D 7.0 program, and (ii) a GEANT4-based code with the addition of appropriate adiabatic invariants in simulating the propagation of the decay electrons and protons in the electromagnetic spectrometer. We use these results to examine the systematic effects and to determine the precision with which the physics parameters a, b, A, and B can be extracted in practice.

  15. High-throughput ab-initio dilute solute diffusion database

    PubMed Central

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  16. Ab initio engineering of materials with stacked hexagonal tin frameworks

    PubMed Central

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  17. Ab initio calculation of the shock Hugoniot of bulk silicon

    NASA Astrophysics Data System (ADS)

    Strickson, Oliver; Artacho, Emilio

    2016-03-01

    We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.

  18. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  19. Non-stoichiometric AB5 alloys for metal hydride electrodes

    DOEpatents

    Reilly, James J.; Adzic, Gordana D.; Johnson, John R.; Vogt, Thomas; McBreen, James

    2001-01-01

    The present invention provides a non-stoichiometric alloy comprising a composition having the formula AB.sub.5+X an atomic ratio wherein A is selected from the group consisting of the rare earth metals, yttrium, mischmetal, or a combination thereof; B is nickel and tin, or nickel and tin and at least a third element selected from the group consisting of the elements in group IVA of the periodic table, aluminum, manganese, iron, cobalt, copper, antimony or a combination thereof; X is greater than 0 and less than or equal to about 2.0; and wherein at least one substituted A site is occupied by at least one of the B elements. An electrode incorporating said alloy and an electrochemical cell incorporating said electrode are also described.

  20. Differential Rotation and Magnetic Polarity Patterns on AB Doradus

    NASA Astrophysics Data System (ADS)

    Donati, J.-F.; Collier Cameron, A.; Hussain, G. A. J.; Semel, M.

    We report new Zeeman-Doppler imaging observations of the rapidly rotating young K0 dwarf AB Doradus, obtained with the Anglo-Australian Telescope in 1996 December. We show simultaneous brightness and magnetic images of the stellar photosphere, reconstructed at three different epochs over the course of a seven-night observing run. Latitude-by-latitude cross-correlation of the resulting images confirms the form and amplitude of the surface differential pattern found in the previous year's observations by Donati & Cameron (1997), with the pole rotating slower than the equator by about one part in 220. We also present dynamic spectra showing the distribution of H alpha-absorbing clouds in the stellar corona at the same epoch.

  1. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations.

    PubMed

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green's function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states. PMID:26671378

  2. Ab initio calculation of thermodynamic properties of silicon

    NASA Astrophysics Data System (ADS)

    Wei, Siqing; Li, Changlin; Chou, M. Y.

    1994-11-01

    We present a fully ab initio calculation of the thermodynamic properties for silicon within the quasiharmonic approximation, making use of volume-dependent phonon frequencies obtained from pseudopotential local-density calculations. The temperature dependence of the thermal-expansion coefficient, specific heat (at constant volume), and other related quantities are studied. We confirm that the thermal-expansion coefficient behaves differently in three temperature regions: positive for temperature below 15 K, negative between 15 and 125 K, and positive again above 125 K. This finding agrees with experiment. The abnormal (negative) thermal-expansion coefficient at low temperatures is explained through a detailed study of mode Grüneisen parameters. Both specific-heat and thermal-expansion-coefficient values calculated are in excellent agreement with experiment up to a few hundred kelvin.

  3. XMVB: a program for ab initio nonorthogonal valence bond computations.

    PubMed

    Song, Lingchun; Mo, Yirong; Zhang, Qianer; Wu, Wei

    2005-04-15

    An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available. PMID:15704237

  4. Ab initio theory of NMR chemical shifts in solids

    SciTech Connect

    Louie, S.G. |

    1997-12-31

    A new formalism for ab initio calculation of the orbital magnetic susceptibility and the NMR chemical shifts in solids and liquids is presented. The approach can be applied to periodic systems such as crystals, surfaces or polymers, and with a supercell technique, to nonperiodic systems such as amorphous materials, liquids, or solids with defects. The formalism is based on the density functional theory in the local density approximation and makes use of a generalized f-sum rule to eliminate the divergent terms that plagued previous theories. Calculations have been successfully carried out for the diamagnetic susceptibility of a number of insulators and for the NMR chemical shifts of a variety of systems including free molecules, ionic crystals, hydrogen-bonded materials and amorphous carbon.

  5. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  6. Ab initio calculations of grain boundaries in bcc metals

    NASA Astrophysics Data System (ADS)

    Scheiber, Daniel; Pippan, Reinhard; Puschnig, Peter; Romaner, Lorenz

    2016-03-01

    In this study, we compute grain boundary (GB) properties for a large set of GBs in bcc transition metals with a special focus on W, Mo and Fe using ab initio density functional theory (DFT) and semi-empirical second nearest neighbour modified embedded atom method (2NN-MEAM) potentials. The GB properties include GB energies, surface energies, GB excess volume and work of separation, which we analyse and then compare to experimental data. We find that the used 2NN-MEAM potentials can predict general trends of GB properties, but do not always reproduce the GB ground state structure and energy found with DFT. In particular, our results explain the experimental finding that W and Mo prefer intergranular fracture, while other bcc metals prefer transgranular cleavage.

  7. Transport coefficients in diamond from ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Löfâs, Henrik; Grigoriev, Anton; Isberg, Jan; Ahuja, Rajeev

    2013-03-01

    By combining the Boltzmann transport equation with ab-initio electronic structure calculations, we obtain transport coefficients for boron-doped diamond. We find the temperature dependence of the resistivity and the hall coefficients in good agreement with experimental measurements. Doping in the samples is treated via the rigid band approximation and scattering is treated in the relaxation time approximation. In contrast to previous results, the acoustic phonon scattering is the dominating scattering mechanism for the considered doping range. At room temperature, we find the thermopower, S, in the range 1-1.6 mV/K and the power factor, S2σ, in the range 0.004-0.16 μW /cm K2.

  8. Ab initio potential energy surface and rovibrational states of HBO

    NASA Astrophysics Data System (ADS)

    Ha, Tae-Kyu; Makarewicz, Jan

    1999-01-01

    The potential energy surface describing the large-amplitude motion of H around the BO core in the HBO molecule has been determined from ab initio calculations. This surface has been sampled by a set of 170 grid points from a two-dimensional space defined by the stretching and the bending coordinates of the H nucleus. At each grid point, the BO bond length has been optimized using the second-order Møller-Plesset perturbation theory with the basis set aug-cc-pVTZ. The surface has a local minimum for the linear as well as the bent configuration of HBO. A low energy barrier to the linear configuration BOH causes a large-amplitude motion and a strong rovibrational interaction in the molecule. Its rovibrational dynamics is different from the dynamics in bent or quasilinear triatomic molecules.

  9. Ab initio engineering of materials with stacked hexagonal tin frameworks

    NASA Astrophysics Data System (ADS)

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-07-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.

  10. Ab initio electronic stopping power of protons in bulk materials

    NASA Astrophysics Data System (ADS)

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

  11. Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy.

    PubMed

    Mladenović, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick

    2009-11-01

    Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space. PMID:19895013

  12. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

    Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-03-01

    Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].

  13. High-throughput ab-initio dilute solute diffusion database.

    PubMed

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  14. Ab initio quantum dynamics using coupled-cluster.

    PubMed

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given. PMID:22612082

  15. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches. PMID:27015491

  16. Ab initio correlated calculations of rare-gas dimer quadrupoles

    NASA Astrophysics Data System (ADS)

    Donchev, Alexander G.

    2007-10-01

    This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.

  17. Ab Initio Screening of CO2-philic Groups.

    PubMed

    Tian, Ziqi; Saito, Tomonori; Jiang, De-En

    2015-04-23

    Ab initio calculations were used to identify CO2-philic groups. Over 55 neutral molecules were screened for CO2 affinity via binding energetics. It is found that poly(ethylene oxide)s (PEO) oligomers with more than three repeating units are good CO2-binding groups, consistent with the high-performance of PEO-based materials for CO2/N2 separation. More interestingly, two triazole groups linked with a methylene chain are also excellent for CO2 binding with a favorable interaction of more than 28 kJ/mol, indicating that polymers or covalent-organic frameworks (COFs) with triazoles may be utilized for CO2 capture. This work provides a useful guide to introduce promising organic groups into polymeric membranes and COFs for CO2/N2 separation media. PMID:25825811

  18. Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism

    SciTech Connect

    Lo, Jonathan; Zheng, Tianyong; Olson, Daniel G.; Ruppertsberger, Natalie; Tripathi, Shital A.; Guss, Adam M.; Lynd, Lee R.

    2015-06-29

    NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP+. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. In this paper, activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H2 formation but otherwise little change in other fermentation products. In two engineered strains with 80% theoretical ethanol yield, loss of nfnAB caused two different responses: in one strain, ethanol yield decreased to about 30% of the theoretical value, while another strain had no change in ethanol yield. Biochemical analysis of cell extracts showed that the ΔnfnAB strain with decreased ethanol yield had NADPH-linked alcohol dehydrogenase (ADH) activity, while the ΔnfnAB strain with unchanged ethanol yield had NADH-linked ADH activity. Deletion of nfnAB caused loss of NADPH-linked ferredoxin oxidoreductase activity in all cell extracts. Significant NADH-linked ferredoxin oxidoreductase activity was seen in all cell extracts, including those that had lost nfnAB. This suggests that there is an unidentified NADH:ferredoxin oxidoreductase (distinct from nfnAB) playing a role in ethanol formation. The NfnAB complex plays a key role in generating NADPH in a strain that had become reliant on NADPH-ADH activity. Importance: Thermophilic anaerobes that can convert biomass-derived sugars into ethanol have been investigated as candidates for biofuel formation. Many anaerobes have been genetically engineered to increase biofuel formation; however, key aspects of metabolism remain unknown and poorly

  19. Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism

    PubMed Central

    Lo, Jonathan; Zheng, Tianyong; Olson, Daniel G.; Ruppertsberger, Natalie; Tripathi, Shital A.; Guss, Adam M.

    2015-01-01

    ABSTRACT NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP+. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. Activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H2 formation but otherwise little change in other fermentation products. In two engineered strains with 80% theoretical ethanol yield, loss of nfnAB caused two different responses: in one strain, ethanol yield decreased to about 30% of the theoretical value, while another strain had no change in ethanol yield. Biochemical analysis of cell extracts showed that the ΔnfnAB strain with decreased ethanol yield had NADPH-linked alcohol dehydrogenase (ADH) activity, while the ΔnfnAB strain with unchanged ethanol yield had NADH-linked ADH activity. Deletion of nfnAB caused loss of NADPH-linked ferredoxin oxidoreductase activity in all cell extracts. Significant NADH-linked ferredoxin oxidoreductase activity was seen in all cell extracts, including those that had lost nfnAB. This suggests that there is an unidentified NADH:ferredoxin oxidoreductase (distinct from nfnAB) playing a role in ethanol formation. The NfnAB complex plays a key role in generating NADPH in a strain that had become reliant on NADPH-ADH activity. IMPORTANCE Thermophilic anaerobes that can convert biomass-derived sugars into ethanol have been investigated as candidates for biofuel formation. Many anaerobes have been genetically engineered to increase biofuel formation; however, key aspects of metabolism remain unknown and poorly understood. One example is the

  20. Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism

    DOE PAGESBeta

    Lo, Jonathan; Zheng, Tianyong; Olson, Daniel G.; Ruppertsberger, Natalie; Tripathi, Shital A.; Guss, Adam M.; Lynd, Lee R.

    2015-06-29

    NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP+. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. In this paper, activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H2 formation butmore » otherwise little change in other fermentation products. In two engineered strains with 80% theoretical ethanol yield, loss of nfnAB caused two different responses: in one strain, ethanol yield decreased to about 30% of the theoretical value, while another strain had no change in ethanol yield. Biochemical analysis of cell extracts showed that the ΔnfnAB strain with decreased ethanol yield had NADPH-linked alcohol dehydrogenase (ADH) activity, while the ΔnfnAB strain with unchanged ethanol yield had NADH-linked ADH activity. Deletion of nfnAB caused loss of NADPH-linked ferredoxin oxidoreductase activity in all cell extracts. Significant NADH-linked ferredoxin oxidoreductase activity was seen in all cell extracts, including those that had lost nfnAB. This suggests that there is an unidentified NADH:ferredoxin oxidoreductase (distinct from nfnAB) playing a role in ethanol formation. The NfnAB complex plays a key role in generating NADPH in a strain that had become reliant on NADPH-ADH activity. Importance: Thermophilic anaerobes that can convert biomass-derived sugars into ethanol have been investigated as candidates for biofuel formation. Many anaerobes have been genetically engineered to increase biofuel formation; however, key aspects of metabolism remain unknown and poorly understood. One

  1. Effect of gamma irradiation on nutritional components and Cry1Ab protein in the transgenic rice with a synthetic cry1Ab gene from Bacillus thuringiensis

    NASA Astrophysics Data System (ADS)

    Wu, Dianxing; Ye, Qingfu; Wang, Zhonghua; Xia, Yingwu

    2004-01-01

    The effects of gamma irradiation on the transgenic rice containing a synthetic cry1Ab gene from Bacillus thuringiensis were investigated. There was almost no difference in the content of the major nutritional components, i.e. crude protein, crude lipid, eight essential amino acids and total ash between the irradiated grains and the non-irradiated transgenic rice. However, the amounts of Cry1Ab protein and apparent amylose in the irradiated transgenic rice were reduced significantly by the doses higher than 200 Gy. In vivo observation showed that Cry1Ab protein contents also decreased in the fresh leaf tissues of survival seedlings after irradiation with 200 Gy or higher doses and showed inhibition of seedling growth. The results indicate that gamma irradiation might improve the quality of transgenic rice due to removal of the toxic Cry1Ab protein.

  2. Molecular parameters for weakly bound 2g(aa, ab) and {0}_{u}^{-}(ab) states of molecular iodine and dipole moment functions of transitions to these states

    NASA Astrophysics Data System (ADS)

    Baturo, V. V.; Cherepanov, I. N.; Lukashov, S. S.; Poretsky, S. A.; Pravilov, A. M.

    2016-06-01

    Weakly bound valence states of 2g symmetry, correlating with the I(2 P 3/2) + I(2 P 3/2) (aa) and I(2 P 3/2) + I(2 P 1/2) (ab) dissociation limits, as well as {0}u-(ab) state, were studied using vibrationally resolved luminescence spectra corresponding to transitions from δ2u(3 P 2) and g {0}g-(3 P 1) ion-pair states, in molecular iodine, respectively, populated using a three-step three-color laser excitation scheme. Spectroscopic constants and potential energy curves of the valence states are determined for the first time. Dipole moment functions of δ2u → 2g(aa, ab) and g {0}g- → {0}u-(ab) transitions are found to exponentially decrease.

  3. Comparison Between Structures and Properties of ABS Nanocomposites Derived from Two Different Kinds of OMT

    NASA Astrophysics Data System (ADS)

    Cai, Yibing; Huang, Fenglin; Xia, Xin; Wei, Qufu; Tong, Xutao; Wei, Anfang; Gao, Weidong

    2010-03-01

    In the present work, the hexadecyl triphenyl phosphonium bromide (P16) and cetyl pyridium chloride (CPC) were used to modify montmorillonite (MMT) based on the structural characteristic of the engineering thermoplastic acrylonitrile-butadiene-styrene copolymer (ABS) and the principle of “like dissolves like”, and then used to prepare the ABS/organic-modified montmorillonite (OMT) nanocomposites by melt-intercalation method. The influences of two different kinds of OMT on the structures and properties of the ABS nanocomposites were characterized by x-ray diffraction (XRD), transmission electron microscopy (TEM), high-resolution electron microscopy (HREM), thermogravimetric analyses (TGA), Cone calorimetry and dynamic mechanical analyses (DMA), respectively. The increased basal spacing showed that ABS intercalated into the gallery of the OMT. The morphology indicated that the OMT dispersed well in the ABS resin and the intercalated structure for ABS/OMT-P16 nanocomposites and intercalated-exfoliated structure for ABS/OMT-CPC nanocomposites were respectively formed. The TGA results revealed that onset temperature of thermal degradation and charred residue at 700 °C of the ABS nanocomposites was remarkably enhanced compared to the pure ABS. It was also found from the Cone calorimetry tests that the peak of heat release rate (PHRR) decreased significantly, contributing to the reduced flammability. The DMA measurements indicated that the loading of silicate clays improved the storage modulus of the ABS resin. The partial exfoliation of the OMT-CPC within ABS nanocomposites was advantageous to increasing thermal stability properties, decreasing flammability properties, and improving mechanical properties.

  4. Ab initio methods for nuclear properties - a computational physics approach

    NASA Astrophysics Data System (ADS)

    Maris, Pieter

    2011-04-01

    A microscopic theory for the structure and reactions of light nuclei poses formidable challenges for high-performance computing. Several ab-initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab-initio no-core full configuration (NCFC) approach is based on basis space expansion methods and uses Slater determinants of single-nucleon basis functions to express the nuclear wave function. In this approach, the quantum many-particle problem becomes a large sparse matrix eigenvalue problem. The eigenvalues of this matrix give us the binding energies, and the corresponding eigenvectors the nuclear wave functions. These wave functions can be employed to evaluate experimental quantities. In order to reach numerical convergence for fundamental problems of interest, the matrix dimension often exceeds 1 billion, and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. I discuss different strategies for distributing and solving this large sparse matrix on current multicore computer architectures, including methods to deal with with memory bottleneck. Several of these strategies have been implemented in the code MFDn, which is a parallel fortran code for nuclear structure calculations. I will show scaling behavior and compare the performance of the pure MPI version with the hybrid MPI/OpenMP code on Cray XT4 and XT5 platforms. For large core counts (typically 5,000 and above), the hybrid version is more efficient than pure MPI. With this code, we have been able to predict properties of the unstable nucleus 14F, which have since been confirmed by experiments. I will also give an overview of other recent results for nuclei in the A = 6 to 16 range with 2- and 3-body interactions. Supported in part by US DOE Grant DE-FC02-09ER41582.

  5. Expression of Cry1Ab and Cry2Ab by a Polycistronic Transgene with a Self-Cleavage Peptide in Rice

    PubMed Central

    Tan, Miaomiao; Gao, Jianhua; Shen, Zhicheng

    2014-01-01

    Insect resistance to Bacillus thuringiensis (Bt) crystal protein is a major threat to the long-term use of transgenic Bt crops. Gene stacking is a readily deployable strategy to delay the development of insect resistance while it may also broaden insecticidal spectrum. Here, we report the creation of transgenic rice expressing discrete Cry1Ab and Cry2Ab simultaneously from a single expression cassette using 2A self-cleaving peptides, which are autonomous elements from virus guiding the polycistronic viral gene expression in eukaryotes. The synthetic coding sequences of Cry1Ab and Cry2Ab, linked by the coding sequence of a 2A peptide from either foot and mouth disease virus or porcine teschovirus-1, regardless of order, were all expressed as discrete Cry1Ab and Cry2Ab at high levels in the transgenic rice. Insect bioassays demonstrated that the transgenic plants were highly resistant to lepidopteran pests. This study suggested that 2A peptide can be utilized to express multiple Bt genes at high levels in transgenic crops. PMID:25333312

  6. Characterization of Cry34Ab1 and Cry35Ab1 insecticidal crystal proteins expressed in transgenic corn plants and Pseudomonas fluorescens.

    PubMed

    Gao, Yong; Schafer, Barry W; Collins, Randy A; Herman, Rod A; Xu, Xiaoping; Gilbert, Jeffrey R; Ni, Weiting; Langer, Vickie L; Tagliani, Laura A

    2004-12-29

    Cry34Ab1 and Cry35Ab1 proteins, identified from Bacillus thuringiensis strain PS149B1, act together to control corn rootworms. Transgenic corn lines coexpressing the two proteins were developed to protect corn against rootworm damage. Large quantities of the two proteins were needed to conduct studies required for assessing the safety of this transgenic corn crop. Because it was technically infeasible to obtain sufficient quantities of high purity Cry34Ab1 and Cry35Ab1 proteins from the transgenic corn plants, the proteins were produced using a recombinant Pseudomonas fluorescens (Pf) production system. The two proteins from both the transgenic corn and the Pf were purified and characterized. The proteins from each host had the expected molecular mass and were immunoreactive to specific antibodies in enzyme-linked immunosorbent assay and Western blot analysis. Data from N-terminal sequencing, tryptic peptide mass fingerprinting, internal peptide sequencing, and biological activity provided direct evidence that the Cry34Ab1 and Cry35Ab1 proteins produced in Pf and transgenic corn were, respectively, comparable or equivalent molecules. In addition, neither protein had detectable glycosylation regardless of the host. PMID:15612796

  7. Expression of Cry1Ab and Cry2Ab by a polycistronic transgene with a self-cleavage peptide in rice.

    PubMed

    Zhao, Qichao; Liu, Minghong; Tan, Miaomiao; Gao, Jianhua; Shen, Zhicheng

    2014-01-01

    Insect resistance to Bacillus thuringiensis (Bt) crystal protein is a major threat to the long-term use of transgenic Bt crops. Gene stacking is a readily deployable strategy to delay the development of insect resistance while it may also broaden insecticidal spectrum. Here, we report the creation of transgenic rice expressing discrete Cry1Ab and Cry2Ab simultaneously from a single expression cassette using 2A self-cleaving peptides, which are autonomous elements from virus guiding the polycistronic viral gene expression in eukaryotes. The synthetic coding sequences of Cry1Ab and Cry2Ab, linked by the coding sequence of a 2A peptide from either foot and mouth disease virus or porcine teschovirus-1, regardless of order, were all expressed as discrete Cry1Ab and Cry2Ab at high levels in the transgenic rice. Insect bioassays demonstrated that the transgenic plants were highly resistant to lepidopteran pests. This study suggested that 2A peptide can be utilized to express multiple Bt genes at high levels in transgenic crops. PMID:25333312

  8. Anti-F(ab')2 antibodies in thrombocytopenic patients at risk for acquired immunodeficiency syndrome.

    PubMed Central

    Yu, J R; Lennette, E T; Karpatkin, S

    1986-01-01

    22 homosexual or narcotic addict patients at risk for acquired immunodeficiency syndrome (AIDS) or with AIDS, were studied for the presence of antiimmunoglobulin antibodies and circulating immune complexes (20 were thrombocytopenic, 6 had AIDS). Circulating immune complex levels were 10-fold higher than levels in normal subjects. IgG anti-F(ab')2 antibodies were noted in homosexual as well as narcotic addict patients. Of 16 homosexual patients, 7 had IgG anti-F(ab')2 antibody of moderate to marked titer with broad reactivity against autologous, homologous, and control F(ab')2 fragments. Three others demonstrated limited reactivity against one or two F(ab')2 fragments. The remaining six patients were negative. Six of six narcotic addict patients had IgG anti-F(ab')2 antibody, five with limited reactivity, one with broad reactivity. In contrast, neither elevated circulating immune complexes nor anti-F(ab')2 antibodies were detectable in six autoimmune thrombocytopenic patients. Anti-F(ab')2 antibody could be affinity purified from serum or circulating immune complexes. Anti-F(ab')2 reactivity correlated with circulating immune complex levels, r = 0.83, P less than 0.01. PMID:3011860

  9. Radiator-induced erythema ab igne in 8-year-old girl.

    PubMed

    Brzezinski, Piotr; Ismail, Samir; Chiriac, Anca

    2014-04-01

    The cutaneous lesion of erythema ab Igne are characterized by a reticulate erythema, hyperpigmentation, fine scaling, epidermal atrophy and telangiectasias, and reticulated erythema. We report a case of erythema ab igne on the hands of a 8-year-old girl, induced by classic homemade radiator. PMID:25697214

  10. Efficacy of VIP3A and Cry1Ab Genotypes against various Lepidopteran Pests.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    2004 through 2005, plots of experimental transgenic cotton lines containing the exotoxin, VIP3A; endotoxin, Cry1Ab; and both VIP3A and Cry1Ab were evaluated for efficacy against certain lepidopteran pests. Results showed that VIP3A was more efficacious against the beet and fall armyworm compared to...

  11. Enhancing Faculty Development: The Impact of AB1725 on California's Community Colleges.

    ERIC Educational Resources Information Center

    Heeren, John W.; Mason, Marylee

    California Assembly Bill (AB) 1725 was passed to improve the operation of the state's community colleges with respect to finance, governance, affirmative action, employment policies, instructional technique, and accountability, providing a $5 million fund for staff development. To assess the effects of AB 1725 on the quantity and quality of…

  12. Dynamics of immature mAb glycoform secretion during CHO cell culture: An integrated modelling framework.

    PubMed

    Jimenez Del Val, Ioscani; Fan, Yuzhou; Weilguny, Dietmar

    2016-05-01

    Ensuring consistent glycosylation-associated quality of therapeutic monoclonal antibodies (mAbs) has become a priority in pharmaceutical bioprocessing given that the distribution and composition of the carbohydrates (glycans) bound to these molecules determines their therapeutic efficacy and immunogenicity. However, the interaction between bioprocess conditions, cellular metabolism and the intracellular process of glycosylation remains to be fully understood. To gain further insight into these interactions, we present a novel integrated modelling platform that links dynamic variations in mAb glycosylation with cellular secretory capacity. Two alternative mechanistic representations of how mAb specific productivity (qp ) influences glycosylation are compared. In the first, mAb glycosylation is modulated by the linear velocity with which secretory cargo traverses the Golgi apparatus. In the second, glycosylation is influenced by variations in Golgi volume. Within our modelling framework, both mechanisms accurately reproduce experimentally-observed dynamic changes in mAb glycosylation. In addition, an optimisation-based strategy has been developed to estimate the concentration of glycosylation enzymes required to minimise mAb glycoform variability. Our results suggest that the availability of glycosylation machinery relative to cellular secretory capacity may play a crucial role in mAb glycosylation. In the future, the modelling framework presented here may aid in selecting and engineering cell lines that ensure consistent mAb glycosylatio. PMID:26743760

  13. AB 3059: A Report to the Governor on the Alternative Child Care Programs, 1976-80.

    ERIC Educational Resources Information Center

    Hailey, Jack

    This publication of the California Governor's Committee on Child Development Programs focuses on the Alternative Child Care Program in California (AB 3059). The report looks back over four years of the AB 3059, reviews the goals of that legislation, and measures the program's accomplishments against those goals. In early 1976, the Governor's…

  14. Comparative Evaluation of AB 3059 Alternative Child Care Programs. Summary Report.

    ERIC Educational Resources Information Center

    Warner, Donna D.; And Others

    Findings from the evaluation of the AB 3059 alternative child care programs are presented in this report. (AB 3059 child care programs were mandated by the California legislature in 1976 with the goals of assessing features that might reduce child care costs, ensuring maximum parental choice among facilities, addressing unmet child care needs…

  15. Development of Novel Analytical Method for Ab Initio Powder Structural Analysis

    NASA Astrophysics Data System (ADS)

    Sakata, Makoto; Nishibori, Eiji; Sawa, Hiroshi

    Genetic Algorithm (GA) applied to ab initio structure determination from synchrotron powder diffraction is described. It seems to have an advantage over other real space methods for ab initio structure determination because of the existence of schema theorem. As an example, the case of Prednisolone Succinate is shown in some detail. Future development of GA in crystallography is briefly described.

  16. 75 FR 70691 - International Game Technology (IGT), Machine Accounting and ABS (Bonusing and BEII), Engineering...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-18

    ..., LLC, Corvallis, Oregon. The notice was published in the Federal Register on June 7, 2010 (75 FR 32223... Employment and Training Administration International Game Technology (IGT), Machine Accounting and ABS... Game Technology (IGT), Machine Accounting and ABS (Bonusing and BEII), Engineering, including...

  17. Process for treating ab5 nickel-metal hydride battery scrap

    SciTech Connect

    Lyman, J.W.; Palmer, G.R.

    1994-12-31

    A process for treating an AB5 Ni-MH battery to recover purified positive and negative electrode components of the battery is disclosed. An AB5 Ni-MH battery is placed in a mineral acid leach solution to cause the positive and negative electrode components of the battery to separate.

  18. Engine with hydraulic fuel injection and ABS circuit using a single high pressure pump

    DOEpatents

    Bartley, Bradley E.; Blass, James R.; Gibson, Dennis H.

    2001-01-01

    An engine system comprises a hydraulically actuated fuel injection system and an ABS circuit connected via a fluid flow passage that provides hydraulic fluid to both the fuel injection system and to the ABS circuit. The hydraulically actuated system includes a high pressure pump. The fluid control passage is in fluid communication with an outlet from the high pressure pump.

  19. Stability of Cry1Ab protein during long-term storage for standardization of insect bioassays.

    PubMed

    Nguyen, Hang Thu; Jehle, Johannes A

    2009-01-01

    The reliable use of purified Cry1Ab protein standards is a prerequisite for ecological studies and resistance monitoring programs of Cry1Ab-expressing transgenic corn. In this study the stability and activity of different Cry1Ab protein batches expressed in and purified from Escherichia coli were determined during two-year storage at different temperature conditions (4 degrees C, -20 degrees C, and -80 degrees C). SDS-Polyacrylamide gel electrophoresis showed degradation of the protein stored at 4 degrees C over four months, whereas no difference in the band intensity of the Cry1Ab proteins stored at -20 degrees C and -80 degrees C was observed. Bioassays with neonate larvae of Ostrinia nubilalis indicated that the biological activity of Cry1Ab varied from batch to batch, depending on the production process. Cry1Ab protein stored at 4 degrees C for four months showed a significantly decreasing activity measured as median lethal concentration (LC(50)), whereas the protein activity declined less than 11-fold after two years storage at -20 degrees C. When stored at -80 degrees C the toxin activity remained relatively stable for at least 30 months, as indicated by low LC(50) values of 7-10 ng Cry1Ab per cm(2) diet. These experiments demonstrate that appropriate long-term storage conditions of Cry1Ab protein standards are crucial for resistance monitoring programs of Bt corn, and storage at -80 degrees C is recommended. PMID:19833078

  20. (abstract) Studies on AB(sub 5) Metal Hydride Alloys with Sn Additives

    NASA Technical Reports Server (NTRS)

    Ratnakumar, B. V.; Surampudi, S.; Stefano, S. Di; Halpert, G.; Witham, C.; Fultz, B.

    1994-01-01

    The use of metal hydrides as negative electrodes in alkaline rechargeable cells is becoming increasingly popular, due to several advantages offered by the metal hydrides over conventional anode materials (such as Zn, Cd) in terms of specific energy environmental cycle life and compatibility. Besides, the similarities in the cell voltage pressure characteristics, and charge control methods of the Ni-MH cells to the commonly used Ni-Cd point to a projected take over of 25% of the Ni-Cd market for consumer electronics by the Ni-MH cells in the next couple of years. Two classes of metal hydrides alloys based on rare earth metals (AB(sub 5)) and titanium (AB(sub 2)) are being currently developed at various laboratories. AB(sub 2) alloys exhibit higher specific energy than the AB(sub 5) alloys but the state of the art commercial Ni-MH cells are predominately manufactured using AB(sub 5) alloys.

  1. Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

  2. Staphylococcus aureus Biofilms Induce Macrophage Dysfunction Through Leukocidin AB and Alpha-Toxin

    PubMed Central

    Scherr, Tyler D.; Hanke, Mark L.; Huang, Ouwen; James, David B. A.; Horswill, Alexander R.; Bayles, Kenneth W.; Fey, Paul D.; Torres, Victor J.

    2015-01-01

    ABSTRACT The macrophage response to planktonic Staphylococcus aureus involves the induction of proinflammatory microbicidal activity. However, S. aureus biofilms can interfere with these responses in part by polarizing macrophages toward an anti-inflammatory profibrotic phenotype. Here we demonstrate that conditioned medium from mature S. aureus biofilms inhibited macrophage phagocytosis and induced cytotoxicity, suggesting the involvement of a secreted factor(s). Iterative testing found the active factor(s) to be proteinaceous and partially agr-dependent. Quantitative mass spectrometry identified alpha-toxin (Hla) and leukocidin AB (LukAB) as critical molecules secreted by S. aureus biofilms that inhibit murine macrophage phagocytosis and promote cytotoxicity. A role for Hla and LukAB was confirmed by using hla and lukAB mutants, and synergy between the two toxins was demonstrated with a lukAB hla double mutant and verified by complementation. Independent confirmation of the effects of Hla and LukAB on macrophage dysfunction was demonstrated by using an isogenic strain in which Hla was constitutively expressed, an Hla antibody to block toxin activity, and purified LukAB peptide. The importance of Hla and LukAB during S. aureus biofilm formation in vivo was assessed by using a murine orthopedic implant biofilm infection model in which the lukAB hla double mutant displayed significantly lower bacterial burdens and more macrophage infiltrates than each single mutant. Collectively, these findings reveal a critical synergistic role for Hla and LukAB in promoting macrophage dysfunction and facilitating S. aureus biofilm development in vivo. PMID:26307164

  3. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  4. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

    Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

  5. Erythema Ab Igne due to Heating Pad Use: A Case Report and Review of Clinical Presentation, Prevention, and Complications

    PubMed Central

    Milchak, Marissa; Smucker, Joanne; Chung, Catherine G.; Seiverling, Elizabeth V.

    2016-01-01

    Erythema ab igne is an asymptomatic cutaneous condition caused by exposure to heat. Cases of erythema ab igne may prove to be diagnostically challenging due to lack of familiarity with the condition. While this dermatosis carries a favorable prognosis, nonmelanoma skin cancers have been reported to arise within lesions of erythema ab igne. Erythema ab igne is preventable, and, thus, clinicians should provide education regarding safe use of heating devices to patients using these products in both outpatient and inpatient settings. PMID:26880929

  6. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

    Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

  7. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  8. Ab initio simulation of gap discrete breathers in strained graphene

    NASA Astrophysics Data System (ADS)

    Lobzenko, I. P.; Chechin, G. M.; Bezuglova, G. S.; Baimova, Yu. A.; Korznikova, E. A.; Dmitriev, S. V.

    2016-03-01

    The methods of the density functional theory were used for the first time for the simulation of discrete breathers in graphene. It is demonstrated that breathers can exist with frequencies lying in the gap of the phonon spectrum, induced by uniaxial tension of a monolayer graphene sheet in the "zigzag" direction (axis X), polarized in the "armchair" direction (axis Y). The found gap breathers are highly localized dynamic objects, the core of which is formed by two adjacent carbon atoms located on the Y axis. The atoms surrounding the core vibrate at much lower amplitudes along both the axes ( X and Y). The dependence of the frequency of these breathers on amplitude is found, which shows a soft type of nonlinearity. No breathers of this type were detected in the gap induced by stretching along the Y axis. It is shown that the breather vibrations may be approximated by the Morse oscillators, the parameters of which are determined from ab initio calculations. The results are of fundamental importance, as molecular dynamics calculations based on empirical potentials cannot serve as a reliable proof of the existence of breathers in crystals.

  9. Volumic omit maps in ab initio dual-space phasing.

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850

  10. Ab initio study of optical excitations in VO2

    NASA Astrophysics Data System (ADS)

    Coulter, John; Gali, Adam; Manousakis, Efstratios

    2014-03-01

    Motivated by recent experimental efforts to fabricate p-n junctions from transition metal oxides (TMOs) and a recent theoretical study claiming TMOs to be good absorbers and promising materials for efficient carrier multiplication, we study the optical properties of a prototypical TMO, the insulator M1 phase of vanadium dioxide (VO2), by ab initio methods. We applied the Bethe-Salpeter equations (BSE) to calculate the optical properties, starting from self-consistent GW quasi-particle energy levels and states. In contrast to expectations, the exciton binding energy obtained by BSE is in good agreement with the experiment. We find that the electron-electron interaction is very strong which makes this material promising for efficient carrier multiplication that might lead to an enhanced efficiency in photo-voltaics applications. To illustrate this more quantitatively, we calculated the impact ionization rate within the independent quasiparticle approximation, and find that the rate is significantly higher than silicon in the region of highest solar intensity, due to the strong multiple carrier excitations.

  11. Ab initio studies of phoshorene island single electron transistor.

    PubMed

    Ray, S J; Venkata Kamalakar, M; Chowdhury, R

    2016-05-18

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications. PMID:27093536

  12. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  13. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

  14. Ab-intitio studies of electronic properties of chalcogenide spinels.

    NASA Astrophysics Data System (ADS)

    Chshiev, Mairbek; Wang, Y.-H. A.; Gupta, Arunava; Bettinger, Joanna; Suzuki, Yuri; Butler, William H.

    2007-03-01

    CuCr2Se4 is a normal chalcogenide spinel which exhibits ferromagnetic properties including a relatively high Curie temperature of 450 K [1] which makes it a promising candidate for use in spintronics devices. Another chalcogenide spinel of enhanced interest for spintronics is CdCr2Se4 which seems to be a promising ferromagnetic semiconductor for electrical spin injection into III-V device heterostructures [2]. We report first principles calculations of the electronic structure of substoichiometric CuCr2Se4-x and CuxCd1-xCrSe4 spinels. The calculations were performed using the Vienna ab-initio simulation program (VASP) within the Generalized Gradient Approximation (GGA) of Density Functional Theory (DFT). Our calculations indicate that both Se deficient CuCr2Se4-x as well as CuxCd1-xCrSe4 show half-metallic behavior over a wide range of x with a gap around the Fermi level in the minority density of states. [1] F.K. Lotgering, Solid State Commun. 2 (1964) 55 [2] G. Kioseoglou et al., Nature Materials 3 (2004) 799

  15. Ab initio description of the exotic unbound 7He nucleus

    DOE PAGESBeta

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

    In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less

  16. Ab initio investigation of grain boundary cohesion in Al alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Shengjun; Kontsevoi, Oleg Y.; Freeman, A. J.; Olson, G. B.

    2010-03-01

    Strength and hardness of aluminum alloys can be substantially increased by alloying with Mg, Zn, Cu, Si, and other elements. The main drawback of Al alloys is their susceptibility to stress corrosion cracking, which is caused by alloying impurities segregated at grain boundaries. We investigated the embrittling and cohesion-enhancing effects of impurities on a σ5(012)[100] grain boundary in Al by means of the full-potential linearized augmented plane-wave (FLAPW) method within the framework of the Rice-Wang thermodynamic model and within the ab initio tensile test approach. We calculated segregation energies, analyzed local atomic configurations, electronic structures and spatial charge density distributions around segregated impurities, and identified the roles of atomic size and the bonding behavior of the impurity with the surrounding Al atoms. The results show that He, H and Na are strong embrittlers, Zn is a weak embrittler, while Sc, B, Cu and Mg are cohesion enhancers. We further evaluated the effect of co-alloying with two or more elements on grain boundary strength. This work provides a fundamental basis for the design of high strength Al alloys.

  17. Ab Initio Simulation of the Photoelectron Spectrum for Methoxy Radical

    NASA Astrophysics Data System (ADS)

    Cheng, Lan; Weichman, Marissa L.; Kim, Jongjin B.; Ichino, Takatoshi; Neumark, Daniel; Stanton, John F.

    2015-06-01

    A theoretical simulation of the photoelectron spectrum for the ground state of methoxy radical is reported based on the quasidiabatic model Hamiltonian originally proposed by Köppel, Domcke, and Cederbaum. The parameters in the model Hamiltonian have been obtained from ab initio coupled-cluster calculations. The linear and quadratic force constants have been calculated using equation-of-motion coupled-cluster ionization potential method with the singles, doubles, and triples (EOMIP-CCSDT) truncation scheme together with atomic natural orbital basis sets of triple-zeta quality (ANO1). The cubic and quartic force constants have been obtained from EOMIP-CCSD calculations with ANO basis sets of double-zeta quality (ANO0), and the spin-orbit coupling constant has been computed at the EOMIP-CCSD/pCVTZ level. The nuclear Schroedinger equation has been solved using the Lanzcos algorithm to obtain vibronic energy levels as well as the corresponding intensities. The simulated spectrum compares favorably with the recent high-resolution slow electron velocity-map imaging experiment for vibronic levels up to 2000 cm-1.

  18. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  19. TOPICAL REVIEW: Ab initio symplectic no-core shell model

    NASA Astrophysics Data System (ADS)

    Dytrych, T.; Sviratcheva, K. D.; Draayer, J. P.; Bahri, C.; Vary, J. P.

    2008-12-01

    The no-core shell model (NCSM) is a prominent ab initio method that yields a good description of the low-lying states in few-nucleon systems as well as in more complex p-shell nuclei. Nevertheless, its applicability is limited by the rapid growth of the many-body basis with larger model spaces and increasing number of nucleons. The symplectic no-core shell model (Sp-NCSM) aspires to extend the scope of the NCSM beyond the p-shell region by augmenting the conventional spherical harmonic oscillator basis with the physically relevant symplectic \\SpR{3} symmetry-adapted configurations of the symplectic shell model that describe naturally the monopole-quadrupole vibrational and rotational modes, and also partially incorporate α-cluster correlations. In this review, the models underpinning the Sp-NCSM approach, namely, the NCSM, the Elliott SU(3) model and the symplectic shell model, are discussed. Following this, a prescription for constructing translationally invariant symplectic configurations in the spherical harmonic oscillator basis is given. This prescription is utilized to unveil the extent to which symplectic configurations enter into low-lying states in 12C and 16O nuclei calculated within the framework of the NCSM with the JISP16 realistic nucleon-nucleon interaction. The outcomes of this proof-of-principle study are presented in detail.

  20. Structure classification of AB solids via machine learning

    NASA Astrophysics Data System (ADS)

    Guberntis, J. E.; Pilania, G.; Lookman, T.

    2015-03-01

    We explored the use of machine learning methods, specifically support vector machines and various forms of cross-validation, for the task of classifying the crystal structures of the octet AB solids. We partitioned a set of 75 solids into rocksalt and non-rocksalt structures and thus performed a binary classification task. We found that using the standard indices (rσ ,rπ) , suggested by St. John and Bloch several decades ago, enabled an average success in classification of 92 % . Our main new result is our finding that using just rσ and the excess Born effective charge ΔZA of the A atom,computed by DFT, enabled an average success of 98 % , prompting us to propose (rσ , ΔZA) as a replacement for the St. John-Bloch pair. In general, we found that adding one or two other features to the St. John-Bloch pair, unless they include the excess Born effective charge, generally decreases the average success rate. Supported by the Department of Energy.

  1. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  2. Ab initio study of MoS2 nanotube bundles

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

  3. Ab initio modelling of methane hydrate thermophysical properties.

    PubMed

    Jendi, Z M; Servio, P; Rey, A D

    2016-04-21

    The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production. PMID:27019976

  4. Mapping α Centauri AB for Possible Habitable Planets

    NASA Astrophysics Data System (ADS)

    Quarles, Billy L.; Lissauer, Jack J.

    2016-06-01

    The alpha Centauri AB star system, our closest stellar neighbors, has been studied for many decades and ACESat (Belikov et al. AAS Meeting #225, #311.01, 2015) is a proposed space mission designed to directly image Earth-sized planets in the habitable zones of both of these stars. The alpha Centauri system is older than our Sun, so any resident planets are expected to occupy long-lived orbits. We evaluate the extent of these trajectories where planets are able to orbit for billion-year timescales. The distribution of long-lived orbits is mapped to the sky plane to indicate regions where planets may appear relative to each stellar component. Our results confirm qualitatively those of Wiegert & Holman (Astron. J. 113, 1445, 1997) regarding the approximate size of the regions of stable orbits, which are larger for retrograde orbits relative to the binary than for prograde orbits. Moreover, we find that orbits beyond each star’s habitable zone are affected by a dynamical imprint from the binary orbit due to mean motion resonances and the Lidov-Kozai Mechanism. Stable planets can exist near the plane of the binary orbit within each stellar habitable zone, whereas highly inclined orbits are typically short-lived. These results are of special interest as they can guide the search process of our stellar neighbors in future missions.

  5. Engineering Room-temperature Superconductors Via ab-initio Calculations

    NASA Astrophysics Data System (ADS)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  6. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  7. A coupled "AB" system: Rogue waves and modulation instabilities

    NASA Astrophysics Data System (ADS)

    Wu, C. F.; Grimshaw, R. H. J.; Chow, K. W.; Chan, H. N.

    2015-10-01

    Rogue waves are unexpectedly large and localized displacements from an equilibrium position or an otherwise calm background. For the nonlinear Schrödinger (NLS) model widely used in fluid mechanics and optics, these waves can occur only when dispersion and nonlinearity are of the same sign, a regime of modulation instability. For coupled NLS equations, rogue waves will arise even if dispersion and nonlinearity are of opposite signs in each component as new regimes of modulation instability will appear in the coupled system. The same phenomenon will be demonstrated here for a coupled "AB" system, a wave-current interaction model describing baroclinic instability processes in geophysical flows. Indeed, the onset of modulation instability correlates precisely with the existence criterion for rogue waves for this system. Transitions from "elevation" rogue waves to "depression" rogue waves are elucidated analytically. The dispersion relation as a polynomial of the fourth order may possess double pairs of complex roots, leading to multiple configurations of rogue waves for a given set of input parameters. For special parameter regimes, the dispersion relation reduces to a cubic polynomial, allowing the existence criterion for rogue waves to be computed explicitly. Numerical tests correlating modulation instability and evolution of rogue waves were conducted.

  8. Ab Initio Investigation of NH_3-O_2 Exciplex

    NASA Astrophysics Data System (ADS)

    Haupert, L. M.; Simpson, G.; Slipchenko, L. V.

    2010-06-01

    In their recent investigation of fluorescence from poly(amido amine) (PAMAM) dendrimers, Chu and Imae suggested an exciplex composed of tertiary amine and oxygen molecules might be responsible for fluorescence in PAMAM dendrimers. In this work, we present an ab initio investigation of the electronic structure of a possible ammonia-oxygen exciplex model system using equation-of-motion coupled cluster techniques. Geometry optimization of the triplet ground state produced a weakly bound state with an equilibrium separation of ˜ 3.5 Å, and an excited state geometry scan revealed a bound, excited triplet state with an equilibrium separation of 2.02 Å, consistent with results of earlier PM3 work by Juranic et al. The energy gap between the triplet ground state and first triplet excited state of the exciplex at 2.02 Å is 412.8 nm, lending support to the exciplex hypothesis. C.-C. Chu, and T. Imae, Macromol. Rapid. Commun., 30, 89-93 (2009). I. Juranic, H. S. Rzepa, and Y. MinYan, J. Chem. Soc. Perkin Trans., 2 (1990)

  9. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  10. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  11. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  12. Ab initio description of p-shell hypernuclei.

    PubMed

    Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

    2014-11-01

    We present the first ab initio calculations for p-shell single-Λ hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Λ and Σ(+),Σ(0),Σ(-) hyperons including Λ-Σ conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to (Λ)(7)Li, (Λ)(9)Be, and (Λ)(13)C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

  13. Ab initio SCF calculations on hydrogen bonded cresol isomers

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Kleinermanns, K.

    1988-12-01

    Ab initio GAUSSIAN 80 calculations with two different basis sets (STO-3G and 4 31 G*) were performed on hydrogen bonded cresol isomers for comparison with experimental data from free jet fluorescence excitation spectroscopy. For m-cresol, the calculated barriers for hindered internal rotation of the OH-group and the CH3-group are in good agreement with experiment. The calculations show the trans-linear configuration of p-cresol· B-clusters ( B = H2O, CH3OH) to be more stable than the all-planar configuration. This agrees with CI calculations and microwave spectroscopic investigations of the water dimer. Calculations of both the intermolecular stretch and bend frequencies of p-cresol· B-clusters show little dependence on the all-planar or trans-linear configuration but a strong dependence on the choice of the basis set. With the minimal basis set STO-3G, the vibrational energies are generally too high. The agreement between the calculated vibrational frequencies from the 4 31 G* basis set and the experimental values is fair.

  14. Predicting lattice thermal conductivity with help from ab initio methods

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

    The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

  15. Ab initio calculation of double ionization of atoms

    SciTech Connect

    Serov, V. V.

    2013-02-15

    The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width {gamma} describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law {gamma} {proportional_to} E{sup 1/4} is applicable at experimentally accessible energies. The Gaussian width {gamma} was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state-specifically, a negative atomic-hydrogen ion H{sup -} and heliumin the 1s2s{sup 1}S and 1s3s{sup 1}S excited states. It was found that this function, {gamma}(E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.

  16. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

  17. Ab initio simulations of peptide-mineral interactions

    NASA Astrophysics Data System (ADS)

    Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko

    We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.

  18. Ab initio study of the phenol-water cation radical

    NASA Astrophysics Data System (ADS)

    Hobza, Pavel; Burcl, Rudolf; Špirko, Vladimír; Dopfer, Otto; Müller-Dethlefs, Klaus; Schlag, Edward W.

    1994-07-01

    The phenol-water cation radical has been investigated by ab initio theory using the spin-restricted open-shell Hartree-Fock and spin-restricted open-shell second-order Møller-Plesset theories with 3-21G*(O) and 6-31G* basis sets. The full geometrical optimization was performed for several hydrogen-bonded structures and one hemibonded structure. Clearly, the most stable structure has been found for Cs symmetry with the linear hydrogen bond between the proton of the OH group of the phenol cation radical and the oxygen of the water, and the water hydrogens pointing away from the phenyl ring. For this structure harmonic (and for some intermolecular modes anharmonic) vibrational frequencies have been computed for various isotopic complexes. The computed shifts of phenol-localized intramolecular modes on complexation and on deuteration as well as the calculated intermolecular frequencies of the different isotopic complexes allow for an assignment of vibrational frequencies observed in the experimental zero-kinetic-energy (ZEKE) photoelectron spectra. Five out of a possible six intermolecular vibrations and several intramolecular modes have been assigned, including the 18b vibration which shows a strong blue shift in frequency upon complexation. Structure and properties of the phenol-water cation radical are compared with those of the corresponding neutral complex.

  19. An efficient approach to ab initio Monte Carlo simulation

    SciTech Connect

    Leiding, Jeff; Coe, Joshua D.

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β{sup 0}), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where—depending on the quality of the reference system potential—acceptance probabilities were enhanced by factors of 1.2–28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  20. Accurate ab initio vibrational energies of methyl chloride.

    PubMed

    Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs. PMID:26133427

  1. Accurate ab initio vibrational energies of methyl chloride

    NASA Astrophysics Data System (ADS)

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-01

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 HL, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm-1, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.

  2. Ab initio study of the bonding in diatomic nickel

    SciTech Connect

    Noell, J.O.; Newton, M.D.; Hay, P.J.; Martin, R.L.; Bobrowicz, F.W.

    1980-09-01

    Hartree--Fock, GVB, and configuration interaction calculations were performed for diatomic nickel using an ab initio effective core potential. A basis set specifically optimized for the /sup 3/D state of atomic nickel is found to be far superior to the more common basis obtained from the /sup 3/F atomic state. Correlation effects are found to be significant in determining the bond energy. In particular, the two electrons of the s--s bond must be appropriately correlated. In addition, correlation effects which one would interpret as being principally intra-atomic in character are found to have a marked effect on the molecular properties. The theoretically predicted bond dissociation energy (D/sub e/) of 43.4 kcal/mol is significantly lower than the experimental estimate of 55 +- 5 kcal/mol. However, molecular partition functions calculated using the present results indicate that the experimental value should be revised downward to a value of approx.46 +- 5 kcal/mol, in good agreement with our calculations. An interatomic distance of 4.27 bohr is computed and compared with experimental estimates. Spectroscopic parameters for dipole-allowed transitions from the ground state were determined from SCF and GVB calculations and discussed in relation to the experimentally observed visible and ultraviolet spectra attributed to Ni/sub 2/.

  3. Ab initio effective interactions for s d -shell valence nucleons

    NASA Astrophysics Data System (ADS)

    Dikmen, E.; Lisetskiy, A. F.; Barrett, B. R.; Maris, P.; Shirokov, A. M.; Vary, J. P.

    2015-06-01

    We perform ab initio no-core shell-model calculations for A =18 and 19 nuclei in a 4 ℏ Ω , or Nmax=4 , model space by using the effective JISP16 and chiral N3LO nucleon-nucleon potentials and transform the many-body effective Hamiltonians into the 0 ℏ Ω model space to construct the A -body effective Hamiltonians in the s d shell. We separate the A -body effective Hamiltonians with A =18 and A =19 into inert core, one-, and two-body components. Then we use these core, one-, and two-body components to perform standard shell-model calculations for the A =18 and A =19 systems with valence nucleons restricted to the s d shell. Finally, we compare the standard shell-model results in the 0 ℏ Ω model space with the exact no-core shell-model results in the 4 ℏ Ω model space for the A =18 and A =19 systems and find good agreement.

  4. Lead-Chalcogenides Under Pressure: Ab-Initio Study

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

    ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.

  5. Amide N-oxides: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

    There are no known examples of amide N-oxides. The present study employs ab initio molecular orbital calculations at the 6-3G ∗ level to explore potential target molecules in this class. Bridgehead bicyclic lactams appear to be attractive targets for oxidation to form the corresponding N-oxides because they have reduced (or zero) amide resonance energy. The amide N-oxide linkage is predicted to have a ca. 9-10 kcal/mol rotational barrier due to eclipsing of nonbonded oxygen atoms in the transition state. The linkage has a nearly flat conformational ( ΦON-CO) profile in the range 120-240° and this suggests that a very sterically hindered acyclic amide N-oxide may be a practical synthetic target. The oxidation of strained amides is calculated to be highly exothermic if dimethyldioxirane is employed. This reagent is predicted to react appreciably exothermically with normal, stable amides such as N, N-dimethylacetamide, thus offering the potential for generating and studying such relatively unstable amide N-oxides at low temperatures.

  6. FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.

    PubMed

    Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B

    2006-02-01

    FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806

  7. Ab initio simulations on rutile-based titania nanowires

    NASA Astrophysics Data System (ADS)

    Zhukovskii, Yu F.; Evarestov, R. A.

    2012-08-01

    The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

  8. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  9. Ab initio study of ice catalyzation of HOCl + HCl reaction

    SciTech Connect

    Zhou, Y.F.; Liu, C.B.

    2000-06-15

    The observations by Farman et al. revealed remarkable depletions in the total atmospheric ozone content in Antarctica. The observed total ozone decreased smoothing during the spring season from about 1975. Satellite observations have proved Antarctic ozone depletions over a very extended region, in general agreement with the local ground-based data of Farman et al. It was suggested that heterogeneous reactions occurring on particles in polar stratospheric clouds (PSCs) play a central role in the depletion of stratospheric ozone. Experiments proved that the reaction of HOCl + HCl was very slow in the gas phase, but on ice surface it was rapid. In this work the ice catalysis of HOCl + HCl reaction was investigated by using ab initio molecular orbital theory. The authors applied the Hartree-Fock self-consistent field and the second-order Moeller-Plesset perturbation theory with the basis sets of 6-31G* to the model system. The complexes and transition state were obtained along the reaction with and without the presence of ice surface. By comparing the results, a possible catalyzation mechanism of ice on the reaction is proposed.

  10. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

    Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia

    Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.

  11. Ab initio modeling of the motional Stark effect on MAST

    SciTech Connect

    De Bock, M. F. M.; Conway, N. J.; Walsh, M. J.; Carolan, P. G.; Hawkes, N. C.

    2008-10-15

    A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the {pi} and {sigma} lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

  12. Cytoskeleton mimetic reinforcement of a self-assembled N,N'-dialkylimidazolium ionic liquid monomer by copolymerization.

    SciTech Connect

    Grubjesic, S.; Seifert, S.; Firestone, M. A.; Materials Science Division

    2009-08-11

    Preparation and photopolymerization of a decylmethylimidazolium ionic liquid (IL) that possesses an acrylate counteranion are described. This IL monomer self-assembles upon addition of water and can be copolymerized with poly(ethylene glycol) diacrylate (PEGDA) in the presence of a photoinitiator, forming a mechanically durable material that adopts a lamellar structure with in-plane hexagonally ordered pores, as evidenced by small-angle X-ray scattering (SAXS). Thermogravimetric analysis, the extent of polymerization, and solubility-swelling studies indicate the formation of a network copolymer of the IL monomer and the PEGDA. Additional evidence for the formation of a nanostructured copolymer is provided by evaluating the product formed by replacement of the IL monomer with the nonpolymerizable analogue, decylmethylimidazolium chloride. The results demonstrate the possibility of designing a self-assembled amiphiphilic bilayer architecture that is reinforced by polymerization and cross-linking.

  13. IL-12 enhances the natural killer cell cytokine response to Ab-coated tumor cells.

    PubMed

    Parihar, Robin; Dierksheide, Julie; Hu, Yan; Carson, William E

    2002-10-01

    The anti-tumor activity of recombinant mAb's directed against tumor cell growth receptors has generally been considered to result from direct antiproliferative effects, the induction of apoptosis, or possibly Ab-dependent cellular cytotoxicity mediated against tumor targets. However, it remains unclear to what degree these mechanisms actually aid in the clearance of Ab-coated tumor cells in vivo. We show here that NK cells secrete a distinct profile of potent immunostimulatory cytokines in response to dual stimulation with Ab-coated tumor cells and IL-12. This response could not be duplicated by costimulation with other ILs and was significantly enhanced in the presence of monocytes. Cytokine production was dependent upon synergistic signals mediated by the activating receptor for the Fc portion of IgG (FcgammaRIII) and the IL-12 receptor expressed on NK cells. Coadministration of Ab-coated tumor cells and IL-12 to BALB/c mice resulted in enhanced circulating levels of NK cell-derived cytokines with the capacity to augment anti-tumor immunity. These findings suggest that, in addition to mediating cellular cytotoxicity and apoptosis, the anti-tumor activity of mAb's might also result from activation of a potent cytokine secretion program within immune effectors capable of recognizing mAb-coated targets. PMID:12370276

  14. Chromatographic purification of equine immunoglobulin G F(ab)2 from plasma.

    PubMed

    Fernandes, Aldon; Kaundinya, John Oswald; Daftary, Gautam; Saxena, Lalit; Banerjee, Subhasis; Pattnaik, Priyabrata

    2008-12-01

    The antibody fragments generated from hyperimmune equine IgG is widely used as anti-snake venom, anti-scorpion venom, anti-diphtheria, anti-tetanus, anti-gangrene and anti-rabies agents. Antibody fragments, F(ab)(2), because of their specificity and absence of undesired reactivity are preferred over complete IgG. This paper discusses a novel purification technique for chromatographic purification of anti-rabies immunoglobulin G (IgG) fragment F(ab)(2) from horse serum. F(ab)(2) was purified by two successive chromatography steps using Cellufine A-200 and ProSep-vA Ultra media. The purified F(ab)(2) was characterized using biochemical and biophysical methods and shown to be pure and homogeneous. The purified F(ab)(2) was reactive to rabies antigen in immuno-electrophoresis and diffusion tests. The purified F(ab)(2) was biologically functional and was found to show a potency of 1500 IU ml(-1). Comparative analysis of the purity with commercially available F(ab)(2) by HPLC analysis and SDS-PAGE indicated that the present product is better in purity. To our knowledge, this is the first report providing evidence on purification of equine antibody fragment using controlled pore glass based protein A chromatography media. PMID:19008160

  15. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    PubMed Central

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  16. A test of Automatic Blowing snow Station (ABS) in the French Alps

    NASA Astrophysics Data System (ADS)

    Ito, Yoichi; Naaim-Bouvet, Florence; Nishimura, Kouichi; Bellot, Hervé; Fontaine, Firmin

    2015-04-01

    Blowing snow is a significant factor to estimate snow distribution in alpine, Arctic and Antarctic regions. The Snow Particle Counter (SPC) is well used for mass flux measurement of the blowing snow, however, the SPC deployment is not always possible for automatic observation under harsh conditions. Recently Automatic Blowing snow Station (ABS), which is a simpler device than the SPC, have been developed in Japan. We installed the ABS system with the SPCs at the Lac Blanc Pass in the French Alps (2700 m a.s.l.) to examine the relationship between the ABS output and snow particle mass flux. The ABS worked well, without problems, for the entire 4-month period in the winter 2014. The ABS output was converted to mass flux using wind-dependent power function which obtained from calibration procedure in a cold wind-tunnel. The mass flux obtained from the ABS showed a good agreement with the SPC, particularly around the peak of blowing snow event. Based on tests under controlled (cold wind-tunnel) and field conditions, we conclude that the ABS is suitable for practical use.

  17. Stacking stability of MoS2 bilayer: An ab initio study

    NASA Astrophysics Data System (ADS)

    Tao, Peng; Guo, Huai-Hong; Yang, Teng; Zhang, Zhi-Dong

    2014-10-01

    The study of the stacking stability of bilayer MoS2 is essential since a bilayer has exhibited advantages over single layer MoS2 in many aspects for nanoelectronic applications. We explored the relative stability, optimal sliding path between different stacking orders of bilayer MoS2, and (especially) the effect of inter-layer stress, by combining first-principles density functional total energy calculations and the climbing-image nudge-elastic-band (CI-NEB) method. Among five typical stacking orders, which can be categorized into two kinds (I: AA, AB and II: AA', AB', A'B), we found that stacking orders with Mo and S superposing from both layers, such as AA' and AB, is more stable than the others. With smaller computational efforts than potential energy profile searching, we can study the effect of inter-layer stress on the stacking stability. Under isobaric condition, the sliding barrier increases by a few eV/(ucGPa) from AA' to AB', compared to 0.1 eV/(ucGPa) from AB to [AB]. Moreover, we found that interlayer compressive stress can help enhance the transport properties of AA'. This study can help understand why inter-layer stress by dielectric gating materials can be an effective means to improving MoS2 on nanoelectronic applications.

  18. Heat shock protein 90AB1 and hyperthermia rescue infectivity of HIV with defective cores.

    PubMed

    Joshi, Pheroze; Sloan, Barbara; Torbett, Bruce E; Stoddart, Cheryl A

    2013-02-01

    We previously showed that reduced infectivity of HIV with incompletely processed capsid-spacer protein 1 (CA-SP1) is rescued by cellular activation or increased expression of HSP90AB1, a member of the cytosolic heat shock protein 90 family. Here we show that HSP90AB1 is present in HIV virions and that HSP90AB1, but not nonfunctional mutated HSP90AB1(E42A+D88A), restores infectivity to HIV with mutations in CA that alter core stability. Further, the CA mutants were hypersensitive to pharmacological inhibition of HSP90AB1. In agreement with Roesch et al. (2012), we found that culturing HIV at 39.5°C enhanced viral infectivity up to 30-fold in human peripheral blood mononuclear cells (p=0.002) and rescued CA-mutant infectivity in nonactivated cells, concurrent with elevated expression of HSP90AB1 during hyperthermia. In sum, the transdominant effect of HSP90AB1 on CA-mutant HIV infectivity suggests a potential role for this class of cellular chaperones in HIV core stability and uncoating. PMID:23200770

  19. 7-(2-Thienyl)-7-Deazaadenosine (AB61), a New Potent Nucleoside Cytostatic with a Complex Mode of Action.

    PubMed

    Perlíková, Pavla; Rylová, Gabriela; Nauš, Petr; Elbert, Tomáš; Tloušťová, Eva; Bourderioux, Aurelie; Slavětínská, Lenka Poštová; Motyka, Kamil; Doležal, Dalibor; Znojek, Pawel; Nová, Alice; Harvanová, Monika; Džubák, Petr; Šiller, Michal; Hlaváč, Jan; Hajdúch, Marián; Hocek, Michal

    2016-05-01

    7-(2-Thienyl)-7-deazaadenosine (AB61) showed nanomolar cytotoxic activities against various cancer cell lines but only mild (micromolar) activities against normal fibroblasts. The selectivity of AB61 was found to be due to inefficient phosphorylation of AB61 in normal fibroblasts. The phosphorylation of AB61 in the leukemic CCRF-CEM cell line proceeds well and it was shown that AB61 is incorporated into both DNA and RNA, preferentially as a ribonucleotide. It was further confirmed that a triphosphate of AB61 is a substrate for both RNA and DNA polymerases in enzymatic assays. Gene expression analysis suggests that AB61 affects DNA damage pathways and protein translation/folding machinery. Indeed, formation of large 53BP1 foci was observed in nuclei of AB61-treated U2OS-GFP-53BP1 cells indicating DNA damage. Random incorporation of AB61 into RNA blocked its translation in an in vitro assay and reduction of reporter protein expression was also observed in mice after 4-hour treatment with AB61. AB61 also significantly reduced tumor volume in mice bearing SK-OV-3, BT-549, and HT-29 xenografts. The results indicate that AB61 is a promising compound with unique mechanism of action and deserves further development as an anticancer agent. Mol Cancer Ther; 15(5); 922-37. ©2016 AACR. PMID:26819331

  20. An operational multispectral scanner for bathymetric surveys - The ABS NORDA scanner

    NASA Technical Reports Server (NTRS)

    Haimbach, Stephen P.; Joy, Richard T.; Hickman, G. Daniel

    1987-01-01

    The Naval Ocean Research and Development Activity (NORDA) is developing the Airborne Bathymetric Survey (ABS) system, which will take shallow water depth soundings from a Navy P-3 aircraft. The system combines active and passive sensors to obtain optical measurements of water depth. The ABS NORDA Scanner is the systems passive multispectral scanner whose design goal is to provide 100 percent coverage of the seafloor, to depths of 20 m in average coastal waters. The ABS NORDA Scanner hardware and operational environment is discussed in detail. The optical model providing the basis for depth extraction is reviewed and the proposed data processing routine discussed.

  1. Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

    We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  2. Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl

    NASA Astrophysics Data System (ADS)

    Halonen, L.; Ha, T.-K.

    1988-03-01

    Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.

  3. Direct Measurement of Ab in Z0 Decays Using Charged Kaon Tagging

    NASA Astrophysics Data System (ADS)

    Abe, Kenji; Abe, Koya; Abe, T.; Adam, I.; Akagi, T.; Allen, N. J.; Arodzero, A.; Ash, W. W.; Aston, D.; Baird, K. G.; Baltay, C.; Band, H. R.; Barakat, M. B.; Bardon, O.; Barklow, T. L.; Bashindzhagyan, G. L.; Bauer, J. M.; Bellodi, G.; Ben-David, R.; Benvenuti, A. C.; Bilei, G. M.; Bisello, D.; Blaylock, G.; Bogart, J. R.; Bolen, B.; Bower, G. R.; Brau, J. E.; Breidenbach, M.; Bugg, W. M.; Burke, D.; Burnett, T. H.; Burrows, P. N.; Byrne, R. M.; Calcaterra, A.; Calloway, D.; Camanzi, B.; Carpinelli, M.; Cassell, R.; Castaldi, R.; Castro, A.; Cavalli-Sforza, M.; Chou, A.; Church, E.; Cohn, H. O.; Coller, J. A.; Convery, M. R.; Cook, V.; Cotton, R.; Cowan, R. F.; Coyne, D. G.; Crawford, G.; Damerell, C. J.; Danielson, M. N.; Daoudi, M.; de Groot, N.; dell'Orso, R.; Dervan, P. J.; de Sangro, R.; Dima, M.; D'Oliveira, A.; Dong, D. N.; Doser, M.; Dubois, R.; Eisenstein, B. I.; Eschenburg, V.; Etzion, E.; Fahey, S.; Falciai, D.; Fan, C.; Fernandez, J. P.; Fero, M. J.; Flood, K.; Frey, R.; Gillman, T.; Gladding, G.; Gonzalez, S.; Goodman, E. R.; Hart, E. L.; Harton, J. L.; Hasan, A.; Hasuko, K.; Hedges, S. J.; Hertzbach, S. S.; Hildreth, M. D.; Huber, J.; Huffer, M. E.; Hughes, E. W.; Huynh, X.; Hwang, H.; Iwasaki, M.; Jackson, D. J.; Jacques, P.; Jaros, J. A.; Jiang, Z. Y.; Johnson, A. S.; Johnson, J. R.; Johnson, R. A.; Junk, T.; Kajikawa, R.; Kalelkar, M.; Kamyshkov, Y.; Kang, H. J.; Karliner, I.; Kawahara, H.; Kim, Y. D.; King, R.; King, M. E.; Kofler, R. R.; Krishna, N. M.; Kroeger, R. S.; Langston, M.; Lath, A.; Leith, D. W.; Lia, V.; Lin, C.-J. S.; Liu, X.; Liu, M. X.; Loreti, M.; Lu, A.; Lynch, H. L.; Ma, J.; Mahjouri, M.; Mancinelli, G.; Manley, S.; Mantovani, G.; Markiewicz, T. W.; Maruyama, T.; Masuda, H.; Mazzucato, E.; McKemey, A. K.; Meadows, B. T.; Menegatti, G.; Messner, R.; Mockett, P. M.; Moffeit, K. C.; Moore, T. B.; Morii, M.; Muller, D.; Murzin, V.; Nagamine, T.; Narita, S.; Nauenberg, U.; Neal, H.; Nussbaum, M.; Oishi, N.; Onoprienko, D.; Osborne, L. S.; Panvini, R. S.; Park, H.; Park, C. H.; Pavel, T. J.; Peruzzi, I.; Piccolo, M.; Piemontese, L.; Pieroni, E.; Pitts, K. T.; Plano, R. J.; Prepost, R.; Prescott, C. Y.; Punkar, G. D.; Quigley, J.; Ratcliff, B. N.; Reeves, T. W.; Reidy, J.; Reinertsen, P. L.; Rensing, P. E.; Rochester, L. S.; Rowson, P. C.; Russell, J. J.; Saxton, O. H.; Schalk, T.; Schindler, R. H.; Schumm, B. A.; Schwiening, J.; Sen, S.; Serbo, V. V.; Shaevitz, M. H.; Shank, J. T.; Shapiro, G.; Sherden, D. J.; Shmakov, K. D.; Simopoulos, C.; Sinev, N. B.; Smith, S. R.; Smy, M. B.; Snyder, J. A.; Staengle, H.; Stahl, A.; Stamer, P.; Steiner, R.; Steiner, H.; Strauss, M. G.; Su, D.; Suekane, F.; Sugiyama, A.; Suzuki, S.; Swartz, M.; Szumilo, A.; Takahashi, T.; Taylor, F. E.; Thom, J.; Torrence, E.; Toumbas, N. K.; Usher, T.; Vannini, C.; Va'Vra, J.; Vella, E.; Venuti, J. P.; Verdier, R.; Verdini, P. G.; Wagner, S. R.; Wagner, D. L.; Waite, A. P.; Walston, S.; Wang, J.; Ward, C.; Watts, S. J.; Weidemann, A. W.; Weiss, E. R.; Whitaker, J. S.; White, S. L.; Wickens, F. J.; Williams, B.; Williams, D. C.; Williams, S. H.; Willocq, S.; Wilson, R. J.; Wisniewski, W. J.; Wittlin, J. L.; Woods, M.; Word, G. B.; Wright, T. R.; Wyss, J.; Yamamoto, R. K.; Yamartino, J. M.; Yang, X.; Yashima, J.; Yellin, S. J.; Young, C. C.; Yuta, H.; Zapalac, G.; Zdarko, R. W.; Zhou, J.

    1999-09-01

    We present a direct measurement of the parity-violating asymmetry Ab in the Z0 to bb¯ coupling using a new technique to distinguish the b and b¯ quarks using charged kaons from B decays. The Z0 bosons are produced in e+e- collisions at the SLC with longitudinally polarized electrons. bb¯ events are selected using a secondary vertex mass tag and Ab is determined from the left-right forward-backward asymmetry. From the 1994-1995 data sample, selected from 100 000 hadronic Z0 decays, we obtain Ab = 0.855+/-0.088stat+/-0.102syst.

  4. Performance of the Molecular Alere i Influenza A&B Test Compared to That of the Xpert Flu A/B Assay

    PubMed Central

    Flores-Cortez, Estefany J.

    2014-01-01

    Data on the performance of rapid molecular point-of-care use platforms for diagnosis of influenza are lacking. We validated nasopharyngeal (NP) flocked specimens in universal transport medium (UTM) and evaluated the clinical sensitivity and specificity of the Alere i influenza A&B test compared to those of the Xpert flu A/B assay. The Alere i influenza A&B test had an overall sensitivity and specificity of 93.8% and 62.5% for influenza A, respectively, and of 91.8% and 53.6% for influenza B, respectively. The poor specificity was due to influenza virus samples determined positive for both type A and B. PMID:25502527

  5. Performance of the molecular Alere I influenza A&B test compared to that of the xpert flu A/B assay.

    PubMed

    Chapin, Kimberle C; Flores-Cortez, Estefany J

    2015-02-01

    Data on the performance of rapid molecular point-of-care use platforms for diagnosis of influenza are lacking. We validated nasopharyngeal (NP) flocked specimens in universal transport medium (UTM) and evaluated the clinical sensitivity and specificity of the Alere i influenza A&B test compared to those of the Xpert flu A/B assay. The Alere i influenza A&B test had an overall sensitivity and specificity of 93.8% and 62.5% for influenza A, respectively, and of 91.8% and 53.6% for influenza B, respectively. The poor specificity was due to influenza virus samples determined positive for both type A and B. PMID:25502527

  6. Atmospheric Characterization of the Hot Jupiter Kepler-13Ab

    NASA Astrophysics Data System (ADS)

    Shporer, Avi; O'Rourke, Joseph G.; Knutson, Heather A.; Szabó, Gyula M.; Zhao, Ming; Burrows, Adam; Fortney, Jonathan; Agol, Eric; Cowan, Nicolas B.; Desert, Jean-Michel; Howard, Andrew W.; Isaacson, Howard; Lewis, Nikole K.; Showman, Adam P.; Todorov, Kamen O.

    2014-06-01

    Kepler-13Ab (= KOI-13.01) is a unique transiting hot Jupiter. It is one of very few known short-period planets orbiting a hot A-type star, making it one of the hottest planets currently known. The availability of Kepler data allows us to measure the planet's occultation (secondary eclipse) and phase curve in the optical, which we combine with occultations observed by warm Spitzer at 4.5 μm and 3.6 μm and a ground-based occultation observation in the Ks band (2.1 μm). We derive a day-side hemisphere temperature of 2750 ± 160 K as the effective temperature of a black body showing the same occultation depths. Comparing the occultation depths with one-dimensional planetary atmosphere models suggests the presence of an atmospheric temperature inversion. Our analysis shows evidence for a relatively high geometric albedo, A g = 0.33^{+0.04}_{-0.06}. While measured with a simplistic method, a high A g is supported also by the fact that the one-dimensional atmosphere models underestimate the occultation depth in the optical. We use stellar spectra to determine the dilution, in the four wide bands where occultation was measured, due to the visual stellar binary companion 1.''15 ± 0.''05 away. The revised stellar parameters measured using these spectra are combined with other measurements, leading to revised planetary mass and radius estimates of Mp = 4.94-8.09 M J and Rp = 1.406 ± 0.038 R J. Finally, we measure a Kepler midoccultation time that is 34.0 ± 6.9 s earlier than expected based on the midtransit time and the delay due to light-travel time and discuss possible scenarios.

  7. Ab initio quantum transport calculations using plane waves

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.

    2015-08-01

    We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.

  8. Internal dynamics in azetidine: A microwave and ab initio study

    NASA Astrophysics Data System (ADS)

    López, Juan C.; Blanco, Susana; Lesarri, Alberto; Alonso, José L.

    2001-02-01

    The internal dynamics of interconversion between equivalent conformations due to the coupling between ring puckering and NH inversion in azetidine has been investigated by rotational spectroscopy and ab initio computations. Analysis of the rotational spectra in the 8-220 GHz region has been completed for the ground state and first four excited states of the ring-puckering vibration. Rotational transitions exhibit a characteristic doubling originated by tunneling between equivalent conformations through a C2v barrier, which is related to symmetric (A1) and antisymmetric (B1) inversion states. Additionally, nuclear quadrupole hyperfine structure arising from the N nucleus could be resolved for low-J transitions. Accurate rotational and centrifugal distortion parameters together with the energy difference between inversion states derived from μc-type inversion transitions have been derived for each ring-puckering state using a two-state Hamiltonian. An effective monodimensional reduced potential function for the ring-puckering vibration V(X)=10.82(X4+14.29X-8.93X2-0.28X3) has been found consistent with the observed experimental variation of the rotational and centrifugal distortion constants with ring-puckering. This asymmetric single minimum potential function supports the existence of only one stable equatorial form. The barrier to interconversion between equivalent equatorial conformers, related to the C2v conformation of azetidine in which the ring atoms and the NH group are coplanar, has been estimated to range between 1900 and 2600 cm-1. The strong dependence of the dipole moment and quadrupole coupling constants with ring-puckering vibrational state evidence structural changes that occur along the ring-puckering coordinate.

  9. Ab initio cluster study of crystalline NaF

    SciTech Connect

    Temple, D.K.

    1992-01-01

    A highly-accurate ab initio cluster model of crystalline NaF has been constructed to explore the limits of cluster methods in the treatment of ionic solids. The focus of this model was the characterization of the lattice environment and its influence on the easily-polarizable fluorine anion. The model consisted of a central all-electron fluorine anion coordinated by pseudopotentials, to represent the nearest-neighbor sodium cations, and a finite array of point charges chosen to generate the correct crystal field from the surrounding infinite ionic lattice. The wavefunction and properties of the anion were calculated using the restricted Hartree-Fock and configuration interaction techniques from quantum chemistry. An extensive analysis of basis set incompleteness errors in the anion wavefunction was performed. Important features were identified in the embedded anion, such as its distortion under the influence of the lattice compressions, its stabilization from the Madelung potential, and its changes in size due to electron correlations. Bulk properties of the rocksalt-structure (B1) NaF crystal were derived from the total mode energies, calculated as a function of the crystal volume. The properties included the zero-pressure lattice constant, cohesive energy, and bulk modulus, and the pressure-volume equation-of-state. A series of test calculations explored the relationships, and their underlying physical mechanisms, between the features of the embedded anion and the bulk properties of the crystal. These features often produced opposing changes in the properties, demonstrating the importance of a thorough and systematic treatment of the embedded anion. The most thorough test calculation gave bulk properties that were within 1% of experiment. Using an embedded anion model for the high-pressure cesium-chloride (B2) phase of NaF, the B1-to-B2 structural transition was correctly predicted at 25 GPa, in excellent agreement with the experimental values of 23 to 27 GPa.

  10. Cosmic-Ray Modulation: an Ab Initio Approach

    NASA Astrophysics Data System (ADS)

    Engelbrecht, N. E.; Burger, R. A.

    2014-10-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.

  11. Chiroptical properties of unsubstituted carbohydrates: Ab initio and semiempirical studies

    NASA Astrophysics Data System (ADS)

    Parra C., Alejandro

    Ab initio calculations support assignment of the vacuum ultraviolet circular dichroism (CD) of simple saccharides to 11A 1 --> 21B1 and 11A 1 --> 11A2 transitions centered on the oxygen atoms of the acetal group treated as two weakly coupled ether chromophores. The calculations are consistent with assignments previously made on the basis of a deconvolution of CD spectra. Estimates of the oxygen centered contributions to magnetic transition dipole moments were made. Semiempirical calculations were performed to model the NaD molar optical rotation of 1,6- and 3,6- anhydrosugars. For 1,6-anhydrosugars, current parameters produce reasonable agreement with experimental values. For 3,6-anhydrosugars, modifications to the ether parameters had to be introduced. The most relevant included a reorientation of the bond-centered s-->s* transition dipole charges in the ether chromophore to a C2v orientation, and a shift from prolate polarizability ellipsoids to general ellipsoids. These changes result in good agreement with experimental Na D molar rotations for 3,6-anhydrosugars. A low energy CD band arises in 3,6- and 1,6-anhydrosugars when agreement with the experimental NaD molar rotations is achieved. It is proposed that this band is a real feature in the spectrum. The origin of the band is primarily the interaction between b1 symmetry- oriented transition dipoles in the COC groups with other transition dipoles in the molecule. Comparison with experimental spectra leads to an assignment of this band to 11A1 --> 21B1 transitions centered on the COC groups.

  12. Efficient conformational space exploration in ab initio protein folding simulation.

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  13. RKKY interaction in AB-stacked multilayer graphene

    NASA Astrophysics Data System (ADS)

    Jiang, Liwei; Lü, Xiaoling; Gao, Wenzhu; Yu, Guodong; Liu, Zhe; Zheng, Yisong

    2012-05-01

    The RKKY interaction between two magnetic impurities absorbed on the surface layer of half-filled AB-stacked multilayer graphene (ABSMLG) is theoretically studied based on the lattice Green’s function technique. In comparison with the case of monolayer graphene, the RKKY interaction in such multilayer graphene presents distinct properties in some aspects. Firstly, from the numerical results, we find that the thickness of the ABSMLG influences the RKKY interaction in a complicated manner, depending on the odd/even parity of the number of layers and the sublattice attribution of the positions of the two magnetic impurities. Then, we derive the asymptotic expressions of the RKKY interactions in ABSMLG in the long-distance limit. For even-layered ABSMLG, we find that the RKKY interactions of the 1A-1A, 1B-1A and 1B-1B couplings fall off as 1/R2, 1/R4 and 1/R6 (1A and 1B stand for, respectively, the sublattice points in the surface layer, which are positioned directly on the plaquette and on a lattice point of the layer underneath). On the other hand, in odd-layered ABSMLG, the decays of these interactions follow the 1/R2, 1/R3 and 1/R3 power laws respectively. In addition, we also find that these analytical expressions are quantitatively valid to describe the RKKY interaction in ABSMLG when the distance between the two magnetic impurities is larger than the lattice constant of graphene by one order of magnitude.

  14. Atmospheric characterization of the hot Jupiter Kepler-13Ab

    SciTech Connect

    Shporer, Avi; O'Rourke, Joseph G.; Knutson, Heather A.; Szabó, Gyula M.; Zhao, Ming; Burrows, Adam; Fortney, Jonathan; Agol, Eric; Cowan, Nicolas B.; Desert, Jean-Michel; Howard, Andrew W.; Isaacson, Howard; Lewis, Nikole K.; Showman, Adam P.; Todorov, Kamen O.

    2014-06-10

    Kepler-13Ab (= KOI-13.01) is a unique transiting hot Jupiter. It is one of very few known short-period planets orbiting a hot A-type star, making it one of the hottest planets currently known. The availability of Kepler data allows us to measure the planet's occultation (secondary eclipse) and phase curve in the optical, which we combine with occultations observed by warm Spitzer at 4.5 μm and 3.6 μm and a ground-based occultation observation in the K{sub s} band (2.1 μm). We derive a day-side hemisphere temperature of 2750 ± 160 K as the effective temperature of a black body showing the same occultation depths. Comparing the occultation depths with one-dimensional planetary atmosphere models suggests the presence of an atmospheric temperature inversion. Our analysis shows evidence for a relatively high geometric albedo, A {sub g} = 0.33{sub −0.06}{sup +0.04}. While measured with a simplistic method, a high A {sub g} is supported also by the fact that the one-dimensional atmosphere models underestimate the occultation depth in the optical. We use stellar spectra to determine the dilution, in the four wide bands where occultation was measured, due to the visual stellar binary companion 1.''15 ± 0.''05 away. The revised stellar parameters measured using these spectra are combined with other measurements, leading to revised planetary mass and radius estimates of M{sub p} = 4.94-8.09 M {sub J} and R{sub p} = 1.406 ± 0.038 R {sub J}. Finally, we measure a Kepler midoccultation time that is 34.0 ± 6.9 s earlier than expected based on the midtransit time and the delay due to light-travel time and discuss possible scenarios.

  15. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

    Engelbrecht, N. E.; Burger, R. A.

    2013-07-20

    A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.

  16. Efficient conformational space exploration in ab initio protein folding simulation

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  17. Ab initio no-core shell model with continuum

    NASA Astrophysics Data System (ADS)

    Navratil, Petr

    2008-04-01

    The ab initio no-core shell model (NCSM) is a many-body approach to nuclear structure of light nuclei. The NCSM adopts an effective interaction theory to transform fundamental inter-nucleon interactions into effective interactions for a specified nucleus in a selected harmonic oscillator basis space [1]. The method is capable of predicting nuclear structure from inter-nucleon forces derived from quantum chromodynamics by means of chiral effective field theory [2]. NCSM extensions to the microscopic description of nuclear reactions are now under development. In my talk, I will first discuss our recent calculations of the ^4He total photo-absorption cross section using two- and three-nucleon interactions from chiral effective field theory [3]. I will then outline our effort to augment the NCSM by the resonating group method (RGM) technique to develop a new method capable of describing simultaneously both bound states and nuclear reactions on light nuclei [4]. This approach, which preserves translational symmetry and the Pauli principle, will allow us to calculate cross sections of reactions important for astrophysics and describe weakly-bound systems from first principles. I will present our first phase shift results for neutron scattering off ^3H, ^4He and ^7Li and proton scattering off ^3He, ^4He and ^7Be using realistic nucleon-nucleon potentials. 3mm [1] P. Navr'atil, J. P. Vary and B. R. Barrett, Phys. Rev. C 62, 054311 (2000). [2] P. Navr'atil and V. G. Gueorguiev and J. P. Vary, W. E. Ormand and A. Nogga, Phys. Rev. Lett. 99, 042501 (2007). [3] S. Quaglioni and P. Navr'atil, Phys. Lett. B 652, 370 (2007). [4] S. Quaglioni and P. Navr'atil, arXiv:0712.0855.

  18. AB-CHMINACA, AB-PINACA, and FUBIMINA: Affinity and Potency of Novel Synthetic Cannabinoids in Producing Δ9-Tetrahydrocannabinol–Like Effects in Mice

    PubMed Central

    Marusich, Julie A.; Lefever, Timothy W.; Antonazzo, Kateland R.; Wallgren, Michael T.; Cortes, Ricardo A.; Patel, Purvi R.; Grabenauer, Megan; Moore, Katherine N.

    2015-01-01

    Diversion of synthetic cannabinoids for abuse began in the early 2000s. Despite legislation banning compounds currently on the drug market, illicit manufacturers continue to release new compounds for recreational use. This study examined new synthetic cannabinoids, AB-CHMINACA (N-[1-amino-3-methyl-oxobutan-2-yl]-1-[cyclohexylmethyl]-1H-indazole-3-carboxamide), AB-PINACA [N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-pentyl-1H-indazole-3-carboxamide], and FUBIMINA [(1-(5-fluoropentyl)-1H-benzo[d]imadazol-2-yl)(naphthalen-1-yl)methanone], with the hypothesis that these compounds, like those before them, would be highly susceptible to abuse. Cannabinoids were examined in vitro for binding and activation of CB1 receptors, and in vivo for pharmacological effects in mice and in Δ9-tetrahydrocannabinol (Δ9-THC) discrimination. AB-CHMINACA, AB-PINACA, and FUBIMINA bound to and activated CB1 and CB2 receptors, and produced locomotor suppression, antinociception, hypothermia, and catalepsy. Furthermore, these compounds, along with JWH-018 [1-pentyl-3-(1-naphthoyl)indole], CP47,497 [rel-5-(1,1-dimethylheptyl)-2-[(1R,3S)-3-hydroxycyclohexyl]-phenol], and WIN55,212-2 ([(3R)-2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl]-1-naphthalenyl-methanone, monomethanesulfonate), substituted for Δ9-THC in Δ9-THC discrimination. Rank order of potency correlated with CB1 receptor-binding affinity, and all three compounds were full agonists in [35S]GTPγS binding, as compared with the partial agonist Δ9-THC. Indeed, AB-CHMINACA and AB-PINACA exhibited higher efficacy than most known full agonists of the CB1 receptor. Preliminary analysis of urinary metabolites of the compounds revealed the expected hydroxylation. AB-PINACA and AB-CHMINACA are of potential interest as research tools due to their unique chemical structures and high CB1 receptor efficacies. Further studies on these chemicals are likely to include research on understanding cannabinoid receptors

  19. Human malignant mesothelioma is recapitulated in immunocompetent BALB/c mice injected with murine AB cells

    PubMed Central

    Mezzapelle, Rosanna; Rrapaj, Eltjona; Gatti, Elena; Ceriotti, Chiara; Marchis, Francesco De; Preti, Alessandro; Spinelli, Antonello E.; Perani, Laura; Venturini, Massimo; Valtorta, Silvia; Moresco, Rosa Maria; Pecciarini, Lorenza; Doglioni, Claudio; Frenquelli, Michela; Crippa, Luca; Recordati, Camilla; Scanziani, Eugenio; de Vries, Hilda; Berns, Anton; Frapolli, Roberta; Boldorini, Renzo; D’Incalci, Maurizio; Bianchi, Marco E.; Crippa, Massimo P.

    2016-01-01

    Malignant Mesothelioma is a highly aggressive cancer, which is difficult to diagnose and treat. Here we describe the molecular, cellular and morphological characterization of a syngeneic system consisting of murine AB1, AB12 and AB22 mesothelioma cells injected in immunocompetent BALB/c mice, which allows the study of the interplay of tumor cells with the immune system. Murine mesothelioma cells, like human ones, respond to exogenous High Mobility Group Box 1 protein, a Damage-Associated Molecular Pattern that acts as a chemoattractant for leukocytes and as a proinflammatory mediator. The tumors derived from AB cells are morphologically and histologically similar to human MM tumors, and respond to treatments used for MM patients. Our system largely recapitulates human mesothelioma, and we advocate its use for the study of MM development and treatment. PMID:26961782

  20. Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  1. Human malignant mesothelioma is recapitulated in immunocompetent BALB/c mice injected with murine AB cells.

    PubMed

    Mezzapelle, Rosanna; Rrapaj, Eltjona; Gatti, Elena; Ceriotti, Chiara; Marchis, Francesco De; Preti, Alessandro; Spinelli, Antonello E; Perani, Laura; Venturini, Massimo; Valtorta, Silvia; Moresco, Rosa Maria; Pecciarini, Lorenza; Doglioni, Claudio; Frenquelli, Michela; Crippa, Luca; Recordati, Camilla; Scanziani, Eugenio; de Vries, Hilda; Berns, Anton; Frapolli, Roberta; Boldorini, Renzo; D'Incalci, Maurizio; Bianchi, Marco E; Crippa, Massimo P

    2016-01-01

    Malignant Mesothelioma is a highly aggressive cancer, which is difficult to diagnose and treat. Here we describe the molecular, cellular and morphological characterization of a syngeneic system consisting of murine AB1, AB12 and AB22 mesothelioma cells injected in immunocompetent BALB/c mice, which allows the study of the interplay of tumor cells with the immune system. Murine mesothelioma cells, like human ones, respond to exogenous High Mobility Group Box 1 protein, a Damage-Associated Molecular Pattern that acts as a chemoattractant for leukocytes and as a proinflammatory mediator. The tumors derived from AB cells are morphologically and histologically similar to human MM tumors, and respond to treatments used for MM patients. Our system largely recapitulates human mesothelioma, and we advocate its use for the study of MM development and treatment. PMID:26961782

  2. The end of a myth—Bt (Cry1Ab) maize does not harm green lacewings

    PubMed Central

    Romeis, Jörg; Meissle, Michael; Naranjo, Steven E.; Li, Yunhe; Bigler, Franz

    2014-01-01

    A concern with Bt-transgenic insect-resistant plants is their potential to harm non-target organisms. Early studies reported that Cry1Ab-producing Bt maize and purified Cry1Ab harmed larvae of the green lacewing, Chrysoperla carnea. Although these effects could not be confirmed in subsequent studies, some authors still refer to them as evidence that Bt maize harms beneficial species. We provide a comprehensive review of the studies evaluating the effects of Bt (Cry1Ab) maize on C. carnea. The evidence indicates that this important predator is not affected by Bt maize or by the produced Cry1Ab protein. We discuss how conceptual models can assist environmental risk assessments, and we emphasize the importance of robust and reproducible studies. PMID:25161661

  3. AdnAB: a new DSB-resecting motor-nuclease from mycobacteria.

    PubMed

    Sinha, Krishna Murari; Unciuleac, Mihaela-Carmen; Glickman, Michael S; Shuman, Stewart

    2009-06-15

    The resection of DNA double-strand breaks (DSBs) in bacteria is a motor-driven process performed by a multisubunit helicase-nuclease complex: either an Escherichia coli-type RecBCD enzyme or a Bacillus-type AddAB enzyme. Here we identify mycobacterial AdnAB as the founder of a new family of heterodimeric helicase-nucleases with distinctive properties. The AdnA and AdnB subunits are each composed of an N-terminal UvrD-like motor domain and a C-terminal nuclease module. The AdnAB ATPase is triggered by dsDNA with free ends and the energy of ATP hydrolysis is coupled to DSB end resection by the AdnAB nuclease. The mycobacterial nonhomologous end-joining (NHEJ) protein Ku protects DSBs from resection by AdnAB. We find that AdnAB incises ssDNA by measuring the distance from the free 5' end to dictate the sites of cleavage, which are predominantly 5 or 6 nucleotides (nt) from the 5' end. The "molecular ruler" of AdnAB is regulated by ATP, which elicits an increase in ssDNA cleavage rate and a distal displacement of the cleavage sites 16-17 nt from the 5' terminus. AdnAB is a dual nuclease with a clear division of labor between the subunits. Mutations in the nuclease active site of the AdnB subunit ablate the ATP-inducible cleavages; the corresponding changes in AdnA abolish ATP-independent cleavage. Complete suppression of DSB end resection requires simultaneous mutation of both subunit nucleases. The nuclease-null AdnAB is a helicase that unwinds linear plasmid DNA without degrading the displaced single strands. Mutations of the phosphohydrolase active site of the AdnB subunit ablate DNA-dependent ATPase activity, DSB end resection, and ATP-inducible ssDNA cleavage; the equivalent mutations of the AdnA subunit have comparatively little effect. AdnAB is a novel signature of the Actinomycetales taxon. Mycobacteria are exceptional in that they encode both AdnAB and RecBCD, suggesting the existence of alternative end-resecting motor-nuclease complexes. PMID:19470566

  4. Increased expression of the multidrug efflux genes acrAB occurs during slow growth of Escherichia coli.

    PubMed

    Rand, Jonathan D; Danby, Simon G; Greenway, David L A; England, Reg R

    2002-01-22

    Intrinsic antimicrobial resistance of Escherichia coli is elicited by the gene products of the multidrug efflux acrAB-tolC operon. In this paper, we have shown that acrAB is regulated as a function of the growth rate of E. coli during growth in batch and chemostat culture. In chemostat culture, expression of acrAB is inversely related to growth rate irrespective of the limiting nutrient. The level of expression of acrAB is greater under glucose limitation compared with either iron or nitrogen limitation. Increase in expression of acrAB confers a greater resistance to ciprofloxacin, and the implications for a clinical situation are discussed. Slow growth rate regulation of acrAB transcription does not require the presence of the stationary-phase sigma factor. A putative gearbox consensus sequence was identified at the -10 region of the acrAB promoter. PMID:11886757

  5. Plasmid-Mediated OqxAB Is an Important Mechanism for Nitrofurantoin Resistance in Escherichia coli

    PubMed Central

    Ng, Ka-Ying; Lo, Wai-U; Law, Pierra Y.; Lai, Eileen Ling-Yi; Wang, Ya; Chow, Kin-Hung

    2015-01-01

    Increasing consumption of nitrofurantoin (NIT) for treatment of acute uncomplicated urinary tract infections (UTI) highlights the need to monitor emerging NIT resistance mechanisms. This study investigated the molecular epidemiology of the multidrug-resistant efflux gene oqxAB and its contribution to nitrofurantoin resistance by using Escherichia coli isolates originating from patients with UTI (n = 205; collected in 2004 to 2013) and food-producing animals (n = 136; collected in 2012 to 2013) in Hong Kong. The oqxAB gene was highly prevalent among NIT-intermediate (11.5% to 45.5%) and -resistant (39.2% to 65.5%) isolates but rare (0% to 1.7%) among NIT-susceptible (NIT-S) isolates. In our isolates, the oqxAB gene was associated with IS26 and was carried by plasmids of diverse replicon types. Multilocus sequence typing revealed that the clones of oqxAB-positive E. coli were diverse. The combination of oqxAB and nfsA mutations was found to be sufficient for high-level NIT resistance. Curing of oqxAB-carrying plasmids from 20 NIT-intermediate/resistant UTI isolates markedly reduced the geometric mean MIC of NIT from 168.9 μg/ml to 34.3 μg/ml. In the plasmid-cured variants, 20% (1/5) of isolates with nfsA mutations were NIT-S, while 80% (12/15) of isolates without nfsA mutations were NIT-S (P = 0.015). The presence of plasmid-based oqxAB increased the mutation prevention concentration of NIT from 128 μg/ml to 256 μg/ml and facilitated the development of clinically important levels of nitrofurantoin resistance. In conclusion, plasmid-mediated oqxAB is an important nitrofurantoin resistance mechanism. There is a great need to monitor the dissemination of this transferable multidrug-resistant efflux pump. PMID:26552976

  6. A KINE-CHEMICAL INVESTIGATION OF THE AB DOR MOVING GROUP 'STREAM'

    SciTech Connect

    Barenfeld, Scott A.; Bubar, Eric J.; Mamajek, Eric E.; Young, Patrick A.

    2013-03-20

    The AB Dor Moving Group consists of a 'nucleus' of {approx}10 stars at d {approx_equal} 20 pc, along with dozens of purported 'stream' members distributed across the sky. We perform a chemical and kinematic analysis of a subsample of AB Dor stream stars to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution spectra taken with the Magellan Clay 6.5 m telescope. Using a {chi}{sup 2} test with the measured abundances for 10 different elements, we find that only half of the purported AB Dor stream members could possibly constitute a statistically chemically homogeneous sample. Some stream members with three-dimensional velocities were hundreds of parsecs from the AB Dor nucleus {approx}10{sup 8} yr ago, and hence were unlikely to share a common origin. We conclude that the published lists of AB Dor moving group stream members are unlikely to represent the dispersed remnant of a single star formation episode. A subsample of the stream stars appears to be both statistically chemically homogeneous and in the vicinity of the AB Dor nucleus at birth. Their mean metallicity is [Fe/H] = 0.02 {+-} 0.02 dex, which we consider representative for the AB Dor group. Finally, we report a strong lower limit on the age of the AB Dor nucleus of >110 Myr based on the pre-main sequence contraction times for K-type members which have reached the main sequence.

  7. A Novel Variant in CMAH Is Associated with Blood Type AB in Ragdoll Cats

    PubMed Central

    Gandolfi, Barbara; Grahn, Robert A.; Gustafson, Nicholas A.; Proverbio, Daniela; Spada, Eva; Adhikari, Badri; Cheng, Janling; Andrews, Gordon; Lyons, Leslie A.; Helps, Chris R.

    2016-01-01

    The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood type B has been achieved, the rare type AB serotype remains genetically uncharacterized. A genome-wide association study in Ragdoll cats (22 cases and 15 controls) detected a significant association between blood type AB and SNPs on cat chromosome B2, with the most highly associated SNP being at position 4,487,432 near the candidate gene cytidine monophospho-N-acetylneuraminic acid hydroxylase. A novel variant, c.364C>T, was identified that is highly associated with blood type AB in Ragdoll cats and, to a lesser degree, with type AB in random bred cats. The newly identified variant is probably linked with blood type AB in Ragdoll cats, and is associated with the expression of both antigens (N-glycolylneuraminic acid and N-acetylneuraminic acid) on the red blood cell membrane. Other variants, not identified by this work, are likely to be associated with blood type AB in other breeds of cat. PMID:27171395

  8. AB3217-A, a novel anti-mite substance produced by a strain of Streptomyces platensis.

    PubMed

    Kanbe, K; Mimura, Y; Tamamura, T; Yatagai, S; Sato, Y; Takahashi, A; Sato, K; Naganawa, H; Nakamura, H; Takeuchi, T

    1992-04-01

    AB3217-A, a novel anti-mite substance, was isolated from the fermentation broth of a streptomycete strain. The strain was isolated from a soil collected at Kita-azumi, Nagano Prefecture, Japan, and identified as Streptomyces platensis AB3217. AB3217-A was purified by Amberlite IR120B, Diaion HP-20 and CM-Sephadex C-25 column chromatographies. The molecular formula was determined as C17H23NO7 by elemental analysis, MS and 13C NMR spectroscopy. The structure of AB3217-A was determined to be (1R,3S,4S,7R,8R,11R,12S,13R)-4,12,13-trihydroxy-8-(4-methoxy phenyl)-6-aza-2,9,14-trioxatricyclo-[9.2.1.0(3,7)]tetradecane by spectroscopic analysis and X-ray crystallographic analysis. The molecule of AB3217-A has unique structure that deacetylanisomycin and beta-D-xylofuranose linked through glycosidic bond and ether bond resulting in the formation of nine-membered ring. AB3217-A showed marked activity against the two spotted spider mite, Tetranychus urticae. PMID:1592678

  9. Bridging the gap: facilities and technologies for development of early stage therapeutic mAb candidates.

    PubMed

    Munro, Trent P; Mahler, Stephen M; Huang, Edwin P; Chin, David Y; Gray, Peter P

    2011-01-01

    Therapeutic monoclonal antibodies (mAbs) currently dominate the biologics marketplace. Development of a new therapeutic mAb candidate is a complex, multistep process and early stages of development typically begin in an academic research environment. Recently, a number of facilities and initiatives have been launched to aid researchers along this difficult path and facilitate progression of the next mAb blockbuster. Complementing this, there has been a renewed interest from the pharmaceutical industry to reconnect with academia in order to boost dwindling pipelines and encourage innovation. In this review, we examine the steps required to take a therapeutic mAb from discovery through early stage preclinical development and toward becoming a feasible clinical candidate. Discussion of the technologies used for mAb discovery, production in mammalian cells and innovations in single-use bioprocessing is included. We also examine regulatory requirements for product quality and characterization that should be considered at the earliest stages of mAb development. We provide details on the facilities available to help researchers and small-biotech build value into early stage product development, and include examples from within our own facility of how technologies are utilized and an analysis of our client base. PMID:21822050

  10. Adsorption of transgenic insecticidal Cry1Ab protein to silica particles. Effects on transport and bioactivity.

    PubMed

    Madliger, Michael; Gasser, Christoph A; Schwarzenbach, René P; Sander, Michael

    2011-05-15

    Bt crops are genetically modified to be resistant against insect pests by expressing insecticidal Cry proteins. The processes governing the fate and bioavailability of the expressed transgenic Cry proteins in soils are poorly understood. We studied adsorption of Cry1Ab to negatively charged silica (SiO(2)) particles, a major soil constituent and a model for negatively charged mineral surfaces, at pH 5 to 10 and ionic strengths I = 10 mM to 250 mM, both in solution depletion and saturated column transport experiments. Cry1Ab-SiO(2) interactions were dominated by patch-controlled electrostatic attraction (PCEA), as evident from increasing Cry1Ab attraction to SiO(2) with decreasing I at pH at which both Cry1Ab and SiO(2) were net negatively charged. Experimental and modeling evidence is provided that the surface heterogeneity of SiO(2) particles modulated PCEA, leading to a fraction of adsorption sites with slow Cry1Ab desorption kinetics. Desorption rates from these sites increased upon increasing the solution pH. In toxicity bioassays, we demonstrated that Cry1Ab retained insecticidal activity when adsorbed to SiO(2), suggesting high protein conformational stability during adsorption-desorption cycles. Models predicting Cry1A protein adsorption in soils therefore need to account for combined effects of the nonuniform protein surface charge distribution and of sorbent surface heterogeneity. PMID:21526821

  11. Treatment with Anti-EGF Ab Ameliorates Experimental Autoimmune Encephalomyelitis via Induction of Neurogenesis and Oligodendrogenesis

    PubMed Central

    Amir-Levy, Yifat; Mausner-Fainberg, Karin; Karni, Arnon

    2014-01-01

    Background. The neural stem cells (NSCs) migrate to the damaged sites in multiple sclerosis (MS) and in experimental autoimmune encephalomyelitis (EAE). However, the differentiation into neurons or oligodendrocytes is blocked. Epidermal growth factor (EGF) stimulates NSC proliferation and mobilization to demyelinated lesions but also induces astrogenesis and glial scar. Objective. To examine the clinical and histopathological effects of EGF neutralization on EAE. Methods. EAE-induced SJL mice were intravenously treated with either anti-EGF neutralizing antibody (Ab) or isotype control or PBS. On day 9 after immunization, 3 mice of each group were daily treated for 9 days with BrdU and then sacrificed for immunohistochemical analysis. Results. Treatment with anti-EGF Ab significantly ameliorated EAE symptoms during the second relapse. Anti-EGF Ab induced a shift from BrdU+GFAP+ NSCs to BrdU+DCX+ neuroblasts in the subventricular zone (SVZ), increased BrdU+NeuN+ neurons in the granular cell layer of the dentate gyrus, and increased BrdU+O4+ oligodendrocytes in the SVZ. There was no change in the inflammatory infiltrates in response to anti-EGF Ab. Conclusions. Therapy with anti-EGF Ab ameliorates EAE via induction of neurogenesis and oligodendrogenesis. No immunosuppressive effect was found. Further investigation is needed to support these notions of beneficial effect of anti-EGF Ab in MS. PMID:25610650

  12. Treatment with Anti-EGF Ab Ameliorates Experimental Autoimmune Encephalomyelitis via Induction of Neurogenesis and Oligodendrogenesis.

    PubMed

    Amir-Levy, Yifat; Mausner-Fainberg, Karin; Karni, Arnon

    2014-01-01

    Background. The neural stem cells (NSCs) migrate to the damaged sites in multiple sclerosis (MS) and in experimental autoimmune encephalomyelitis (EAE). However, the differentiation into neurons or oligodendrocytes is blocked. Epidermal growth factor (EGF) stimulates NSC proliferation and mobilization to demyelinated lesions but also induces astrogenesis and glial scar. Objective. To examine the clinical and histopathological effects of EGF neutralization on EAE. Methods. EAE-induced SJL mice were intravenously treated with either anti-EGF neutralizing antibody (Ab) or isotype control or PBS. On day 9 after immunization, 3 mice of each group were daily treated for 9 days with BrdU and then sacrificed for immunohistochemical analysis. Results. Treatment with anti-EGF Ab significantly ameliorated EAE symptoms during the second relapse. Anti-EGF Ab induced a shift from BrdU(+)GFAP(+) NSCs to BrdU(+)DCX(+) neuroblasts in the subventricular zone (SVZ), increased BrdU(+)NeuN(+) neurons in the granular cell layer of the dentate gyrus, and increased BrdU(+)O4(+) oligodendrocytes in the SVZ. There was no change in the inflammatory infiltrates in response to anti-EGF Ab. Conclusions. Therapy with anti-EGF Ab ameliorates EAE via induction of neurogenesis and oligodendrogenesis. No immunosuppressive effect was found. Further investigation is needed to support these notions of beneficial effect of anti-EGF Ab in MS. PMID:25610650

  13. Hepatoma-Targeted Radionuclide Immune Albumin Nanospheres: 131I-antiAFPMcAb-GCV-BSA-NPs

    PubMed Central

    Lin, Mei; Huang, Junxing; Zhang, Dongsheng; Jiang, Xingmao; Zhang, Jia; Yu, Hong; Xiao, Yanhong; Shi, Yujuan; Guo, Ting

    2016-01-01

    An effective strategy has been developed for synthesis of radionuclide immune albumin nanospheres (131I-antiAFPMcAb-GCV-BSA-NPs). In vitro as well as in vivo targeting of 131I-antiAFPMcAb-GCV-BSA-NPs to AFP-positive hepatoma was examined. In cultured HepG2 cells, the uptake and retention rates of 131I-antiAFPMcAb-GCV-BSA-NPs were remarkably higher than those of 131I alone. As well, the uptake rate and retention ratios of 131I-antiAFPMcAb-GCV-BSA-NPs in AFP-positive HepG2 cells were also significantly higher than those in AFP-negative HEK293 cells. Compared to 131I alone, 131I-antiAFPMcAb-GCV-BSA-NPs were much more easily taken in and retained by hepatoma tissue, with a much higher T/NT. Due to good drug-loading, high encapsulation ratio, and highly selective affinity for AFP-positive tumors, the 131I-antiAFPMcAb-GCV-BSA-NPs are promising for further effective radiation-gene therapy of hepatoma. PMID:26981334

  14. The multidrug resistance efflux complex, EmrAB from Escherichia coli forms a dimer in vitro

    SciTech Connect

    Tanabe, Mikio; Szakonyi, Gerda; Brown, Katherine A.; Henderson, Peter J.F.; Nield, Jon; Byrne, Bernadette

    2009-03-06

    Tripartite efflux systems are responsible for the export of toxins across both the inner and outer membranes of Gram negative bacteria. Previous work has indicated that EmrAB-TolC from Escherichia coli is such a tripartite system, comprised of EmrB an MFS transporter, EmrA, a membrane fusion protein and TolC, an outer membrane channel. The whole complex is predicted to form a continuous channel allowing direct export from the cytoplasm to the exterior of the cell. Little is known, however, about the interactions between the individual components of this system. Reconstitution of EmrA + EmrB resulted in co-elution of the two proteins from a gel filtration column indicating formation of the EmrAB complex. Electron microscopic single particle analysis of the reconstituted EmrAB complex revealed the presence of particles approximately 240 x 140 A, likely to correspond to two EmrAB dimers in a back-to-back arrangement, suggesting the dimeric EmrAB form is the physiological state contrasting with the trimeric arrangement of the AcrAB-TolC system.

  15. Yeast killer toxin-like candidacidal Ab6 antibodies elicited through the manipulation of the idiotypic cascade.

    PubMed

    Polonelli, Luciano; Beninati, Concetta; Teti, Giuseppe; Felici, Franco; Ciociola, Tecla; Giovati, Laura; Sperindè, Martina; Lo Passo, Carla; Pernice, Ida; Domina, Maria; Arigò, Milena; Papasergi, Salvatore; Mancuso, Giuseppe; Conti, Stefania; Magliani, Walter

    2014-01-01

    A mouse anti-anti-anti-idiotypic (Id) IgM monoclonal antibody (mAb K20, Ab4), functionally mimicking a Wyckerhamomyces anomalus (Pichia anomala) killer toxin (KT) characterized by fungicidal activity against yeasts presenting specific cell wall receptors (KTR) mainly constituted by β-1,3-glucan, was produced from animals presenting anti-KT Abs (Ab3) following immunization with a rat IgM anti-Id KT-like mAb (mAb K10, Ab2). MAb K10 was produced by immunization with a KT-neutralizing mAb (mAb KT4, Ab1) bearing the internal image of KTR. MAb K20, likewise mAb K10, proved to be fungicidal in vitro against KT-sensitive Candida albicans cells, an activity neutralized by mAb KT4, and was capable of binding to β-1,3-glucan. MAb K20 and mAb K10 competed with each other and with KT for binding to C. albicans KTR. MAb K20 was used to identify peptide mimics of KTR by the selection of phage clones from random peptide phage display libraries. Using this strategy, four peptides (TK 1-4) were selected and used as immunogen in mice in the form of either keyhole limpet hemocyanin (KLH) conjugates or peptide-encoding minigenes. Peptide and DNA immunization could induce serum Abs characterized by candidacidal activity, which was inhibited by laminarin, a soluble β-1,3-glucan, but not by pustulan, a β-1,6-glucan. These findings show that the idiotypic cascade can not only overcome the barrier of animal species but also the nature of immunogens and the type of technology adopted. PMID:25162681

  16. Different evolutionary stages in S235A-B

    NASA Astrophysics Data System (ADS)

    Felli, Marcello; Massi, Fabrizio; Cesaroni, Riccardo

    The star forming region S235A-B has been studied at high resolution with radio (IRAM Interferometer and VLA) and infrared (JCMT and Spitzer) observations. The region was mapped in HCO^+, C^34S, H[2]CS, SO[2] and CH[3]CN as well as in the 1.2 and 3.3 continuum, in the cm continuum at 6, 3.6, 1.3 and 0.7 cm and in the 22 GHz water maser line, in the far infrared at 450 and 850 micron and in the mid infrared from 3.6 to 8 micron. Use was made of the Medicina water maser patrol, from 1987 to 2005, to study the maser variability. S235A is a classical HII region, well resolved and with a very good match between radio and infrared images. To the south of it, molecular and continuum mm observations as well as infrared observations reveal the presence of newly formed YSOs placed in between S235A and S235B: a molecular core and an unresolved mm source centred on one maser component, with indication of mass infall onto the core. Two bipolar outflows and a jet originate from the same position. No cm radio continuum emission is detected either from the compact molecular core or from the jet-like structure, suggesting emission from dust in both cases. Evidence is found for a molecular rotating disk perpendicular to the main bipolar outflow. The derived parameters indicate that the YSO is an intermediate luminosity object in a very early evolutionary phase. Its main source of energy could come from gravitational infall thus making this YSO a rare link between the earliest evolutionary phases of massive stars and low mass protostars of class 0-I. Two compact radio continuum sources (VLA-1 and VLA-2) and three separate maser spots were found. VLA-1 coincides with one of the maser spots and with an IR source (M1). VLA-2 lies towards S235B and represents the first radio detection from this peculiar nebula. The two other maser spots coincide with the rotating disk perpendicular to the bipolar molecular outflow. The Spitzer images reveal a red object towards the molecular core which is

  17. Large scale production of Bacillus thuringiensis PS149B1 insecticidal proteins Cry34Ab1 and Cry35Ab1 from Pseudomonas fluorescens.

    PubMed

    Huang, Ke-Xue; Badger, Monty; Haney, Keith; Evans, Steve L

    2007-06-01

    The 14kDa (Cry34Ab1) and 44kDa (Cry35Ab1) binary insecticidal proteins are produced naturally by Bacillus thuringiensis PS149B1 as parasporal inclusion bodies. Here, we show production of these two insecticidal proteins in recombinant Pseudomonas fluorescens and their subsequent purification to near homogeneity to provide large quantities of protein for safety-assessment studies associated with the registration of transgenic corn plants. The gene sequence specific for each protein was expressed in P. fluorescens and fermented at the 75-L scale. For Cry34Ab1, the protein accumulated as insoluble inclusion bodies, and was purified by extraction directly from the cell pastes at pH 3.4 with a sodium acetate buffer, selective precipitation at pH 7.0, and differential centrifugation. For Cry35Ab1, the protein was extracted from the purified inclusion bodies with sodium acetate buffer (pH 3.5) containing 0.5M urea, followed by diafiltration. No chromatography steps were required to produce over 30g of lyophilized protein powder with purity greater than 98%, while retaining full insecticidal activity against Western corn rootworm larvae. The proteins were further characterized to assure identity and suitability for use in safety-assessment studies. PMID:17337206

  18. Complexation of AB+, AB+C, ACB+, and A(B+-stat-C) block copolymer micelles with poly(styrene sulfonate) as models for tunable gene delivery vectors

    NASA Astrophysics Data System (ADS)

    Laaser, Jennifer; Jiang, Yaming; Lohmann, Elise; Reineke, Theresa; Lodge, Timothy

    We investigate the complexation of poly(styrene sulfonate) with micelles with mixed cationic/hydrophilic coronas as models for tunable gene delivery vectors. The micelles are self-assembled from AB+, AB+C, ACB+, and A(B+-stat-C) block polymer architectures, where the hydrophobic A blocks (poly(styrene)) form the micelle cores, and the cationic B blocks (poly(dimethylamino ethyl methacrylate)) and hydrophilic, nonionic C blocks (poly(poly(ethylene glycol) methyl ether methacrylate)) form the coronas. We find that hydrophilic units do not change the colloidal stability of the complexes, and complexes based on all four micelle architectures form broad, multimodal size distributions. While complexes based on the AB+, AB+C, and ACB+polymer architectures are kinetically trapped at low ionic strength, however, those based on the A(B+-stat-C) architecture rapidly rearrange into single-micelle complexes when the linear polyanion is in excess. This suggests that the randomly-placed hydrophilic units break up the ion pairing between the cationic and anionic chains and promote formation of over-charged complexes. Design of the micelle architecture may thus provide a powerful way control the structure and stability of micelle-polyelectrolyte complexes for gene delivery applications.

  19. Report on Distance Education and AB606 Funding Prepared for the 70th Nevada Legislature (in Accordance with AB 606, 1997 Session).

    ERIC Educational Resources Information Center

    Nevada Univ. and Community Coll. System, Reno. Office of the Chancellor.

    In 1997 the Nevada State Legislature approved Assembly Bill 606 (AB606), which appropriated funds to the University and Community College System of Nevada (UCCSN) for the purchase of computer hardware and software, and communication services. In July of that year, the K-16 Partnership for Distance Learning adopted three priorities that have guided…

  20. Characterization of the mechanism of action of the genetically modified Cry1AbMod toxin that is active against Cry1Ab-resistant insects.

    PubMed

    Muñóz-Garay, Carlos; Portugal, Leivi; Pardo-López, Liliana; Jiménez-Juárez, Nuria; Arenas, Ivan; Gómez, Isabel; Sánchez-López, Rosana; Arroyo, Raquel; Holzenburg, Andreas; Savva, Christos G; Soberón, Mario; Bravo, Alejandra

    2009-10-01

    Bacillus thuringiensis Cry toxins are used in the control of insect pests. They are pore-forming toxins with a complex mechanism that involves the sequential interaction with receptors. They are produced as protoxins, which are activated by midgut proteases. Activated toxin binds to cadherin receptor, inducing an extra cleavage including helix alpha-1, facilitating the formation of a pre-pore oligomer. The toxin oligomer binds to secondary receptors such as aminopeptidase and inserts into lipid rafts forming pores and causing larval death. The primary threat to efficacy of Bt-toxins is the evolution of insect resistance. Engineered Cry1AMod toxins, devoid of helix alpha-1, could be used for the control of resistance in lepidopterans by bypassing the altered cadherin receptor, killing resistant insects affected in this receptor. Here we analyzed the mechanism of action of Cry1AbMod. We found that alkaline pH and the presence of membrane lipids facilitates the oligomerization of Cry1AbMod. In addition, tryptophan fluorescence emission spectra, ELISA binding to pure aminopeptidase receptor, calcein release assay and analysis of ionic-conductance in planar lipid bilayers, indicated that the secondary steps in mode of action that take place after interaction with cadherin receptor such as oligomerization, receptor binding and pore formation are similar in the Cry1AbMod and in the wild type Cry1Ab. Finally, the membrane-associated structure of Cry1AbMod oligomer was analyzed by electron crystallography showing that it forms a complex with a trimeric organization. PMID:19559004

  1. An Absolute Index (Ab-index) to Measure a Researcher’s Useful Contributions and Productivity

    PubMed Central

    Biswal, Akshaya Kumar

    2013-01-01

    Bibliographic analysis has been a very powerful tool in evaluating the effective contributions of a researcher and determining his/her future research potential. The lack of an absolute quantification of the author’s scientific contributions by the existing measurement system hampers the decision-making process. In this paper, a new metric system, Absolute index (Ab-index), has been proposed that allows a more objective comparison of the contributions of a researcher. The Ab-index takes into account the impact of research findings while keeping in mind the physical and intellectual contributions of the author(s) in accomplishing the task. The Ab-index and h-index were calculated for 10 highly cited geneticists and molecular biologist and 10 young researchers of biological sciences and compared for their relationship to the researchers input as a primary author. This is the first report of a measuring method clarifying the contributions of the first author, corresponding author, and other co-authors and the sharing of credit in a logical ratio. A java application has been developed for the easy calculation of the Ab-index. It can be used as a yardstick for comparing the credibility of different scientists competing for the same resources while the Productivity index (Pr-index), which is the rate of change in the Ab-index per year, can be used for comparing scientists of different age groups. The Ab-index has clear advantage over other popular metric systems in comparing scientific credibility of young scientists. The sum of the Ab-indices earned by individual researchers of an institute per year can be referred to as Pr-index of the institute. PMID:24391941

  2. HEK293 cells express dystrophin Dp71 with nucleus-specific localization of Dp71ab.

    PubMed

    Nishida, Atsushi; Yasuno, Sato; Takeuchi, Atsuko; Awano, Hiroyuki; Lee, Tomoko; Niba, Emma Tabe Eko; Fujimoto, Takahiro; Itoh, Kyoko; Takeshima, Yasuhiro; Nishio, Hisahide; Matsuo, Masafumi

    2016-09-01

    The dystrophin gene consists of 79 exons and encodes tissue-specific isoforms. Mutations in the dystrophin gene cause Duchenne muscular dystrophy, of which a substantial proportion of cases are complicated by non-progressive mental retardation. Abnormalities of Dp71, an isoform transcribed from a promoter in intron 62, are a suspected cause of mental retardation. However, the roles of Dp71 in human brain have not been fully elucidated. Here, we characterized dystrophin in human HEK293 cells with the neuronal lineage. Reverse transcription-PCR amplification of the full-length dystrophin transcript revealed the absence of fragments covering the 5' part of the dystrophin cDNA. In contrast, fragments covering exons 64-79 were present. The Dp71 promoter-specific exon G1 was shown spliced to exon 63. We demonstrated that the Dp71 transcript comprised two subisoforms: one lacking exon 78 (Dp71b) and the other lacking both exons 71 and 78 (Dp71ab). Western blotting of cell lysates using an antibody against the dystrophin C-terminal region revealed two bands, corresponding to Dp71b and Dp71ab. Immunohistochemical examination with the dystrophin antibody revealed scattered punctate signals in the cytoplasm and the nucleus. Western blotting revealed one band corresponding to Dp71b in the cytoplasm and two bands corresponding to Dp71b and Dp71ab in the nucleus, with Dp71b being predominant. These results indicated that Dp71ab is a nucleus-specific subisoform. We concluded that Dp71, comprising Dp71b and Dp71ab, was expressed exclusively in HEK293 cells and that Dp71ab was specifically localized to the nucleus. Our findings suggest that Dp71ab in the nucleus contributes to the diverse functions of HEK293 cells. PMID:27109495

  3. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  4. Identification and quantification of metabolites of AB-CHMINACA in a urine specimen of an abuser.

    PubMed

    Wurita, Amin; Hasegawa, Koutaro; Minakata, Kayoko; Gonmori, Kunio; Nozawa, Hideki; Yamagishi, Itaru; Suzuki, Osamu; Watanabe, Kanako

    2016-03-01

    We experienced an autopsy case in which the cause of death was judged as poisoning by multiple new psychoactive substances, including AB-CHMINACA, 5-fluoro-AMB and diphenidine [Forensic Toxicol. 33 (2015): 45-53]. Although unchanged AB-CHMINACA could be detected from 8 solid tissues, it could neither be detected from blood nor urine specimens. In this article, we obtained eight kinds of reference standards of AB-CHMINACA metabolites from a commercial source. The AB-CHMINACA metabolites from the urine specimen of the abuser were extracted by a modified QuEChERS method and analyzed by liquid chromatography-tandem mass spectrometry before and after hydrolysis with β-glucuronidase. Among the eight AB-CHMINACA metabolites tested, only 2 metabolites could be identified in the urine specimen of the deceased. After hydrolysis with β-glucuronidase, the concentrations of the two metabolites were not increased, suggesting that the metabolites were not in the conjugated forms. The metabolites detected were 4-hydroxycyclohexylmethyl AB-CHMINACA (M1), followed by N-[[1-(cyclohexylmethyl)-1H-indazol-3-yl]carbonyl]-l-valine (M3). Their concentrations were 52.8±3.44 and 41.3±5.04ng/ml (n=10) for M1 and M3, respectively. Although there is one preceding report showing the estimations of metabolism of AB-CHMINACA without reference standards, this is the first report dealing with exact identification using reference standards, and quantification of M1 and M3 in an authentic urine specimen. PMID:26257317

  5. High-throughput mAb expression and purification platform based on transient CHO.

    PubMed

    Barnard, Gavin C; Hougland, Maria D; Rajendra, Yashas

    2015-01-01

    A high-cell-density transient transfection system was recently developed in our laboratory based on a CHO-GS-KO cell line. This method yields monoclonal antibody titers up to 350 mg/L from a simple 7-day process, in volumes ranging from 2 mL to 2 L. By performing transfections in 24-deep-well plates, a large number of mAbs can be expressed simultaneously. We coupled this new high-throughput transfection process to a semiautomated protein A purification process. Using a Biomek FX(p) liquid handling robot, up to 72 unique mAbs can be simultaneously purified. Our primary goal was to obtain >0.25 mg of purified mAb at a concentration of >0.5 mg/mL, without any concentration or buffer-exchange steps. We optimized both the batch-binding and the batch elution steps. The length of the batch-binding step was important to minimize mAb losses in the flowthrough fraction. The elution step proved to be challenging to simultaneously maximize protein recovery and protein concentration. We designed a variable volume elution strategy based on the average supernatant titer. Finally, we present two case studies. In the first study, we produced 56 affinity maturation mAb variants at an average yield of 0.33 ± 0.05 mg (average concentration of 0.65 ± 0.10 mg/mL). In a second study, we produced 42 unique mAbs, from an early-stage discovery effort, at an average yield of 0.79 ± 0.31 mg (average concentration of 1.59 ± 0.63 mg/mL). The combination of parallel high-yielding transient transfection and semiautomated high-throughput protein A purification represents a valuable mAb drug discovery tool. PMID:25403790

  6. Islet biology, the CDKN2A/B locus and type 2 diabetes risk.

    PubMed

    Kong, Yahui; Sharma, Rohit B; Nwosu, Benjamin U; Alonso, Laura C

    2016-08-01

    Type 2 diabetes, fuelled by the obesity epidemic, is an escalating worldwide cause of personal hardship and public cost. Diabetes incidence increases with age, and many studies link the classic senescence and ageing protein p16(INK4A) to diabetes pathophysiology via pancreatic islet biology. Genome-wide association studies (GWASs) have unequivocally linked the CDKN2A/B locus, which encodes p16 inhibitor of cyclin-dependent kinase (p16(INK4A)) and three other gene products, p14 alternate reading frame (p14(ARF)), p15(INK4B) and antisense non-coding RNA in the INK4 locus (ANRIL), with human diabetes risk. However, the mechanism by which the CDKN2A/B locus influences diabetes risk remains uncertain. Here, we weigh the evidence that CDKN2A/B polymorphisms impact metabolic health via islet biology vs effects in other tissues. Structured in a bedside-to-bench-to-bedside approach, we begin with a summary of the evidence that the CDKN2A/B locus impacts diabetes risk and a brief review of the basic biology of CDKN2A/B gene products. The main emphasis of this work is an in-depth look at the nuanced roles that CDKN2A/B gene products and related proteins play in the regulation of beta cell mass, proliferation and insulin secretory function, as well as roles in other metabolic tissues. We finish with a synthesis of basic biology and clinical observations, incorporating human physiology data. We conclude that it is likely that the CDKN2A/B locus influences diabetes risk through both islet and non-islet mechanisms. PMID:27155872

  7. Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter

    PubMed Central

    Szollosi, Andras; Vieira-Pires, Ricardo S.; Teixeira-Duarte, Celso M.; Rocha, Rita; Morais-Cabral, João H.

    2016-01-01

    KtrAB belongs to the Trk/Ktr/HKT superfamily of monovalent cation (K+ and Na+) transport proteins that closely resemble K+ channels. These proteins underlie a plethora of cellular functions that are crucial for environmental adaptation in plants, fungi, archaea, and bacteria. The activation mechanism of the Trk/Ktr/HKT proteins remains unknown. It has been shown that ATP stimulates the activity of KtrAB while ADP does not. Here, we present X-ray structural information on the KtrAB complex with bound ADP. A comparison with the KtrAB-ATP structure reveals conformational changes in the ring and in the membrane protein. In combination with a biochemical and functional analysis, we uncover how ligand-dependent changes in the KtrA ring are propagated to the KtrB membrane protein and conclude that, despite their structural similarity, the activation mechanism of KtrAB is markedly different from the activation mechanism of K+ channels. PMID:26771197

  8. Visual search is postponed during the period of the AB: An event-related potential study.

    PubMed

    Lagroix, Hayley E P; Grubert, Anna; Spalek, Thomas M; Di Lollo, Vincent; Eimer, Martin

    2015-08-01

    In the phenomenon known as the attentional blink (AB), perception of the second of two rapidly sequential targets (T2) is impaired when presented shortly after the first (T1). Studies in which T2 consisted of a pop-out search array provided evidence suggesting that visual search is postponed during the AB. In the present work, we used behavioral and electrophysiological measures to test this postponement hypothesis. The behavioral measure was reaction time (RT) to T2; the electrophysiological measure was the onset latency of an ERP index of attentional selection, known as the N2pc. Consistent with the postponement hypothesis, both measures were delayed during the AB. The delay in N2pc was substantially shorter than that in RT, pointing to multiple sources of delay in the chain of processing events, as distinct from the single source postulated in current theories of the AB. Finally, the finding that the N2pc was delayed during the AB strongly suggests that attention is involved in the processing of pop-out search arrays. PMID:25871502

  9. Characterization of Two Novel mAbs Recognizing Different Epitopes on CD43

    PubMed Central

    Kim, Soseul; Hong, Jeong won; Cho, Woon-Dong; Moon, Yoo Ri; Yoon, Sang Soon; Kim, Min-Young; Hong, Kwon Pyo; Lee, Yong-Moon; Yi, Jae Hyuk; Ham, Young Jun; Rah, Hyung Chul; Kim, Seung Ryul

    2014-01-01

    JL1, a specific epitope on CD43, is a potential biomarker for the diagnosis of acute leukemia. Although qualitative assays for detecting leukemia-specific CD43 exist, there is a need to develop quantitative assays for the same. Here, we developed two novel monoclonal antibodies (mAbs), 2C8 and 8E10, recognizing different epitopes on CD43. These clones are capable of pairing with YG5, another mAb against JL1 epitope, because they were selectively obtained using sandwich ELISA. Antigens recognized by 2C8 and 8E10 were confirmed as CD43 by western blotting using the CD43-hFC recombinant protein. When expression on various leukemic cell lines was investigated, 2C8 and 8E10 displayed a disparity in the distribution of the epitope. Enzyme assays revealed that these mAbs recognized a sialic acid-dependent epitope on CD43. Using normal thymus and lymph node paraffin-embedded tissues, we confirmed a difference in the epitopes recognized by the two mAbs that was predicted based on the maturity of the cells in the tissue. In summary, we developed and characterized two mAbs, 2C8 and 8E10, which can be used with YG5 in a sandwich ELISA for detecting leukemia-specific CD43. PMID:24999313

  10. Water body mapping method with HJ-1A/B satellite imagery

    NASA Astrophysics Data System (ADS)

    Lu, Shanlong; Wu, Bingfang; Yan, Nana; Wang, Hao

    2011-06-01

    This paper proposes an integrated water body mapping method with HJ-1A/B satellite imagery, the CCD (charge coupled device) data of the Chinese environmental satellites that were launched on September 6th, 2008. It combines the difference between NDVI and NDWI (NDVI-NDWI) with SLOPE and near-infrared (NIR) band. The NDVI-NDWI index is used to enhance the contrast between water bodies and the surrounding surface features; the topographic SLOPE is used to eliminate the mountain shadow; and the NIR band is used to reduce the effects of artificial construction land. The objectives are evaluating the potential of the HJ-1A/B imagery on water body monitoring, and proposing ideally mapping method. The test study results indicated that the NDVI-NDWI index is superior to the single index of NDVI and NDWI to enhance the contrast between water bodies and the rest of the features. On the basis of the accurately mapped water bodies in the HJ-1A/B CCD images of the study area, we conclude that the HJ-1A/B multi-spectral satellite images is an ideal data source for high spatial and temporal resolution water bodies monitoring. And the integrated water body mapping method is suitable for the applications of HJ-1A/B multi-spectral satellite images in this field.

  11. Solitaire AB Stent-Assisted Coiling of Wide-Neck Micro Aneurysms

    PubMed Central

    Li, Xue-dong; Qin, Jun; Xiao, Zhen-yong; Feng, Yi

    2016-01-01

    Objective Solitaire AB stent-assisted coiling facilitates the endovascular treatment of wide-necked intracranial aneurysms. We present our experience of coiling the micro-aneurysms of wide-neck with Solitaire AB stent assisting in a single center. Methods Thirty-one Solitaire AB stents were used to treat via endovascular approach patients with 31 wide-neck micro aneurysms in a single center in China. Technical and clinical complications were recorded. Modified Rankin Scale was used to evaluate the patients' conditions via clinic and telephone follow-up. Results The mean width of aneurysm sac was 2.30±0.42 mm, and the mean diameter of aneurysm neck was 2.83±0.48 mm. Complete occlusion was achieved in 28 aneurysms (90.32%); neck remnant was seen in 3 aneurysms (9.68%). Technical and clinical complications related to the procedure were encountered in four patients (12.5%). Two patients died (6.25%). No patient had a permanent deficit. Conclusion Solitaire AB stent was a safe and efficiency tool in assisting coiling of micro aneurysms with wide neck, but may be not suitable for a blaster-like one. Mid- and long-term follow-up will be required to elucidate the impact of the Solitaire AB stent on recanalization rate. PMID:27446513

  12. Small-Angle Neutron Scattering study of the NIST mAb reference material

    NASA Astrophysics Data System (ADS)

    Castellanos, Maria Monica; Liu, Yun; Krueger, Susan; Curtis, Joseph

    Monoclonal antibodies (mAbs) are of great interest to the biopharmaceutical industry because they can be engineered to target specific antigens. Due to their importance, the biomanufacturing initiative at NIST is developing an IgG1 mAb reference material `NIST mAb', which can be used by industry, academia, and regulatory authorities. As part of this collaborative effort, we aim at characterizing the reference material using neutron scattering techniques. We have studied the small-angle scattering profile of the NIST mAb in a histidine buffer at 0 and 150 mM NaCl. Using Monte Carlo simulations, we generate an ensemble of structures and calculate their theoretical scattering profile, which can be directly compared with experimental data. Moreover, we analyze the structure factor to understand the effect of solution conditions on the protein-protein interactions. Finally, we have measured the solution scattering of the NIST mAb, while simultaneously performing freeze/thaw cycles, in order to investigate if the solution structure was affected upon freezing. The results from neutron scattering not only support the development of the reference material, but also provide insights on its stability and guide efforts for its development under different formulations.

  13. A binding site for Bacillus thuringiensis Cry1Ab toxin is lost during larval development in two forest pests.

    PubMed

    Rausell, C; Martínez-Ramírez, A C; García-Robles, I; Real, M D

    2000-04-01

    The insecticidal activity and receptor binding properties of Bacillus thuringiensis Cry1A toxins towards the forest pests Thaumetopoea pityocampa (processionary moth) and Lymantria monacha (nun moth) were investigated. Cry1Aa, Cry1Ab, and Cry1Ac were highly toxic (corresponding 50% lethal concentration values: 956, 895, and 379 pg/microl, respectively) to first-instar T. pityocampa larvae. During larval development, Cry1Ab and Cry1Ac toxicity decreased with increasing age, although the loss of activity was more pronounced for Cry1Ab. Binding assays with (125)I-labelled Cry1Ab and brush border membrane vesicles from T. pityocampa first- and last-instar larvae detected a remarkable decrease in the overall Cry1Ab binding affinity in last-instar larvae, although saturable Cry1Ab binding to both instars was observed. Homologous competition experiments demonstrated the loss of one of the two Cry1Ab high-affinity binding sites detected in first-instar larvae. Growth inhibition assays with sublethal doses of Cry1Aa, Cry1Ab, and Cry1Ac in L. monacha showed that all three toxins were able to delay molting from second instar to third instar. Specific saturable binding of Cry1Ab was detected only in first- and second-instar larvae. Cry1Ab binding was not detected in last-instar larvae, although specific binding of Cry1Aa and Cry1Ac was observed. These results demonstrate a loss of Cry1Ab binding sites during development on the midgut epithelium of T. pityocampa and L. monacha, correlating in T. pityocampa with a decrease in Cry1Ab toxicity with increasing age. PMID:10742241

  14. A Binding Site for Bacillus thuringiensis Cry1Ab Toxin Is Lost during Larval Development in Two Forest Pests

    PubMed Central

    Rausell, Carolina; Martínez-Ramírez, Amparo Consuelo; García-Robles, Inmaculada; Real, María Dolores

    2000-01-01

    The insecticidal activity and receptor binding properties of Bacillus thuringiensis Cry1A toxins towards the forest pests Thaumetopoea pityocampa (processionary moth) and Lymantria monacha (nun moth) were investigated. Cry1Aa, Cry1Ab, and Cry1Ac were highly toxic (corresponding 50% lethal concentration values: 956, 895, and 379 pg/μl, respectively) to first-instar T. pityocampa larvae. During larval development, Cry1Ab and Cry1Ac toxicity decreased with increasing age, although the loss of activity was more pronounced for Cry1Ab. Binding assays with 125I-labelled Cry1Ab and brush border membrane vesicles from T. pityocampa first- and last-instar larvae detected a remarkable decrease in the overall Cry1Ab binding affinity in last-instar larvae, although saturable Cry1Ab binding to both instars was observed. Homologous competition experiments demonstrated the loss of one of the two Cry1Ab high-affinity binding sites detected in first-instar larvae. Growth inhibition assays with sublethal doses of Cry1Aa, Cry1Ab, and Cry1Ac in L. monacha showed that all three toxins were able to delay molting from second instar to third instar. Specific saturable binding of Cry1Ab was detected only in first- and second-instar larvae. Cry1Ab binding was not detected in last-instar larvae, although specific binding of Cry1Aa and Cry1Ac was observed. These results demonstrate a loss of Cry1Ab binding sites during development on the midgut epithelium of T. pityocampa and L. monacha, correlating in T. pityocampa with a decrease in Cry1Ab toxicity with increasing age. PMID:10742241

  15. Plant-derived anti-Lewis Y mAb exhibits biological activities for efficient immunotherapy against human cancer cells

    PubMed Central

    Brodzik, Robert; Glogowska, Magdalena; Bandurska, Katarzyna; Okulicz, Monika; Deka, Deepali; Ko, Kisung; van der Linden, Joke; Leusen, Jeanette H. W.; Pogrebnyak, Natalia; Golovkin, Maxim; Steplewski, Zenon; Koprowski, Hilary

    2006-01-01

    Although current demands for therapeutic mAbs are growing quickly, production methods to date, including in vitro mammalian tissue culture and transgenic animals, provide only limited quantities at high cost. Several tumor-associated antigens in tumor cells have been identified as targets for therapeutic mAbs. Here we describe the production of mAb BR55-2 (IgG2a) in transgenic plants that recognizes the nonprotein tumor-associated antigen Lewis Y oligosaccharide overexpressed in human carcinomas, particularly breast and colorectal cancers. Heavy and light chains of mAb BR55-2 were expressed separately and assembled in plant cells of low-alkaloid tobacco transgenic plants (Nicotiana tabacum cv. LAMD609). Expression levels of plant-derived mAb (mAbP) were high (30 mg/kg of fresh leaves) in T1 generation plants. Like the mammalian-derived mAbM, the plant mAbP bound specifically to both SK-BR3 breast cancer cells and SW948 colorectal cancer cells. The Fc domain of both mAbP and mAbM showed the similar binding to FcγRI receptor (CD64). Comparable levels of cytotoxicity against SK-BR3 cells were also shown for both mAbs in antibody-dependent cell-mediated cytotoxicity assay. Furthermore, plant-derived BR55-2 efficiently inhibited SW948 tumor growth xenografted in nude mice. Altogether, these findings suggest that mAbP originating from low-alkaloid tobacco exhibit biological activities suitable for efficient immunotherapy. PMID:16720700

  16. Reassessment of the cancer mortality risk among Hiroshima atomic-bomb survivors using a new dosimetry system, ABS2000D, compared with ABS93D.

    PubMed

    Katayama, Hiroaki; Matsuura, Masaaki; Endo, Satoru; Hoshi, Masaharu; Ohtaki, Megu; Hayakawa, Norihiko

    2002-03-01

    The aim of the present study was to examine the excess relative risk for leukemia mortality and all cancers, except leukemia, among Hiroshima atomic-bomb survivors by applying ABS93D and ABS2000D. Particular attention was given to any difference in the neutron-dose estimates between the two dosimetry systems. The study subjects were 51,532 atomic-bomb survivors registered in a database of the Research Institute for Radiation Biology and Medicine of Hiroshima University (RIRBM). The results obtained by both dosimetry systems are similar: the excess relative risk per Sv for leukemia mortality and all cancers except leukemia is significantly higher compared to the control group. In addition, the difference in the excess relative risks between the two systems is not significant. Therefore, it is indicated that a modification of the neutron-dose estimates would not markedly change the conclusions about the cancer mortality risk. PMID:12056330

  17. Dynamics of A-B transition of the DNA double helices

    NASA Astrophysics Data System (ADS)

    Wang, Hao; Cheatham, Thomas; Gannett, Peter; Lewis, James

    2008-03-01

    The conformational transitions of DNA and the sensitivity of DNA structure to the surrounding environment are very relevant to its chemical and biological function and potential applications in nano-technology. Different conformations of DNA, even with the same sequence, exhibit different electronic structures, resulting in different conduction properties. We present theoretical work on the dynamical features of electronic states in the A-B transition of a model DNA duplex of d(CGCGCGCGCG)2 (10 base-pairs, 628 atoms) as the molecule undergoes conformational changes and thermal fluctuations at room temperature. We couple state-of-the art empirical force field molecular dynamics (MD) simulations with an ab-initio electronic structure method based on density-functional theory, called FIREBALL. For the A-B transition, we calculated the effects of conformational change on the electronic structure for each snapshot obtained from nanosecond MD simulations.

  18. Efficient ab initio free energy calculations by classically assisted trajectory sampling

    NASA Astrophysics Data System (ADS)

    Wilson, Hugh F.

    2015-12-01

    A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.

  19. Ab Initio and Phenomenological Modeling of the Phonon Spectrum of Superhard cp-BC2N

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Kopytov, A. V.; Pavlova, T. Yu.; Poplavnoi, A. S.

    2015-11-01

    The phonon spectrum of hypothetical superhard cp-BC2N is calculated based on ab initio method of density functional in the center of the Brillouin zone and interpolated over the entire Brillouin zone using the Keating phenomenological model. The interaction parameters are determined by optimization of the IR- and Ramanactive frequencies for a phenomenological model by their comparison with the results of ab initio calculations. Numerical values of short-range interaction constants and charges are in agreement with the characteristics of the chemical bond calculated ab initio. These parameters have transparent physical meaning and chemical nature and can further be used for both qualitative estimations of any physical and physico-chemical quantities and quantitative calculations of the phonon spectra of a number of isostructural compounds. The Keating phenomenological model is used to study the genesis of the phonon spectrum from the spectra of sublattices.

  20. Numerical Simulation of the Microtron Electron Beam Absorption by the Modified ABS-Plastic

    NASA Astrophysics Data System (ADS)

    Stuchebrov, S. G.; Miloichikova, I. A.; Melnikov, A. L.; Pereverzeva, M. A.

    2016-01-01

    Each specific task of the electron beam application imposes requirements for the beam profile and shape. One of the methods allows achieving high accuracy and low cost of the filters production is the 3D print method. The required properties of the electron beam interaction with the material can be achieved by using the modified plastic filaments. In this paper, the results of the model creation of the electron beams interaction with the ABS-plastic doped with different concentrations are presented. The depth dose distributions of the electron beam in the modified ABS-plastic are sown. The electron beam profiles and the electron beam distribution in the modified ABS-plastic are illustrated.

  1. Platelet-derived growth factor (PDGF)-AB-mediated phosphorylation of PDGF beta receptors.

    PubMed Central

    Coats, S R; Love, H D; Pledger, W J

    1994-01-01

    Platelet-derived growth factor (PDGF) stimulates the proliferation of Balb/c-3T3 fibroblasts through binding and subsequent activation of PDGF receptors. Activation of the PDGF receptors has been proposed to involve receptor dimerization. PDGF-AB has been shown to bind PDGF alpha and beta receptor subunits to form PDGF alpha beta and alpha alpha receptor dimers. In this paper we demonstrate that, following the down-regulation of PDGF alpha receptors, the binding of PDGF-AB to beta receptors occurred at 37 degrees C but not at 4 degrees C. PDGF-AB stimulated the phosphorylation of PDGF beta receptor monomers in cells depleted of PDGF alpha receptors by prior exposure to PDGF-AA. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8297345

  2. Periodic arrays of intercalated atoms in twisted bilayer graphene: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Miwa, R. H.; Venezuela, P.; Morell, Eric Suárez

    2015-09-01

    We have performed an ab initio investigation of transition metals (TMs =Mo ,Ru ,Co ,andPt ) embedded in twisted bilayer graphene (tBG) layers. Our total energy results reveal that, triggered by the misalignment between the graphene layers, Mo and Ru atoms may form a quasiperiodic (triangular) array of intercalated atoms. In contrast, the formation of those structures is not expected for the other TMs, the Co and Pt atoms. The net magnetic moment (m ) of Mo and Ru atoms may be quenched upon intercalation, depending on the stacking region (AA or AB). For instance, we find a magnetic moment of 0.3 μB(1.8 μB) for Ru atoms intercalated between the AA (AB) regions of the stacked twisted layers. Through simulated scanning tunneling microscopy (STM) images, we verify that the presence of intercalated TMs can be identified by the formation of bright (hexagonal) spots lying on the graphene surface.

  3. Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling

    PubMed Central

    Kenyon, Emma J.; Campos, Isabel; Bull, James C.; Williams, P. Huw; Stemple, Derek L.; Clark, Matthew D.

    2015-01-01

    The RAB5 gene family is the best characterised of all human RAB families and is essential for in vitro homotypic fusion of early endosomes. In recent years, the disruption or activation of Rab5 family proteins has been used as a tool to understand growth factor signal transduction in whole animal systems such as Drosophila melanogaster and zebrafish. In this study we have examined the functions for four rab5 genes in zebrafish. Disruption of rab5ab expression by antisense morpholino oligonucleotide (MO) knockdown abolishes nodal signalling in early zebrafish embryos, whereas overexpression of rab5ab mRNA leads to ectopic expression of markers that are normally downstream of nodal signalling. By contrast MO disruption of other zebrafish rab5 genes shows little or no effect on expression of markers of dorsal organiser development. We conclude that rab5ab is essential for nodal signalling and organizer specification in the developing zebrafish embryo. PMID:25478908

  4. Semirational solutions and baseband modulational instability of the AB system in fluid mechanics

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Wang, Zi-Zhe; Jiang, Dong-Yang; Qi, Feng-Hua; Guo, Rui

    2015-10-01

    Under investigation in this paper is the AB system describing marginally unstable baroclinic wave packets in geophysical fluids. By means of the n -fold modified Darboux transformation, the semirational solutions in terms of the determinants of the AB system are derived. These solutions, which are a combination of rational and exponential functions, can be used to model the nonlinear superposition of the Akhmediev breathers (or the Kuznetsov-Ma breathers) and the rogue waves. The k -order rogue wave of the AB system is produced by the interaction between the l-order rogue wave with 1/2(k-l)(k+l+1) neighboring elements in the (k-l)-order breathers (0

  5. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    NASA Astrophysics Data System (ADS)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  6. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

    SciTech Connect

    Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  7. Structural features of Chi recognition in AddAB with implications for RecBCD

    PubMed Central

    Wilkinson, Martin; Wigley, Dale B

    2014-01-01

    AddAB and RecBCD-type helicase-nuclease complexes control the first stage of bacterial homologous recombination (HR) – the resection of double strand DNA breaks. A switch in the activities of the complexes to initiate repair by HR is regulated by a short, species-specific DNA sequence known as a Crossover Hotspot Instigator (Chi) site. It has been shown that, upon encountering Chi, AddAB and RecBCD pause translocation before resuming at a reduced rate. Recently, the structure of B.subtilis AddAB in complex with its regulatory Chi sequence revealed the nature of Chi binding and the paused translocation state. Here the structural features associated with Chi binding are described in greater detail and discussed in relation to the related E.coli RecBCD system. PMID:25486468

  8. An ab initio-based Er–He interatomic potential in hcp Er

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2014-09-01

    We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.

  9. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  10. Evaluation of corn hybrids expressing Cry34Ab1/Cry35Ab1 and Cry3BbL against the western corn rootworm (Coleoptera: Chrysomelidae).

    PubMed

    Prasifka, P L; Rule, D M; Storer, N P; Nolting, S P; Hendrix, W H

    2013-04-01

    Studies were conducted across nine U.S. states, over 5 yr, to characterize the efficacy of transgenic corn (Zea mays L.) hybrids producing insecticidal proteins derived from Bacillus thuringiensis (Bt) for control of western corn rootworm, Diabrotica virgifera virgifera Le Conte. Hybrids tested had the same genetic background, contained one of two single events (DAS-59122-7 expressing Cry34Ab1/Cry35Ab1 or MON 88017 expressing Cry3Bb1) or a pyramid consisting of both rootworm-active events (SmartStax traits) and were compared with a non-Bt near isoline. Frequency analyses of root feeding data showed that hybrids containing both events sustained less root damage (0-3 node injury scale) than hybrids containing either event alone. The levels of root protection provided by MON 88017 and DAS-59122-7 were not different from each other. Efficacy was also evaluated based on consistency of protection, based on the proportion of plants with root ratings of either < or = 0.25 or < 1.00 on the node injury scale. The combination of two modes of action in SmartStax provided greater product consistency over a single mode of action at the 0.25 level and all hybrids producing Bt proteins provided equally high consistency at the 1.00 level. Overall these data show single and multiple mode of action hybrids provided high, consistent protection over the past 5 yr across the trial geography; however, pyramiding the rootworm Bt events provided greater and more consistent root protection. These findings also support that pyramided traits like SmartStax (Cry3Bb1 + Cry34Ab1/Cry35Ab1) remain a viable strategy for delaying resistance to either trait. PMID:23786070

  11. ORBITAL AND PHYSICAL PROPERTIES OF THE σ Ori Aa, Ab, B TRIPLE SYSTEM

    SciTech Connect

    Simón-Díaz, S.; Caballero, J. A.; Apellániz, J. Maíz; Lorenzo, J.; Negueruela, I.; Dorda, R.; Marco, A.; Schneider, F. R. N.; Barbá, R. H.; Montes, D.; Pellerin, A.; Sanchez-Bermudez, J.; Sota, A.

    2015-02-01

    We provide a complete characterization of the astrophysical properties of the σ Ori Aa, Ab, B hierarchical triple system and an improved set of orbital parameters for the highly eccentric σ Ori Aa, Ab spectroscopic binary. We compiled a spectroscopic data set comprising 90 high-resolution spectra covering a total time span of 1963 days. We applied the Lehman-Filhés method for a detailed orbital analysis of the radial velocity curves and performed a combined quantitative spectroscopic analysis of the σ Ori Aa, Ab, B system by means of the stellar atmosphere code FASTWIND. We used our own plus other available information on photometry and distance to the system for measuring the radii, luminosities, and spectroscopic masses of the three components. We also inferred evolutionary masses and stellar ages using the Bayesian code BONNSAI. The orbital analysis of the new radial velocity curves led to a very accurate orbital solution of the σ Ori Aa, Ab pair. We provided indirect arguments indicating that σ Ori B is a fast-rotating early B dwarf. The FASTWIND+BONNSAI analysis showed that the Aa, Ab pair contains the hottest and most massive components of the triple system while σ Ori B is a bit cooler and less massive. The derived stellar ages of the inner pair are intriguingly younger than the one widely accepted for the σ Orionis cluster, at 3 ± 1 Ma. The outcome of this study will be of key importance for a precise determination of the distance to the σ Orionis cluster, the interpretation of the strong X-ray emission detected for σ Ori Aa, Ab, B, and the investigation of the formation and evolution of multiple massive stellar systems and substellar objects.

  12. The mechanochemical cycle of mammalian kinesin-2 KIF3A/B under load

    PubMed Central

    Andreasson, Johan O.L.; Shastry, Shankar; Hancock, William O.; Block, Steven M.

    2015-01-01

    Summary The response of motor proteins to external loads underlies their ability to work in teams and determines the net speed and directionality of cargo transport. The mammalian kinesin-2, KIF3A/B, is a heterotrimeric motor involved in intraflagellar transport and vesicle motility in neurons. Bidirectional cargo transport is known to result from the opposing activities of KIF3A/B and dynein bound to the same cargo, but the load-dependent properties of kinesin-2 are poorly understood. We used a feedback-controlled optical trap to probe the velocity, run length and unbinding kinetics of mouse KIF3A/B under various loads and nucleotide conditions. The kinesin-2 motor velocity is less sensitive than kinesin-1 to external forces, but its processivity diminishes steeply with load, and the motor was observed occasionally to slip and reattach. Each motor domain was characterized by studying homodimeric constructs, and a global fit to the data resulted in a comprehensive pathway that quantifies the principal force-dependent kinetic transitions. The properties of the KIF3A/B heterodimer are intermediate between the two homodimers, and the distinct load-dependent behavior is attributable to the properties of the motor domains, and not to the neck-linkers or the coiled-coil stalk. We conclude that the force-dependent movement of KIF3A/B differs significantly from conventional kinesin-1. Against opposing dynein forces, KIF3A/B motors are predicted to rapidly unbind and rebind, resulting in qualitatively different transport behavior from kinesin-1. PMID:25866395

  13. Successful radioimmunotherapy of established syngeneic rat colon carcinoma with 211At-mAb

    PubMed Central

    2013-01-01

    Background Most carcinomas are prone to metastasize despite successful treatment of the primary tumor. One way to address this clinical challenge may be targeted therapy with α-emitting radionuclides such as astatine-211 (211At). Radioimmunotherapy utilizing α-particle emitting radionuclides is considered especially suitable for the treatment of small cell clusters and single cells, although lesions of different sizes may also be present in the patient. The aim of this study was primarily to evaluate the toxicity and secondarily in vivo efficacy of a 211At-labeled monoclonal antibody (mAb) directed against colon carcinoma with tumor diameters of approximately 10 mm. Methods Eighteen rats with subperitoneal syngeneic colon carcinoma were allocated to three groups of six animals together with three healthy rats in each group. The groups were injected intravenously with either 150 μg of unlabeled mAbs (controls) or 2.5 or 5 MBq 211At-mAbs directed towards the Lewis Y antigen expressed on the cell membrane of several carcinomas. Tumor volume, body weight, and blood cell counts were monitored for 100 days after treatment. Results Local tumors were non-palpable in five out of six rats after treatment with both activities of 211At-mAbs, compared to one out of six in the control group. At the study end, half of the animals in each group given 211At-BR96 and one animal in the control group were free from disease. Radioimmunotherapy resulted in dose-dependent, transient weight loss and myelotoxicity. Survival was significantly better in the groups receiving targeted alpha therapy than in those receiving unlabeled mAbs. Conclusions This study demonstrates the possibility of treating small, solid colon carcinoma tumors with α-emitting radionuclides such as 211At bound to mAbs, with tolerable toxicity. PMID:23557183

  14. Biodistribution of charged F(ab')2 photoimmunoconjugates in a xenograft model of ovarian cancer.

    PubMed

    Duska, L R; Hamblin, M R; Bamberg, M P; Hasan, T

    1997-01-01

    The effect of charge modification of photoimmunoconjugates (PICs) on their biodistribution in a xenograft model of ovarian cancer was investigated. Chlorin(e6)c(e6) was attached site specifically to the F(ab')2 fragment of the murine monoclonal antibody OC125, directed against human ovarian cancer cells, via poly-1-lysine linkers carrying cationic or anionic charges. Preservation of immunoreactivity was checked by enzyme-linked immunosorbent assay (ELISA). PICs were radiolabelled with 125I and compared with non-specific rabbit IgG PICs after intraperitoneal (i.p.) injection into nude mice. Samples were taken from normal organs and tumour at 3 h and 24 h. Tumour to normal 125I ratios showed that the cationic OC125F(ab')2 PIC had the highest tumour selectivity. Ratios for c(e6) were uniformly higher than for 125I, indicating that c(e6) became separated from 125I. OC125F(ab')2 gave highest tissue values of 125I, followed by cationic OC125F(ab')2 PIC; other species were much lower. The amounts of c(e6) delivered per gram of tumour were much higher for cationic OC125F(ab')2 PIC than for other species. The results indicate that cationic charge stimulates the endocytosis and lysosomal degradation of the OC125F(ab')2-pl-c(e6) that has bound to the i.p. tumour. Positively charged PICs may have applications in the i.p. photoimmunotherapy of minimal residual ovarian cancer. PMID:9062404

  15. Circulating microRNA-196a/b are novel biomarkers associated with metastatic gastric cancer.

    PubMed

    Tsai, Ming-Ming; Wang, Chia-Siu; Tsai, Chung-Ying; Huang, Chung-Guei; Lee, Kam-Fai; Huang, Hsiang-Wei; Lin, Yang-Hsiang; Chi, Hsiang-Cheng; Kuo, Liang-Mou; Lu, Pei-Hsuan; Lin, Kwang-Huei

    2016-09-01

    miR-196a and/or miR-196b, involved in cancer initiation and progression, are frequently upregulated in tumour tissues. However, the clinical significance of these microRNAs in gastric cancer (GC) remains to be clarified. In the current study, we investigated the potential utility of circulating miR-196a/b as novel biomarkers for early detection and/or metastatic prognosis of GC. The quantitative real time-polymerase chain reaction data revealed markedly higher pre-operative circulating miR-196a and miR-196b levels in GC patients than healthy controls. Receiver-operating characteristics curve analysis showed that circulating miR-196a, miR-196b and combined miR-196a and miR-196b (miR-196a/b) are more effective than carcinoembryonic antigen or carbohydrate antigen 19-9 alone in distinguishing GC patients from healthy controls, with higher sensitivity and specificity. Circulating miR-196a exhibited higher diagnostic capacity than combined miR-196a/b or miR-196b alone, highlighting its potential as an effective plasma biomarker for GC. In clinicopathological analysis, elevated circulating miR-196a/b levels were highly correlated with metastatic potential or more advanced stages of disease and poorer survival. In addition, the expression levels of circulating miR-196a/b were reduced after surgical resection in GC patients. Taken together, we propose that circulating miR-196a/b serve as a more sensitive and specific novel biomarker than carbohydrate antigen 19-9 for GC monitor, diagnosis and prognosis. PMID:27420607

  16. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dixit, Mudit; Major, Dan Thomas; Pal, Sourav

    2016-05-01

    Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.

  17. Abū’l Faẓl, independent discoverer of the Great Comet of 1577

    NASA Astrophysics Data System (ADS)

    Kapoor, R. C.

    2015-11-01

    Abū’l Faẓl, the celebrated Prime Minister of the Mughal Emperor Akbar, has recorded in the Akbarnāmā (a highly-acclaimed biographical account of the Emperor) the appearance of a comet during the 22nd year of Akhar's reign, in 985 A.H. From the recorded date, it turns out that Abū’l Faẓl was an independent discoverer of one of the most famous comets in history—the Great Comet of 1577 (C/1577 V1).

  18. Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  19. Spectroscopic signatures of AA' and AB stacking of chemical vapor deposited bilayer MoS2

    DOE PAGESBeta

    Xia, Ming; Li, Bo; Yin, Kuibo; Capellini, Giovanni; Niu, Gang; Gong, Yongji; Zhou, Wu; Ajayan, Pulickel M.; Xie, Ya -Hong

    2015-11-04

    We discuss prominent resonance Raman and photoluminescence spectroscopic differences between AA'and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Also, resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom.

  20. Attenuation coefficient determination of printed ABS and PLA samples in diagnostic radiology standard beams

    NASA Astrophysics Data System (ADS)

    Veneziani, G. R.; Corrêa, E. L.; Potiens, M. P. A.; Campos, L. L.

    2016-07-01

    IAEA code of practice TRS-457 states that standard phantoms should offer the same primary attenuation and scatter production as relevant body section of a representative patient. Material cost, availability and dimensional stability must also be considered. The goal of this study is to determine the attenuation coefficient of printed ABS and PLA samples in standard X-ray beams, verifying if phantoms printed with these materials could be an easier-handle substitute for PMMA, enabling the creation of different designs in an easier and cheaper way. Results show that PMMA presents higher attenuation coefficient, followed by PLA and ABS, which means that thinner PMMA layer creates higher radiation attenuation.

  1. Research and development of therapeutic mAbs: An analysis based on pipeline projects.

    PubMed

    Geng, Xiaomei; Kong, Xiangjun; Hu, Hao; Chen, Jiayu; Yang, Fengqing; Liang, Hongyu; Chen, Xin; Hu, Yuanjia

    2015-01-01

    As the subject of active research and development (R&D) in recent decades, monoclonal antibodies have emerged among the major classes of therapeutic agents for treatment of many human diseases, especially cancers, infections, and immunological disorders. This article surveys the landscape of R&D projects of therapeutic monoclonal antibodies (mAbs), which are mostly used for disease immunotherapy, from a number of perspectives, including therapeutic indications, development phases, participants, and citation of related patents. The results of this research can be used as a reference resource for pharmaceutical researchers, investors, and policymakers in the field of therapeutic mAbs. PMID:26211701

  2. AB 327 A Look At Renewable Energy in Los Angeles County, California

    NASA Astrophysics Data System (ADS)

    Schevker, Marla

    AB 327 was passed in the California State Assembly in October of 2013. This affected not only the way that investor-owned utility companies but also consumers who are interested in or have already invested in solar or other electricity efficiency efforts. This project looks at the way that AB 327 affects consumers and power companies, who supported it and who is against it and what consumers are doing to make their homes more environmentally friendly. Please note this project is intended to be viewed on the web and can be seen at: http://marla.schevker.com/marla/USC_Thesis/index.html.

  3. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

    NASA Astrophysics Data System (ADS)

    Lawan, Narin; Ranaghan, Kara E.; Manby, Frederick R.; Mulholland, Adrian J.

    2014-07-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme.

  4. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    SciTech Connect

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-08-15

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  5. Spectroscopic Signatures of AA' and AB Stacking of Chemical Vapor Deposited Bilayer MoS2.

    PubMed

    Xia, Ming; Li, Bo; Yin, Kuibo; Capellini, Giovanni; Niu, Gang; Gong, Yongji; Zhou, Wu; Ajayan, Pulickel M; Xie, Ya-Hong

    2015-12-22

    Prominent resonance Raman and photoluminescence spectroscopic differences between AA' and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom will be discussed. PMID:26536495

  6. Resistance to Bacillus thuringiensis Toxin Cry2Ab in Trichoplusia ni Is Conferred by a Novel Genetic Mechanism.

    PubMed

    Song, Xiaozhao; Kain, Wendy; Cassidy, Douglas; Wang, Ping

    2015-08-01

    The resistance to the Bacillus thuringiensis (Bt) toxin Cry2Ab in a greenhouse-originated Trichoplusia ni strain resistant to both Bt toxins Cry1Ac and Cry2Ab was characterized. Biological assays determined that the Cry2Ab resistance in the T. ni strain was a monogenic recessive trait independent of Cry1Ac resistance, and there existed no significant cross-resistance between Cry1Ac and Cry2Ab in T. ni. From the dual-toxin-resistant T. ni strain, a strain resistant to Cry2Ab only was isolated, and the Cry2Ab resistance trait was introgressed into a susceptible laboratory strain to facilitate comparative analysis of the Cry2Ab resistance with the susceptible T. ni strain. Results from biochemical analysis showed no significant difference between the Cry2Ab-resistant and -susceptible T. ni larvae in midgut proteases, including caseinolytic proteolytic activity and zymogram profile and serine protease activities, in midgut aminopeptidase and alkaline phosphatase activity, and in midgut esterases and hemolymph plasma melanization activity. For analysis of genetic linkage of Cry2Ab resistance with potential Cry toxin receptor genes, molecular markers for the midgut cadherin, alkaline phosphatase (ALP), and aminopeptidase N (APN) genes were identified between the original greenhouse-derived dual-toxin-resistant and the susceptible laboratory T. ni strains. Genetic linkage analysis showed that the Cry2Ab resistance in T. ni was not genetically associated with the midgut genes coding for the cadherin, ALP, and 6 APNs (APN1 to APN6) nor associated with the ABC transporter gene ABCC2. Therefore, the Cry2Ab resistance in T. ni is conferred by a novel but unknown genetic mechanism. PMID:26025894

  7. Adsorption of transgenic insecticidal Cry1Ab protein to SiO2. 2. Patch-controlled electrostatic attraction.

    PubMed

    Madliger, Michael; Sander, Michael; Schwarzenbach, René P

    2010-12-01

    Adsorption governs the fate of Cry proteins from genetically modified Bt crops in soils. The effect of ionic strength (I) on the adsorption of Cry1Ab (isoelectric point IEP(Cry1Ab) ≈ 6) to negatively charged quartz (SiO(2)) and positively charged poly-L-lysine (PLL) was investigated at pH 5 to 8, using quartz crystal microbalance with dissipation monitoring and optical waveguide lightmode spectroscopy. Cry1Ab adsorbed via positively and negatively charged surface patches to SiO(2) and PLL, respectively. This patch controlled electrostatic attraction (PCEA) explains the observed increase in Cry1Ab adsorption to sorbents that carried the same net charge as the protein (SiO(2) at pH > IEP(Cry1Ab) and PLL at pH < IEP(Cry1Ab)) with decreasing I. In contrast, the adsorption of two reference proteins, BSA and HEWL, with different adsorption mechanism, were little affected by similar changes of I. Consistent with PCEA, Cry1Ab desorption from SiO(2) at pH > IEP(Cry1Ab) increased with increasing I and pH. Weak Cry1Ab-SiO(2) PCEA above pH 7 resulted in reversible, concentration dependent adsorption. Solution depletion experiments showed that PCEA also governed Cry1Ab adsorption to SiO(2) particles at environmentally relevant concentrations (a few ng mL(-1)). These results imply that models describing Cry1Ab adsorption to charged surfaces in soils need to account for the nonuniform surface charge distribution of the protein. PMID:21033744

  8. Resistance to Bacillus thuringiensis Toxin Cry2Ab in Trichoplusia ni Is Conferred by a Novel Genetic Mechanism

    PubMed Central

    Song, Xiaozhao; Kain, Wendy; Cassidy, Douglas

    2015-01-01

    The resistance to the Bacillus thuringiensis (Bt) toxin Cry2Ab in a greenhouse-originated Trichoplusia ni strain resistant to both Bt toxins Cry1Ac and Cry2Ab was characterized. Biological assays determined that the Cry2Ab resistance in the T. ni strain was a monogenic recessive trait independent of Cry1Ac resistance, and there existed no significant cross-resistance between Cry1Ac and Cry2Ab in T. ni. From the dual-toxin-resistant T. ni strain, a strain resistant to Cry2Ab only was isolated, and the Cry2Ab resistance trait was introgressed into a susceptible laboratory strain to facilitate comparative analysis of the Cry2Ab resistance with the susceptible T. ni strain. Results from biochemical analysis showed no significant difference between the Cry2Ab-resistant and -susceptible T. ni larvae in midgut proteases, including caseinolytic proteolytic activity and zymogram profile and serine protease activities, in midgut aminopeptidase and alkaline phosphatase activity, and in midgut esterases and hemolymph plasma melanization activity. For analysis of genetic linkage of Cry2Ab resistance with potential Cry toxin receptor genes, molecular markers for the midgut cadherin, alkaline phosphatase (ALP), and aminopeptidase N (APN) genes were identified between the original greenhouse-derived dual-toxin-resistant and the susceptible laboratory T. ni strains. Genetic linkage analysis showed that the Cry2Ab resistance in T. ni was not genetically associated with the midgut genes coding for the cadherin, ALP, and 6 APNs (APN1 to APN6) nor associated with the ABC transporter gene ABCC2. Therefore, the Cry2Ab resistance in T. ni is conferred by a novel but unknown genetic mechanism. PMID:26025894

  9. Evolution and dissemination of OqxAB-like efflux pumps, an emerging quinolone resistance determinant among members of Enterobacteriaceae.

    PubMed

    Wong, Marcus Ho Yin; Chan, Edward Wai Chi; Chen, Sheng

    2015-01-01

    The OqxAB efflux pump, a plasmid-mediated quinolone resistance (PMQR) determinant, has become increasingly prevalent among members of Enterobacteriaceae over the past decade. To investigate the evolution and dissemination routes of the oqxAB operon, we assessed the prevalence of oqxAB-like elements among various Gram-negative bacterial species and analyzed the genotypic and phenotypic characteristics of organisms harboring such elements. With a comprehensive genotyping approach, a chromosome-based oqxAB operon was detectable in all Klebsiella pneumoniae strains tested, including organisms isolated before the year 1984. Sequence and phylogenetic analyses confirmed that the oqxAB operon in K. pneumoniae isolates was genetically closest to their plasmid-borne counterparts recoverable only from Escherichia coli and Salmonella isolates collected from the year 2003 onward. Chromosomal elements with much lower sequence homology were also found among the Enterobacter spp. but not other Gram-negative species. Contrary to the quinolone resistance phenotypes which were consistently observable among organisms with oqxAB-harboring plasmids, chromosomal oqxAB elements generally did not confer quinolone resistance, except for K. pneumoniae strains, which exhibited a typical oqxAB-mediated phenotype characterized by cross-resistance to olaquindox, chloramphenicol, and the quinolones. Gene expression analysis illustrated that such phenotypes were due to elevated expression of the chromosomal oqxAB operon. Furthermore, transposition of the oqxAB operon from the bacterial chromosome to plasmids was found to result in a >80-fold increase in the level of expression of the OqxAB pump, confirming its status as the first constitutively expressed efflux system located in bacterial mobile elements. PMID:25801572

  10. Subtilase cytotoxin-encoding subAB2 variants in verotoxin-producing Escherichia coli strains isolated from goats and sheep.

    PubMed

    Orden, José A; Domínguez-Bernal, Gustavo; de la Fuente, Ricardo; Carrión, Javier

    2016-04-01

    Subtilase cytotoxin (SubAB) is a cytotoxin which might contribute to the virulence of verotoxin-producing Escherichia coli (VTEC) strains in humans. Three variants of SubAB encoding genes have been described (subAB1, subAB2-1, and subAB2-2) and it has been suggested that the strains positive for two variants of subAB may be more pathogenic for humans. In this study, 188 subAB2-positive VTEC strains isolated from goats and sheep were investigated for the presence of the subAB2-1 and subAB2-2 variants by PCR. Eighty-one of the 132 (61.4%) caprine strains and 36 of the 56 (64.3%) ovine strains possessed the subAB2-1 variant and all ovine and caprine strains, except one, were positive for the subAB2-2 variant. The results of this study show for first time that the subAB2-1 and subAB2-2 variants are found in caprine subAB2-positive VTEC strains and confirm that both subAB2 variants are detected in ovine subAB2-positive VTEC strains. Since no significant difference in the presence of both subAB2 variants was found among strains belonging to serotypes associated with severe illness in humans and strains not belonging to these serotypes, the occurrence of two subAB2 variants seems not to be associated with a higher risk of severe disease in humans. PMID:27033912

  11. 76 FR 53301 - Airworthiness Directives; Saab AB, Saab Aerosystems Model SAAB 2000 Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-26

    ...-16787; AD 2011-18-05] RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab Aerosystems Model SAAB 2000... specified products. That NPRM was published in the Federal Register on June 1, 2011 (76 FR 31508). That NPRM... air commerce by prescribing regulations for practices, methods, and procedures the Administrator...

  12. Method for the separation of high impact polystyrene (HIPS) and acrylonitrile butadiene styrene (ABS) plastics

    DOEpatents

    Jody, Bassam J.; Arman, Bayram; Karvelas, Dimitrios E.; Pomykala, Jr., Joseph A.; Daniels, Edward J.

    1997-01-01

    An improved method is provided for separating acrylonitrile butadiene styrene (ABS) and high impact polystyrene (HIPS) plastics from each other. The ABS and HIPS plastics are shredded to provide a selected particle size. The shredded particles of the ABS and HIPS plastics are applied to a solution having a solution density in a predefined range between 1.055 gm/cm.sup.3 and 1.07 gm/cm.sup.3, a predefined surface tension in a range between 22 dynes/cm to 40 dynes/cm and a pH in the range of 1.77 and 2.05. In accordance with a feature of the invention, the novel method is provided for separating ABS and HIPS, two solid thermoplastics which have similar densities by selectively modifying the effective density of the HIPS using a binary solution with the appropriate properties, such as pH, density and surface tension, such as a solution of acetic acid and water or a quaternary solution having the appropriate density, surface tension, and pH.

  13. The 1-AB block fields-a giant oil accumulation in Eastern Peru

    SciTech Connect

    Jarvis, H.A.; Lay, V. ); Orosco, C. )

    1993-02-01

    The 1-Ab block fields are located in the northeastern part of Peru. Geologically, the area is the sub-Andean Maranon Basin, a continuation of the Napo Basin from eastern Ecuador. During the 20 years that Occidental has operated Block 1-AB, approximately 11,500 km of seismic data has been recorded and 34 exploratory wells have been drilled, resulting in the discovery of 18 fields, or 53% exploration success. The 1-AB oil accumulation discovered in 1972 is a group of medium to small asymmetric anticlines distributed along six northwest-southeast trending structural alignments: North Capahuari-South Capahuari-Tambo, Carmen-North San Jaacinto and Bartra. This concentration of productive structures in a relative small area is unique within the Maranon basin. The controlling factors include exceptional pre-Cretaceous uplifting and the presence of very good to excellent Cretaceous sandstones reservoirs. The two major Cretaceous producing zones, the Chonta and Vivian sandstones, have been defined within the Coniacian and Campanian ages respectively. The Chonta sands are related to shelfal deposition across Block 1-AB, represented by strand plain and barrier island sediments. The Vivian formation is a massive fluvial sandstone covering all of the Maranon basin and ranging in thickness between 40 and 200 feet. After oil was accumulated, fresh water influxes into the reservoirs of the northern and eastern fields caused oil biodegradation and salinity variation of the reservoir waters, depending upon the intensity of biodegradation. Oil remigration also has been documented for the South Huayari field.

  14. Possible Future Monoclonal Antibody (mAb)-Based Therapy against Arbovirus Infections

    PubMed Central

    Mancini, Nicasio; Gorini, Giacomo; Clementi, Massimo; Burioni, Roberto

    2013-01-01

    More than 150 arboviruses belonging to different families are known to infect humans, causing endemic infections as well as epidemic outbreaks. Effective vaccines to limit the occurrence of some of these infections have been licensed, while for the others several new immunogens are under development mostly for their improvements concerning safety and effectiveness profiles. On the other hand, specific and effective antiviral drugs are not yet available, posing an urgent medical need in particular for emergency cases. Neutralizing monoclonal antibodies (mAbs) have been demonstrated to be effective in the treatment of several infectious diseases as well as in preliminary in vitro and in vivo models of arbovirus-related infections. Given their specific antiviral activity as well-tolerated molecules with limited side effects, mAbs could represent a new therapeutic approach for the development of an effective treatment, as well as useful tools in the study of the host-virus interplay and in the development of more effective immunogens. However, before their use as candidate therapeutics, possible hurdles (e.g., Ab-dependent enhancement of infection, occurrence of viral escape variants) must be carefully evaluated. In this review are described the main arboviruses infecting humans and candidate mAbs to be possibly used in a future passive immunotherapy. PMID:24058915

  15. 45 CFR 233.21 - Budgeting methods for OAA, AB, APTD, and AABD.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 2 2011-10-01 2011-10-01 false Budgeting methods for OAA, AB, APTD, and AABD. 233... COVERAGE AND CONDITIONS OF ELIGIBILITY IN FINANCIAL ASSISTANCE PROGRAMS § 233.21 Budgeting methods for OAA... specify if assistance payments shall be computed using a prospective budgeting system or a...

  16. 45 CFR 233.21 - Budgeting methods for OAA, AB, APTD, and AABD.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Budgeting methods for OAA, AB, APTD, and AABD. 233... COVERAGE AND CONDITIONS OF ELIGIBILITY IN FINANCIAL ASSISTANCE PROGRAMS § 233.21 Budgeting methods for OAA... specify if assistance payments shall be computed using a prospective budgeting system or a...

  17. Adaptation of the ABS-S:2 for Use in Spain with Children with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Garcia Alonso, Isabel; De La Fuente Anuncibay, Raquel; Fernandez Hawrylak, Maria

    2010-01-01

    As there is a dearth of Spanish-language standardized scales that assess adaptive behavior in children and adolescents with intellectual disabilities (ID), the authors adapted one of the most widely used and studied scales of adaptive behavior in the U.S., the ABS-S:2 (Adaptive Behavior Scale-School, 2nd Edition), and validated it for use in…

  18. Detection and analysis of tupaia hepatocytes via mAbs against tupaia serum albumin

    PubMed Central

    Liu, Xuan; Yuan, Lunzhi; Yuan, Quan; Zhang, Yali; Wu, Kun; Zhang, Tianying; Wu, Yong; Hou, Wangheng; Wang, Tengyun; Liu, Pingguo; Shih, James Wai Kuo; Cheng, Tong; Xia, Ningshao

    2015-01-01

    On the basis of its close phylogenetic relationship with primates, the development of Tupaia belangeri as an infection animal model and drug metabolism model could provide a new option for preclinical studies, especially in hepatitis virus research. As a replacement for primary human hepatocytes (PHHs), primary tupaia hepatocytes (PTHs) have been widely used. Similar to human serum albumin, tupaia serum albumin (TSA) is the most common liver synthesis protein and is an important biomarker for PTHs and liver function. However, no detection or quantitative method for TSA has been reported. In this study, mouse monoclonal antibodies (mAbs) 4G5 and 9H3 against TSA were developed to recognize PTHs, and they did not show cross-reactivity with serum albumin from common experimental animals, such as the mouse, rat, cow, rabbit, goat, monkey, and chicken. The two mAbs also exhibited good performance in fluorescence activated cell sorting (FACS) analysis and immunofluorescence (IF) detection of PTHs. A chemiluminescent enzyme immune assay method using the two mAbs, with a linear range from 96.89 pg/ml to 49,609.38 pg/ml, was developed for the quantitative detection of TSA. The mAbs and the CLEIA method provide useful tools for research on TSA and PTHs. PMID:26597317

  19. Detection and analysis of tupaia hepatocytes via mAbs against tupaia serum albumin.

    PubMed

    Liu, Xuan; Yuan, Lunzhi; Yuan, Quan; Zhang, Yali; Wu, Kun; Zhang, Tianying; Wu, Yong; Hou, Wangheng; Wang, Tengyun; Liu, Pingguo; Shih, James Wai Kuo; Cheng, Tong; Xia, Ningshao

    2016-05-20

    On the basis of its close phylogenetic relationship with primates, the development of Tupaia belangeri as an infection animal model and drug metabolism model could provide a new option for preclinical studies, especially in hepatitis virus research. As a replacement for primary human hepatocytes (PHHs), primary tupaia hepatocytes (PTHs) have been widely used. Similar to human serum albumin, tupaia serum albumin (TSA) is the most common liver synthesis protein and is an important biomarker for PTHs and liver function. However, no detection or quantitative method for TSA has been reported. In this study, mouse monoclonal antibodies (mAbs) 4G5 and 9H3 against TSA were developed to recognize PTHs, and they did not show cross-reactivity with serum albumin from common experimental animals, such as the mouse, rat, cow, rabbit, goat, monkey, and chicken. The two mAbs also exhibited good performance in fluorescence activated cell sorting (FACS) analysis and immunofluorescence (IF) detection of PTHs. A chemiluminescent enzyme immune assay method using the two mAbs, with a linear range from 96.89 pg/ml to 49,609.38 pg/ml, was developed for the quantitative detection of TSA. The mAbs and the CLEIA method provide useful tools for research on TSA and PTHs. PMID:26597317

  20. 76 FR 28169 - Airworthiness Directives; Agusta S.p.A. Model AB412 Helicopters

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-16

    ... Procedures (44 FR 11034, February 26, 1979); and 3. Will not have a significant economic impact, positive or...-27-AD; Amendment 39-16692; AD 2011-10-11] RIN 2120-AA64 Airworthiness Directives; Agusta S.p.A. Model... Agusta S.p.A. (Agusta) Model AB412 helicopters. This AD results from mandatory continuing...

  1. Variability in the cadherin gene in an Ostrinia nubilalis strain selected for Cry1Ab resistance.

    PubMed

    Bel, Yolanda; Siqueira, Herbert A A; Siegfried, Blair D; Ferré, Juan; Escriche, Baltasar

    2009-03-01

    Transgenic corn expressing Cry1Ab (a Bacillus thuringiensis toxin) is highly effective in the control of Ostrinia nubilalis. For its toxic action, Cry1Ab has to bind to specific insect midgut proteins. To date, in three Lepidoptera species resistance to a Cry1A toxin has been conferred by mutations in cadherin, a protein of the Lepidoptera midgut membrane. The implication of cadherin in the resistance of an Ostrinia nubilalis colony (Europe-R) selected with Bacillus thuringiensis Cry1Ab protoxin was investigated. Several major mutations in the cadherin (cdh) gene were found, which introduced premature termination codons and/or large deletions (ranging from 1383 to 1701bp). The contribution of these major mutations to the resistance was analyzed in resistant individuals that survived exposure to a high concentration of Cry1Ab protoxin. The results indicated that the presence of major mutations was drastically reduced in individuals that survived exposure. Previous inheritance experiments with the Europe-R strain indicated the involvement of more than one genetic locus and reduced amounts of the cadherin receptor. The results of the present work support a polygenic inheritance of resistance in the Europe-R strain, in which mutations in the cdh gene would contribute to resistance by means of an additive effect. PMID:19114103

  2. Ab initio electronic structure study for TTF-TCNQ under uniaxial compression

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Hashimoto, Tamotsu; Kohyama, Masanori; Terakura, Kiyoyuki

    2004-04-01

    We have investigated the electronic structure of TTF-TCNQ under uniaxial compression with ab initio plane-wave pseudopotential calculations within the local-density approximation and generalized gradient approximation. Depending on the compression direction, the constituent molecules are deformed in different ways. Along with these structural deformations, quasi-one-dimensional Fermi surfaces show dramatic changes in their shapes and sizes.

  3. Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2011-01-01

    A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

  4. Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

  5. Isotopic composition of trace elements in presolar silicon carbide A+B grains

    NASA Astrophysics Data System (ADS)

    Savina, M.; Tripa, C.; Pellin, M.; Davis, A.; Clayton, R.; Lewis, R.; Amari, S.

    2003-04-01

    Presolar SiC are classified into several types based on C, N, and Si isotopic compositions. Most are mainstream, which are generally believed to derive from low-mass asymptotic giant branch (AGB) stars. Among the less common grains, A+B grains, which comprise ˜3-4% of presolar SiC, are perhaps the least well understood. Recent measurements of trace element concentration patterns in individual grains suggest that A+B grains can be divided into at least 4 groups, and thus have multiple astrophysical sites of origin^1. We report here our Resonant Ionization Mass Spectrometry (RIMS) measurements of Zr, Mo, Ba, and Fe isotopic compositions in individual mainstream and type A+B presolar SiC. While the mainstream grains show isotopic compositions compatible with condensation around low-mass AGB stars, most A+B grains have near-solar isotopic compositions, though some show Zr, Mo, and Fe isotope patterns that have not been observed in other types of presolar SiC grains. We discuss these results in terms of possible astrophysical sites for the production of these unusual grains. This work was supported in part by the Department of Energy, BES-Materials Sciences through Contract No. W-31-109-ENG-38. ^1 Amari S., Nittler L. R., Zinner E., Lodders K., and Lewis R. S. (2001) Astrophys. J. 559, 463-483.

  6. Accurate radio and optical positions for the radio star HD 36705 (AB Doradus)

    NASA Technical Reports Server (NTRS)

    White, Graeme L.; Jauncey, David L.; Batty, Michael J.; Peters, W. L.; Gulkis, S.

    1988-01-01

    Arc-second position measurements of the active star HD 36705 (AB Dor) and of the variable radio source found nearby are presented. These measurements show that the radio source is clearly identified with HD 36705 and not with the nearby red-dwarf star Rst 137B.

  7. Instructional Leaders' Perceptions of the Impact of AB 1725 on Faculty Hiring in California Community Colleges

    ERIC Educational Resources Information Center

    Hebert-Swartzer, Cathleen

    2009-01-01

    The purpose of this study was to analyze how administrators and faculty leaders perceive the impact of AB 1725 on faculty hiring in California community colleges. Employing a qualitative case study approach, this research presented the findings from interviews and document analysis for the cases included in this effort. Four California community…

  8. The College & Financial Aid Guide for: AB540 Undocumented Immigrant Students

    ERIC Educational Resources Information Center

    Oliverez, Paz M., Ed.; Chavez, Maria Lucia, Ed.; Soriano, Mayra, Ed.; Tierney, William G., Ed.

    2006-01-01

    Since the passage of California Assembly Bill 540 in 2001, authored by the late Assemblyman, Marco Antonio Firebaugh, more than 5,000 undocumented students in California have had improved financial access to higher education. AB 540 has become a pinnacle in the lives of students, who because of their immigration status, have historically been…

  9. Improvements to a five-phase ABS algorithm for experimental validation

    NASA Astrophysics Data System (ADS)

    Gerard, Mathieu; Pasillas-Lépine, William; de Vries, Edwin; Verhaegen, Michel

    2012-10-01

    The anti-lock braking system (ABS) is the most important active safety system for passenger cars. Unfortunately, the literature is not really precise about its description, stability and performance. This research improves a five-phase hybrid ABS control algorithm based on wheel deceleration [W. Pasillas-Lépine, Hybrid modeling and limit cycle analysis for a class of five-phase anti-lock brake algorithms, Veh. Syst. Dyn. 44 (2006), pp. 173-188] and validates it on a tyre-in-the-loop laboratory facility. Five relevant effects are modelled so that the simulation matches the reality: oscillations in measurements, wheel acceleration reconstruction, brake pressure dynamics, brake efficiency changes and tyre relaxation. The time delays in measurement and actuation have been identified as the main difficulty for the initial algorithm to work in practice. Three methods are proposed in order to deal with these delays. It is verified that the ABS limit cycles encircle the optimal braking point, without assuming any tyre parameter being a priori known. The ABS algorithm is compared with the commercial algorithm developed by Bosch.

  10. Using the TxtAB Operon to Quantify Pathogenic Streptomyces in Potato Tubers and Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phytotoxin thaxtomin, produced by plant pathogenic Streptomyces species, is a pathogenicity determinant for common scab. In this study a SYBR Green quantitative real-time PCR assay using primers targeted on the txtAB operon of Streptomyces was developed to quantify pathogenic bacterial populati...

  11. A Comparison of Two Approaches to Training Visual Analysis of AB Graphs

    ERIC Educational Resources Information Center

    Wolfe, Katie; Slocum, Timothy A.

    2015-01-01

    Visual analysis is the primary method of evaluating data in single-subject research. Few studies have evaluated interventions to teach visual analysis skills. The purpose of this study was to evaluate systematic instruction, delivered using computer-based intervention or a recorded lecture, on identifying changes in slope and level in AB graphs.…

  12. AB 1725 Human Resources Development Plan for the Period July 1, 1989-June 30, 1990.

    ERIC Educational Resources Information Center

    Desert Community Coll. District, Palm Desert, CA.

    Funds set aside by California Assembly Bill (AB) 1725 for staff development programs were used by the Desert Community College District (DCCD) to supplement its existing human resources development plan (HRDP). The HRDP, which was based on the results of a needs assessment of all employees, was designed to respond to the changing professional…

  13. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    NASA Astrophysics Data System (ADS)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  14. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    PubMed

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms. PMID:27394094

  15. Environment-friendly Pd free surface activation technics for ABS surface

    NASA Astrophysics Data System (ADS)

    Shu, Zengnian; Wang, Xu

    2012-05-01

    An environment-friendly surface etching and activation technics for acrylonitrile-butadiene-styrene (ABS) surface metallization were investigated as a replacement for conventional chromic acid etching bath and palladium catalyst. After etching by H2SO4-MnO2 colloid, the ABS surfaces became roughness; meanwhile the carboxyl and hydroxyl groups were formed on the surface. With absorption and a reduction by a dimethylamineborane solution, copper particles were deposited on the ABS surface, which serves as a catalyst replacement for SnCl2/PdCl2 colloid. The effects of CuSO4 concentration, (CH3)2NHBH3 concentration, reduction temperature and reduction time on the adhesion strength between the ABS surface and the electroless copper film were investigated. And the average adhesion strengths reached 1.31 kN m-1, which is near the values (1.19 kN m-1) obtained by SnCl2/PdCl2 colloid.

  16. Predicting materials for solar energy conversion: ab-initio spectroscopy of heterogeneous interfaces

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    We will discuss some progress in predicting materials for solar energy conversion using ab initio calculations, in particular we will focus on heterogeneous interfaces between photo-electrodes and water and between nanocomposites. We will also address the problem of building much needed tighter connections between computational and laboratory experiments.

  17. 46 CFR 12.403 - Service or training requirements for able seaman (A/B) endorsements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false Service or training requirements for able seaman (A/B) endorsements. 12.403 Section 12.403 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MERCHANT MARINE OFFICERS AND SEAMEN REQUIREMENTS FOR RATING ENDORSEMENTS Requirements for National Deck Rating Endorsements § 12.403 Service or...

  18. Protoporphyrin (PPIX) efflux by the MacAB-TolC pump in Escherichia coli.

    PubMed

    Turlin, Evelyne; Heuck, Gesine; Simões Brandão, Maria Inês; Szili, Noémie; Mellin, J R; Lange, Norbert; Wandersman, Cécile

    2014-12-01

    In most organisms, heme biosynthesis is strictly controlled so as to avoid heme and heme precursor accumulation, which is toxic. Escherichia coli regulates heme biosynthesis by a feedback loop involving heme-induced proteolytic cleavage of HemA, glutamyl-tRNA reductase, which is the first enzyme in the heme biosynthetic pathway. We show here that heme homeostasis can be disrupted by overproduction of YfeX, a cytoplasmic protein that captures iron from heme that we named deferrochelatase. We also show that it is disrupted by iron chelation, which reduces the intracellular iron concentration necessary for loading iron into protoporphyrin IX (PPIX, the immediate heme precursor). In both cases, we established that there is an increased PPIX concentration and we demonstrate that this compound is expelled by the MacAB-TolC pump, an efflux pump involved in E. coli and Salmonella for macrolide efflux. The E. coli macAB and tolC mutants accumulate PPIX and are sensitive to photo-inactivation. The MacAB-TolC pump is required for Salmonella typhimurium survival in macrophages. We propose that PPIX is an endogenous substrate of the MacAB-TolC pump in E. coli and S. typhimurium and that this compound is produced inside bacteria when natural heme homeostasis is disrupted by iron shortage, as happens when bacteria invade the mammalian host. PMID:25257218

  19. Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava; Hanagud, Sathya

    2009-06-01

    Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

  20. Introductory Physical and Earth Science 8AB. An Instructional Course Outline. Publication No. SC-864.

    ERIC Educational Resources Information Center

    Los Angeles Unified School District, CA. Office of Secondary Instruction.

    Introductory Physical and Earth Science 8AB, a required course in the Los Angeles Unified School District, covers skills and concepts related to matter, energy, space science, weather, and oceanography with particular emphasis on the investigative approach. This instructional outline contains teacher guidelines and course content information.…

  1. CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.

    PubMed

    Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G

    2006-11-28

    The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700

  2. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  3. The transcription factors STAT5A/B regulate GM-CSF-mediated granulopoiesis.

    PubMed

    Kimura, Akiko; Rieger, Michael A; Simone, James M; Chen, Weiping; Wickre, Mark C; Zhu, Bing-Mei; Hoppe, Philipp S; O'Shea, John J; Schroeder, Timm; Hennighausen, Lothar

    2009-11-19

    Neutrophils play a vital role in the immune defense, which is evident by the severity of neutropenia causing life-threatening infections. Granulocyte macrophage-colony stimulating factor (GM-CSF) controls homeostatic and emergency development of granulocytes. However, little is known about the contribution of the downstream mediating transcription factors signal transducer and activator of transcription 5A and 5B (STAT5A/B). To elucidate the function of this pathway, we generated mice with complete deletion of both Stat5a/b genes in hematopoietic cells. In homeostasis, peripheral neutrophils were markedly decreased in these animals. Moreover, during emergency situations, such as myelosuppression, Stat5a/b-mutant mice failed to produce enhanced levels of neutrophils and were unable to respond to GM-CSF. Both the GM-CSF-permitted survival of mature neutrophils and the generation of granulocytes from granulocyte-macrophage progenitors (GMPs) were markedly reduced in Stat5a/b mutants. GMPs showed impaired colony-formation ability with reduced number and size of colonies on GM-CSF stimulation. Moreover, continuous cell fate analyses by time-lapse microscopy and single cell tracking revealed that Stat5a/b-null GMPs showed both delayed cell-cycle progression and increased cell death. Finally, transcriptome analysis indicated that STAT5A/B directs GM-CSF signaling through the regulation of proliferation and survival genes. PMID:19779039

  4. When Does Rank(ABC)= Rank(AB) + Rank(BC) - Rank(B) Hold?

    ERIC Educational Resources Information Center

    Tian, Yongge; Styan, George P. H.

    2002-01-01

    The well-known Frobenius rank inequality established by Frobenius in 1911 states that the rank of the product ABC of three matrices satisfies the inequality rank(ABC) [greater than or equal]rank(AB) + rank(BC) - rank(B) A new necessary and sufficient condition for equality to hold is presented and then some interesting consequences and…

  5. Ribosomal protein L18aB is required for both male gametophyte function and embryo development in Arabidopsis.

    PubMed

    Yan, Hailong; Chen, Dan; Wang, Yifan; Sun, Yang; Zhao, Jing; Sun, Mengxiang; Peng, Xiongbo

    2016-01-01

    Ribosomal proteins are involved in numerous essential cell activities in plants. However, the regulatory role in specific plant developmental processes has not yet been fully elucidated. Here we identified the new ribosomal protein L18aB, which is specifically involved in sexual reproduction and plays a critical role in male gametophyte development and embryo pattern formation. In rpl18aB mutant plants, the mature pollen grains can germinate normally, but their competitiveness for growing in the style is significantly reduced. More interestingly, RPL18aB is required in early embryogenesis. rpl18aB embryos displayed irregular cell division orientations in the early pro-embryo and arrested at the globular stage with possible, secondary pattern formation defects. Further investigations revealed that the polar transportation of auxin is disturbed in the rpl18aB mutant embryos, which may explain the observed failure in embryo pattern formation. The cell type-specific complementation of RPL18aB in rpl18aB was not able to recover the phenotype, indicating that RPL18aB may play an essential role in early cell fate determination. This work unravels a novel role in embryo development for a ribosomal protein, and provides insight into regulatory mechanism of early embryogenesis. PMID:27502163

  6. Struggling for Opportunity: Undocumented AB 540 Students in the Latina/o Education Pipeline. CSRC Research Report. Number 13

    ERIC Educational Resources Information Center

    Huber, Lindsay Perez; Malagon, Maria C.; Solorzano, Daniel G.

    2009-01-01

    Assembly Bill 540 (AB 540) was passed into law by the California state legislature in October 2001 and was implemented on January 1, 2002. Under AB 540, an undocumented student pays resident (in-state) fees at California's public colleges and universities if the student 1) attended a high school in California for at least three years (schooling…

  7. Ribosomal protein L18aB is required for both male gametophyte function and embryo development in Arabidopsis

    PubMed Central

    Yan, Hailong; Chen, Dan; Wang, Yifan; Sun, Yang; Zhao, Jing; Sun, Mengxiang; Peng, Xiongbo

    2016-01-01

    Ribosomal proteins are involved in numerous essential cell activities in plants. However, the regulatory role in specific plant developmental processes has not yet been fully elucidated. Here we identified the new ribosomal protein L18aB, which is specifically involved in sexual reproduction and plays a critical role in male gametophyte development and embryo pattern formation. In rpl18aB mutant plants, the mature pollen grains can germinate normally, but their competitiveness for growing in the style is significantly reduced. More interestingly, RPL18aB is required in early embryogenesis. rpl18aB embryos displayed irregular cell division orientations in the early pro-embryo and arrested at the globular stage with possible, secondary pattern formation defects. Further investigations revealed that the polar transportation of auxin is disturbed in the rpl18aB mutant embryos, which may explain the observed failure in embryo pattern formation. The cell type-specific complementation of RPL18aB in rpl18aB was not able to recover the phenotype, indicating that RPL18aB may play an essential role in early cell fate determination. This work unravels a novel role in embryo development for a ribosomal protein, and provides insight into regulatory mechanism of early embryogenesis. PMID:27502163

  8. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1...

  9. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1...

  10. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1...

  11. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1...

  12. Different mechanisms by which anti-DNA MoAbs bind to human endothelial cells and glomerular mesangial cells.

    PubMed Central

    Chan, T M; Frampton, G; Staines, N A; Hobby, P; Perry, G J; Cameron, J S

    1992-01-01

    The mechanisms by which anti-DNA MoAbs derived from MRL-lpr/lpr mice, bind to human umbilical vein endothelial cells (HUVEC) and glomerular mesangial cells were studied using a cellular ELISA. DNAse-treatment of either the MoAb or HUVEC followed by reconstitution with DNA and/or histones was performed to determine whether DNA and histones mediated such binding. It was found that MoAb410 bound to HUVEC and mesangial cells in the form of preformed DNA/anti-DNA immune complex, and such binding was facilitated by histones. In contrast, MoAb 152 bound directly to cell membrane-associated DNA, and adding DNA to MoAb 152 reduced its cellular binding. DNA binds endothelial cell surface and histones enhance the binding of both MoAb 410 and MoAb 152 to HUVEC by increasing cell membrane-associated DNA. Finally, the degree of MoAb binding to HUVEC is critically influenced by the relative concentrations of antibody, DNA, and histones. PMID:1563108

  13. Greatwall-phosphorylated Endosulfine is both an inhibitor and a substrate of PP2A-B55 heterotrimers

    PubMed Central

    Williams, Byron C; Filter, Joshua J; Blake-Hodek, Kristina A; Wadzinski, Brian E; Fuda, Nicholas J; Shalloway, David; Goldberg, Michael L

    2014-01-01

    During M phase, Endosulfine (Endos) family proteins are phosphorylated by Greatwall kinase (Gwl), and the resultant pEndos inhibits the phosphatase PP2A-B55, which would otherwise prematurely reverse many CDK-driven phosphorylations. We show here that PP2A-B55 is the enzyme responsible for dephosphorylating pEndos during M phase exit. The kinetic parameters for PP2A-B55’s action on pEndos are orders of magnitude lower than those for CDK-phosphorylated substrates, suggesting a simple model for PP2A-B55 regulation that we call inhibition by unfair competition. As the name suggests, during M phase PP2A-B55’s attention is diverted to pEndos, which binds much more avidly and is dephosphorylated more slowly than other substrates. When Gwl is inactivated during the M phase-to-interphase transition, the dynamic balance changes: pEndos dephosphorylated by PP2A-B55 cannot be replaced, so the phosphatase can refocus its attention on CDK-phosphorylated substrates. This mechanism explains simultaneously how PP2A-B55 and Gwl together regulate pEndos, and how pEndos controls PP2A-B55. DOI: http://dx.doi.org/10.7554/eLife.01695.001 PMID:24618897

  14. AB1725 and the Vanishing Human Being: How Pluralism Is Giving Way to Special Privilege in the California Community Colleges.

    ERIC Educational Resources Information Center

    Reeb, Richard H.

    This paper argues against the affirmative action legislation contained in Assembly Bill (AB) 1725, putting forth the position that affirmative action policies in faculty hiring and student admissions represent de facto racial and gender discrimination. The paper criticizes the purely formal language of AB 1725, arguing that it blurs the…

  15. Biocontrol of the oriental armyworm, Mythimna separata, by the tachinid fly Exorista civilis is synergized by Cry1Ab protoxin

    PubMed Central

    Jiang, Xingfu; Zhang, Lei; Yang, Haixia; Sappington, Thomas W.; Cheng, Yunxia; Luo, Li zhi

    2016-01-01

    Tritrophic interactions between Mythimna separata, its tachinid parasite Exorista civilis and the Cry1Ab were examined. Although 6th instar M. separata mortality increased with increasing Cry1Ab concentration, some tolerance was evident. Likewise, parasitization by E. civilis resulted in only 18% host mortality. However, combination of Cry1Ab and E. civilis parasitization resulted in a significant Cry1Ab dose-dependent increase in mortality over that of either alone, including a 50–56% synergistic increase in efficacy at the two concentrations tested. Pupal weight, adult emergence and lifetime fecundity of M. separata derived from larvae surviving both agents were negatively affected. The ability of E. civilis to parasitize and subsequently develop on the host was not adversely influenced by Cry1Ab. Instead, pupation rate increased significantly among host larvae fed 3.125 μg/g Cry1Ab diet. Overall, our results demonstrate that use of Cry1Ab to control M. separata not only is compatible with the use of the tachinid parasitoid, but that the two methods can act synergistically to manage this destructive pest, provide support for the safety of transgenic Cry1Ab Bt plants in China. This example of two independent pest management strategies acting synergistically against a difficult pest offers a new perspective of broad significance in striving for agricultural sustainability. PMID:27324469

  16. The end of a myth – Bt(Cry1Ab) maize does not harm green lacewings

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A concern with Bt-transgenic insect-resistant plants is their potential to harm non-target organisms. Early studies reported that Cry1Ab-producing Bt maize and purified Cry1Ab harmed larvae of the green lacewing, Chrysoperla carnea. Although these effects could not be confirmed in subsequent studies...

  17. Biocontrol of the oriental armyworm, Mythimna separata, by the tachinid fly Exorista civilis is synergized by Cry1Ab protoxin.

    PubMed

    Jiang, Xingfu; Zhang, Lei; Yang, Haixia; Sappington, Thomas W; Cheng, Yunxia; Luo, Li Zhi

    2016-01-01

    Tritrophic interactions between Mythimna separata, its tachinid parasite Exorista civilis and the Cry1Ab were examined. Although 6th instar M. separata mortality increased with increasing Cry1Ab concentration, some tolerance was evident. Likewise, parasitization by E. civilis resulted in only 18% host mortality. However, combination of Cry1Ab and E. civilis parasitization resulted in a significant Cry1Ab dose-dependent increase in mortality over that of either alone, including a 50-56% synergistic increase in efficacy at the two concentrations tested. Pupal weight, adult emergence and lifetime fecundity of M. separata derived from larvae surviving both agents were negatively affected. The ability of E. civilis to parasitize and subsequently develop on the host was not adversely influenced by Cry1Ab. Instead, pupation rate increased significantly among host larvae fed 3.125 μg/g Cry1Ab diet. Overall, our results demonstrate that use of Cry1Ab to control M. separata not only is compatible with the use of the tachinid parasitoid, but that the two methods can act synergistically to manage this destructive pest, provide support for the safety of transgenic Cry1Ab Bt plants in China. This example of two independent pest management strategies acting synergistically against a difficult pest offers a new perspective of broad significance in striving for agricultural sustainability. PMID:27324469

  18. Multicenter Evaluation of the Clostridium difficile TOX A/B TEST

    PubMed Central

    Lyerly, D. M.; Neville, L. M.; Evans, D. T.; Fill, J.; Allen, S.; Greene, W.; Sautter, R.; Hnatuck, P.; Torpey, D. J.; Schwalbe, R.

    1998-01-01

    Clostridium difficile, the primary cause of nosocomial diarrhea in the United States and many other industrialized countries, is recognized as a major health concern because of its ability to cause severe intestinal disease leading to complications such as relapses and infections due to vancomycin-resistant enterococci. The disease results from two toxins, toxins A and B, produced by this pathogen. In this study, we evaluated the TOX A/B TEST, a new 1-h enzyme immunoassay (EIA) that detects toxins A and B. We compared the test with the tissue culture assay, which is recognized as the “gold standard” for C. difficile testing. Evaluations were performed in-house at TechLab, Inc. (Blacksburg, Va.) and off-site at four clinical laboratories. Of 1,152 specimens tested, 165 were positive by the TOX A/B TEST and tissue culture and 973 were negative by both tests. The sensitivity and specificity were 92.2 and 100%, respectively. The positive and negative predictive values were 100 and 98.6%, respectively, and the correlation of the TOX A/B TEST with tissue culture was 98.8%. When discrepant samples were resolved by culture, the sensitivity and specificity were 93.2 and 98.9%, respectively. The positive and negative predictive values were 100 and 98.8%, respectively, with a correlation of 99.0%. There were no specimens that were positive by the TOX A/B TEST and negative by tissue culture. Fourteen specimens were negative by the TOX A/B TEST but positive by tissue culture. Of these, two were negative by toxigenic culture, five were positive by toxigenic culture, and seven were not available for further testing. There were no indeterminate results, since the test does not have an indeterminant zone. In a separate study, 102 specimens that were positive by tissue culture and the TOX A/B TEST were examined in toxin A-specific EIAs. Two specimens that presumptively contained toxin A-negative, toxin B-positive (toxA−/toxB+) isolates were identified. One specimen was from a

  19. Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa.

    PubMed

    Pan, Ya-Ping; Xu, Yuan-Hong; Wang, Zhong-Xin; Fang, Ya-Ping; Shen, Ji-Lu

    2016-08-01

    Efflux pump systems are one of the most important mechanisms conferring multidrug resistance in Pseudomonas aeruginosa. MexAB-OprM efflux pump is one of the largest multi-drug resistant efflux pumps with high-level expression, which is controlled by regulatory genes mexR, nalC, and nalD. This study investigated the role of efflux pump MexAB-OprM in 75 strains of carbapenem-resistant P. aeruginosa and evaluated the influence of point mutation of the regulatory genes. The minimum inhibitory concentrations of imipenem and meropenem, with or without MC207110, an efflux pump inhibitor, were determined by agar dilution method to select the positive strains for an overexpressed active efflux pump. Carba NP test and EDTA-disk synergy test were used for the detection of carbapenemase and metallo-β-lactamases, respectively. The gene mexA, responsible for the fusion protein structure, and the reference gene rpoD of the MexAB-OprM pump were amplified by real-time PCR. The quantity of relative mRNA expression was determined simultaneously. By PCR method, the efflux regulatory genes mexR, nalC, and nalD and outer membrane protein OprD2 were amplified for the strains showing overexpression of MexAB-OprM and subsequently analyzed by BLAST. Among the 75 P. aeruginosa strains, the prevalence of efflux pump-positive phenotype was 17.3 % (13/75). Carba NP test and EDTA-disk synergy test were all negative in the 13 strains. PCR assay results showed that ten strains overexpressed the MexAB-OprM efflux pump and were all positive for the regulatory genes mexR, nalC, and nalD. Sequence analysis indicated that of the ten isolates, nine had a mutation (Gly → Glu) at 71st amino acid position in NalC, and eight also had a mutation (Ser → Arg) at 209th position in NalC. Only one strain had a mutation (Thr → Ile) at the 158th amino acid position in NalD, whereas eight isolates had mutations in MexR. In conclusion, overexpression of efflux pump MexAB-OprM plays an important role in

  20. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

    PubMed Central

    Hu, Hao; Yang, Weitao

    2013-01-01

    Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

  1. Fitness costs and stability of Cry1Ab resistance in sugarcane borer, Diatraea saccharalis (F.).

    PubMed

    Zhang, Liping; Leonard, B Rogers; Chen, Mao; Clark, Thomas; Anilkumar, Konasale; Huang, Fangneng

    2014-03-01

    The sugarcane borer, Diatraea saccharalis (F.), is a major target species of transgenic corn expressing Bacillus thuringiensis (Bt) proteins in South America and the U.S. mid-south region. In this study, the fitness of seven insect genotypes of D. saccharalis were assayed on non-toxic diet, which included a Cry1Ab-susceptible strain (SS-2009), two Cry1Ab-resistant strains (RR-43A(BC), RR-L5B(BC)), and four F1 hybrids (F1-R43A(m)S(f), F1-R43A(f)S(m), F1-R5B(m)S(f), and F1-R5B(f)S(m)). The F1 hybrids were generated by reciprocal crosses of SS-2009 with RR-43ABC and RR-L5BBC, respectively. Biological parameters measured were neonate-to-pupa survivorship, neonate-to-pupa development time, pupal mass, pupa-to-adult emergence rate, and progeny (neonates) production. The overall performance of the two resistant strains and the four F1 genotypes was either similar or better than SS-2009 for all biological parameters measured, suggesting a lack of fitness costs associated with the Cry1Ab resistance traits in both RR-43A(BC) and RR-L5B(BC). In addition, resistance stability was evaluated by measuring the Cry1Ab susceptibility of RR-43A(BC) and RR-L5B(BC) in the absence of selection pressure. Laboratory bioassays showed that larval mortality of the two resistant strains did not significantly increase after selection pressure was removed for 16 generations across all Cry1Ab concentrations assayed. The results provide valuable information on assessing resistance risk and developing effective management strategies for the sustainable use of Bt corn technology. PMID:24503242

  2. Brown Dwarfs in Young Moving Groups from Pan-STARRS1. I. AB Doradus

    NASA Astrophysics Data System (ADS)

    Aller, Kimberly M.; Liu, Michael C.; Magnier, Eugene A.; Best, William M. J.; Kotson, Michael C.; Burgett, William S.; Chambers, Kenneth C.; Hodapp, Klaus W.; Flewelling, Heather; Kaiser, Nick; Metcalf, Nigel; Tonry, John L.; Wainscoat, Richard J.; Waters, Christopher

    2016-04-01

    Substellar members of young (≲150 Myr) moving groups are valuable benchmarks to empirically define brown dwarf evolution with age and to study the low-mass end of the initial mass function. We have combined Pan-STARRS1 (PS1) proper motions with optical–IR photometry from PS1, Two Micron All Sky Survey (2MASS), and WISE to search for substellar members of the AB Dor Moving Group within ≈50 pc and with spectral types of late M to early L, corresponding to masses down to ≈30 MJup at the age of the group (≈125 Myr). Including both photometry and proper motions allows us to better select candidates by excluding field dwarfs whose colors are similar to young AB Dor Moving Group members. Our near-IR spectroscopy has identified six ultracool dwarfs (M6–L4 ≈30–100 MJup) with intermediate surface gravities (int-g) as candidate members of the AB Dor Moving Group. We find another two candidate members with spectra showing hints of youth but consistent with field gravities. We also find four field brown dwarfs unassociated with the AB Dor Moving Group, three of which have int-g gravity classification. While signatures of youth are present in the spectra of our ≈125 Myr objects, neither their J – K nor W1 – W2 colors are significantly redder than field dwarfs with the same spectral types, unlike younger ultracool dwarfs. We also determined PS1 parallaxes for eight of our candidates and one previously identified AB Dor Moving Group candidate. Although radial velocities (and parallaxes, for some) are still needed to fully assess membership, these new objects provide valuable insight into the spectral characteristics and evolution of young brown dwarfs.

  3. The Use of Solitaire AB Stents in Coil Embolization of Wide-Necked Cerebral Aneurysms

    PubMed Central

    Han, Xin-Wei; Yan, Lei; Ma, Ji; Guo, Dong; Zhu, Hong-Can; Wang, Shu-Kai; He, Yuan-Hong; Chen, Wen-Wu; Wei, Li-Ping; Wang, Ming-Ke; Song, Tai-Min

    2015-01-01

    Background The Solitaire AB stent is one of many assistant stents used for treating wide-necked cerebral aneurysm, and has been used since 2003. However, large sample studies on its safety and effectiveness are lacking. The objective of this study was to evaluate the effectiveness and safety of the Solitaire AB stent in the coil embolization of wide-necked cerebral aneurysms. Methods Retrospective review of the clinical and image data of 116 patients with wide-necked cerebral aneurysms who had been enrolled at six interventional neuroradiology centers from February 2010 to February 2014 and had been treated by coil embolization; in total, 120 Solitaire AB stents were used. The degree of aneurysm occlusion was examined using digital subtraction angiography (DSA) immediately after the procedure and during follow-up, and was graded using the modified Raymond classification. We also observed complications to evaluate the safety and effectiveness of this therapy. Results The 120 Solitaire AB stents (4 mm × 15 mm, four stents; 4 mm × 20 mm, 16 stents; 6 mm × 20 mm, 36 stents; 6 mm × 30 mm, 64 stents) were inserted to treat 120 wide-necked cerebral aneurysms. All stents were inserted successfully. DSA immediately post-surgery revealed 55 cases of complete occlusion, 59 cases of neck remnant, and six cases of aneurysm remnant. Perioperatively, there were four cases of hemorrhage and four cases of stent thrombosis. The follow-up spanned 3–37 months; of 92 patients examined by DSA at the 6-month follow up, 12 had disease recurrence. Conclusions The Solitaire AB stent is effective with a good technical success rate and short-term effect for assisting coil embolization of wide-necked cerebral aneurysms. PMID:26426804

  4. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  5. NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies.

    PubMed

    Pisitkun, Trairak; Hoffert, Jason D; Saeed, Fahad; Knepper, Mark A

    2012-01-01

    Investigation of physiological mechanisms at a cellular level often requires production of high-quality antibodies, frequently using synthetic peptides as immunogens. Here we describe a new, web-based software tool called NHLBI-AbDesigner that allows the user to visualize the information needed to choose optimal peptide sequences for peptide-directed antibody production (http://helixweb.nih.gov/AbDesigner/). The choice of an immunizing peptide is generally based on a need to optimize immunogenicity, antibody specificity, multispecies conservation, and robustness in the face of posttranslational modifications (PTMs). AbDesigner displays information relevant to these criteria as follows: 1) "Immunogenicity Score," based on hydropathy and secondary structure prediction; 2) "Uniqueness Score," a predictor of specificity of an antibody against all proteins expressed in the same species; 3) "Conservation Score," a predictor of ability of the antibody to recognize orthologs in other animal species; and 4) "Protein Features" that show structural domains, variable regions, and annotated PTMs that may affect antibody performance. AbDesigner displays the information online in an interactive graphical user interface, which allows the user to recognize the trade-offs that exist for alternative synthetic peptide choices and to choose the one that is best for a proposed application. Several examples of the use of AbDesigner for the display of such trade-offs are presented, including production of a new antibody to Slc9a3. We also used the program in large-scale mode to create a database listing the 15-amino acid peptides with the highest Immunogenicity Scores for all known proteins in five animal species, one plant species (Arabidopsis thaliana), and Saccharomyces cerevisiae. PMID:21956165

  6. EVIDENCE FOR RADIOGENIC SULFUR-32 IN TYPE AB PRESOLAR SILICON CARBIDE GRAINS?

    SciTech Connect

    Fujiya, Wataru; Hoppe, Peter; Zinner, Ernst; Pignatari, Marco; Herwig, Falk E-mail: peter.hoppe@mpic.de E-mail: mpignatari@gmail.com

    2013-10-20

    We report C, Si, and S isotope measurements on 34 presolar silicon carbide grains of Type AB, characterized by {sup 12}C/{sup 13}C < 10. Nitrogen, Mg-Al-, and Ca-Ti-isotopic compositions were measured on a subset of these grains. Three grains show large {sup 32}S excesses, a signature that has been previously observed for grains from supernovae (SNe). Enrichments in {sup 32}S may be due to contributions from the Si/S zone and the result of S molecule chemistry in still unmixed SN ejecta or due to incorporation of radioactive {sup 32}Si from C-rich explosive He shell ejecta. However, a SN origin remains unlikely for the three AB grains considered here, because of missing evidence for {sup 44}Ti, relatively low {sup 26}Al/{sup 27}Al ratios (a few times 10{sup –3}), and radiogenic {sup 32}S along with low {sup 12}C/{sup 13}C ratios. Instead, we show that born-again asymptotic giant branch (AGB) stars that have undergone a very-late thermal pulse (VLTP), known to have low {sup 12}C/{sup 13}C ratios and enhanced abundances of the light s-process elements, can produce {sup 32}Si, which makes such stars attractive sources for AB grains with {sup 32}S excesses. This lends support to the proposal that at least some AB grains originate from born-again AGB stars, although uncertainties in the born-again AGB star models and possible variations of initial S-isotopic compositions in the parent stars of AB grains make it difficult to draw a definitive conclusion.

  7. Evidence for Radiogenic Sulfur-32 in Type AB Presolar Silicon Carbide Grains?

    NASA Astrophysics Data System (ADS)

    Fujiya, Wataru; Hoppe, Peter; Zinner, Ernst; Pignatari, Marco; Herwig, Falk

    2013-10-01

    We report C, Si, and S isotope measurements on 34 presolar silicon carbide grains of Type AB, characterized by 12C/13C < 10. Nitrogen, Mg-Al-, and Ca-Ti-isotopic compositions were measured on a subset of these grains. Three grains show large 32S excesses, a signature that has been previously observed for grains from supernovae (SNe). Enrichments in 32S may be due to contributions from the Si/S zone and the result of S molecule chemistry in still unmixed SN ejecta or due to incorporation of radioactive 32Si from C-rich explosive He shell ejecta. However, a SN origin remains unlikely for the three AB grains considered here, because of missing evidence for 44Ti, relatively low 26Al/27Al ratios (a few times 10-3), and radiogenic 32S along with low 12C/13C ratios. Instead, we show that born-again asymptotic giant branch (AGB) stars that have undergone a very-late thermal pulse (VLTP), known to have low 12C/13C ratios and enhanced abundances of the light s-process elements, can produce 32Si, which makes such stars attractive sources for AB grains with 32S excesses. This lends support to the proposal that at least some AB grains originate from born-again AGB stars, although uncertainties in the born-again AGB star models and possible variations of initial S-isotopic compositions in the parent stars of AB grains make it difficult to draw a definitive conclusion.

  8. Characterization of a Novel Pyranopyridine Inhibitor of the AcrAB Efflux Pump of Escherichia coli

    PubMed Central

    Kwasny, Steven M.; Kim, Hong-Suk; Nguyen, Son T.; Houseweart, Chad; D'Souza, Sanjay; Walker, Graham C.; Peet, Norton P.; Nikaido, Hiroshi; Bowlin, Terry L.

    2014-01-01

    Members of the resistance-nodulation-division (RND) family of efflux pumps, such as AcrAB-TolC of Escherichia coli, play major roles in multidrug resistance (MDR) in Gram-negative bacteria. A strategy for combating MDR is to develop efflux pump inhibitors (EPIs) for use in combination with an antibacterial agent. Here, we describe MBX2319, a novel pyranopyridine EPI with potent activity against RND efflux pumps of the Enterobacteriaceae. MBX2319 decreased the MICs of ciprofloxacin (CIP), levofloxacin, and piperacillin versus E. coli AB1157 by 2-, 4-, and 8-fold, respectively, but did not exhibit antibacterial activity alone and was not active against AcrAB-TolC-deficient strains. MBX2319 (3.13 μM) in combination with 0.016 μg/ml CIP (minimally bactericidal) decreased the viability (CFU/ml) of E. coli AB1157 by 10,000-fold after 4 h of exposure, in comparison with 0.016 μg/ml CIP alone. In contrast, phenyl-arginine-β-naphthylamide (PAβN), a known EPI, did not increase the bactericidal activity of 0.016 μg/ml CIP at concentrations as high as 100 μM. MBX2319 increased intracellular accumulation of the fluorescent dye Hoechst 33342 in wild-type but not AcrAB-TolC-deficient strains and did not perturb the transmembrane proton gradient. MBX2319 was broadly active against Enterobacteriaceae species and Pseudomonas aeruginosa. MBX2319 is a potent EPI with possible utility as an adjunctive therapeutic agent for the treatment of infections caused by Gram-negative pathogens. PMID:24247144

  9. Promoter analysis and RNA interference of CYP6ab4 in the silkworm Bombyx mori.

    PubMed

    Zhao, Guo-Dong; Zhang, Yi-Ling; Liu, Yun-Lei; Li, Bing; Chen, Yu-Hua; Xu, Ya-Xiang; Xia, Qing-You; Shen, Wei-De; Wei, Zheng-Guo

    2015-10-01

    In insects, cytochrome P450 monooxygenases (P450s) are involved in the metabolism of endogenous compounds such as steroid hormones and lipids. In this study, we measured the 20-hydroxyecdysone (20E)-induced transcriptional level of the CYP6ab4 gene using reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) with a dual spike-in strategy. We then probed possible physiological functions using RNAi experiments in the silkworm Bombyx mori. The activity of the CYP6ab4 promoter in various silkworm tissues was measured by firefly luciferase activity and normalized by Renilla luciferase activity. Our results showed that the activity of the CYP6ab4 promoter was highest in the malpighian tubule, followed by the fat body, the silk gland, the midgut, the epidermis, and the hemocyte. The essential region for basal and 20E-induced transcriptional activity was between -908 and -456 bp from the transcription start site. Through promoter truncation analysis using a dual-luciferase reporter assay in B. mori ovary cells (BmN), we showed that the region between -827 and -722 bp was essential for basal and 20E-induced transcriptional activity. Sequence analysis of this region revealed several potential transcriptional regulatory elements such as Hunchback (Hb) and BR-C Z. Mutation of the core bases of the BR-C Z binding site demonstrated that BR-C Z induces 20E-mediated CYP6ab4 transcription. Further identification of cis- and trans-elements and their roles in the upregulation of CYP6ab4 may be useful for elucidating the contribution of P450 to the response mechanism to 20E. PMID:25920486

  10. Data characteristics and preliminary results from the atacama b-mode search (ABS)

    NASA Astrophysics Data System (ADS)

    Visnjic, Catherine

    The Atacama B-Mode Search (ABS) is a 145 GHz polarimeter located at a high altitude site on Cerro Toco, in the Andes of northern Chile. Having deployed in early 2012, it is currently in its second year of operation, observing the polarization of the Cosmic Microwave Background (CMB). It seeks to probe the as yet undetected odd-parity B-modes of the polarization, which would have been created by the primordial gravitational wave background (GWB) predicted by theories of inflation. The magnitude of the B-mode signal is characterized by the tensor-to-scalar ratio, r. ABS features 60 cm cryogenic reflectors in the crossed-Dragone configuration, and a warm, continuously rotating sapphire half-wave plate to modulate the polarization of incoming radiation. The focal plane consists of 480 antenna-coupled transition edge sensor bolometers, arranged in orthogonal pairs for polarization sensitivity, and coupled to feedhorns in a hexagonal array. In this thesis we describe the ABS instrument in the state in which it is now operating, outline the first season of observations, and characterize the data obtained. Focusing on observations of the primary CMB field during a one month reference period, we detail the algorithms currently used to select the data suitable for making maps. This is the first pass at data cuts and provides a conservative estimate for the sensitivity of ABS to the polarization modes in the sky. We project that with one year total observation time of the primary CMB field, ABS should be able to detect the B-mode signal at roughly the level of r = 0.03.

  11. Tobacco plants expressing the Cry1AbMod toxin suppress tolerance to Cry1Ab toxin of Manduca sexta cadherin-silenced larvae.

    PubMed

    Porta, Helena; Jiménez, Gladys; Cordoba, Elizabeth; León, Patricia; Soberón, Mario; Bravo, Alejandra

    2011-07-01

    Cry toxins produced by Bacillus thuringiensis bacteria are insecticidal proteins used worldwide in the control of different insect pests. Alterations in toxin-receptor interaction represent the most common mechanism to induce resistance to Cry toxins in lepidopteran insects. Cry toxins bind with high affinity to the cadherin protein present in the midgut cells and this interaction facilitates the proteolytic removal of helix α-1 and pre-pore oligomer formation. Resistance to Cry toxins has been linked with mutations in the cadherin gene. One strategy effective to overcome larval resistance to Cry1A toxins is the production of Cry1AMod toxins that lack helix α-1. Cry1AMod are able to form oligomeric structures without binding to cadherin receptor and were shown to be toxic to cadherin-silenced Manduca sexta larvae and Pectinophora gossypiella strain with resistance linked to mutations in a cadherin gene. We developed Cry1AbMod tobacco transgenic plants to analyze if Cry1AMod toxins can be expressed in transgenic crops, do not affect plant development and are able to control insect pests. Our results show that production of the Cry1AbMod toxin in transgenic plants does not affect plant development, since these plants exhibited healthy growth, produced abundant seeds, and were virtually undistinguishable from control plants. Most importantly, Cry1AbMod protein produced in tobacco plants retains its functional toxic activity against susceptible and tolerant M. sexta larvae due to the silencing of cadherin receptor by RNAi. These results suggest that CryMod toxins could potentially be expressed in other transgenic crops to protect them against both toxin-susceptible and resistant lepidopteran larvae affected in cadherin gene. PMID:21621616

  12. Some aspects of the recombinantly expressed humanised superagonist anti-CD28 mAb, TGN1412 trial catastrophe lessons to safeguard mAbs and vaccine trials.

    PubMed

    Mehrishi, Jitendra N; Szabó, Miklós; Bakács, Tibor

    2007-05-01

    We consider essential, still ignored, basic research aspects of the failed clinical trial (13 March 2006) of a recombinantly expressed humanised superagonist anti-CD28 mAb, TGN14122. Without hindsight, if for approval of the first ever recombinantly expressed anti-CD28 mAb use in humans attention had been paid to the physico-chemical factors and receptor saturation, the possible catastrophe will have been predictable and preventable. To understand what went wrong and, crucially, to prevent any future disasters to safeguard human health, safety and welfare, the information provided is likely to be of wide interest. We present calculations to show CD28 receptors on T cells of the six healthy volunteers by the anti-CD28 mAb superagonist, TGN1412. This led to the over activation of T cells and the violent cytokine storm precipitating the cascade and the release of endogenous molecules affecting other cells. Monocytes and plasma cells are likely to have been affected. We discuss briefly the role of neutrophils and activation releasing the surface-located sialidase affecting cell coats, such as, of T lymphocytes exposing galactose receptors that could have been involved in antigen presenting cell interactions. The role of the cell surface thiols of lymphocytes in forming mixed disulphides with endogenous ligands and in the REDOX system are briefly mentioned. Consideration of these various factors and a critical evaluation of the receptor occupancy data before injecting 0.1 mg/kg TGN1412 will have rung alarm bells about possible serious side effects and the catastrophe will have been averted. PMID:17397974

  13. Decline in Titers of Anti-Idiotypic Antibodies Specific to Autoantibodies to GAD65 (GAD65Ab) Precedes Development of GAD65Ab and Type 1 Diabetes

    PubMed Central

    Larsson, Helena Elding; Jönsson, Ida; Lernmark, Åke; Ivarsson, Sten; Radtke, Jared R.; Hampe, Christiane S.

    2013-01-01

    The humoral Idiotypic Network consisting of antibodies and their anti-idiotypic antibodies (anti-Id) can be temporarily upset by antigen exposure. In the healthy immune response the original equilibrium is eventually restored through counter-regulatory mechanisms. In certain autoimmune diseases however, autoantibody levels exceed those of their respective anti-Id, indicating a permanent disturbance in the respective humoral Idiotypic Network. We investigated anti-Id directed to a major Type 1 diabetes (T1D)-associated autoantibody (GAD65Ab) in two independent cohorts during progression to disease. Samples taken from participants of the Natural History Study showed significantly lower anti-Id levels in individuals that later progressed to T1D compared to non-progressors (anti-Id antibody index of 0.06 vs. 0.08, respectively, p = 0.02). We also observed a significant inverse correlation between anti-Id levels and age at sampling, but only in progressors (p = 0.014). Finally, anti-Id levels in progressors showed a significant decline during progression as compared to longitudinal anti-Id levels in non-progressors (median rate of change: −0.0004 vs. +0.0004, respectively, p = 0.003), suggesting a loss of anti-Id during progression. Our analysis of the Diabetes Prediction in Skåne cohort showed that early in life (age 2) individuals at risk have anti-Id levels indistinguishable from those in healthy controls, indicating that low anti-Id levels are not an innate characteristic of the immune response in individuals at risk. Notably, anti-Id levels declined significantly in individuals that later developed GAD65Ab suggesting that the decline in anti-Id levels precedes the emergence of GAD65Ab (median rate of change: −0.005) compared to matched controls (median rate of change: +0.001) (p = 0.0016). We conclude that while anti-Id are present early in life, their levels decrease prior to the appearance of GAD65Ab and to the development of T1D. PMID

  14. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  15. Poly(ethylene oxide)-Assisted Macromolecular Self-Assembly of Lignin in ABS Matrix for Sustainable Composite Applications

    DOE PAGESBeta

    Akato, Kokouvi M.; Tran, Chau D.; Chen, Jihua; Naskar, Amit K.

    2015-11-05

    Here we report the compatibilization of biomass-derived lignin polymer in acrylonitrile butadiene styrene (ABS) thermoplastic matrix without loss of mechanical properties via poly(ethylene oxide) (PEO)-mediated macromolecular self-assembly. ABS was blended with lignin in different concentrations, and blends with 10 wt % PEO (relative to lignin) were prepared. The relative tensile strength improved slightly at low lignin content but diminished rapidly as the lignin content was increased. However, the inclusion of PEO as an interfacial adhesion promoter helped avoid deleterious effects. Dynamic mechanical analysis showed that PEO plasticized the hard phase and thus lowered the activation energy (Ea) for its relaxationmore » but caused stiffening of the soft phase and increased its Ea. Microscopy revealed that incorporating lignin in ABS led to the statistical dispersion of discrete lignin domains (300–1000 nm) which, after PEO addition, were reduced to smaller interconnected particles (200–500 nm). The lignin-extended partially renewable ABS resins showed shear-thinning behavior and reduced viscosity compared to neat ABS. The preferred lignin-loaded compositions reinforced with 20 vol % chopped carbon fibers exhibited mechanical performances (77–80 MPa) equivalent to those of reinforced ABS materials reportedly used in 3D printing applications. In conclusion, this approach could lower the cost of ABS while reducing its carbon footprint.« less

  16. Expression of cry1Ab gene from a novel Bacillus thuringiensis strain SY49-1 active on pest insects.

    PubMed

    Azizoglu, Ugur; Ayvaz, Abdurrahman; Yılmaz, Semih; Karabörklü, Salih; Temizgul, Rıdvan

    2016-01-01

    In this study, the cry1Ab gene of previously characterized and Lepidoptera-, Diptera-, and Coleoptera-active Bacillus thuringiensis SY49-1 strain was cloned, expressed and individually tested on Ephestia kuehniella (Lepidoptera: Pyralidae) and Plodia interpunctella (Lepidoptera: Pyralidae) larvae. pET-cry1Ab plasmids were constructed by ligating the cry1Ab into pET28a (+) expression vector. Constructed plasmids were transferred to an Escherichia coli BL21 (DE3) strain rendered competent with CaCl2. Isopropyl β-d-1-thiogalactopyranoside was used to induce the expression of cry1Ab in E. coli BL21(DE3), and consequently, ∼130kDa of Cry1Ab was obtained. Bioassay results indicated that recombinant Cry1Ab at a dose of 1000μgg(-1) caused 40% and 64% mortality on P. interpunctella and E. kuehniella larvae, respectively. However, the mortality rates of Bt SY49-1 strains' spore-crystal mixture at the same dose were observed to be 70% on P. interpunctella and 90% on E. kuehniella larvae. The results indicated that cry1Ab may be considered as a good candidate in transgenic crop production and as an alternative biocontrol agent in controlling stored product moths. PMID:27143037

  17. High-yield chemical vapor deposition growth of high-quality large-area AB-stacked bilayer graphene.

    PubMed

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-09-25

    Bernal-stacked (AB-stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electric field. Mechanical exfoliation can be used to produce AB-stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB- and randomly stacked structures. Herein we report a rational approach to produce large-area high-quality AB-stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H(2)/CH(4) ratio in a low-pressure CVD process to enable the continued growth of bilayer graphene. A high-temperature and low-pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90%) and high coverage (up to 99%). The electrical transport studies demonstrate that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB-stacked bilayer graphene with the highest carrier mobility exceeding 4000 cm(2)/V · s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  18. Isolation and Characterization of a Light-Harvesting Chlorophyll a/b Protein Complex Associated with Photosystem I 1

    PubMed Central

    Lam, Eric; Oritz, William; Mayfield, Stephen; Malkin, Richard

    1984-01-01

    A chlorophyll a/b protein complex has been isolated from a resolved native photosystem I complex by mildly dissociating sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The chlorophyll a/b protein contains a single polypeptide of molecular weight 20 kilodaltons, and has a chlorophyll a/b ratio of 3.5 to 4.0. The visible absorbance spectrum of the chlorophyll a/b protein complex showed a maximum at 667 nanometers in the red region and a 77 K fluorescence emission maximum at 681 nanometers. Alternatively, by treatment of the native photosystem I complex with lithium dodecyl sulfate and Triton, the chlorophyll a/b protein complex could be isolated by chromatography on Sephadex G-75. Immunological assays using antibodies to the P700-chlorophyll a-protein and the photosystem II light-harvesting chlorophyll a/b protein show no cross-reaction between the photosystem I chlorophyll a/b protein and the other two chlorophyll-containing protein complexes. Images Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:16663476

  19. Poly(ethylene oxide)-Assisted Macromolecular Self-Assembly of Lignin in ABS Matrix for Sustainable Composite Applications

    SciTech Connect

    Akato, Kokouvi M.; Tran, Chau D.; Chen, Jihua; Naskar, Amit K.

    2015-11-05

    Here we report the compatibilization of biomass-derived lignin polymer in acrylonitrile butadiene styrene (ABS) thermoplastic matrix without loss of mechanical properties via poly(ethylene oxide) (PEO)-mediated macromolecular self-assembly. ABS was blended with lignin in different concentrations, and blends with 10 wt % PEO (relative to lignin) were prepared. The relative tensile strength improved slightly at low lignin content but diminished rapidly as the lignin content was increased. However, the inclusion of PEO as an interfacial adhesion promoter helped avoid deleterious effects. Dynamic mechanical analysis showed that PEO plasticized the hard phase and thus lowered the activation energy (Ea) for its relaxation but caused stiffening of the soft phase and increased its Ea. Microscopy revealed that incorporating lignin in ABS led to the statistical dispersion of discrete lignin domains (300–1000 nm) which, after PEO addition, were reduced to smaller interconnected particles (200–500 nm). The lignin-extended partially renewable ABS resins showed shear-thinning behavior and reduced viscosity compared to neat ABS. The preferred lignin-loaded compositions reinforced with 20 vol % chopped carbon fibers exhibited mechanical performances (77–80 MPa) equivalent to those of reinforced ABS materials reportedly used in 3D printing applications. In conclusion, this approach could lower the cost of ABS while reducing its carbon footprint.

  20. AB209630, a long non-coding RNA decreased expression in hypopharyngeal squamous cell carcinoma, influences proliferation, invasion, metastasis, and survival

    PubMed Central

    Li, Wenming; Wang, Juan; Xiang, Xuan; Li, Guojun; Pan, Xinliang; Lei, Dapeng

    2016-01-01

    Long noncoding RNAs (lncRNAs) are associated with the development, progression, and prognosis of human cancers. However, the clinical significance and biological function of lncRNAs in hypopharyngeal squamous cell carcinoma (HSCC) remain largely unknown. We characterized the novel lncRNA AB209630 in vivo and in vitro. First, using qRT-PCR, we evaluated whether AB209630 levels differ between HSCC tissues/cell lines and adjacent normal tissues/cell lines. We then assessed whether AB209630 expression levels stimulate or inhibit proliferation, invasion, apoptosis, and metastasis in vitro. Finally, we investigated whether AB209630 levels in tumor tissues were associated with survival outcomes. Our results demonstrated that AB209630 levels were markedly lower in HSCC tissues and cells than in normal tissues and cells, and increased expression of AB209630 level significantly inhibited growth, metastasis, and invasion and stimulated apoptosis in vitro. In addition, patients with decreased expression of AB209630 had a significantly poorer prognosis than those with high AB209630 expression. These data suggest that increased expression of AB209630 might either stimulate or inhibit biological activities involved in HSCC development, indicating a potential application of AB209630 in future treatment for this disease. This study suggest that AB209630 functions as a tumor suppressor in HSCC, and its decreased expression may help predict a poor prognostic outcome of HSCC. Our future work will focus on the mechanisms of whether and how AB209630 as a tumor suppressor gene is involved in HSCC development. PMID:26895099

  1. 40 CFR 174.519 - Bacillus thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Bacillus thuringiensis Cry2Ab2 protein... thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry2Ab2 protein in or on corn or cotton are exempt from the requirement of...

  2. 40 CFR 174.519 - Bacillus thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Bacillus thuringiensis Cry2Ab2 protein... thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry2Ab2 protein in or on corn or cotton are exempt from the requirement of...

  3. 40 CFR 174.519 - Bacillus thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Bacillus thuringiensis Cry2Ab2 protein... thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry2Ab2 protein in or on corn or cotton are exempt from the requirement of...

  4. 40 CFR 174.511 - Bacillus thuringiensis Cry1Ab protein in all plants; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Bacillus thuringiensis Cry1Ab protein... Cry1Ab protein in all plants; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry1Ab protein in all plants are exempt from the requirement of a tolerance when used as...

  5. 40 CFR 174.519 - Bacillus thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Bacillus thuringiensis Cry2Ab2 protein... thuringiensis Cry2Ab2 protein in corn and cotton; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry2Ab2 protein in or on corn or cotton are exempt from the requirement of...

  6. 40 CFR 174.511 - Bacillus thuringiensis Cry1Ab protein in all plants; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Bacillus thuringiensis Cry1Ab protein... Cry1Ab protein in all plants; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry1Ab protein in all plants are exempt from the requirement of a tolerance when used as...

  7. 40 CFR 174.511 - Bacillus thuringiensis Cry1Ab protein in all plants; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Bacillus thuringiensis Cry1Ab protein... Cry1Ab protein in all plants; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry1Ab protein in all plants are exempt from the requirement of a tolerance when used as...

  8. 40 CFR 174.511 - Bacillus thuringiensis Cry1Ab protein in all plants; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Bacillus thuringiensis Cry1Ab protein... Cry1Ab protein in all plants; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry1Ab protein in all plants are exempt from the requirement of a tolerance when used as...

  9. Cooperative mixtures of bispecific F(ab')2 antibodies for delivering saporin to lymphoma in vitro and in vivo

    SciTech Connect

    French, R.R.; Courtenay, A.E.; Ingamells, S.; Stevenson, G.T.; Glennie, M.J. )

    1991-05-01

    We report that selected combinations of two or more monoclonal bispecific F(ab')2 antibodies (BsAbs) far outperform single derivatives in the delivery of the ribosome-inactivating protein, saporin, to guinea pig L2C leukemic cells. Throughout the work, BsAbs were constructed by thioether-linking the hinges of two Fab'gamma, one from monoclonal anti-L2C-idiotype antibody and the other from anti-saporin antibody. The latter was either affinity-purified rabbit polyclonal or one of a panel of five mouse monoclonal antibodies. In vitro cytotoxicity studies showed that, though all derivatives were effective, the BsAb made with the polyclonal antibody was always 10 to 20 times more potent than those made with a monoclonal antibody in yielding 50% inhibition of (3H)leucine uptake. This superior activity could be matched by selective mixtures of two or more of the monoclonal derivatives. Furthermore, in immunotherapeutic delivery of saporin to tumor, a pair of BsAbs performed significantly better than did either individually. Binding and uptake studies with radiolabeled saporin demonstrated a 20-fold increase in functional affinity when saporin was held at the cell surface by an appropriate BsAb mixture rather than by a single BsAb. In contrast, only small differences were recorded in the rate at which saporin was internalized as a result of the same maneuver. We conclude that the improved performance of combinations of BsAbs arises from their ability to provide multiple linkages between saporin molecules and cell surfaces, increasing the functional affinity with which saporin is tethered to the cell, but, in this system at least, having only a minor effect on the rate at which it is internalized. Cocktails of two or more BsAbs, selected to bind to multiple epitopes on ribosome-inactivating proteins could provide an important new strategy in immunotherapy.

  10. The therapeutic efficacy of I131-PSCA-mAb in orthotopic mouse models of prostate cancer

    PubMed Central

    2013-01-01

    Background Prostate stem cell antigen (PSCA) is upregulated in prostate cancer tissues. Here we aimed to study the therapeutic efficacy of a monoclonal antibody of PSCA-labeled I131 (I131-PSCA-mAb) in orthotopic mouse models of prostate cancer. Methods The proliferation, apoptosis and invasion abilities of PC-3 and LNCaP cells treated with I131-PSCA-mAb were measured by methyl thiazolyl tetrazolium assay, flow cytometry and transwell culture, respectively. The human prostate cancer models were established by orthotopic implantation of PC-3 and LNCaP cells in nude mice. I131-PSCA-mAb distribution and tumor cell apoptosis in the tumor-bearing nude mice were measured. Results The inhibitory and apoptosis rates of PC-3 and LNCaP cells treated with I131-PSCA-mAb reached a maximum of 84%, 80% and 50%, 46%, respectively, which were obviously higher than in the cells treated with I131-IgG or PSCA-mAb. The invaded number of PC-3 and LNCaP cells treated with I131-PSCA-mAbe was significantly reduced (P < 0.01) compared with the control group. The ratios of I131-PSCA-mAb in tumor to intramuscular I131-PSCA-mAb (T/NT) in tumor-bearing nude mice were increased with time and reached the highest level after 8 h. T/NT stayed above 3.0 after 12 h, and the tumor could still be developed after 24 h. The number of apoptotic cells in tumor tissue of nude mice treated with I131-PSCA-mAb was larger than that in the control group. Conclusion I131-PSCA-mAb has the potential to become a new targeted therapy drug for the treatment of prostate cancer. PMID:24330823

  11. Fibrin biomatrix-conjugated platelet-derived growth factor AB accelerates wound healing in severe thermal injury.

    PubMed

    Mittermayr, Rainer; Branski, Ludwik; Moritz, Martina; Jeschke, Marc G; Herndon, David N; Traber, Daniel; Schense, Jason; Gampfer, Jörg; Goppelt, Andreas; Redl, Heinz

    2016-05-01

    Controlled delivery of growth factors from biodegradable biomatrices could accelerate and improve impaired wound healing. The study aim was to determine whether platelet-derived growth factor AB (PDGF.AB) with a transglutaminase (TG) crosslinking substrate site released from a fibrin biomatrix improves wound healing in severe thermal injury. The binding and release kinetics of TG-PDGF.AB were determined in vitro. Third-degree contact burns (dorsum of Yorkshire pigs) underwent epifascial necrosectomy 24 h post-burn. Wound sites were covered with autologous meshed (3:1) split-thickness skin autografts and either secured with staples or attached with sprayed fibrin sealant (FS; n = 8/group). TG-PDGF.AB binds to the fibrin biomatrix using the TG activity of factor XIIIa, and is subsequently released through enzymatic cleavage. Three doses of TG-PDGF.AB in FS (100 ng, 1 µg and 11 µg/ml FS) were tested. TG-PDGF.AB was bound to the fibrin biomatrix as evidenced by western blot analysis and subsequently released by enzymatic cleavage. A significantly accelerated and improved wound healing was achieved using sprayed FS containing TG-PDGF.AB compared to staples alone. Low concentrations (100 ng-1 µg TG-PDGF.AB/ml final FS clot) demonstrated to be sufficient to attain a nearly complete closure of mesh interstices 14 days after grafting. TG-PDGF.AB incorporated in FS via a specific binding technology was shown to be effective in grafted third-degree burn wounds. The adhesive properties of the fibrin matrix in conjunction with the prolonged growth factor stimulus enabled by this binding technology could be favourable in many pathological situations associated with wound-healing disturbances. Copyright © 2013 John Wiley & Sons, Ltd. PMID:23723146

  12. Inhibition of Stat5a/b enhances proteasomal degradation of androgen receptor liganded by antiandrogens in prostate cancer

    PubMed Central

    Hoang, David T.; Gu, Lei; Liao, Zhiyong; Talati, Pooja G.; Shen, Feng; Koptyra, Mateusz; Tan, Shyh-Han; Ellsworth, Elyse; Gupta, Shilpa; Montie, Heather; Dagvadorj, Ayush; Savolainen, Saija; Leiby, Benjamin; Mirtti, Tuomas; Merry, Diane E.; Nevalainen, Marja T.

    2015-01-01

    Although poorly understood, androgen receptor (AR) signaling is sustained despite treatment of prostate cancer with antiandrogens and potentially underlies development of incurable castrate-resistant prostate cancer. However, therapies targeting the AR signaling axis eventually fail when prostate cancer progresses to the castrate-resistant stage. Stat5a/b, a candidate therapeutic target protein in prostate cancer, synergizes with AR to reciprocally enhance signaling of both proteins. In this work, we demonstrate that Stat5a/b sequesters antiandrogen-liganded (MDV3100, Bicalutamide, Flutamide) AR in prostate cancer cells and protects it against proteasomal degradation in prostate cancer. Active Stat5a/b increased nuclear levels of both unliganded and antiandrogen-liganded AR, as demonstrated in prostate cancer cell lines, xenograft tumors and clinical patient-derived prostate cancer samples. Physical interaction between Stat5a/b and AR in prostate cancer cells was mediated by the DNA-binding domain of Stat5a/b and the N-terminal domain of AR. Moreover, active Stat5a/b increased AR occupancy of the Prostate Specific Antigen promoter and AR-regulated gene expression in prostate cancer cells. Mechanistically, both Stat5a/b genetic knockdown and antiandrogen treatment induced proteasomal degradation of AR in prostate cancer cells, with combined inhibition of Stat5a/b and AR leading to maximal loss of AR protein and prostate cancer cell viability. Our results indicate that therapeutic targeting of AR in prostate cancer using antiandrogens may be substantially improved by targeting of Stat5a/b. PMID:25552366

  13. Impact of enrofloxacin and florfenicol therapy on the spread of OqxAB gene and intestinal microbiota in chickens.

    PubMed

    Chen, Yi; Sun, Jian; Liao, Xiao-Ping; Shao, Yang; Li, Liang; Fang, Liang-Xing; Liu, Ya-Hong

    2016-08-30

    Horizontal transfer of plasmid-encoded multidrug-resistant determinants is a major health problem and has attracted much public attention. We studied the dissemination of the efflux pump gene oqxAB located on transferable plasmid pHXY0908 between Salmonella Typhimurium and Escherichia coli in the gut of chickens. After an inoculation with Salmonella Typhimurium harboring oqxAB-bearing plasmid pHXY0908, chickens were treated with enrofloxacin and florfenicol. Inoculated, but non-treated chickens were included as a control group. Our results revealed that commensal E. coli isolates from the gut of chickens acquired the oqxAB-bearing plasmid in both treated and non-treated groups. Additionally, in the florfenicol treatment group, the average isolation rate of oqxAB-positive E. coli was significantly higher than that in the non-treated group. PFGE analysis showed that oqxAB-positive E. coli strains belonged to different patterns with one predominating. Moreover, multilocus sequence typing analysis revealed that E. coli ST533 was closely associated with the spread of oqxAB gene. qPCR analysis indicated that antibiotic administration provided selective advantages for sustaining a significantly high level of oqxAB gene from the DNA extracted from the feces. There was also a fluctuation in the intestinal microbiota with antibiotic therapy. In conclusion, the present study indicates that the oqxAB gene could be readily spread within the intestinal microflora. This could be enhanced by administrated with clinical doses of florfenicol and enrofloxacin, resulting in the enlargement of resistance gene reservoirs. In addition, ST533 E. coli isolates were found to contribute to transfer of the oqxAB gene. PMID:27527758

  14. Direct measurements of Ab and Ac using vertex and kaon charge tags at the SLAC detector.

    PubMed

    Abe, Koya; Abe, Kenji; Abe, T; Adam, I; Akimoto, H; Aston, D; Baird, K G; Baltay, C; Band, H R; Barklow, T L; Bauer, J M; Bellodi, G; Berger, R; Blaylock, G; Bogart, J R; Bower, G R; Brau, J E; Breidenbach, M; Bugg, W M; Burke, D; Burnett, T H; Burrows, P N; Calcaterra, A; Cassell, R; Chou, A; Cohn, H O; Coller, J A; Convery, M R; Cook, V; Cowan, R F; Crawford, G; Damerell, C J S; Daoudi, M; Dasu, S; de Groot, N; de Sangro, R; Dong, D N; Doser, M; Dubois, R; Erofeeva, I; Eschenburg, V; Etzion, E; Fahey, S; Falciai, D; Fernandez, J P; Flood, K; Frey, R; Hart, E L; Hasuko, K; Hertzbach, S S; Huffer, M E; Huynh, X; Iwasaki, M; Jackson, D J; Jacques, P; Jaros, J A; Jiang, Z Y; Johnson, A S; Johnson, J R; Kajikawa, R; Kalelkar, M; Kang, H J; Kofler, R R; Kroeger, R S; Langston, M; Leith, D W G; Lia, V; Lin, C; Mancinelli, G; Manly, S; Mantovani, G; Markiewicz, T W; Maruyama, T; McKemey, A K; Messner, R; Moffeit, K C; Moore, T B; Morii, M; Muller, D; Murzin, V; Narita, S; Nauenberg, U; Neal, H; Nesom, G; Oishi, N; Onoprienko, D; Osborne, L S; Panvini, R S; Park, C H; Peruzzi, I; Piccolo, M; Piemontese, L; Plano, R J; Prepost, R; Prescott, C Y; Ratcliff, B N; Reidy, J; Reinertsen, P L; Rochester, L S; Rowson, P C; Russell, J J; Saxton, O H; Schalk, T; Schumm, B A; Schwiening, J; Serbo, V V; Shapiro, G; Sinev, N B; Snyder, J A; Staengle, H; Stahl, A; Stamer, P; Steiner, H; Su, D; Suekane, F; Sugiyama, A; Suzuki, A; Swartz, M; Taylor, F E; Thom, J; Torrence, E; Usher, T; Va'vra, J; Verdier, R; Wagner, D L; Waite, A P; Walston, S; Weidemann, A W; Weiss, E R; Whitaker, J S; Williams, S H; Willocq, S; Wilson, R J; Wisniewski, W J; Wittlin, J L; Woods, M; Wright, T R; Yamamoto, R K; Yashima, J; Yellin, S J; Young, C C; Yuta, H

    2005-03-11

    Exploiting the manipulation of the SLAC Linear Collider electron-beam polarization, we present precise direct measurements of the parity-violation parameters A(c) and A(b) in the Z-boson-c-quark and Z-boson-b-quark coupling. Quark-antiquark discrimination is accomplished via a unique algorithm that takes advantage of the precise SLAC Large Detector charge coupled device vertex detector, employing the net charge of displaced vertices as well as the charge of kaons that emanate from those vertices. From the 1996-1998 sample of 400 000 Z decays, produced with an average beam polarization of 73.4%, we find A(c)=0.673+/-0.029(stat)+/-0.023(syst) and A(b)=0.919+/-0.018(stat)+/-0.017(syst). PMID:15783953

  15. Low temperature edge dynamics of AB-stacked bilayer graphene: naturally favored closed zigzag edges.

    PubMed

    Zhan, Da; Liu, Lei; Xu, Ya Nan; Ni, Zhen Hua; Yan, Jia Xu; Zhao, Chun; Shen, Ze Xiang

    2011-01-01

    Closed edges bilayer graphene (CEBG) is a recent discovered novel form of graphene structures, whose regulated edge states may critically change the overall electronic behaviors. If stacked properly with the AB style, the bilayer graphene with closed zigzag edges may even present amazing electronic properties of bandgap opening and charge separation. Experimentally, the CEBG has been confirmed recently with HRTEM observations after extremely high temperature annealing (2000 °C). From the application point of view, the low temperature closing of the graphene edges would be much more feasible for large-scale graphene-based electronic devices fabrication. Here, we demonstrate that the zigzag edges of AB-stacked bilayer graphene will form curved close structure naturally at low annealing temperature (< 500 °C) based on Raman observation and first principles analysis. Such findings may illuminate a simple and easy way to engineer graphene electronics. PMID:22355531

  16. Melting of sodium under high pressure. An ab-initio study

    SciTech Connect

    González, D. J.; González, L. E.

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

  17. Ab initio calculations on the magnetic properties of transition metal complexes

    SciTech Connect

    Bodenstein, Tilmann; Fink, Karin

    2015-12-31

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.

  18. Polysiloxanes: ab initio force field and structural, conformational and thermophysical properties

    NASA Astrophysics Data System (ADS)

    Sun, Huai; Rigby, David

    1997-07-01

    Various levels of ab initio calculation have been performed to determine the optimum strategy for parameterization of the valence parameters of a CFF-type force field for siloxanes and polysiloxanes. Electrostatic nonbond parameters have been determined using scaled electrostatic potential (ESP) charges adjusted for known systematic differences between ab initio and experimental data, while van der Waals nonbond parameters have been determined using a classical approach involving fitting to experimental liquid density and cohesive energy density data measured at atmospheric pressure and a single temperature for a set of four small molecules. Simulations have been performed on molecular crystals, liquids and isolated molecules, yielding results which agree favorably with available experimental data. Properties calculated include unit cell parameters and crystal densities, liquid densities from 303-473 K and 0-1800 bar, dependence of oligomer density and solubility parameters on chain length and temperature, gas-phase geometries and vibrational frequencies, and gas and liquid-phase conformational behavior.

  19. Spectroscopic evidence supporting the gravitational lens hypothesis for 1635+267 A,B

    NASA Technical Reports Server (NTRS)

    Turner, Edwin L.; Hillenbrand, Lynne A.; Schneider, Donald P.; Hewitt, Jacqueline N.; Burke, Bernard F.

    1988-01-01

    The gravitational lens hypothesis is tested for 1613+267 A,B by comparing the detailed line widths and shapes of the 2799-A Mg II and semiforbidden 1909-A C-III lines in each component. Following subtraction of an interpolating polynomial fit to the continua and the determination of a single optimum scaling factor (an amplification ratio of 2.83), reasonable agreement between the profiles of both lines in the two composites is obtained. Comparison of these lines to those in an unrelated quasar with a similar redshift and apparent magnitude does not produce a good match. It is suggested that the observed match in the 1635+267 A,B spectra arises from gravitational lensing.

  20. Comparison between ab initio and semiempirical net atomic charges of some nicotinic acetylcholine receptor agonists

    SciTech Connect

    Yadav, J.S.; Hermsmeier, M.; Gund, T. )

    1989-01-01

    We have calculated the net atomic charges and molecular electrostatic potentials of two potent nicotinic acetylcholine receptor agonists, isoarecolone and acetylpiperazine, by three different methods to see how well they correlate and if the simplest method gives the same predictive results. The calculational methods involved calculating net atomic charges by semiempirical (MNDO from MOPAC) and ab initio (Mulliken) and ab initio (potential derived) at STO-3G basis set level. Some deviations were observed when comparisons were made atom by atom, but when group comparisons were made, good correlations were observed. When these partial charges were used to calculate the respective molecular electrostatic potentials on the van der Waals surface, very good correlations were obtained. This study shows that for routine electrostatic calculations, semiempirical MNDO Calculations give similar results and thus lead to similar predictions.