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Sample records for single ion binding

  1. The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

    NARCIS (Netherlands)

    Vos, H.L.; Lee, F.M. van der; Sussenbach, J.S.

    1988-01-01

    We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that

  2. Binding energy of protonium ions

    Science.gov (United States)

    Assad Abdel-Raouf, Mohamed

    2009-11-01

    The goal of the present work is to calculate the binding energy of the protonium ions bar PPe+ and bar PPe- using Rayleigh- Ritz variational method. It is indicated that an employment of 21 components of the trial wavefunction yields -0.08793 eV as the ground state energy of these ions. Our result agrees quite well with recently obtained results based on elaborate Monte Carlo approximations. It confirms the possible formation of these ions in laboratory.

  3. Dissociation kinetics of excited ions: PEPICO measurements of Os3(CO)12 — The 7-35 eV single ionization binding energy region

    Science.gov (United States)

    Schalk, Oliver; Josefsson, Ida; Geng, Ting; Richter, Robert; Sa'adeh, Hanan; Thomas, Richard D.; Mucke, Melanie

    2018-02-01

    In this article, we study the photoinduced dissociation pathways of a metallocarbonyl, Os3(CO)12, in particular the consecutive loss of CO groups. To do so, we performed photoelectron-photoion coincidence (PEPICO) measurements in the single ionization binding energy region from 7 to 35 eV using 45-eV photons. Zero-energy ion appearance energies for the dissociation steps were extracted by modeling the PEPICO data using the statistical adiabatic channel model. Upon ionization to the excited ionic states above 13 eV binding energy, non-statistical behavior was observed and assigned to prompt CO loss. Double ionization was found to be dominated by the knockout process with an onset of 20.9 ± 0.4 eV. The oscillator strength is significantly larger for energies above 26.6 ± 0.4 eV, corresponding to one electron being ejected from the Os3 center and one from the CO ligands. The cross section for double ionization was found to increase linearly up to 35 eV ionization energy, at which 40% of the generated ions are doubly charged.

  4. Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein.

    Science.gov (United States)

    Politis, Argyris; Park, Ah Young; Hall, Zoe; Ruotolo, Brandon T; Robinson, Carol V

    2013-11-29

    DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit clamp loader complex, is responsible for loading the sliding clamp (β2) onto DNA. Here, we use structural information derived from ion mobility mass spectrometry (IM-MS) to build three-dimensional models of one form of the full clamp loader complex, γ3δδ'ψχ (254 kDa). By probing the interaction between the clamp loader and a single-stranded DNA (ssDNA) binding protein (SSB4) and by identifying two distinct conformational states, with and without ssDNA, we assemble models of ψχ-SSB4 (108 kDa) and the clamp loader-SSB4 (340 kDa) consistent with IM data. A significant increase in measured collision cross-section (~10%) of the clamp loader-SSB4 complex upon DNA binding suggests large conformational rearrangements. This DNA bound conformation represents the active state and, along with the presence of ψχ, stabilises the clamp loader-SSB4 complex. Overall, this study of a large heteromeric complex analysed by IM-MS, coupled with integrative modelling, highlights the potential of such an approach to reveal structural features of previously unknown complexes of high biological importance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Single Cathode Ion Thruster

    Data.gov (United States)

    National Aeronautics and Space Administration — Objective is to design an electrostatic ion thruster that is more efficient, simpler, and lower cost than the current gridded ion thruster. Initial objective is to...

  6. Binding of corroded ions to human saliva.

    Science.gov (United States)

    Mueller, H J

    1985-05-01

    Employing equilibrium dialysis, the binding abilities of Cu, Al, Co and Cr ions from corroded Cu-Al and Co-Cr dental casting alloys towards human saliva and two of its gel chromatographic fractions were determined. Results indicate that both Cu and Co bind to human saliva i.e. 0.045 and 0.027 mg/mg protein, respectively. Besides possessing the largest binding ability, Cu also possessed the largest binding capacity. The saturation of Cu binding was not reached up to the limit of 0.35 mg protein/ml employed in the tests, while Co reached full saturation at about 0.2 mg protein/ml. Chromium showed absolutely no binding to human saliva while Al ions did not pass through the dialysis membranes. Compared to the binding with solutions that were synthetically made up to contain added salivary-type proteins, it is shown that the binding to human saliva is about 1 order of magnitude larger, at least for Cu ions.

  7. Europium ion as a probe for binding sites to carrageenans

    International Nuclear Information System (INIS)

    Ramos, Ana P.; Goncalves, Rogeria R.; Serra, Osvaldo A.; Zaniquelli, Maria Elisabete D.; Wong, Kenneth

    2007-01-01

    Carrageenans, sulfated polysaccharides extracted from red algae, present a coil-helix transition and helix aggregation dependence on the type and concentration of counterions. In this study, we focus attention on a mixed valence counterion system: Eu 3+ /Na + or K + with different gel-forming carrageenans: kappa, iota, and kappa-2. Results of stationary and time-dependent luminescence showed to be a suitable tool to probe ion binding to both the negatively charged sulfate group and the hydroxyl groups present in the biopolymer. For lower europium ion concentrations, a single longer decay emission lifetime was detected, which was attributed to the binding of europium ion to the carrageenan sulfate groups. An additional decay ascribed to europium binding to hydroxyl groups was observed above a threshold concentration, and this decay was dependent on the carrageenan charge density. Symmetry of the europium ion microenvironment was estimated by the ratio between the intensities of its emission bands, which has been shown to depend on the concentration of europium ions and on the specificity of the monovalent counterion bound to the carrageenan

  8. Metal ion binding with dehydroannulenes – Plausible two ...

    Indian Academy of Sciences (India)

    WINTEC

    Abstract. Theoretical investigations have been carried out at B3LYP/6-311++G** level of theory to study the binding interaction of various metal ions, Li+, Na+ and K+ with dehydroannulene systems. The present study reveals that alkali metal ions bind strongly to dehydroannulenes and the passage through the central.

  9. Importance of diffuse metal ion binding to RNA.

    Science.gov (United States)

    Tan, Zhi-Jie; Chen, Shi-Jie

    2011-01-01

    RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

  10. Single ion dynamics in molten sodium bromide

    Energy Technology Data Exchange (ETDEWEB)

    Alcaraz, O.; Trullas, J. [Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, 08034 Barcelona (Spain); Demmel, F. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom)

    2014-12-28

    We present a study on the single ion dynamics in the molten alkali halide NaBr. Quasielastic neutron scattering was employed to extract the self-diffusion coefficient of the sodium ions at three temperatures. Molecular dynamics simulations using rigid and polarizable ion models have been performed in parallel to extract the sodium and bromide single dynamics and ionic conductivities. Two methods have been employed to derive the ion diffusion, calculating the mean squared displacements and the velocity autocorrelation functions, as well as analysing the increase of the line widths of the self-dynamic structure factors. The sodium diffusion coefficients show a remarkable good agreement between experiment and simulation utilising the polarisable potential.

  11. Metal ion binding with dehydroannulenes – Plausible two ...

    Indian Academy of Sciences (India)

    WINTEC

    has highest interaction energy of –50∙6 kcal/mol at. B3LYP/6-311++G** level and is 128∙0 kcal/mol more than 1′-K+ complex. Understandably, the binding energy of metal complexes decreases with increase in the size of the metal ion, in accordance with ear- lier results.16,21. Placement of the metal ions at the centroid of ...

  12. High Affinity Binding of Indium and Ruthenium Ions by Gastrins.

    Directory of Open Access Journals (Sweden)

    Graham S Baldwin

    Full Text Available The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd of 3.3 x 10-7 and 1.1 x 10-6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10-15 and 1.7 x 10-7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10-13 and 1.2 x 10-5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0-3.3 Å, the Ru complex clearly demonstrated a short range Ru-Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy.

  13. Single-ion nonlinear mechanical oscillator

    International Nuclear Information System (INIS)

    Akerman, N.; Kotler, S.; Glickman, Y.; Dallal, Y.; Keselman, A.; Ozeri, R.

    2010-01-01

    We study the steady-state motion of a single trapped ion oscillator driven to the nonlinear regime. Damping is achieved via Doppler laser cooling. The ion motion is found to be well described by the Duffing oscillator model with an additional nonlinear damping term. We demonstrate here the unique ability of tuning both the linear as well as the nonlinear damping coefficients by controlling the laser-cooling parameters. Our observations pave the way for the investigation of nonlinear dynamics on the quantum-to-classical interface as well as mechanical noise squeezing in laser-cooling dynamics.

  14. Chirality-induced conformational preferences in peptide-metal ion binding revealed by IR spectroscopy

    NARCIS (Netherlands)

    Dunbar, R.C.; Steill, J.D.; Oomens, J.

    2011-01-01

    Chirality reversal of a residue in a peptide can change its mode of binding to a metal ion, as shown here experimentally by gas-phase IR spectroscopy of peptide−metal ion complexes. The binding conformations of Li+, Na+, and H+ with the ll and dl stereoisomers of PhePhe were compared through IR ion

  15. Chirality-Induced Conformational Preferences in Peptide-Metal Ion Binding Revealed by IR Spectroscopy

    NARCIS (Netherlands)

    Dunbar, R. C.; Steill, J. D.; Oomens, J.

    2011-01-01

    Chirality reversal of a residue in a peptide can change its mode of binding to a metal ion, as shown here experimentally by gas-phase IR spectroscopy of peptide metal ion complexes. The binding conformations of Li+, Na+, and H+ with the LL and DL stereoisomers of PhePhe were compared through IR ion

  16. Towards single Ce ion detection in a bulk crystal for the development of a single-ion qubit readout scheme

    OpenAIRE

    Yan, Ying

    2013-01-01

    The work presented in this thesis was concerned with investigating the relevant spectroscopic properties of Ce ions randomly doped in an Y2SiO5 crystal at low temperatures (around 4 K), in order to develop a technique and an experimental set-up to detect the fluorescence photons emitted by a single Ce ion. The aim of the work was to determine whether a single Ce ion (referred to as the readout ion) can be used as a local probe to sense the quantum state of a neighbouring single-ion qubit via ...

  17. Coherent Control of a Single Trapped Rydberg Ion

    Science.gov (United States)

    Higgins, Gerard; Pokorny, Fabian; Zhang, Chi; Bodart, Quentin; Hennrich, Markus

    2017-12-01

    Trapped Rydberg ions are a promising novel approach to quantum computing and simulations. They are envisaged to combine the exquisite control of trapped ion qubits with the fast two-qubit Rydberg gates already demonstrated in neutral atom experiments. Coherent Rydberg excitation is a key requirement for these gates. Here, we carry out the first coherent Rydberg excitation of an ion and perform a single-qubit Rydberg gate, thus demonstrating basic elements of a trapped Rydberg ion quantum computer.

  18. Single ion counting with a MCP (microchannel plate) detector

    Energy Technology Data Exchange (ETDEWEB)

    Tawara, Hiroko; Sasaki, Shinichi; Miyajima, Mitsuhiro [National Lab. for High Energy Physics, Tsukuba, Ibaraki (Japan); Shibamura, Eido

    1996-07-01

    In this study, a single-ion-counting method using alpha-particle-impact ionization of Ar atoms is demonstrated and the preliminary {epsilon}{sub mcp} for Ar ions with incident energies of 3 to 4.7 keV is determined. The single-ion counting by the MCP is aimed to be performed under experimental conditions as follows: (1) A signal from the MCP is reasonably identified as incidence of single Ar-ion. (2) The counting rate of Ar ions is less than 1 s{sup -1}. (3) The incident Ar ions are not focused on a small part of an active area of the MCP, namely, {epsilon}{sub mcp} is determined with respect to the whole active area of the MCP. So far, any absolute detection efficiency has not been reported under these conditions. (J.P.N.)

  19. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

    Energy Technology Data Exchange (ETDEWEB)

    Lipfert, Jan; Sim, Adelene Y.L.; Herschlag, Daniel; Doniach, Sebastian (Stanford)

    2010-09-17

    Riboswitches are gene-regulating RNAs that are usually found in the 5{prime}-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg{sup 2+}, Ca{sup 2+}, and Mn{sup 2+} facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.

  20. SINGLE AND DOUBLE IMPRINTED POLYMER FOR SELECTIVE RECOGNITION OF Cd(II IONS IN AQUEOUS MEDIA

    Directory of Open Access Journals (Sweden)

    Ebru Birlik ÖZKÜTÜK

    2010-12-01

    Full Text Available In this paper, we have reported the synthesis of a new single and double-imprinted polymeric material for the separation of Cd(II ions in aqueous solutions. Chitosan has choosen as the Cd(II metal complexing big polymer for single and double imprinted polymers. In the synthesis of single imprinted polymer, Cd(II-complexed chitosan has crosslinked by epichlorohydrin. In the synthesis of double imprinted polymer, Cd(II-complexed chitosan was reacted with 3-mercaptopropyl-trimethoxysilane. Then, the polymeric beads have crosslinked with tetraethoxysilane (TEOS. The imprinted cadmium ions have removed from the polymeric matrix by 0.1M HNO3 (to prepare Cd(II templates. Optimum pH for rebinding of Cd(II on the single and double-imprinted polymers was 7.0. Equilibrium binding time and sorbent capacity have been found as 120 and 60 min, 342 and 172 mg g-1 for single and double imprinted polymers, respectively. In selectivity studies, it has been found that double imprinted results in increased affinity of the material toward Cd(II ion over other competitor metal ions with the same charge. The prepared single and double-imprinted polymers have repeatedly used and regenerated for thirty times without a significant decrease in polymer binding affinities.

  1. Automated parallel recordings of topologically identified single ion channels.

    Science.gov (United States)

    Kawano, Ryuji; Tsuji, Yutaro; Sato, Koji; Osaki, Toshihisa; Kamiya, Koki; Hirano, Minako; Ide, Toru; Miki, Norihisa; Takeuchi, Shoji

    2013-01-01

    Although ion channels are attractive targets for drug discovery, the systematic screening of ion channel-targeted drugs remains challenging. To facilitate automated single ion-channel recordings for the analysis of drug interactions with the intra- and extracellular domain, we have developed a parallel recording methodology using artificial cell membranes. The use of stable lipid bilayer formation in droplet chamber arrays facilitated automated, parallel, single-channel recording from reconstituted native and mutated ion channels. Using this system, several types of ion channels, including mutated forms, were characterised by determining the protein orientation. In addition, we provide evidence that both intra- and extracellular amyloid-beta fragments directly inhibit the channel open probability of the hBK channel. This automated methodology provides a high-throughput drug screening system for the targeting of ion channels and a data-intensive analysis technique for studying ion channel gating mechanisms.

  2. Single track regime in ion implanted polystyrene

    Energy Technology Data Exchange (ETDEWEB)

    Licciardello, A.; Puglisi, O.; Calcagno, L.; Foti, G.

    1988-05-01

    The molecular weight distribution (MWD) of nearly monodisperse polystyrene thin films is heavily affected by ion bombardment. The main effect is an increase of the MW and is detectable at fluences as low as 10/sup 11/ ions cm/sup -2/ for 400 keV Ar/sup +/ bombardment. A statistical model, here outlined for the first time, allows us the predict the size distribution of these high MW components. From the analysis of the MWD curves one can extract useful information concerning the lateral dimensions of the ion tracks.

  3. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry.

    Science.gov (United States)

    Krainer, Georg; Keller, Sandro

    2015-04-01

    Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Generic NICA-Donnan model parameters for metal-ion binding by humic substances

    NARCIS (Netherlands)

    Milne, C.J.; Kinniburgh, D.G.; Riemsdijk, van W.H.; Tipping, E.

    2003-01-01

    A total of 171 datasets of literature and experimental data for metal-ion binding by fulvic and humic acids have been digitized and re-analyzed using the NICA-Donnan model. Generic parameter values have been derived that can be used for modeling in the absence of specific metal-ion binding

  5. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-01-01

    Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

  6. Engineering bispecificity into a single albumin-binding domain.

    Directory of Open Access Journals (Sweden)

    Johan Nilvebrant

    Full Text Available Bispecific antibodies as well as non-immunoglobulin based bispecific affinity proteins are considered to have a very high potential in future biotherapeutic applications. In this study, we report on a novel approach for generation of extremely small bispecific proteins comprised of only a single structural domain. Binding to tumor necrosis factor-α (TNF-α was engineered into an albumin-binding domain while still retaining the original affinity for albumin, resulting in a bispecific protein composed of merely 46 amino acids. By diversification of the non albumin-binding side of the three-helix bundle domain, followed by display of the resulting library on phage particles, bispecific single-domain proteins were isolated using selections with TNF-α as target. Moreover, based on the obtained sequences from the phage selection, a second-generation library was designed in order to further increase the affinity of the bispecific candidates. Staphylococcal surface display was employed for the affinity maturation, enabling efficient isolation of improved binders as well as multiparameter-based sortings with both TNF-α and albumin as targets in the same selection cycle. Isolated variants were sequenced and the binding to albumin and TNF-α was analyzed. This analysis revealed an affinity for TNF-α below 5 nM for the strongest binders. From the multiparameter sorting that simultaneously targeted TNF-α and albumin, several bispecific candidates were isolated with high affinity to both antigens, suggesting that cell display in combination with fluorescence activated cell sorting is a suitable technology for engineering of bispecificity. To our knowledge, the new binders represent the smallest engineered bispecific proteins reported so far. Possibilities and challenges as well as potential future applications of this novel strategy are discussed.

  7. Studies on the Binding of Lead and Zinc Ions by Modified Cellulosic ...

    African Journals Online (AJOL)

    substrate contact time, the metal ion concentration, the metal ion type and the substrate type. The amount of these ions absorbed varies with the cellulosic material and in the order Pb (II) > Zn (II). It is shown that the cellulosic materials could bind ...

  8. A compact source for bunches of singly charged atomic ions

    Science.gov (United States)

    Murböck, T.; Schmidt, S.; Andelkovic, Z.; Birkl, G.; Nörtershäuser, W.; Vogel, M.

    2016-04-01

    We have built, operated, and characterized a compact ion source for low-energy bunches of singly charged atomic ions in a vacuum beam line. It is based on atomic evaporation from an electrically heated oven and ionization by electron impact from a heated filament inside a grid-based ionization volume. An adjacent electrode arrangement is used for ion extraction and focusing by applying positive high-voltage pulses to the grid. The method is particularly suited for experimental environments which require low electromagnetic noise. It has proven simple yet reliable and has been used to produce μs-bunches of up to 106 Mg+ ions at a repetition rate of 1 Hz. We present the concept, setup and characterizing measurements. The instrument has been operated in the framework of the SpecTrap experiment at the HITRAP facility at GSI/FAIR to provide Mg+ ions for sympathetic cooling of highly charged ions by laser-cooled 24Mg+.

  9. short communication binding of nickel and zinc ions with activated ...

    African Journals Online (AJOL)

    a

    Equilibrium sorption of nickel and zinc ions by the activated carbon was studied using a range of metal ion concentrations. The sorption data was observed to have an adequate fit for the. Langmuir isotherm equation. The level of metal ion uptake was found to be of the order: Ni2+ >. Zn2+. The difference in the removal ...

  10. Anisotropic Lithium Ion Conductivity in Single-Ion Diblock Copolymer Electrolyte Thin Films

    NARCIS (Netherlands)

    Aissou, Karim; Mumtaz, Muhammad; Usluer, Özlem; Pécastaings, Gilles; Portale, Giuseppe; Fleury, Guillaume; Cloutet, Eric; Hadziioannou, Georges

    Well-defined single-ion diblock copolymers consisting of a Li-ion conductive poly(styrenesulfonyllithium(trifluoromethylsulfonyl)imide) (PSLiTFSI) block associated with a glassy polystyrene (PS) block have been synthesized via reversible addition fragmentation chain transfer polymerization.

  11. Conduction in ion implanted single crystal diamond

    International Nuclear Information System (INIS)

    Hunn, J.D.; Parikh, N.R.; Swanson, M.L.

    1992-01-01

    We have implanted sodium, phosphorus and arsenic into single crystal type IIa diamond as possible n-type dopants. Particular emphasis was applied to the implantation of sodium at different temperatures and doses; combined implantation energies of 55,80 and 120 keV were used to provide a uniformly doped layer over approximately 100 nm depth. The implanted layers exhibited semiconducting behavior with a single exponential activation energy between 0.40 and 0.48 eV, as determined by temperature dependent resistance measurements. A sample implanted to a concentration of 5.10 19 Na + /cm 3 at 550 degrees C exhibited a single activation energy of 0.415 eV over a temperature range from 25 to 500 degrees C. Thermal annealing above 900 degrees C was found to remove implantation damage as measured by optical absorption and RBS/channeling. However, concomitant increases in the resistance and the activation energy were observed. Implantation of 22 Ne was used to introduce a damage density equivalent to the 23 Na implant, while not introducing an electrically active species. The activation energy and electrical resistance were similar but higher than those produced by implantation with sodium. We conclude that the electrical properties of the Na-implanted samples were at least partly due to electrically active Na, but that residual implantation damage was still important

  12. Localization Spectroscopy of a Single Ion in an Optical Lattice

    DEFF Research Database (Denmark)

    Legrand, Olivier Philippe Alexandre

    2015-01-01

    The work reported in this thesis primarily focuses on studies of the dynamics of a single laser-cooled ion, simultaneously confined in the harmonic potential of a linear Paul trap and a rapidly varying periodic potential – a so-called optical lattice – generated from an optical standing-wave. Bes......The work reported in this thesis primarily focuses on studies of the dynamics of a single laser-cooled ion, simultaneously confined in the harmonic potential of a linear Paul trap and a rapidly varying periodic potential – a so-called optical lattice – generated from an optical standing...... calibration and analysis of the detection system, several theoretical simulations of the expected dynamics and associated optical response of the ion were undertaken. Finally, a new laser source based on second harmonic generation was developed in order to perform laser-cooling of Ca+ ions, and to serve...

  13. Calculated distortions induced by metal-ion binding to simple oligonucleotide systems: Implications for toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Turner, J.E.; Hingerty, B.E.; England, M.W.; Jacobson, K.B.

    1990-01-01

    We have previously published detailed results of calculations of the binding of the metal ions, Cd{sup 2+} and Ca{sup 2+}, to the dinucleoside monophosphate GpC in water. These ions, which have the same charge and radius, differ enormously in their toxicity to man and other biological systems. Our calculations showed contrasting behavior in the binding of these two metal ions to GpC. We suggest the hypothesis that structural distortions calculated for metal ions binding to simple nucleic-acid systems might serve as a indicator of an ion's potential ability to alter molecular activity and hence to be toxic to an organism. Furthermore, the degree of distortion might be correlated with the degree of toxicity as measured by some suitable criteria. The present paper reports the results of binding calculations for a number of other metal ions, of different valence states, with several dinucleoside monophosphates in water. A general trend of distortion with the type of binding of the metal ions is found. We are seeking quantitative measures of distortion to correlate with indicators of acute toxicity that we have measured for 24 metal ions using mice, Drosophila, and CHO cells. 3 refs., 3 figs.

  14. Ion implantation induced blistering of rutile single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Bing-Xi [School of Physics, Shandong University, Jinan, Shandong 250100 (China); Jiao, Yang [College of Physics and Electronics, Shandong Normal University, Jinan, Shandong 250100 (China); Guan, Jing [School of Physics, Shandong University, Jinan, Shandong 250100 (China); Wang, Lei [School of Physics, Shandong University, Jinan, Shandong 250100 (China); Key Laboratory of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences (China)

    2015-07-01

    The rutile single crystals were implanted by 200 keV He{sup +} ions with a series fluence and annealed at different temperatures to investigate the blistering behavior. The Rutherford backscattering spectrometry, optical microscope and X-ray diffraction were employed to characterize the implantation induced lattice damage and blistering. It was found that the blistering on rutile surface region can be realized by He{sup +} ion implantation with appropriate fluence and the following thermal annealing.

  15. Single Ion Trapping for the Enriched Xenon Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Waldman, Samuel J.; /Stanford U., Phys. Dept. /SLAC

    2006-03-28

    In the last decade, a variety of neutrino oscillation experiments have established that there is a mass difference between neutrino flavors, without determining the absolute neutrino mass scale. The Enriched Xenon Observatory for neutrinoless double beta decay (EXO) will search for the rare decays of xenon to determine the absolute value of the neutrino mass. The experiment uses a novel technique to minimize backgrounds, identifying the decay daughter product in real time using single ion spectroscopy. Here, we describe single ion trapping and spectroscopy compatible with the EXO detector. We extend the technique of single ion trapping in ultrahigh vacuum to trapping in xenon gas. With this technique, EXO will achieve a neutrino mass sensitivity of {approx_equal} .010 eV.

  16. Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

    International Nuclear Information System (INIS)

    Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

    2012-01-01

    Highlights: ► Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio. ► The binding constant between Hg 2+ and the T:T mismatched base pair was 10 6 M −1 . ► The binding constant was larger than those for nonspecific metal–DNA interactions. ► The binding constant for the second Hg 2+ was larger than that for the first Hg 2+ . ► The positive cooperative binding was observed between Hg 2+ and multiple T:T. - Abstract: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg 2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg 2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 10 6 M −1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg 2+ –double T:T mismatched base pair interaction, the affinity for the second Hg 2+ binding was significantly larger than that for the first Hg 2+ binding. The positively cooperative binding may be favorable to align multiple Hg 2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

  17. Molecular mechanism of ATP binding and ion channel activation in P2X receptors

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, Motoyuki; Gouaux, Eric (Oregon HSU)

    2012-10-24

    P2X receptors are trimeric ATP-activated ion channels permeable to Na{sup +}, K{sup +} and Ca{sup 2+}. The seven P2X receptor subtypes are implicated in physiological processes that include modulation of synaptic transmission, contraction of smooth muscle, secretion of chemical transmitters and regulation of immune responses. Despite the importance of P2X receptors in cellular physiology, the three-dimensional composition of the ATP-binding site, the structural mechanism of ATP-dependent ion channel gating and the architecture of the open ion channel pore are unknown. Here we report the crystal structure of the zebrafish P2X4 receptor in complex with ATP and a new structure of the apo receptor. The agonist-bound structure reveals a previously unseen ATP-binding motif and an open ion channel pore. ATP binding induces cleft closure of the nucleotide-binding pocket, flexing of the lower body {beta}-sheet and a radial expansion of the extracellular vestibule. The structural widening of the extracellular vestibule is directly coupled to the opening of the ion channel pore by way of an iris-like expansion of the transmembrane helices. The structural delineation of the ATP-binding site and the ion channel pore, together with the conformational changes associated with ion channel gating, will stimulate development of new pharmacological agents.

  18. Ion Source Multiplexing on a Single Mass Spectrometer.

    Science.gov (United States)

    Kostyukevich, Yury; Nikolaev, Eugene

    2018-03-06

    We present the simple approach for the combination of different ion sources on a single mass spectrometer without any interference between them. Each ion source can be positioned as far as 1 m from the mass spectrometer; ions are transported by the means of flexible copper tubes, which are connected, to the separate inlet capillaries. Special valves enable switching channels on and off. Using this approach, we successfully combined native electrospray ionization (ESI), regular ESI, β-electrons ionization, and atmospheric pressure photoionization (APPI) of thermally desorbed vapors of petroleum on a single mass spectrometer. In addition, separate channels allow infusing internal calibration mixture or performing ion molecular reactions in one channel and using the other as a reference. Using this idea, we have developed an original sequential window acquisition of all theoretical mass spectra (SWATH MS) approach in which peptide ions are transported in different channels, one of which is heated to high temperature so that ions are thermally fragmented, and the other channel ensures the presence of nonfragmented ions in the spectrum. Also, we demonstrated the possibility to perform gas phase H/D exchange reaction in one channel and using another as reference. Use of valves makes it possible to exclude any interference between them. Thus, we have demonstrated the possibility to create a multichannel system in which ions would be transported through several inlet tubes in which different ion molecular reactions such as Paternò-Büchi, ozonation, or H/D exchange will occur. Comparison of mass spectra recorded when different channels are open will provide structural and chemical information about unknown species.

  19. Modification of ion implanted or irradiated single crystal sapphire

    International Nuclear Information System (INIS)

    Song Yin; Zhang Chonghong; Wang Zhiguang; Zhao Zhiming; Yao Cunfeng; Zhou Lihong; Jin Yunfan

    2006-01-01

    Single crystal sapphire (Al 2 O 3 ) samples were implanted at 600 K by He, Ne and Ar ions with energy of 110 keV to doses ranging from 5 x 10 16 to 2 x 10 17 ion/cm 2 or irradiated at 320 K by 208 Pb 27+ ion with energy of 1.1 MeV/u to the fluences ranging from 1 x 10 12 to 5 x 10 14 ion/cm 2 . The modification of structure and optical properties induced by ion implantation or irradiation were analyzed by using photoluminescence (PL) and Fourier transformation infrared spectrum (FTIR) spectra and transmission electron microscopy (TEM) measurements. The PL measurements showed that absorption peaks located at 375, 413 and 450 nm appeared in all the implanted or irradiated samples, the PL intensities reached up to the maximum for the 5 x 10 16 ion/cm 2 implanted samples. After Pb-ion irradiation, a new peak located at 390 nm formed. TEM analyses showed that small size voids (1-2 nm) with high density were formed in the region from the surface till to about 100 nm in depth and also large size Ne-bubble formed in the Ne-doped region. Form the obtained FTIR spectra, it was found that Pb-ion irradiation induced broadening of the absorption band in 460-510 cm -1 and position shift of the absorption band in 1000-1300 cm -1 towards to high wavenumber. The possible damage mechanism in single crystal sapphire induced by energetic ion implantation or irradiation was briefly discussed. (authors)

  20. short communication binding of nickel and zinc ions with activated ...

    African Journals Online (AJOL)

    a

    ABSTRACT. Activated carbon was prepared from sugar cane fibre by carbonizing at 500 oC for 30 minutes. ... Equilibrium sorption of nickel and zinc ions by the activated carbon was studied using a range of metal ion .... which means that limited sorption cycles will be required in the treatment of waste water containing the ...

  1. Single Molecule Kinetics of ENTH Binding to Lipid Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Rozovsky, Sharon [Univ. of Delaware, Newark, DE (United States); Forstner, Martin B. [Syracuse Univ., NY (United States); Sondermann, Holger [Cornell Univ., Ithaca, NY (United States); Groves, Jay T. [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-04-03

    Transient recruitment of proteins to membranes is a fundamental mechanism by which the cell exerts spatial and temporal control over proteins’ localization and interactions. Thus, the specificity and the kinetics of peripheral proteins’ membrane residence are an attribute of their function. In this article, we describe the membrane interactions of the interfacial epsin N-terminal homology (ENTH) domain with its target lipid phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2). The direct visualization and quantification of interactions of single ENTH molecules with supported lipid bilayers is achieved using total internal reflection fluorescence microscopy (TIRFM) with a time resolution of 13 ms. This enables the recording of the kinetic behavior of ENTH interacting with membranes with physiologically relevant concentrations of PtdIns(4,5)P2 despite the low effective binding affinity. Subsequent single fluorophore tracking permits us to build up distributions of residence times and to measure ENTH dissociation rates as a function of membrane composition. In addition, due to the high time resolution, we are able to resolve details of the motion of ENTH associated with a simple, homogeneous membrane. In this case ENTH’s diffusive transport appears to be the result of at least three different diffusion processes.

  2. Surface noise analysis using a single-ion sensor

    Science.gov (United States)

    Daniilidis, N.; Gerber, S.; Bolloten, G.; Ramm, M.; Ransford, A.; Ulin-Avila, E.; Talukdar, I.; Häffner, H.

    2014-06-01

    We use a single-ion electric-field noise sensor in combination with in situ surface treatment and analysis tools, to investigate the relationship between electric-field noise from metal surfaces in vacuum and the composition of the surface. These experiments are performed in a setup that integrates ion trapping capabilities with surface analysis tools. We find that treatment of an aluminum-copper surface with energetic argon ions significantly reduces the level of room-temperature electric-field noise, but the surface does not need to be atomically clean to show noise levels comparable to those of the best cryogenic traps. The noise levels after treatment are low enough to allow fault-tolerant trapped-ion quantum information processing on a microfabricated surface trap at room temperature.

  3. Ions in size-selected aqueous nanodrops: sequential water molecule binding energies and effects of water on ion fluorescence.

    Science.gov (United States)

    Donald, William A; Leib, Ryan D; Demireva, Maria; Williams, Evan R

    2011-11-23

    The effects of water on ion fluorescence were investigated, and average sequential water molecule binding energies to hydrated ions, M(z)(H(2)O)(n), at large cluster size were measured using ion nanocalorimetry. Upon 248-nm excitation, nanodrops with ~25 or more water molecules that contain either rhodamine 590(+), rhodamine 640(+), or Ce(3+) emit a photon with average energies of approximately 548, 590, and 348 nm, respectively. These values are very close to the emission maxima of the corresponding ions in solution, indicating that the photophysical properties of these ions in the nanodrops approach those of the fully hydrated ions at relatively small cluster size. As occurs in solution, these ions in nanodrops with 8 or more water molecules fluoresce with a quantum yield of ~1. Ce(3+) containing nanodrops that also contain OH(-) fluoresce, whereas those with NO(3)(-) do not. This indirect fluorescence detection method has the advantages of high sensitivity, and both the size of the nanodrops as well as their constituents can be carefully controlled. For ions that do not fluoresce in solution, such as protonated tryptophan, full internal conversion of the absorbed 248-nm photon occurs, and the average sequential water molecule binding energies to the hydrated ions can be accurately obtained at large cluster sizes. The average sequential water molecule binding energies for TrpH(+)(H(2)O)(n) and a doubly protonated tripeptide, [KYK + 2H](2+)(H(2)O)(n), approach asymptotic values of ~9.3 (n ≥ 11) and ~10.0 kcal/mol (n ≥ 25), respectively, consistent with a liquidlike structure of water in these nanodrops.

  4. Production and Characterization of Desmalonichrome Relative Binding Affinity for Uranyl Ions in Relation to Other Siderophores

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Kai-For; Dai, Ziyu; Wunschel, David S.

    2016-06-24

    Siderophores are Fe binding secondary metabolites that have been investigated for their uranium binding properties. Much of the previous work has focused on characterizing hydroxamate types of siderophores, such as desferrioxamine B, for their uranyl binding affinity. Carboxylate forms of these metabolites hold potential to be more efficient chelators of uranyl, yet they have not been widely studied and are more difficult to obtain. Desmalonichrome is a carboxylate siderophore which is not commercially available and so was obtained from the ascomycete fungus Fusarium oxysporum cultivated under Fe depleted conditions. The relative affinity for uranyl binding of desmalonichrome was investigated using a competitive analysis of binding affinities between uranyl acetate and different concentrations of iron(III) chloride using electrospray ionization mass spectrometry (ESI-MS). In addition to desmalonichrome, three other siderophores, including two hydroxamates (desferrioxamine B and desferrichrome) and one carboxylate (desferrichrome A) were studied to understand their relative affinities for the uranyl ion at two pH values. The binding affinities of hydroxymate siderophores to uranyl ion were found to decrease to a greater degree at lower pH as the concentration of Fe (III) ion increases. On the other hand, lowering pH has little impact on the binding affinities between carboxylate siderophores and uranyl ion. Desmalonichrome was shown to have the greatest relative affinity for uranyl at any pH and Fe(III) concentration. These results suggest that acidic functional groups in the ligands are critical for strong chelation with uranium at lower pH.

  5. MeRNA: a Database of Metal Ion Binding Sites in RNAStructures

    Energy Technology Data Exchange (ETDEWEB)

    Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E.; Holbrook, Stephen R.

    2005-10-05

    Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

  6. Single qubit manipulation in a microfabricated surface electrode ion trap

    Science.gov (United States)

    Mount, Emily; Baek, So-Young; Blain, Matthew; Stick, Daniel; Gaultney, Daniel; Crain, Stephen; Noek, Rachel; Kim, Taehyun; Maunz, Peter; Kim, Jungsang

    2013-09-01

    We trap individual 171Yb+ ions in a surface trap microfabricated on a silicon substrate, and demonstrate a complete set of high fidelity single qubit operations for the hyperfine qubit. Trapping times exceeding 20 min without laser cooling, and heating rates as low as 0.8 quanta ms-1, indicate stable trapping conditions in these microtraps. A coherence time of more than 1 s, high fidelity qubit state detection and single qubit rotations are demonstrated. The observation of low heating rates and demonstration of high quality single qubit gates at room temperature are critical steps toward scalable quantum information processing in microfabricated surface traps.

  7. Single qubit manipulation in a microfabricated surface electrode ion trap

    International Nuclear Information System (INIS)

    Mount, Emily; Baek, So-Young; Gaultney, Daniel; Crain, Stephen; Noek, Rachel; Kim, Taehyun; Maunz, Peter; Kim, Jungsang; Blain, Matthew; Stick, Daniel

    2013-01-01

    We trap individual 171 Yb + ions in a surface trap microfabricated on a silicon substrate, and demonstrate a complete set of high fidelity single qubit operations for the hyperfine qubit. Trapping times exceeding 20 min without laser cooling, and heating rates as low as 0.8 quanta ms −1 , indicate stable trapping conditions in these microtraps. A coherence time of more than 1 s, high fidelity qubit state detection and single qubit rotations are demonstrated. The observation of low heating rates and demonstration of high quality single qubit gates at room temperature are critical steps toward scalable quantum information processing in microfabricated surface traps. (paper)

  8. Enriching lanthanide single-ion magnetism through symmetry and axiality.

    Science.gov (United States)

    Gupta, Sandeep K; Murugavel, Ramaswamy

    2018-04-10

    Rapidly growing modern information technology demands energy and cost efficient tools that can efficiently store and process a large amount of data. However, the miniaturization technology that was being used to boost the performance of the electronic devices, keeping up with the pace as estimated by Moore's law, is reaching its limit. To overcome these challenges, several alternative routes that can eventually mimic the modern electronics fabrication using silicon have been proposed. Single molecule magnets (SMMs), being considered as one of the potential alternatives, have gone through significant progress and the focus has shifted from the use of polynuclear clusters to mononuclear complexes in the last few years. The recent frenzy in the field of SMMs is driven by a better understanding of the effects of crystal field (CF) and molecular symmetry on the magnetic properties, especially in the case of mononuclear paramagnetic complexes, apart from other controlling factors. This has led to the advent of highly anisotropic single-ion magnets (SIMs) with magnetic blocking temperatures as high as 60 K and anisotropic energy barriers over 1800 K. This article overviews our recent research in the light of the emergence of the importance of CF and symmetry in 4f ion based single-ion magnets (SIMs), especially in the context of SIMs with D5h symmetry, apart from commenting on the synthetic efforts adopted to place these metal ions in unusual coordination geometries.

  9. NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.

    Science.gov (United States)

    Gu, Xiaobo; Park, Sun-Young; Tonelli, Marco; Cornilescu, Gabriel; Xia, Tianbing; Zhong, Dongping; Schroeder, Susan J

    2016-10-06

    Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.

  10. The conserved potassium channel filter can have distinct ion binding profiles: structural analysis of rubidium, cesium, and barium binding in NaK2K.

    Science.gov (United States)

    Lam, Yee Ling; Zeng, Weizhong; Sauer, David Bryant; Jiang, Youxing

    2014-08-01

    Potassium channels are highly selective for K(+) over the smaller Na(+). Intriguingly, they are permeable to larger monovalent cations such as Rb(+) and Cs(+) but are specifically blocked by the similarly sized Ba(2+). In this study, we used structural analysis to determine the binding profiles for these permeant and blocking ions in the selectivity filter of the potassium-selective NaK channel mutant NaK2K and also performed permeation experiments using single-channel recordings. Our data revealed that some ion binding properties of NaK2K are distinct from those of the canonical K(+) channels KcsA and MthK. Rb(+) bound at sites 1, 3, and 4 in NaK2K, as it does in KcsA. Cs(+), however, bound predominantly at sites 1 and 3 in NaK2K, whereas it binds at sites 1, 3, and 4 in KcsA. Moreover, Ba(2+) binding in NaK2K was distinct from that which has been observed in KcsA and MthK, even though all of these channels show similar Ba(2+) block. In the presence of K(+), Ba(2+) bound to the NaK2K channel at site 3 in conjunction with a K(+) at site 1; this led to a prolonged block of the channel (the external K(+)-dependent Ba(2+) lock-in state). In the absence of K(+), however, Ba(2+) acts as a permeating blocker. We found that, under these conditions, Ba(2+) bound at sites 1 or 0 as well as site 3, allowing it to enter the filter from the intracellular side and exit from the extracellular side. The difference in the Ba(2+) binding profile in the presence and absence of K(+) thus provides a structural explanation for the short and prolonged Ba(2+) block observed in NaK2K. © 2014 Lam et al.

  11. Single Gold Nanorod Charge Modulation in an Ion Gel Device.

    Science.gov (United States)

    Collins, Sean S E; Wei, Xingzhan; McKenzie, Thomas G; Funston, Alison M; Mulvaney, Paul

    2016-11-09

    A reliable and reproducible method to rapidly charge single gold nanocrystals in a solid-state device is reported. Gold nanorods (Au NRs) were integrated into an ion gel capacitor, enabling them to be charged in a transparent and highly capacitive device, ideal for optical transmission. Changes in the electron concentration of a single Au NR were observed with dark-field imaging spectroscopy via localized surface plasmon resonance (LSPR) shifts in the scattering spectrum. A time-resolved, laser-illuminated, dark-field system was developed to enable direct measurement of single particle charging rates with time resolution below one millisecond. The added sensitivity of this new approach has enabled the optical detection of fewer than 110 electrons on a single Au NR. Single wavelength resonance shifts provide a much faster, more sensitive method for all surface plasmon-based sensing applications.

  12. Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease.

    Science.gov (United States)

    Wallin, Cecilia; Kulkarni, Yashraj S; Abelein, Axel; Jarvet, Jüri; Liao, Qinghua; Strodel, Birgit; Olsson, Lisa; Luo, Jinghui; Abrahams, Jan Pieter; Sholts, Sabrina B; Roos, Per M; Kamerlin, Shina C L; Gräslund, Astrid; Wärmländer, Sebastian K T S

    2016-12-01

    Growing evidence links neurodegenerative diseases to metal exposure. Aberrant metal ion concentrations have been noted in Alzheimer's disease (AD) brains, yet the role of metals in AD pathogenesis remains unresolved. A major factor in AD pathogenesis is considered to be aggregation of and amyloid formation by amyloid-β (Aβ) peptides. Previous studies have shown that Aβ displays specific binding to Cu(II) and Zn(II) ions, and such binding has been shown to modulate Aβ aggregation. Here, we use nuclear magnetic resonance (NMR) spectroscopy to show that Mn(II) ions also bind to the N-terminal part of the Aβ(1-40) peptide, with a weak binding affinity in the milli- to micromolar range. Circular dichroism (CD) spectroscopy, solid state atomic force microscopy (AFM), fluorescence spectroscopy, and molecular modeling suggest that the weak binding of Mn(II) to Aβ may not have a large effect on the peptide's aggregation into amyloid fibrils. However, identification of an additional metal ion displaying Aβ binding reveals more complex AD metal chemistry than has been previously considered in the literature. Copyright © 2016 Elsevier GmbH. All rights reserved.

  13. Quaternary Benzyltriethylammonium Ion Binding to the Na,K-ATPase: a Tool to Investigate Extracellular K+ Binding Reactions†

    Science.gov (United States)

    Peluffo, R. Daniel; González-Lebrero, Rodolfo M.; Kaufman, Sergio B.; Kortagere, Sandhya; Orban, Branly; Rossi, Rolando C.; Berlin, Joshua R.

    2009-01-01

    This study examined how the quaternary organic ammonium ion, benzyltriethylamine (BTEA), binds to the Na,K-ATPase to produce membrane potential (VM)-dependent inhibition and tested the prediction that such a VM-dependent inhibitor would display electrogenic binding kinetics. BTEA competitively inhibited K+ activation of Na,K-ATPase activity and steady-state 86Rb+ occlusion. The initial rate of 86Rb+ occlusion was decreased by BTEA to a similar degree whether it was added to the enzyme prior to or simultaneously with Rb+, a demonstration that BTEA inhibits the Na,K-ATPase without being occluded. Several BTEA structural analogues reversibly inhibited Na,K-pump current, but none blocked current in a VM-dependent manner except BTEA and its para-nitro derivative, pNBTEA. Under conditions that promoted electroneutral K+-K+ exchange by the Na,K-ATPase, step changes in VM elicited pNBTEA-activated ouabain-sensitive transient currents that had similarities to those produced with the K+ congener, Tl+. pNBTEA- and Tl+-dependent transient currents both displayed saturation of charge moved at extreme negative and positive VM, equivalence of charge moved during and after step changes in VM, and similar apparent valence. The rate constant (ktot) for Tl+-dependent transient current asymptotically approached a minimum value at positive VM. In contrast, ktot for pNBTEA-dependent transient current was a “U”-shaped function of VM with a minimum value near 0 mV. Homology models of the Na,K-ATPase alpha subunit suggested that quaternary amines can bind to two extracellularly-accessible sites, one of them located at K+ binding sites positioned between transmembrane helices 4, 5, and 6. Altogether, these data revealed important information about electrogenic ion binding reactions of the Na,K-ATPase that are not directly measurable during ion transport by this enzyme. PMID:19621894

  14. Single ion impact detection and scanning probe aligned ion implantation for quantum bit formation

    International Nuclear Information System (INIS)

    Weis, Christoph D.

    2011-01-01

    Quantum computing and quantum information processing is a promising path to replace classical information processing via conventional computers which are approaching fundamental physical limits. Instead of classical bits, quantum bits (qubits) are utilized for computing operations. Due to quantum mechanical phenomena such as superposition and entanglement, a completely different way of information processing is achieved, enabling enhanced performance for certain problem sets. Various proposals exist on how to realize a quantum bit. Among them are electron or nuclear spins of defect centers in solid state systems. Two such candidates with spin degree of freedom are single donor atoms in silicon and nitrogen vacancy (NV) defect centers in diamond. Both qubit candidates possess extraordinary qualities which makes them promising building blocks. Besides certain advantages, the qubits share the necessity to be placed precisely in their host materials and device structures. A commonly used method is to introduce the donor atoms into the substrate materials via ion implantation. For this, focused ion beam systems can be used, or collimation techniques as in this work. A broad ion beam hits the back of a scanning probe microscope (SPM) cantilever with incorporated apertures. The high resolution imaging capabilities of the SPM allows the non destructive location of device areas and the alignment of the cantilever and thus collimated ion beam spot to the desired implant locations. In this work, this technique is explored, applied and pushed forward to meet necessary precision requirements. The alignment of the ion beam to surface features, which are sensitive to ion impacts and thus act as detectors, is demonstrated. The technique is also used to create NV center arrays in diamond substrates. Further, single ion impacts into silicon device structures are detected which enables deliberate single ion doping.

  15. Single ion impact detection and scanning probe aligned ion implantation for quantum bit formation

    Energy Technology Data Exchange (ETDEWEB)

    Weis, Christoph D.

    2011-10-04

    Quantum computing and quantum information processing is a promising path to replace classical information processing via conventional computers which are approaching fundamental physical limits. Instead of classical bits, quantum bits (qubits) are utilized for computing operations. Due to quantum mechanical phenomena such as superposition and entanglement, a completely different way of information processing is achieved, enabling enhanced performance for certain problem sets. Various proposals exist on how to realize a quantum bit. Among them are electron or nuclear spins of defect centers in solid state systems. Two such candidates with spin degree of freedom are single donor atoms in silicon and nitrogen vacancy (NV) defect centers in diamond. Both qubit candidates possess extraordinary qualities which makes them promising building blocks. Besides certain advantages, the qubits share the necessity to be placed precisely in their host materials and device structures. A commonly used method is to introduce the donor atoms into the substrate materials via ion implantation. For this, focused ion beam systems can be used, or collimation techniques as in this work. A broad ion beam hits the back of a scanning probe microscope (SPM) cantilever with incorporated apertures. The high resolution imaging capabilities of the SPM allows the non destructive location of device areas and the alignment of the cantilever and thus collimated ion beam spot to the desired implant locations. In this work, this technique is explored, applied and pushed forward to meet necessary precision requirements. The alignment of the ion beam to surface features, which are sensitive to ion impacts and thus act as detectors, is demonstrated. The technique is also used to create NV center arrays in diamond substrates. Further, single ion impacts into silicon device structures are detected which enables deliberate single ion doping.

  16. Scaling properties in single collision model of light ion reflection

    International Nuclear Information System (INIS)

    Vukanic, J.; Simovic, R.

    2004-01-01

    Light ion reflection from solids in the keV energy region has been studied within the single collision model. Particle and energy reflection coefficients as functions of the scaled transport cross section have been calculated numerically by utilizing the exact scattering function for the Kr-C potential and analytically with an effective power approximation for the same potential. The obtained analytical formulae approximate very accurately to the numerical results. Comparison of the calculated reflection coefficients with the experimental data and computer simulations for different light ion-heavy target combinations shows that the scaled transport cross section remains a convenient scaling parameter in the single collision domain, as adopted previously in multiple collision theory

  17. Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions.

    Science.gov (United States)

    Tomlinson, Christopher G; Syson, Karl; Sengerová, Blanka; Atack, John M; Sayers, Jon R; Swanson, Linda; Tainer, John A; Williams, Nicholas H; Grasby, Jane A

    2011-09-02

    Flap endonucleases (FENs) are divalent metal ion-dependent phosphodiesterases. Metallonucleases are often assigned a "two-metal ion mechanism" where both metals contact the scissile phosphate diester. The spacing of the two metal ions observed in T5FEN structures appears to preclude this mechanism. However, the overall reaction catalyzed by wild type (WT) T5FEN requires three Mg(2+) ions, implying that a third ion is needed during catalysis, and so a two-metal ion mechanism remains possible. To investigate the positions of the ions required for chemistry, a mutant T5FEN was studied where metal 2 (M2) ligands are altered to eliminate this binding site. In contrast to WT T5FEN, the overall reaction catalyzed by D201I/D204S required two ions, but over the concentration range of Mg(2+) tested, maximal rate data were fitted to a single binding isotherm. Calcium ions do not support FEN catalysis and inhibit the reactions supported by viable metal cofactors. To establish participation of ions in stabilization of enzyme-substrate complexes, dissociation constants of WT and D201I/D204S-substrate complexes were studied as a function of [Ca(2+)]. At pH 9.3 (maximal rate conditions), Ca(2+) substantially stabilized both complexes. Inhibition of viable cofactor supported reactions of WT, and D201I/D204S T5FENs was biphasic with respect to Ca(2+) and ultimately dependent on 1/[Ca(2+)](2). By varying the concentration of viable metal cofactor, Ca(2+) ions were shown to inhibit competitively displacing two catalytic ions. Combined analyses imply that M2 is not involved in chemical catalysis but plays a role in substrate binding, and thus a two-metal ion mechanism is plausible.

  18. Neutralizing Mutations of Carboxylates That Bind Metal 2 in T5 Flap Endonuclease Result in an Enzyme That Still Requires Two Metal Ions*

    Science.gov (United States)

    Tomlinson, Christopher G.; Syson, Karl; Sengerová, Blanka; Atack, John M.; Sayers, Jon R.; Swanson, Linda; Tainer, John A.; Williams, Nicholas H.; Grasby, Jane A.

    2011-01-01

    Flap endonucleases (FENs) are divalent metal ion-dependent phosphodiesterases. Metallonucleases are often assigned a “two-metal ion mechanism” where both metals contact the scissile phosphate diester. The spacing of the two metal ions observed in T5FEN structures appears to preclude this mechanism. However, the overall reaction catalyzed by wild type (WT) T5FEN requires three Mg2+ ions, implying that a third ion is needed during catalysis, and so a two-metal ion mechanism remains possible. To investigate the positions of the ions required for chemistry, a mutant T5FEN was studied where metal 2 (M2) ligands are altered to eliminate this binding site. In contrast to WT T5FEN, the overall reaction catalyzed by D201I/D204S required two ions, but over the concentration range of Mg2+ tested, maximal rate data were fitted to a single binding isotherm. Calcium ions do not support FEN catalysis and inhibit the reactions supported by viable metal cofactors. To establish participation of ions in stabilization of enzyme-substrate complexes, dissociation constants of WT and D201I/D204S-substrate complexes were studied as a function of [Ca2+]. At pH 9.3 (maximal rate conditions), Ca2+ substantially stabilized both complexes. Inhibition of viable cofactor supported reactions of WT, and D201I/D204S T5FENs was biphasic with respect to Ca2+ and ultimately dependent on 1/[Ca2+]2. By varying the concentration of viable metal cofactor, Ca2+ ions were shown to inhibit competitively displacing two catalytic ions. Combined analyses imply that M2 is not involved in chemical catalysis but plays a role in substrate binding, and thus a two-metal ion mechanism is plausible. PMID:21734257

  19. Single event upsets caused by solar energetic heavy ions

    International Nuclear Information System (INIS)

    Tylka, A.J.; Adams, J.H. Jr.; Boberg, P.R.; Smith, E.C.

    1996-01-01

    The authors calculate single event upset (SEU) rates due to protons, alphas, and heavier ions in two satellite systems for the major solar particle events of 1989--92, using a new and complete analysis of GOES proton data and high-energy heavy-ion fluences from the University of Chicago Cosmic Ray Telescope on IMP-8. These measurements cover the entire range of energies relevant to SEU studies and therefore overcome shortcomings of previous studies, which relied upon theoretical or semi-empirical estimates of high-energy heavy-ion spectra. They compare the results to the observed SEU rates in these events. The SEU rates in one device were overwhelmingly dominated by protons. However, even after taking into account uncertainties in the ground-test cross-section data, the authors find that at least ∼45% of the SEUs in the other device must have been caused by heavy ions. The results demonstrate that both protons and heavy ions must be considered in order to make a reliable assessment of SEU vulnerabilities. Furthermore, the GOES/Chicago database of solar particle events provides a basis for making accurate solar particle SEU calculations and credible worst-case estimates. In particular, measurements of the historic solar particle events of October 1989 are used in worst week and worst day environment models in CREME96, a revision of NRL's Cosmic Ray Effects on MicroElectronics code

  20. Conduction Mechanisms and Structure of Ionomeric Single-Ion Conductors

    Energy Technology Data Exchange (ETDEWEB)

    Colby, Ralph H. [Pennsylvania State Univ., University Park, PA (United States); Maranas, Janna K. [Pennsylvania State Univ., University Park, PA (United States); Mueller, Karl T. [Pennsylvania State Univ., University Park, PA (United States); Runt, James [Pennsylvania State Univ., University Park, PA (United States); Winey, Karen I. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    2015-03-01

    Our team has designed using DFT (Gaussian) and synthesized low glass transition temperature single-ion conductors that are either polyanions that conduct small cations Li+, Na+, Cs+ or polycations that conduct small anions F-, OH-, Br-. We utilize a wide range of complimentary experimental materials characterization tools to understand ion transport; differential scanning calorimetry, dielectric relaxation spectroscopy, infrared spectroscopy, nuclear magnetic resonance spectroscopy, linear viscoelasticity, X-ray scattering and molecular dynamics simulations. The glass transition temperature Tg needs to be as low as possible to facilitate ion transport, so the nonionic parts of the polymer need to be polar, flexible and have strong solvation interactions with the ions. The lowest Tg we have managed for polyanions conducting Li+ is -60 °C. In contrast, polysiloxanes with PEO side chains and tetrabutylphosphonium cationic side groups have Tg ≈ -75 °C that barely increases with ion content, as anticipated by DFT. A survey of all polyanions in the literature suggests that Tg < -80 °C is needed to achieve the 10-4 S/cm conductivity needed for battery separators.

  1. Applications of heavy ion microprobe for single event effects analysis

    International Nuclear Information System (INIS)

    Reed, Robert A.; Vizkelethy, Gyorgy; Pellish, Jonathan A.; Sierawski, Brian; Warren, Kevin M.; Porter, Mark; Wilkinson, Jeff; Marshall, Paul W.; Niu, Guofu; Cressler, John D.; Schrimpf, Ronald D.; Tipton, Alan; Weller, Robert A.

    2007-01-01

    The motion of ionizing-radiation-induced rogue charge carriers in a semiconductor can create unwanted voltage and current conditions within a microelectronic circuit. If sufficient unwanted charge or current occurs on a sensitive node, a variety of single event effects (SEEs) can occur with consequences ranging from trivial to catastrophic. This paper describes the application of heavy ion microprobes to assist with calibration and validation of SEE modeling approaches

  2. Single water entropy: hydrophobic crossover and application to drug binding.

    Science.gov (United States)

    Sasikala, Wilbee D; Mukherjee, Arnab

    2014-09-11

    Entropy of water plays an important role in both chemical and biological processes e.g. hydrophobic effect, molecular recognition etc. Here we use a new approach to calculate translational and rotational entropy of the individual water molecules around different hydrophobic and charged solutes. We show that for small hydrophobic solutes, the translational and rotational entropies of each water molecule increase as a function of its distance from the solute reaching finally to a constant bulk value. As the size of the solute increases (0.746 nm), the behavior of the translational entropy is opposite; water molecules closest to the solute have higher entropy that reduces with distance from the solute. This indicates that there is a crossover in translational entropy of water molecules around hydrophobic solutes from negative to positive values as the size of the solute is increased. Rotational entropy of water molecules around hydrophobic solutes for all sizes increases with distance from the solute, indicating the absence of crossover in rotational entropy. This makes the crossover in total entropy (translation + rotation) of water molecule happen at much larger size (>1.5 nm) for hydrophobic solutes. Translational entropy of single water molecule scales logarithmically (Str(QH) = C + kB ln V), with the volume V obtained from the ellipsoid of inertia. We further discuss the origin of higher entropy of water around water and show the possibility of recovering the entropy loss of some hypothetical solutes. The results obtained are helpful to understand water entropy behavior around various hydrophobic and charged environments within biomolecules. Finally, we show how our approach can be used to calculate the entropy of the individual water molecules in a protein cavity that may be replaced during ligand binding.

  3. Toward Molecular 4f Single-Ion Magnet Qubits.

    Science.gov (United States)

    Pedersen, Kasper S; Ariciu, Ana-Maria; McAdams, Simon; Weihe, Høgni; Bendix, Jesper; Tuna, Floriana; Piligkos, Stergios

    2016-05-11

    Quantum coherence is detected in the 4f single-ion magnet (SIM) Yb(trensal), by isotope selective pulsed EPR spectroscopy on an oriented single crystal. At X-band, the spin-lattice relaxation (T1) and phase memory (Tm) times are found to be independent of the nuclei bearing, or not, a nuclear spin. The observation of Rabi oscillations of the spin echo demonstrates the possibility to coherently manipulate the system for more than 70 rotations. This renders Yb(trensal), a sublimable and chemically modifiable SIM, an excellent candidate for quantum information processing.

  4. Binding of ligands to the catalytic zinc ion in horse liver alcohol dehydrogenase.

    Science.gov (United States)

    Syvertsen, C; McKinley-McKee, J S

    1984-01-01

    The affinity of nitrogen and sulfur ligands for the catalytic zinc ion in horse liver alcohol dehydrogenase has been investigated by their influence on the affinity labeling reaction with iodoacetate. All the nitrogen compounds including ammonia, a primary and a secondary amine, and heterocycles containing a pyridine-type nitrogen with the exception of 2,2-dipyridyl were found to activate the affinity labeling reaction. Activation results from inner-sphere ligand coordination to the catalytic zinc ion. Closely related pyridine compounds gave a regular increase in affinity for the enzyme with increasing basicity, as expected for coordination to a metal ion. The sulfur compounds penicillamine and mercaptoethanol also activated the affinity labeling reaction, but dimercaptopropanol bound very tightly as a bidentate inhibited the reaction. The anions hydrosulfide, diethyldithiocarbamate, and cyanide coordinated to the catalytic zinc ion, whereas azide, thiocyanate, tetrazole, and iodide complexed the anion-binding site. The anionic metal ligands increased the rate of inactivation of the enzyme with iodoacetamide by binding to the catalytic zinc ion, while the binding of iodoacetate to the anion-binding site was prevented.

  5. Design of a single ion facility and its applications

    Energy Technology Data Exchange (ETDEWEB)

    Cholewa, M.; Saint, A.; Legge, G.J.F. [Melbourne Univ., Parkville, VIC (Australia). School of Physics

    1996-12-31

    The use of micro-irradiation techniques in radiobiology is not new; however, the current techniques take advantage of recent developments in particle delivery, focussing detection, image processing, cell recognition and computer control. These developments have generally come from other fields, for example microbeam elemental analysis techniques and single-event upset testing of semiconductor devices. Also in radiation biology there have been important advances in developments of individual cell assays, which allow a wide range of endpoints to be studied with good accuracy at low doses. Many of the studies that are planned involve following the responses of individual cells after a programmed exposure to charged-particle traversals. To probe the radiation sensitivity of a single cell and/or its constituents with a submicron resolution several developments are needed. The essential parameters of the proposed system can be summarised as follows: a focussed beam of ions of 300nm or less at the cell; a reliable (close to 100%) single ion detection; a fast beam switch to prevent second hits; a target holder adapted for the irradiation of wet cells and a fully automated system for cell recognition and single hits. 1 fig.

  6. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory.

    Science.gov (United States)

    Chu, Vincent B; Bai, Yu; Lipfert, Jan; Herschlag, Daniel; Doniach, Sebastian

    2007-11-01

    Poisson-Boltzmann (PB) theory is among the most widely applied electrostatic theories in biological and chemical science. Despite its reasonable success in explaining a wide variety of phenomena, it fails to incorporate two basic physical effects, ion size and ion-ion correlations, into its theoretical treatment. Recent experimental work has shown significant deviations from PB theory in competitive monovalent and divalent ion binding to a DNA duplex. The experimental data for monovalent binding are consistent with a hypothesis that attributes these deviations to counterion size. To model the observed differences, we have generalized an existing size-modified Poisson-Boltzmann (SMPB) theory and developed a new numerical implementation that solves the generalized theory around complex, atomistic representations of biological molecules. The results of our analysis show that good agreement to data at monovalent ion concentrations up to approximately 150 mM can be attained by adjusting the ion-size parameters in the new size-modified theory. SMPB calculations employing calibrated ion-size parameters predict experimental observations for other nucleic acid structures and salt conditions, demonstrating that the theory is predictive. We are, however, unable to model the observed deviations in the divalent competition data with a theory that only accounts for size but neglects ion-ion correlations, highlighting the need for theoretical descriptions that further incorporate ion-ion correlations. The accompanying numerical solver has been released publicly, providing the general scientific community the ability to compute SMPB solutions around a variety of different biological structures with only modest computational resources.

  7. Metal Cation Binding to Gas-Phase Pentaalanine: Divalent Ions Restructure the Complex

    NARCIS (Netherlands)

    Dunbar, R.C.; Steill, J.D.; Polfer, N.C.; Oomens, J.

    2013-01-01

    Ion-neutral complexes of pentaalalanine with several singly- and doubly charged metal ions are examined using conformation analysis by infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) computations. The infrared spectroscopy in the 1500-1800 cm(-1) region

  8. Binding of ArgTX-636 in the NMDA receptor ion channel

    DEFF Research Database (Denmark)

    Poulsen, Mette H; Andersen, Jacob; Christensen, Rune

    2015-01-01

    The N-methyl-d-aspartate receptors (NMDARs) constitute an important class of ligand-gated cation channels that are involved in the majority of excitatory neurotransmission in the human brain. Compounds that bind in the NMDAR ion channel and act as blockers are use- and voltage-dependent inhibitor...

  9. Spectrofluorometric and Molecular Modeling Studies on Binding of Nitrite Ion with Bovine Hemoglobin: Effect of Nitrite Ion on Amino Acid Residues

    Science.gov (United States)

    Madrakian, T.; Bagheri, H.; Afkhami, A.

    2015-05-01

    The interaction between nitrite ion and bovine hemoglobin was investigated by a spectrofluorometric technique. The experimental results indicated that the interaction causes a static quenching of the fluorescence of bovine hemoglobin, that the binding reaction is spontaneous, and that H-bonding interactions play a major role in binding of this ion to bovine hemoglobin. The formation constant for this interaction was calculated. Based on Förster's theory of nonradiative energy transfer, the binding distance between this ion and bovine hemoglobin was determined. Furthermore, the interaction of nitrite ion with tyrosine and tryptophan was investigated with synchronous fluorescence. There was no significant shift of the maximum emission wavelength with interactions of the mentioned ion with bovine hemoglobin, which implies that interaction of nitrite ion with bovine hemoglobin does not affect the microenvironment around the tryptophan and tyrosine residues. Furthermore, the effect of nitrite ion on amino acid residues of bovine hemoglobin was studied by a molecular docking technique.

  10. A mononuclear non-heme manganese(IV)-oxo complex binding redox-inactive metal ions.

    Science.gov (United States)

    Chen, Junying; Lee, Yong-Min; Davis, Katherine M; Wu, Xiujuan; Seo, Mi Sook; Cho, Kyung-Bin; Yoon, Heejung; Park, Young Jun; Fukuzumi, Shunichi; Pushkar, Yulia N; Nam, Wonwoo

    2013-05-01

    Redox-inactive metal ions play pivotal roles in regulating the reactivities of high-valent metal-oxo species in a variety of enzymatic and chemical reactions. A mononuclear non-heme Mn(IV)-oxo complex bearing a pentadentate N5 ligand has been synthesized and used in the synthesis of a Mn(IV)-oxo complex binding scandium ions. The Mn(IV)-oxo complexes were characterized with various spectroscopic methods. The reactivities of the Mn(IV)-oxo complex are markedly influenced by binding of Sc(3+) ions in oxidation reactions, such as a ~2200-fold increase in the rate of oxidation of thioanisole (i.e., oxygen atom transfer) but a ~180-fold decrease in the rate of C-H bond activation of 1,4-cyclohexadiene (i.e., hydrogen atom transfer). The present results provide the first example of a non-heme Mn(IV)-oxo complex binding redox-inactive metal ions that shows a contrasting effect of the redox-inactive metal ions on the reactivities of metal-oxo species in the oxygen atom transfer and hydrogen atom transfer reactions.

  11. A Mononuclear Non-Heme Manganese(IV)-Oxo Complex Binding Redox-Inactive Metal Ions

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Junying; Lee, Yong-Min; Davis, Katherine M.; Wu, Xiujuan; Seo, Mi Sook; Cho, Kyung-Bin; Yoon, Heejung; Park, Young Jun; Fukuzumi, Shunichi; Pushkar, Yulia N.; Nam, Wonwoo [Ewha; (Purdue); (Osaka)

    2013-05-29

    Redox-inactive metal ions play pivotal roles in regulating the reactivities of high-valent metal–oxo species in a variety of enzymatic and chemical reactions. A mononuclear non-heme Mn(IV)–oxo complex bearing a pentadentate N5 ligand has been synthesized and used in the synthesis of a Mn(IV)–oxo complex binding scandium ions. The Mn(IV)–oxo complexes were characterized with various spectroscopic methods. The reactivities of the Mn(IV)–oxo complex are markedly influenced by binding of Sc3+ ions in oxidation reactions, such as a ~2200-fold increase in the rate of oxidation of thioanisole (i.e., oxygen atom transfer) but a ~180-fold decrease in the rate of C–H bond activation of 1,4-cyclohexadiene (i.e., hydrogen atom transfer). The present results provide the first example of a non-heme Mn(IV)–oxo complex binding redox-inactive metal ions that shows a contrasting effect of the redox-inactive metal ions on the reactivities of metal–oxo species in the oxygen atom transfer and hydrogen atom transfer reactions.

  12. The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange.

    Science.gov (United States)

    Qian, Yufeng; Johnson, Kenneth A

    2017-08-04

    The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB) 30 and (SSB) 60 , defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB) 60 and (SSB) 30 complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 10 9 m -1 s -1 ) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Simple molecular model for the binding of antibiotic molecules to bacterial ion channels

    Science.gov (United States)

    Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

    2003-10-01

    A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill's theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of interacting sites facilitates drug binding. The dependence of the number of ampicillin binding events per second with the solution pH and salt concentration is explained qualitatively using a reduced number of fundamental concepts.

  14. Identification of metal ion binding sites based on amino acid sequences

    Science.gov (United States)

    Cao, Xiaoyong; Zhang, Xiaojin; Gao, Sujuan; Ding, Changjiang; Feng, Yonge; Bao, Weihua

    2017-01-01

    The identification of metal ion binding sites is important for protein function annotation and the design of new drug molecules. This study presents an effective method of analyzing and identifying the binding residues of metal ions based solely on sequence information. Ten metal ions were extracted from the BioLip database: Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+ and Co2+. The analysis showed that Zn2+, Cu2+, Fe2+, Fe3+, and Co2+ were sensitive to the conservation of amino acids at binding sites, and promising results can be achieved using the Position Weight Scoring Matrix algorithm, with an accuracy of over 79.9% and a Matthews correlation coefficient of over 0.6. The binding sites of other metals can also be accurately identified using the Support Vector Machine algorithm with multifeature parameters as input. In addition, we found that Ca2+ was insensitive to hydrophobicity and hydrophilicity information and Mn2+ was insensitive to polarization charge information. An online server was constructed based on the framework of the proposed method and is freely available at http://60.31.198.140:8081/metal/HomePage/HomePage.html. PMID:28854211

  15. Binding of monovalent alkali metal ions with negatively charged phospholipid membranes.

    Science.gov (United States)

    Maity, Pabitra; Saha, Baishakhi; Kumar, Gopinatha Suresh; Karmakar, Sanat

    2016-04-01

    We have systematically investigated the effect of various alkali metal ions with negatively charged phospholipid membranes. Size distributions of large unilamellar vesicles have been confirmed using dynamic light scattering. Zeta potential and effective charges per vesicle in the presence of various alkali metal ions have been estimated from the measured electrophoretic mobility. We have determined the intrinsic binding constant from the zeta potential using electrostatic double layer theory. The reasonable and consistent value of the intrinsic binding constant of Na(+), found at moderate NaCl concentration (10-100 mM), indicates that the Gouy-Chapman theory cannot be applied for very high (> 100mM) and very low (concentrations. The isothermal titration calorimetry study has revealed that the net binding heat of interaction of the negatively charged vesicles with monovalent alkali metal ions is small and comparable to those obtained from neutral phosphatidylcholine vesicles. The overall endothermic response of binding heat suggests that interaction is primarily entropy driven. The entropy gain might arise due to the release of water molecules from the hydration layer vicinity of the membranes. Therefore, the partition model which does not include the electrostatic contribution suffices to describe the interaction. The binding constant of Na(+) (2.4 ± 0.1 M(-1)), obtained from the ITC, is in agreement with that estimated from the zeta potential (-2.0 M(-1)) at moderate salt concentrations. Our results suggest that hydration dynamics may play a vital role in the membrane solution interface which strongly affects the ion-membrane interaction. Copyright © 2016 Elsevier B.V. All rights reserved

  16. Selective binding of oligonucleotide on TiO{sub 2} surfaces modified by swift heavy ion beam lithography

    Energy Technology Data Exchange (ETDEWEB)

    Vicente Pérez-Girón, J. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Emerging Viruses Department Heinrich Pette Institute, Hamburg 20251 (Germany); Hirtz, M. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); McAtamney, C.; Bell, A.P. [Advanced Microscopy Laboratory, CRANN, Trinity College Dublin, Dublin 2 (Ireland); Antonio Mas, J. [Laboratorio de Genómica del Centro de Apoyo Tecnológico, Universidad Rey Juan Carlos, Campus de Alcorcón 28922, Madrid (Spain); Jaafar, M. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Luis, O. de [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Bioquímica, Fisiología y Genética Molecular, Facultad de Ciencias de la Salud, Universidad Rey Juan Carlos, Campus de Alcorcón, 28922 Madrid (Spain); Fuchs, H. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Physical Institute and Center for Nanotechnology (CeNTech), Wilhelm-Klemm-Straße 10, University of Münster (Germany); and others

    2014-11-15

    We have used swift heavy-ion beam based lithography to create patterned bio-functional surfaces on rutile TiO{sub 2} single crystals. The applied lithography method generates a permanent and well defined periodic structure of micrometre sized square holes having nanostructured TiO{sub 2} surfaces, presenting different physical and chemical properties compared to the surrounding rutile single crystal surface. On the patterned substrates selective binding of oligonucleotides molecules is possible at the surfaces of the holes. This immobilisation process is only being controlled by UV light exposure. The patterned transparent substrates are compatible with fluorescence detection techniques, are mechanically robust, have a high tolerance to extreme chemical and temperature environments, and apparently do not degrade after ten cycles of use. These qualities make the patterned TiO{sub 2} substrates useful for potential biosensor applications.

  17. Mechanism of DNA–binding loss upon single-point mutation in p53

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    provides an excellent prototype system to elucidate the different mechanisms underlying the loss in DNA binding affinity and specificity upon single point mutation because over 50% of all human cancers involve p53 mutations, which occur mostly in the sequence–specific DNA–binding central domain (residues 102–292, ...

  18. Single-ion quantum lock-in amplifier.

    Science.gov (United States)

    Kotler, Shlomi; Akerman, Nitzan; Glickman, Yinnon; Keselman, Anna; Ozeri, Roee

    2011-05-05

    Quantum metrology uses tools from quantum information science to improve measurement signal-to-noise ratios. The challenge is to increase sensitivity while reducing susceptibility to noise, tasks that are often in conflict. Lock-in measurement is a detection scheme designed to overcome this difficulty by spectrally separating signal from noise. Here we report on the implementation of a quantum analogue to the classical lock-in amplifier. All the lock-in operations--modulation, detection and mixing--are performed through the application of non-commuting quantum operators to the electronic spin state of a single, trapped Sr(+) ion. We significantly increase its sensitivity to external fields while extending phase coherence by three orders of magnitude, to more than one second. Using this technique, we measure frequency shifts with a sensitivity of 0.42 Hz Hz(-1/2) (corresponding to a magnetic field measurement sensitivity of 15 pT Hz(-1/2)), obtaining an uncertainty of less than 10 mHz (350 fT) after 3,720 seconds of averaging. These sensitivities are limited by quantum projection noise and improve on other single-spin probe technologies by two orders of magnitude. Our reported sensitivity is sufficient for the measurement of parity non-conservation, as well as the detection of the magnetic field of a single electronic spin one micrometre from an ion detector with nanometre resolution. As a first application, we perform light shift spectroscopy of a narrow optical quadrupole transition. Finally, we emphasize that the quantum lock-in technique is generic and can potentially enhance the sensitivity of any quantum sensor. ©2011 Macmillan Publishers Limited. All rights reserved

  19. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding

    National Research Council Canada - National Science Library

    Hanke, Andreas

    2008-01-01

    ... may open up spontaneously due to thermal activation. By rising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA...

  20. Single event monitoring system based on Java 3D and XML data binding

    International Nuclear Information System (INIS)

    Wang Liang; Chinese Academy of Sciences, Beijing; Zhu Kejun; Zhao Jingwei

    2007-01-01

    Online single event monitoring is important to BESIII DAQ System. Java3D is extension of Java Language in 3D technology, XML data binding is more efficient to handle XML document than SAX and DOM. This paper mainly introduce the implementation of BESIII single event monitoring system with Java3D and XML data binding, and interface for track fitting software with JNI technology. (authors)

  1. New generation of composite inorganic ion-exchangers with polyacrylonitrile binding matrix

    International Nuclear Information System (INIS)

    Sebesta, F.; John, J.; Motl, A.; Uvirova, K.; Smrckova, S.

    1998-01-01

    General procedure for treatment of powdered inorganic ion-exchangers using binding polymer - modified polyacrylonitrile (PAN) into beads suitable for the application in column packed beds was proposed earlier. These composite ion-exchangers were tested for many applications, some of them are used in the full-scale treatment of liquid radioactive wastes and/or for radioanalytical purposes. New generation of the composite ion-exchangers was developed to improve their volume exchange capacity and mechanical strength. Further, composite absorbers with new active components or their mixtures were prepared. The possibility of preparation of magnetic composite adsorbers and magnetic composite ion-exchangers was also studied. The new prepared materials were mainly tested for their application in caesium separation from highly active acidic waste streams. The efficiency of AMP-PAN (ammonium molybdophosphate active component) and ferrocyanides based composite ion-exchangers for caesium separation was studied in more details. Possibilities of regeneration of the above mentioned composite ion-exchangers were also studied. In preliminary experiments, mercury sorption from model mixed radioactive wastes onto ferro- and ferricyanide based absorbers was tested. The new generation of composite ion-exchangers with hydrated titanium oxide or sodium titanate as active component was tested for strontium separation from alkaline solutions. (author)

  2. Micro-Capillary Coatings Based on Spiropyran Polymeric Brushes for Metal Ion Binding, Detection, and Release in Continuous Flow

    Directory of Open Access Journals (Sweden)

    Aishling Dunne

    2018-04-01

    Full Text Available Micro-capillaries, capable of light-regulated binding and qualitative detection of divalent metal ions in continuous flow, have been realised through functionalisation with spiropyran photochromic brush-type coatings. Upon irradiation with UV light, the coating switches from the passive non-binding spiropyran form to the active merocyanine form, which binds different divalent metal ions (Zn2+, Co2+, Cu2+, Ni2+, Cd2+, as they pass through the micro-capillary. Furthermore, the merocyanine visible absorbance spectrum changes upon metal ion binding, enabling the ion uptake to be detected optically. Irradiation with white light causes reversion of the merocyanine to the passive spiropyran form, with simultaneous release of the bound metal ion from the micro-capillary coating.

  3. DNA-cisplatin binding mechanism peculiarities studied with single molecule stretching experiments

    Science.gov (United States)

    Crisafuli, F. A. P.; Cesconetto, E. C.; Ramos, E. B.; Rocha, M. S.

    2012-02-01

    We propose a method to determine the DNA-cisplatin binding mechanism peculiarities by monitoring the mechanical properties of these complexes. To accomplish this task, we have performed single molecule stretching experiments by using optical tweezers, from which the persistence and contour lengths of the complexes can be promptly measured. The persistence length of the complexes as a function of the drug total concentration in the sample was used to deduce the binding data, from which we show that cisplatin binds cooperatively to the DNA molecule, a point which so far has not been stressed in binding equilibrium studies of this ligand.

  4. Photodynamic membrane damage at the level of single ion channels.

    Science.gov (United States)

    Kunz, L; Stark, G

    1997-07-05

    Illumination of cellular membranes by visible light in the presence of appropriate photosensitizers is known to inactivate specific ionic pathways and to increase the unspecific leak conductance of the membranes. While previous studies have concentrated on the macroscopic ionic currents, the present study separates the two phenomena at the microscopic level. Using opossum kidney (OK) cells as epithelial model system and photofrin II as sensitizer, the patch-clamp technique in inside-out configuration has been applied to show the inactivation of single ion channels immediately after start of illumination and the subsequent strong increase of the leak conductance. Inactivation is shown for two kinds of channels: the large-conductance Ca2+-dependent K+ channel (maxi-K(Ca)) and the stretch-activated nonselective cation channel (SA-cat).

  5. Effects of single-stranded DNA binding proteins on primer extension by telomerase.

    Science.gov (United States)

    Cohen, Shlomit; Jacob, Eyal; Manor, Haim

    2004-08-12

    We present a biochemical analysis of the effects of three single-stranded DNA binding proteins on extension of oligonucleotide primers by the Tetrahymena telomerase. One of them, a human protein designated translin, which was shown to specifically bind the G-rich Tetrahymena and human telomeric repeats, slightly stimulated the primer extension reactions at molar ratios of translin/primer of primers, rather than by a direct interaction of this protein with telomerase. A second protein, the general human single-stranded DNA binding protein Replication Protein A (RPA), similarly affected the primer extension by telomerase, even though its mode of binding to DNA differs from that of translin. A third protein, the E. coli single-stranded DNA binding protein (SSB), whose binding to DNA is highly cooperative, caused more substantial stimulation and inhibition at the lower and the higher molar ratios of SSB/primer, respectively. Both telomere-specific and general single-stranded DNA binding proteins are found in living cells in telomeric complexes. Based on our data, we propose that these proteins may exert either stimulatory or inhibitory effects on intracellular telomerases, depending on their local concentrations. Copyright 2004 Elsevier B.V.

  6. Combined sodium ion sensitivity in agonist binding and internalization of vasopressin V1b receptors.

    Science.gov (United States)

    Koshimizu, Taka-Aki; Kashiwazaki, Aki; Taniguchi, Junichi

    2016-05-03

    Reducing Na(+) in the extracellular environment may lead to two beneficial effects for increasing agonist binding to cell surface G-protein coupled receptors (GPCRs): reduction of Na(+)-mediated binding block and reduce of receptor internalization. However, such combined effects have not been explored. We used Chinese Hamster Ovary cells expressing vasopressin V1b receptors as a model to explore Na(+) sensitivity in agonist binding and receptor internalization. Under basal conditions, a large fraction of V1b receptors is located intracellularly, and a small fraction is in the plasma membrane. Decreases in external Na(+) increased cell surface [(3)H]AVP binding and decreased receptor internalization. Substitution of Na(+) by Cs(+) or NH4(+) inhibited agonist binding. To suppress receptor internalization, the concentration of NaCl, but not of CsCl, had to be less than 50 mM, due to the high sensitivity of the internalization machinery to Na(+) over Cs(+). Iso-osmotic supplementation of glucose or NH4Cl maintained internalization of the V1b receptor, even in a low-NaCl environment. Moreover, iodide ions, which acted as a counter anion, inhibited V1b agonist binding. In summary, we found external ionic conditions that could increase the presence of high-affinity state receptors at the cell surface with minimum internalization during agonist stimulations.

  7. Quantitative Molecular Imaging with a Single Gd-Based Contrast Agent Reveals Specific Tumor Binding and Retention in Vivo.

    Science.gov (United States)

    Johansen, Mette L; Gao, Ying; Hutnick, Melanie A; Craig, Sonya E L; Pokorski, Jonathan K; Flask, Chris A; Brady-Kalnay, Susann M

    2017-06-06

    Magnetic resonance imaging (MRI) has become an indispensable tool in the diagnosis and treatment of many diseases, especially cancer. However, the poor sensitivity of MRI relative to other imaging modalities, such as PET, has hindered the development and clinical use of molecular MRI contrast agents that could provide vital diagnostic information by specifically locating a molecular target altered in the disease process. This work describes the specific and sustained in vivo binding and retention of a protein tyrosine phosphatase mu (PTPμ)-targeted, molecular magnetic resonance (MR) contrast agent with a single gadolinium (Gd) chelate using a quantitative MRI T 1 mapping technique in glioma xenografts. Quantitative T 1 mapping is an imaging method used to measure the longitudinal relaxation time, the T 1 relaxation time, of protons in a magnetic field after excitation by a radiofrequency pulse. T 1 relaxation times can in turn be used to calculate the concentration of a gadolinium-containing contrast agent in a region of interest, thereby allowing the retention or clearance of an agent to be quantified. In this context, retention is a measure of molecular contrast agent binding. Using conventional peptide chemistry, a PTPμ-targeted peptide was linked to a chelator that had been conjugated to a lysine residue. Following complexation with Gd, this PTPμ-targeted molecular contrast agent containing a single Gd ion showed significant tumor enhancement and a sustained increase in Gd concentration in both heterotopic and orthotopic tumors using dynamic quantitative MRI. This single Gd-containing PTPμ agent was more effective than our previous version with three Gd ions. Differences between nonspecific and specific agents, due to specific tumor binding, can be determined within the first 30 min after agent administration by examining clearance rates. This more facile chemistry, when combined with quantitative MR techniques, allows for widespread adoption by academic

  8. Application of equilibrium binding model for analysis of conformational transitions in poly(rApoly(rU complexes with metal ions

    Directory of Open Access Journals (Sweden)

    Sorokin V. A.

    2010-09-01

    Full Text Available Aim. The study is aimed at generalization of the previous experimental results on the metal ion (Mg2+, Ni2+, Cd2+ effects on conformation transitions in poly(rA·poly(rU. The objective was to find out how the type of a metal ion-polynucleotide complex influences the phase transitions and to estimate the constants (K of ions binding to polymers of different structures. Methods. The K values were obtained upon theoretical and experimental transition temperature fitting by the least-square method with the root mean square deviation minimized through the procedure of the gradient descent in the multidimensional space. Results. Calcula- tions of diagrams with Mg2+ are shown to permit obtaining satisfactory results if concentration-independent, mean values of constants are used. For Ni2+ and Cd2+ the concentration dependence of K must be taken into account, especially for high ion contents at which compaction of single-stranded poly(rA emerges. It was revealed that the main factor responsible for the differences in diagrams with Ni2+ and Cd2+ is a significant distinction of their constants of binding to poly(rA and poly(rU. Conclusions. The model theory of equilibrium binding is capable to describe adequately conformation transitions in polynucleotides in the presence of metal ions.

  9. MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode.

    Science.gov (United States)

    Wagner, Tristan; Ermler, Ulrich; Shima, Seigo

    2016-06-21

    In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA-H of methanogenic archaea has a key function in energy conservation by catalysing the methyl transfer from methyl-tetrahydromethanopterin to coenzyme M and its coupling with sodium-ion translocation. The cobalamin-binding subunit MtrA is not homologous to any known B12-binding proteins and is proposed as the motor of the sodium-ion pump. Here, we present crystal structures of the soluble domain of the membrane-associated MtrA from Methanocaldococcus jannaschii and the cytoplasmic MtrA homologue/cobalamin complex from Methanothermus fervidus. The MtrA fold corresponds to the Rossmann-type α/β fold, which is also found in many cobalamin-containing proteins. Surprisingly, the cobalamin-binding site of MtrA differed greatly from all the other cobalamin-binding sites. Nevertheless, the hydrogen-bond linkage at the lower axial-ligand site of cobalt was equivalently constructed to that found in other methyltransferases and mutases. A distinct polypeptide segment fixed through the hydrogen-bond linkage in the relaxed Co(III) state might be involved in propagating the energy released upon corrinoid demethylation to the sodium-translocation site by a conformational change.

  10. Nonlinearly Additive Forces in Multivalent Ligand Binding to a Single Protein Revealed with Force Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, T V; Rudd, R E; Langry, K C; Balhorn, R L; McElfresh, M W

    2005-07-15

    We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

  11. Synthesis and ion-binding properties of polymeric pseudocrown ethers II: Template ion induced cyclization of oligomeric ethylene glycol diacrylates

    Energy Technology Data Exchange (ETDEWEB)

    Mathur, A.M.; Scranton, A.B. [Michigan State Univ., East Lansing, MI (United States)

    1997-01-01

    Inexpensive polymeric pseudocrown ethers have been synthesized based upon a {open_quotes}template ion{close_quotes} effect in which oligomeric ethylene glycol diacrylates are induced to assume a circular conformation in which the unsaturated end-groups are in proximity. This synthetic scheme has considerable potential for the development of inexpensive materials for binding of target cations. In this contribution, the authors report a spectroscopic study of the induced cyclization caused by ion-dipole interactions between the templating cation and the electron lone pairs of the ethylene glycol ether linkages. Fluorescence spectroscopy was used to provide insight into the templatization process by examining excimer formation in pyrene end-labeled oligomeric ethylene glycol both in the absence and in the presence of the templating ion. Pyrene end-labeled tetraethylene glycol and pentaethylene glycol were synthesized and excimer fluorescence enhancement was studied with the introduction of cations such as nickel, chromium and tin in solvents such as tetrahydrofuran and chloroform. An increase in excimer fluorescence indicated enhanced excimer formation due to the templating effect of the cation which results in the end groups being close to each other. Molecular dynamics simulations of pyrene end-labeled ligands were performed to elucidate the effect of the large fluorescent chromophores on the chain conformations.

  12. Characteristics of the brown hagfish Paramyxine atami transthyretin: Metal ion-dependent thyroid hormone binding.

    Science.gov (United States)

    Suzuki, Shunsuke; Kasai, Kentaro; Nishiyama, Norihito; Ishihara, Akinori; Yamauchi, Kiyoshi

    2017-08-01

    Transthyretin (TTR) is a vertebrate-specific protein involved in thyroid hormone distribution in plasma, and its gene is thought to have emerged by gene duplication from the gene for the ancient TTR-related protein, 5-hydroxyisourate hydrolase, at some early stage of chordate evolution. We investigated the molecular and hormone-binding properties of the brown hagfish Paramyxine atami TTR. The amino acid sequence deduced from the cloned hagfish TTR cDNA shared 33-50% identities with those of other vertebrate TTRs but less than 24% identities with those of vertebrate and deuterostome invertebrate 5-hydroxyisourate hydrolases. Hagfish TTR, as well as lamprey and little skate TTRs, had an N-terminal histidine-rich segment, allowing purification by metal-affinity chromatography. The affinity of hagfish TTR for 3,3',5-triiodo-L-thyronine (T3) was 190 times higher than that for L-thyroxine, with a dissociation constant of 1.5-3.9nM at 4°C. The high-affinity binding sites were strongly sensitive to metal ions. Zn 2+ and Cu 2+ decreased the dissociation constant to one-order of magnitude, whereas a chelator, o-phenanthroline, increased it four times. The number of metal ions (mainly Zn 2+ and Cu 2+ ) was approximately 12/TTR (mol/mol). TTR was also a major T3-binding protein in adult hagfish sera and its serum concentration was approximately 8μM. These results suggest that metal ions and the acquisition of N-terminal histidine-rich segment may cooperatively contribute to the evolution toward an ancient TTR with high T3 binding activity from either 5-hydroxyisourate hydrolase after gene duplication. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

    Science.gov (United States)

    Marinsky, J.A.; Reddy, M.M.

    1984-01-01

    A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

  14. Change of conformation and internal dynamics of supercoiled DNA upon binding of Escherichia coli single-strand binding protein

    International Nuclear Information System (INIS)

    Langowski, J.; Benight, A.S.; Fujimoto, B.S.; Schurr, J.M.; Schomburg, U.

    1985-01-01

    The influence of Escherichia coli single-strand binding (SSB) protein on the conformation and internal dynamics of pBR322 and pUC8 supercoiled DNAs has been investigated by using dynamic light scattering at 632.8 and 351.1 nm and time-resolved fluorescence polarization anisotropy of intercalated ethidium. SSB protein binds to both DNAs up to a stoichiometry that is sufficient to almost completely relax the superhelical turns. Upon saturation binding, the translational diffusion coefficients (D 0 ) of both DNAs decrease by approximately 20%. Apparent diffusion coefficients (D/sub app/) obtained from dynamic light scattering display the well-known increase with K 2 (K = scattering vector), leveling off toward a plateau value (D/sub plat/) at high K 2 . For both DNAs, the difference D/sub plat/ - D 0 increases upon relaxation of supercoils by SSB protein, which indicates a corresponding enhancement of the subunit mobilities in internal motions. Fluorescence polarization anisotropy measurements on free and complexed pBR322 DNA indicate a (predominantly) uniform torsional rigidity for the saturated DNA/SSB protein complex that is significantly reduced compared to the free DNA. These observations are all consistent with the notion that binding of SSB protein is accompanied by a gradual loss of supercoils and saturates when the superhelical twist is largely removed

  15. Determining ERβ Binding Affinity to Singly Mutant ERE Using Dual Polarization Interferometry

    Science.gov (United States)

    Song, Hong Yan; Su, Xiaodi

    In a classic mode of estrogen action, estrogen receptors (ERs) bind to estrogen responsive element (ERE) to activate gene transcription. A perfect ERE contains a 13-base pair sequence of a palindromic repeat separated by a three-base spacer, 5‧-GGTCAnnnTGACC-3‧. In addition to the consensus or wild-type ERE (wtERE), naturally occurring EREs often have one or two base pairs’ alternation. Based on the newly constructed Thermodynamic Modeling of ChIP-seq (TherMos) model, binding energy between ERβ and a series of 34-bp mutant EREs (mutERE) was simulated to predict the binding affinity between ERs and EREs with single base pair deviation at different sites of the 13-bp inverted sequence. Experimentally, dual polarization interferometry (DPI) method was developed to measure ERβ-mutEREs binding affinity. On a biotin-NeutrAvidin (NA)-biotin treated DPI chip, wtERE is immobilized. In a direct binding assay, ERβ-wtERE binding affinity is determined. In a competition assay, ERβ was preincubated with mutant EREs before being added for competitive binding to the immobilized wtERE. This competition strategy provided a successful platform to evaluate the binding affinity variation among large number of ERE with different base mutations. The experimental result correlates well with the mathematically predicted binding energy with a Spearman correlation coefficient of 0.97.

  16. Metal ion interaction of an oligopeptide fragment representing the regulatory metal binding site of a CueR protein

    DEFF Research Database (Denmark)

    Jancsó, Attila; Szokolai, Hajnalka; Roszahegyi, Livia

    2013-01-01

    Metalloregulatory proteins of the MerR family are transcriptional activators that sense/control the concentration of various metal ions inside bacteria.1 The Cu+ efflux regulator CueR, similarly to other MerR proteins, possesses a short multiple Cys-containing metal binding loop close to the C......-terminus. CueR has a high selectivity for Cu+, Ag+ and Au+, but exhibits no transcriptional activity for the divalent ions Hg2+ and Zn2+.2 The two Cys- residues of the metal binding loop were shown to settle M+ ions into a linear coordination environment but other factors may also play a role in the recognition...... of cognate metal ions.2 Nevertheless, it is an interesting question whether the same sequence, when removed from the protein, shows a flexibility to adopt different coordination environments and may efficiently bind metal ions having preferences for larger coordination numbers....

  17. Single-ion and single-chain magnetism in triangular spin-chain oxides

    Science.gov (United States)

    Seikh, Md. Motin; Caignaert, Vincent; Perez, Olivier; Raveau, Bernard; Hardy, Vincent

    2017-05-01

    S r4 -xC axM n2Co O9 oxides (x =0 and x =2 ) are found to exhibit magnetic responses typical of single-chain magnets (SCMs) and single-ion magnets (SIMs), two features generally investigated in coordination polymers or complexes. The compound x =0 appears to be a genuine SCM, in that blocking effects associated with slow spin dynamics yield remanence and coercivity in the absence of long-range ordering (LRO). In addition, SIM signatures of nearly identical nature are detected in both compounds, coexisting with SCM in x =0 and with LRO in x =2 . It is also observed that a SCM response can be recovered in x =2 after application of magnetic field. These results suggest that purely inorganic systems could play a valuable role in the topical issue of the interplay among SIM, SCM, and LRO phenomena in low-dimensional magnetism.

  18. Stepwise bending of DNA by a single TATA box binding protein

    DEFF Research Database (Denmark)

    Tolic-Nørrelykke, Simon F; Rasmussen, Mette B; Pavone, Francesco S

    2006-01-01

    The TATA-box binding protein (TBP) is required by all three eucaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called "TATA-boxes" in the DNA. We present results from the study of individual Saccharomyces...... cerevisiae TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of the beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tehtered...

  19. Short term memory for single surface features and bindings in ageing: A replication study.

    Science.gov (United States)

    Isella, Valeria; Molteni, Federica; Mapelli, Cristina; Ferrarese, Carlo

    2015-06-01

    In the present study we replicated a previous experiment investigating visuo-spatial short term memory binding in young and older healthy individuals, in the attempt to verify the pattern of impairment that can be observed in normal elderly for short term memory for single items vs short term memory for bindings. Assessing a larger sample size (25 young and 25 older subjects), using a more appropriate measure of accuracy for a change detection task (A'), and adding the evaluation of speed of performance, we confirmed that old normals show a decline in short term memory for bindings of shape and colour that is of comparable extent, and not major, to the decline in memory for single shapes and single colours. The absence of a specific deficit of short term memory for conjunctions of surface features seems to distinguish cognitive ageing from Alzheimer's Disease. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Cellulose Nanocrystals Obtained from Rice By-Products and Their Binding Potential to Metallic Ions

    Directory of Open Access Journals (Sweden)

    Vanessa L. Albernaz

    2015-01-01

    Full Text Available The present study aimed to develop and optimize a method to obtain cellulose nanocrystals from the agricultural by-products rice husk and straw and to evaluate their electrostructural modifications in the presence of metallic ions. First, different particle formation conditions and routes were tested and analyzed by spectrophotometry, dynamic light scattering (DLS, and Zeta potential measurements. Then, electrostructural effects of ions Na(I, Cd(II, and Al(III on the optimized nanoparticles were analyzed by atomic force microscopy (AFM, scanning electron microscopy (SEM, and electrical conductivity (EC assessments. The produced cellulose nanocrystals adopted a rod-like shape. AFM height distribution and EC data indicated that the nanocrystals have more affinity in binding with Na(I > Al(III > Cd(II. These data suggest that the use of these cellulose nanocrystals in the bioremediation field is promising, both in metal sorption from wastewater and as an alternative for water desalination.

  1. Composite sorbents of inorganic ion-exchangers and polyacrylonitrile binding matrix. Methods of modification of properties of inorganic ion-exchangers for application in column packed beds

    International Nuclear Information System (INIS)

    Sebesta, F.

    1997-01-01

    Methods of preparation of granules of inorganic ion exchangers as well as methods for improvement of granular strength of these materials are reviewed. The resulting ion exchangers are classified in three groups - 'intrinsic', supported and composite ion exchangers. Their properties are compared and possibilities of their technological application are evaluated. A new method of preparation of inorganic-organic composite sorbents of inorganic ion-exchangers and polyacrylonitrile binding matrix is described, advantages and disadvantages of such sorbents are discussed. Proposed fields of application include tratment of liquid radioactive and/or hazardous wastes, decontamination of natural water as well as analytical applications. (author)

  2. POT1-independent single-strand telomeric DNA binding activities in Brassicaceae.

    Science.gov (United States)

    Shakirov, Eugene V; McKnight, Thomas D; Shippen, Dorothy E

    2009-06-01

    Telomeres define the ends of linear eukaryotic chromosomes and are required for genome maintenance and continued cell proliferation. The extreme ends of telomeres terminate in a single-strand protrusion, termed the G-overhang, which, in vertebrates and fission yeast, is bound by evolutionarily conserved members of the POT1 (protection of telomeres) protein family. Unlike most other model organisms, the flowering plant Arabidopsis thaliana encodes two divergent POT1-like proteins. Here we show that the single-strand telomeric DNA binding activity present in A. thaliana nuclear extracts is not dependent on POT1a or POT1b proteins. Furthermore, in contrast to POT1 proteins from yeast and vertebrates, recombinant POT1a and POT1b proteins from A. thaliana, and from two additional Brassicaceae species, Arabidopsis lyrata and Brassica oleracea (cauliflower), fail to bind single-strand telomeric DNA in vitro under the conditions tested. Finally, although we detected four single-strand telomeric DNA binding activities in nuclear extracts from B. oleracea, partial purification and DNA cross-linking analysis of these complexes identified proteins that are smaller than the predicted sizes of BoPOT1a or BoPOT1b. Taken together, these data suggest that POT1 proteins are not the major single-strand telomeric DNA binding activities in A. thaliana and its close relatives, underscoring the remarkable functional divergence of POT1 proteins from plants and other eukaryotes.

  3. Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

    Directory of Open Access Journals (Sweden)

    Qingling Hang

    2009-02-01

    Full Text Available The surface attachment properties of the Creutz-Taube ion, i.e., [(NH35Ru(pyrazineRu(NH35]5+, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS. The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO2 and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH3 terminated organic SAMs and poly(methylmethacrylate (PMMA thin films covered gold or SiO2 substrates was observed. Further ellipsometric, atomic force microscopy (AFM and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO2 substrate with a “lying-down” orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO2 surface was believed to account for these observations. Based on its selective binding property, patterning of wide (~200 nm and narrow (~35 nm lines of the Creutz-Taube ions on SiO2 surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL.

  4. Binding of Cu(II) ions to peptides studied by fluorescence spectroscopy and isothermal titration calorimetry

    Science.gov (United States)

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

    2016-01-01

    Steady-state and time-resolved fluorescence quenching measurements supported by Isothermal Titration Calorimetry (ITC) were used to study the interactions of Cu2 + with four peptides. Two of them were taken from the N-terminal part of the FBP28 protein (formin binding protein) WW domain: Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr-NH2 (D9) and its mutant Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr-NH2 (D9_M) as well as two mutated peptides from the B3 domain of the immunoglobulin binding protein G derived from Streptococcus: Asp-Val-Ala-Thr-Tyr-Thr-NH2 (J1) and Glu-Val-Ala-Thr-Tyr-Thr-NH2 (J2). The measurements were carried out at 298.15 K in 20 mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution with a pH of 6. The fluorescence of all peptides was quenched by Cu2 + ions. The stoichiometry, conditional stability constants and thermodynamic parameters for the interactions of the Cu2 + ions with D9 and D9_M were determined from the calorimetric data. The values of the conditional stability constants were additionally determined from fluorescence quenching measurements and compared with those obtained from calorimetric studies. There was a good correlation between data obtained from the two techniques. On the other hand, the studies revealed that J1 and J2 do not exhibit an affinity towards metal ions. The obtained results prove that fluorescence quenching experiments may be successfully used in order to determine stability constants of complexes with fluorescent ligands. Finally, based on the obtained results, the coordinating properties of the peptides towards the Cu2 + ions are discussed.

  5. Single-Molecule Counting of Point Mutations by Transient DNA Binding

    Science.gov (United States)

    Su, Xin; Li, Lidan; Wang, Shanshan; Hao, Dandan; Wang, Lei; Yu, Changyuan

    2017-03-01

    High-confidence detection of point mutations is important for disease diagnosis and clinical practice. Hybridization probes are extensively used, but are hindered by their poor single-nucleotide selectivity. Shortening the length of DNA hybridization probes weakens the stability of the probe-target duplex, leading to transient binding between complementary sequences. The kinetics of probe-target binding events are highly dependent on the number of complementary base pairs. Here, we present a single-molecule assay for point mutation detection based on transient DNA binding and use of total internal reflection fluorescence microscopy. Statistical analysis of single-molecule kinetics enabled us to effectively discriminate between wild type DNA sequences and single-nucleotide variants at the single-molecule level. A higher single-nucleotide discrimination is achieved than in our previous work by optimizing the assay conditions, which is guided by statistical modeling of kinetics with a gamma distribution. The KRAS c.34 A mutation can be clearly differentiated from the wild type sequence (KRAS c.34 G) at a relative abundance as low as 0.01% mutant to WT. To demonstrate the feasibility of this method for analysis of clinically relevant biological samples, we used this technology to detect mutations in single-stranded DNA generated from asymmetric RT-PCR of mRNA from two cancer cell lines.

  6. Zinc(II) and the single-stranded DNA binding protein of bacteriophage T4

    International Nuclear Information System (INIS)

    Gauss, P.; Krassa, K.B.; McPheeters, D.S.; Nelson, M.A.; Gold, L.

    1987-01-01

    The DNA binding domain of the gene 32 protein of the bacteriophage T4 contains a single zinc-finger sequence. The gene 32 protein is an extensively studied member of a class of proteins that bind relatively nonspecifically to single-stranded DNA. The authors have sequenced and characterized mutations in gene 32 whose defective proteins are activated by increasing the Zn(II) concentration in the growth medium. The results identify a role for the gene 32 protein in activation of T4 late transcription. Several eukaryotic proteins with zinc fingers participate in activation of transcription, and the gene 32 protein of T4 should provide a simple, well-characterized system in which genetics can be utilized to study the role of a zinc finger in nucleic acid binding and gene expression

  7. Genetic and biochemical identification of a novel single-stranded DNA binding complex in Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Amy eStroud

    2012-06-01

    Full Text Available Single-stranded DNA binding proteins play an essential role in DNA replication and repair. They use oligosaccharide-binding folds, a five-stranded ß-sheet coiled into a closed barrel, to bind to single-stranded DNA thereby protecting and stabilizing the DNA. In eukaryotes the single-stranded DNA binding protein is known as replication protein A (RPA and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed single-stranded DNA-binding protein (SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3 exist in operons with a novel gene specific to Euryarchaeota, this gene encodes a protein that we have termed rpa-associated protein (RPAP. The rpap genes encode proteins belonging to COG3390 group and feature oligosaccharide-binding folds, suggesting that they might cooperate with RPA in binding to single-stranded DNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only ∆rpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins. We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA binding complex that is unique to Euryarchaeota.

  8. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nilsson, A.S.; Lehnherr, H.

    2002-01-01

    Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit...

  9. Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Macek, B

    2006-01-01

    by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation...

  10. Single aromatic residue location alters nucleic acid binding and chaperone function of FIV nucleocapsid protein

    Science.gov (United States)

    Wu, Hao; Wang, Wei; Naiyer, Nada; Fichtenbaum, Eric; Qualley, Dominic F.; McCauley, Micah J.; Gorelick, Robert J.; Rouzina, Ioulia; Musier-Forsyth, Karin; Williams, Mark C.

    2014-01-01

    Feline immunodeficiency virus (FIV) is a retrovirus that infects domestic cats, and is an excellent animal model for human immunodeficiency virus type 1 (HIV-1) pathogenesis. The nucleocapsid (NC) protein is critical for replication in both retroviruses. FIV NC has several structural features that differ from HIV-1 NC. While both NC proteins have a single conserved aromatic residue in each of the two zinc fingers, the aromatic residue on the second finger of FIV NC is located on the opposite C-terminal side relative to its location in HIV-1 NC. In addition, whereas HIV-1 NC has a highly charged cationic N-terminal tail and a relatively short C-terminal extension, the opposite is true for FIV NC. To probe the impact of these differences on the nucleic acid (NA) binding and chaperone properties of FIV NC, we carried out ensemble and single-molecule assays with wild-type (WT) and mutant proteins. The ensemble studies show that FIV NC binding to DNA is strongly electrostatic, with a higher effective charge than that observed for HIV-1 NC. The C-terminal basic domain contributes significantly to the NA binding capability of FIV NC. In addition, the non-electrostatic component of DNA binding is much weaker for FIV NC than for HIV-1 NC. Mutation of both aromatic residues in the zinc fingers to Ala (F12A/W44A) further increases the effective charge of FIV NC and reduces its non-electrostatic binding affinity. Interestingly, switching the location of the C-terminal aromatic residue to mimic the HIV-1 NC sequence (N31W/W44A) reduces the effective charge of FIV NC and increases its non-electrostatic binding affinity to values similar to HIV-1 NC. Consistent with the results of these ensemble studies, single-molecule DNA stretching studies show that while WT FIV NC has reduced stacking capability relative to HIV-1 NC, the aromatic switch mutant recovers the ability to intercalate between the DNA bases. Our results demonstrate that altering the position of a single aromatic

  11. Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

    Science.gov (United States)

    McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; Adams, C.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; Gómez-Cadenas, J. J.; González-Díaz, D.; Gutiérrez, R. M.; Guenette, R.; Hafidi, K.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Johnston, S.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Monrabal, F.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Repond, J.; Renner, J.; Riordan, S.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Simón, A.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.; NEXT Collaboration

    2018-03-01

    A new method to tag the barium daughter in the double-beta decay of Xe 136 is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba++ ) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (˜2 nm ), and detected with a statistical significance of 12.9 σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

  12. Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, A. D.; Jones, B. J. P.; Nygren, D. R.; Adams, C.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; Gómez-Cadenas, J. J.; González-Díaz, D.; Gutiérrez, R. M.; Guenette, R.; Hafidi, K.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Johnston, S.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; Monrabal, F.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Repond, J.; Renner, J.; Riordan, S.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Simón, A.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.

    2018-03-01

    A new method to tag the barium daughter in the double beta decay of $^{136}$Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba$^{++}$) resolution at a transparent scanning surface has been demonstrated. A single-step photo-bleach confirms the single ion interpretation. Individual ions are localized with super-resolution ($\\sim$2~nm), and detected with a statistical significance of 12.9~$\\sigma$ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

  13. EMF signals and ion/ligand binding kinetics: prediction of bioeffective waveform parameters.

    Science.gov (United States)

    Pilla, A A; Muehsam, D J; Markov, M S; Sisken, B F

    1999-02-01

    The kinetics of an electromagnetic field (EMF) target pathway are used to estimate frequency windows for EMF bioeffects. Ion/ligand binding is characterized via first order kinetics from which a specific electrical impedance can be derived. The resistance/capacitance properties of the binding pathway impedance, determined by the kinetics of the rate-determining step, define the frequency range over which the target pathway is most sensitive to external EMF. Applied signals may thus be configured such that their spectral content closely matches that of the target, using evaluation of the signal to thermal noise ratio to optimize waveform parameters. Using the approach proposed in this study, a pulsed radio frequency (PRF) waveform, currently employed clinically for soft tissue repair, was returned by modulation of burst duration, producing significant bioeffects at substantially reduced signal amplitude. Application is made to Ca2+/Calmodulin-dependent myosin phosphorylation, for which the binding time constants may be estimated from reported kinetics, neurite outgrowth from embryonic chick dorsal root explants and bone repair in a fracture model. The results showed that the retuned signal produced increased phosphorylation rates, neurite outgrowth and biomechanical strength that were indistinguishable from those produced by the clinical signal, but with a tenfold reduction in peak signal amplitude, approximately 800-fold reduction in average amplitude and approximately 10(6)-fold reduction in average power.

  14. Native Mass Spectrometry, Ion mobility, and Collision-Induced Unfolding Categorize Malaria Antigen/Antibody Binding

    Science.gov (United States)

    Huang, Yining; Salinas, Nichole D.; Chen, Edwin; Tolia, Niraj H.; Gross, Michael L.

    2017-09-01

    Plasmodium vivax Duffy Binding Protein (PvDBP) is a promising vaccine candidate for P. vivax malaria. Recently, we reported the epitopes on PvDBP region II (PvDBP-II) for three inhibitory monoclonal antibodies (2D10, 2H2, and 2C6). In this communication, we describe the combination of native mass spectrometry and ion mobility (IM) with collision induced unfolding (CIU) to study the conformation and stabilities of three malarial antigen-antibody complexes. These complexes, when collisionally activated, undergo conformational changes that depend on the location of the epitope. CIU patterns for PvDBP-II in complex with antibody 2D10 and 2H2 are highly similar, indicating comparable binding topology and stability. A different CIU fingerprint is observed for PvDBP-II/2C6, indicating that 2C6 binds to PvDBP-II on an epitope different from 2D10 and 2H2. This work supports the use of CIU as a means of classifying antigen-antibody complexes by their epitope maps in a high throughput screening workflow. [Figure not available: see fulltext.

  15. Towards the role of metal ions in the structural variability of proteins: CdII speciation of a metal ion binding loop motif

    DEFF Research Database (Denmark)

    Jancsó, Attila; Szunyogh, Dániel; Gyurcsik, Béla

    2011-01-01

    A de novo designed dodecapeptide (HS), inspired by the metal binding loops of metal-responsive transcriptional activators, was synthesized. The aim was to create a model system for structurally promiscuous and intrinsically unstructured proteins, and explore the effect of metal ions on their stru...... the peptide is exchanging between a number of structures also in its metal ion bound state(s), as indicated by NMR and PAC data. © 2011 The Royal Society of Chemistry....

  16. Novel, Solvent-Free, Single Ion Conductive Polymer Electrolytes

    National Research Council Canada - National Science Library

    Florjanczyk, Zbigniew

    2008-01-01

    This project report concerns studies on the synthesis of new polymer electrolytes for application in lithium and lithium-ion batteries characterized by limited participation of anions in the transport...

  17. Selective Binding and Precipitation of Cesium Ions from Aqueous Solutions: A Size-Driven Supramolecular Reaction.

    Science.gov (United States)

    Bengiat, Ravell; Bogoslavsky, Benny; Mandler, Daniel; Almog, Joseph

    2018-03-02

    The nuclear disasters of Chernobyl and Fukushima presented an urgent need for finding solutions to treatment of radioactive wastes. Among the by-products of nuclear fission is radioactive 137 Cs, which evokes an environmental hazard due to its long half-life (>30 years) and high solubility in water. In this work, a water-soluble organic ligand, readily obtained from alloxan and 1,3,5-benzenetriol, has been found to selectively bind and precipitate Cs + ions from aqueous solutions. The special rigid structure of the ligand, which consists of a "tripodal" carbonyl base above and below an aromatic plane, contributes to the size-driven selectivity towards the large Cs + ions and the formation of a giant, insoluble supramolecular complex. In addition to the low costs of the ligand, high yields and effectiveness in precipitating Cs + ions, the Cs-complex revealed a high endurance to continuous doses of γ-radiation, increasing its potential to act as a precipitating agent for 137 Cs. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis.

    Science.gov (United States)

    Olszewski, Marcin; Mickiewicz, Małgorzata; Kur, Józef

    2008-07-01

    The thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular mass of 17.29 and 16.96 kDa, respectively. They are the smallest known bacterial SSB proteins. The homology between amino acid sequences of these proteins is 40% identity and 53% similarity. They are functional as homotetramers, with each monomer encoding one single-stranded DNA binding domain (OB-fold). In fluorescence titrations with poly(dT), both proteins bind single-stranded DNA with a binding site size of about 40 nt per homotetramer. Thermostability with half-life of about 30 s at 95 degrees C makes TteSSB3 similar to the known SSB of Thermus aquaticus (TaqSSB). The TteSSB2 was fully active even after 6 h incubation at 100 degrees C. Here, we show for the first time paralogous thermostable homotetrameric SSBs, which could be an attractive alternative for known homodimeric thermostable SSB proteins in their applications for molecular biology methods and analytical purposes.

  19. High-affinity single-domain binding proteins with a binary-code interface.

    Science.gov (United States)

    Koide, Akiko; Gilbreth, Ryan N; Esaki, Kaori; Tereshko, Valentina; Koide, Shohei

    2007-04-17

    High degrees of sequence and conformation complexity found in natural protein interaction interfaces are generally considered essential for achieving tight and specific interactions. However, it has been demonstrated that specific antibodies can be built by using an interface with a binary code consisting of only Tyr and Ser. This surprising result might be attributed to yet undefined properties of the antibody scaffold that uniquely enhance its capacity for target binding. In this work we tested the generality of the binary-code interface by engineering binding proteins based on a single-domain scaffold. We show that Tyr/Ser binary-code interfaces consisting of only 15-20 positions within a fibronectin type III domain (FN3; 95 residues) are capable of producing specific binding proteins (termed "monobodies") with a low-nanomolar K(d). A 2.35-A x-ray crystal structure of a monobody in complex with its target, maltose-binding protein, and mutation analysis revealed dominant contributions of Tyr residues to binding as well as striking molecular mimicry of a maltose-binding protein substrate, beta-cyclodextrin, by the Tyr/Ser binary interface. This work suggests that an interaction interface with low chemical diversity but with significant conformational diversity is generally sufficient for tight and specific molecular recognition, providing fundamental insights into factors governing protein-protein interactions.

  20. The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays.

    Science.gov (United States)

    Hua, Boyang; Wang, Yanbo; Park, Seongjin; Han, Kyu Young; Singh, Digvijay; Kim, Jin H; Cheng, Wei; Ha, Taekjip

    2018-03-13

    Here, we demonstrate that the use of the single-molecule centroid localization algorithm can improve the accuracy of fluorescence binding assays. Two major artifacts in this type of assay, i.e., nonspecific binding events and optically overlapping receptors, can be detected and corrected during analysis. The effectiveness of our method was confirmed by measuring two weak biomolecular interactions, the interaction between the B1 domain of streptococcal protein G and immunoglobulin G and the interaction between double-stranded DNA and the Cas9-RNA complex with limited sequence matches. This analysis routine requires little modification to common experimental protocols, making it readily applicable to existing data and future experiments.

  1. Effects of urea, metal ions and surfactants on the binding of baicalein with bovine serum albumin

    Directory of Open Access Journals (Sweden)

    Atanu Singha Roy

    2016-08-01

    Full Text Available The interaction of baicalein with bovine serum albumin (BSA was investigated with the help of spectroscopic and molecular docking studies. The binding affinity of baicalein towards BSA was estimated to be in order of 105 M−1 from fluorescence quenching studies. Negative ΔH° (−5.66±0.14 kJ/mol and positive (ΔS° (+79.96±0.65 J/mol K indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°. The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate (SDS due to probable hydrophobic association of baicalein with SDS, resulting in a negative ΔS° (−40.65±0.87 J/mol K. Matrix-assisted laser desorption ionization/time of flight (MALDI--TOF experiments indicate a 1:1 complexation between baicalein and BSA. The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements. It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA. The presence of metal ions (Ag+, Mg2+, Ni2+, Mn2+, Co2+and Zn2+ increased the binding affinity of ligand towards BSA. The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism (CD and Fourier transform infrared (FT-IR spectroscopic techniques. Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1 (subdomain IIA of BSA.

  2. Features of polyatomic ion emission under sputtering of a silicon single crystal by Au sub m sup - cluster ions

    CERN Document Server

    Akhunov, S; Rasulev, U K

    2003-01-01

    Comparative studies of the emission of secondary cluster Si sub n sup + ions (n=1-11) and polyatomic Si sub n X sub l Y sub k sup + ions (X, Y are Au, B, C, N), as well as doubly charged Si sup 2 sup + ions under bombardment of single crystalline silicon by cluster Au sub m sup - (m=1-5) ions with energy E sub 0 =4-18 keV have been carried out. High non-additivity enhancement of the yield of the Si sub n sup + ions and most polyatomic ones has been observed with an increase of the number of atoms in the projectiles. For Si sup 2 sup + ions the negative non-additive effect has been observed. The increase in the yield of impurity-containing cluster Si sub n X sup + ions allows for an increase by a factor of 100-1000 for the sensitivity of the SIMS analysis of the Au, B, C, N impurities in Si with the use of cluster ions as primary and secondary ones.

  3. Development of a keV single-ion-implanter for nanofabrication

    International Nuclear Information System (INIS)

    Yang, C.; Jamieson, D.N.; Hopf, T.; Tamanyan, G.; Spizziri, P.; Pakes, C.; Andresen, S.E.; Hudson, F.; Gauja, E.; Dzurak, A.; Clark, R.G.

    2005-01-01

    Traditional methods of doping semiconductors have a difficulty meeting the demand for high precision doping due to large statistical fluctuations in the numbers of dopant atoms introduced in the ever shrinking volume in micro- and nano-electronics devices, especially when the fabrication process approaches the nanometre scale. The statistical fluctuations in doping semiconductors for the fabrication of devices with a very small feature size may lead to inconsistent and unreliable performance. This paper describes the adaptation of a commercial ion implanter into a single-ion-implantation system for the accurate delivery of dopants into a nanometre or micrometre area in a silicon substrate. All the implanted ions can be accurately counted with near 100% certainty through online detection using the silicon substrate itself as an ion detector. A variety of ion species including B + , N + , P + at the energy range of 10-15 keV can be delivered in the single ion implantation system. (author). 6 refs., 6 figs

  4. Optimization of ECR singly-charged ion sources for the radioactive ion beam production

    CERN Document Server

    Jardin, P; Gaubert, G; Pacquet, J Y; Drobert, T; Cornell, J; Barue, C; Canet, C; Dupuis, M; Flambard, J L; Lecesne, N; Leherissier, P; Lemagnen, F; Leroy, R

    2003-01-01

    Measurements of the transformation time of atoms into ions were carried out with two 2.45 GHz electron cyclotron resonance ion sources (ECRIS) in the case of the simple ionization of He, Ne, Ar and Kr gases. The effect of the plasma volume, of the dead volumes and of the ionization efficiency are presented. Some rules are deduced for the design of the next ECRIS dedicated to radioactive ion production with noble gases.

  5. Ion beam induced single phase nanocrystalline TiO2 formation

    Science.gov (United States)

    Rukade, Deepti A.; Tribedi, L. C.; Bhattacharyya, Varsha

    2014-06-01

    Single phase TiO2 nanostructures are fabricated by oxygen ion implantation (60 keV) at fluence ranging from 1×1016 ions/cm2 to 1×1017 ions/cm2 in titanium thin films deposited on fused silica substrate and subsequent thermal annealing in argon atmosphere. GAXRD and Raman spectroscopy study reveals formation of single rutile phases of TiO2. Particle size is found to vary from 29 nm to 35 nm, establishing nanostructure formation. Nanostructure formation is also confirmed by the quantum confinement effect manifested by the blueshift of the UV-vis absorption spectra. Photoluminescence spectra show peaks corresponding to TiO2 rutile phase and reveal the presence of oxygen defects due to implantation. The controlled synthesis of single phase nanostructure is attributed to ion induced defects and post-implantation annealing. It is observed that the size of the nanostructures formed is strongly dependent on the ion fluence.

  6. Development of heavy-ion irradiation technique for single-event in semiconductor devices

    Energy Technology Data Exchange (ETDEWEB)

    Nemoto, Norio; Akutsu, Takao; Matsuda, Sumio [National Space Development Agency of Japan, Tsukuba, Ibaraki (Japan). Tsukuba Space Center; Naitoh, Ichiro; Itoh, Hisayoshi; Agematsu, Takashi; Kamiya, Tomihiro; Nashiyama, Isamu

    1997-03-01

    Heavy-ion irradiation technique has been developed for the evaluation of single-event effects on semiconductor devices. For the uniform irradiation of high energy heavy ions to device samples, we have designed and installed a magnetic beam-scanning system in a JAERI cyclotron beam course. It was found that scanned area was approximately 4 x 2 centimeters and that the deviation of ion fluence from the average value was less than 7%. (author)

  7. Action of age-hardening on the copper single crystals after ion implantation

    International Nuclear Information System (INIS)

    Kul'ment'eva, O.P.; Kul'ment'ev, A.I.

    2007-01-01

    High-dose implantation (up to (1-5)·10 17 cm -2 ) of tantalum ions into a copper single crystal of (100), (110) and (111) orientation has been investigated. Modified properties just after ion implantation and subsequent age-hardening during ten years were studied. It was shown that ion implantation and subsequent masstransfer process results in sufficient long-term stable changes of the microhardness. (authors)

  8. The bacterial DnaA-trio replication origin element specifies single-stranded DNA initiator binding.

    Science.gov (United States)

    Richardson, Tomas T; Harran, Omar; Murray, Heath

    2016-06-16

    DNA replication is tightly controlled to ensure accurate inheritance of genetic information. In all organisms, initiator proteins possessing AAA+ (ATPases associated with various cellular activities) domains bind replication origins to license new rounds of DNA synthesis. In bacteria the master initiator protein, DnaA, is highly conserved and has two crucial DNA binding activities. DnaA monomers recognize the replication origin (oriC) by binding double-stranded DNA sequences (DnaA-boxes); subsequently, DnaA filaments assemble and promote duplex unwinding by engaging and stretching a single DNA strand. While the specificity for duplex DnaA-boxes by DnaA has been appreciated for over 30 years, the sequence specificity for single-strand DNA binding has remained unknown. Here we identify a new indispensable bacterial replication origin element composed of a repeating trinucleotide motif that we term the DnaA-trio. We show that the function of the DnaA-trio is to stabilize DnaA filaments on a single DNA strand, thus providing essential precision to this binding mechanism. Bioinformatic analysis detects DnaA-trios in replication origins throughout the bacterial kingdom, indicating that this element is part of the core oriC structure. The discovery and characterization of the novel DnaA-trio extends our fundamental understanding of bacterial DNA replication initiation, and because of the conserved structure of AAA+ initiator proteins these findings raise the possibility of specific recognition motifs within replication origins of higher organisms.

  9. Binding of iron, zinc, and lead ions from aqueous solution by shea butter (Butyrospermun Parkii) seed husks

    Energy Technology Data Exchange (ETDEWEB)

    Eromosele, I.C.; Otitolaye, O.O. (Federal Univ. of Technology, Yola, Adamawa State (Nigeria))

    1994-08-01

    Several workers have reported on the potential use of agricultural products as substrates for the removal of metal ions from aqueous solutions. These studies demonstrated that considerable amounts of metal ions can be removed from aqueous solutions by cellulosic materials. The merit in the use of the latter is their relative abundance and cheapness compared to conventional materials for the removal of toxic metal ions from waste-waters. In some of the studies, chemical modification of cellulosic materials significantly enhanced their ion-binding properties, providing greater flexibility in their applications to a wide range of heavy metal ions. Shea butter plant (Butyrospermun Parkii) normally grows in the wild within the guinea-savana zone of Nigeria. The seeds are a rich source of edible oils and the husks are usually discarded. The husk is thus available in abundance and, hence, there is reason to examine its ion-binding properties for its possible application in the removal of toxic metal ions from industrial waste-waters. This paper reports on preliminary studies of the sorption of iron, zinc and lead ions from aqueous solution by modified and unmodified shea butter seed husks. 8 refs., 5 figs., 1 tab.

  10. Production of multi-, oligo- and single-pore membranes using a continuous ion beam

    Czech Academy of Sciences Publication Activity Database

    Apel, P. Yu.; Ivanov, O.; Lizunov, N. E.; Mamonova, T. I.; Nechaev, A. N.; Olejniczak, K.; Vacík, Jiří; Dmitriev, S. N.

    2015-01-01

    Roč. 365, DEC (2015), s. 641-645 ISSN 0168-583X R&D Projects: GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : ion beam * irradiation * ion track * etching * single nanopore Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.389, year: 2015

  11. Measuring p53 Binding to Single DNA Molecules in a Nanofluidic Device

    Science.gov (United States)

    Whelsky, Amber; Gonzalez, Nicholas, Jr.; Gal, Susannah; Levy, Stephen

    2012-02-01

    Protein-DNA binding is central to several important cellular processes, for instance, the transfer of genetic information into proteins. The p53 protein plays a central role in regulating several major cell cycle pathways, in part by binding to well-characterized DNA sequences in the promoters of specific genes. Recent studies show that the most common mutation to the protein occurs in the region responsible for its binding to DNA. We have fabricated slit-like nanofluidic devices that allow us to trap and stretch single molecules of DNA containing a known recognition sequence of p53. We use fluorescent microscopy to observe the diffusion of a single p53 protein as it searches for its DNA recognition site. We measure the reaction rates of binding to selected DNA sequences as well as the one-dimensional, non-sequence specific diffusion of p53 along a stretched DNA molecule as a function of salt concentration. The mechanism of facilitated diffusion attempts to explain how proteins seem able to find their DNA target sequences much more quickly than would be expected from three-dimensional diffusion alone. We compare the observed search mechanism used by normal and mutated p53 from cancer cells to predictions based on this theory.

  12. Lattice location of platinum ions implanted into single crystal zirconia and their annealing behaviour

    Energy Technology Data Exchange (ETDEWEB)

    Cao, D.X. [Royal Melbourne Inst. of Tech., VIC (Australia); Sood, D.K. [Academia Sinica, Shanghai, SH (China). Shanghai Inst. of Nuclear Research; Brown, I.G. [Lawrence Berkeley Lab., CA (United States)

    1993-12-31

    Single crystal samples of (100) oriented cubic zirconia stabilised with 9.5 mol % yttria were implanted with platinum ions, using a metal vapour vacuum arc (MEVVA) high current ion implanter, to a nominal dose of 1x10{sup 17} ions/cm{sup 2}. The implanted samples were annealed isothermally in air ambient at 1200 deg C, from 1-24 hours. Rutherford Backscattering Spectrometry and Channeling (RBSC) of 2 MeV He ions are employed to determine depth distributions of ion damage, Pt ions and substitutionality of Pt ions before and after annealing. The damage behaviour, Pt migration and lattice location are discussed in terms of metastable phase formation and solid solubility considerations. 7 refs., 3 figs.

  13. Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction

    Science.gov (United States)

    Gomes, Antonio L.C.; Abeel, Thomas; Peterson, Matthew; Azizi, Elham; Lyubetskaya, Anna; Carvalho, Luís

    2014-01-01

    The comprehension of protein and DNA binding in vivo is essential to understand gene regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a global map of the regulatory binding network. Most ChIP-seq analysis tools focus on identifying binding regions from coverage enrichment. However, less work has been performed to infer the physical and regulatory details inside the enriched regions. This research extends a previous blind-deconvolution approach to develop a post-peak–calling algorithm that improves binding site resolution and predicts cooperative interactions. At the core of our new method is a physically motivated model that characterizes the binding signal as an extreme value distribution. This model suggests a mathematical framework to study physical properties of DNA shearing from the ChIP-seq coverage. The model explains the ChIP-seq coverage with two signals: The first considers DNA fragments with only a single binding event, whereas the second considers fragments with two binding events (a double-binding signal). The model incorporates motif discovery and is able to detect multiple sites in an enriched region with single-nucleotide resolution, high sensitivity, and high specificity. Our method improves peak caller sensitivity, from less than 45% up to 94%, at a false positive rate ChIP-seq analysis: the identification of cooperative interaction. Predictions of known cooperative binding sites show a 0.85 area under an ROC curve. PMID:25024162

  14. Single ion induced surface nanostructures: a comparison between slow highly charged and swift heavy ions.

    Science.gov (United States)

    Aumayr, Friedrich; Facsko, Stefan; El-Said, Ayman S; Trautmann, Christina; Schleberger, Marika

    2011-10-05

    This topical review focuses on recent advances in the understanding of the formation of surface nanostructures, an intriguing phenomenon in ion-surface interaction due to the impact of individual ions. In many solid targets, swift heavy ions produce narrow cylindrical tracks accompanied by the formation of a surface nanostructure. More recently, a similar nanometric surface effect has been revealed for the impact of individual, very slow but highly charged ions. While swift ions transfer their large kinetic energy to the target via ionization and electronic excitation processes (electronic stopping), slow highly charged ions produce surface structures due to potential energy deposited at the top surface layers. Despite the differences in primary excitation, the similarity between the nanostructures is striking and strongly points to a common mechanism related to the energy transfer from the electronic to the lattice system of the target. A comparison of surface structures induced by swift heavy ions and slow highly charged ions provides a valuable insight to better understand the formation mechanisms. © 2011 IOP Publishing Ltd

  15. A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies.

    Directory of Open Access Journals (Sweden)

    Kevin A Henry

    Full Text Available Staphylococcal protein A (SpA and streptococcal protein G (SpG affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species.

  16. Binding of antioxidant flavonol morin to the native state of bovine serum albumin: Effects of urea and metal ions on the binding

    Energy Technology Data Exchange (ETDEWEB)

    Singha Roy, Atanu; Dinda, Amit Kumar; Chaudhury, Susmitnarayan; Dasgupta, Swagata, E-mail: swagata@chem.iitkgp.ernet.in

    2014-01-15

    In consideration of the various medicinal aspects of the flavonoid polyphenols, the interaction of morin with bovine serum albumin (BSA) has been investigated using multi-spectroscopic approaches. The pKa{sub 1} of morin being 5.09, which is below physiological pH, binding studies provide important insights into its potential use as a biotherapeutic. The binding was performed under different pH (5, 7 and 9) conditions and in absence and presence of Cu(II) and Fe(III) ions. It is observed that the presence of metal ions affect the binding of morin towards BSA. The binding with BSA results in a motional restriction of morin in solution that causes an increase in anisotropy (r), rotational correlation time (t{sub r}) and steady-state lifetime (t{sub av}) of the ligand. Urea causes denaturation of BSA resulting in the release of morin from the protein core as determined from both the steady-state fluorescence and anisotropy (r) measurements. The possibility of non-radiative energy transfer from the donor tryptophan to the acceptor morin is detected following the Förster's theory. The site marker displacement studies along with the molecular docking results indicated that morin binds to the hydrophobic pocket of site 1 (subdomain IIA) near Trp 213 of BSA. -- Highlights: • Binding mainly occurs through the electrostatic forces with partial hydrophobic association. • Negative ΔG° indicates the spontaneity of the complexation between morin and BSA. • Morin binds near Trp 213 (site 1, subdomain IIA) of BSA only in its native state. • Lifetime of morin increases as a function of BSA. • Motional restriction of morin occurs in the presence of BSA.

  17. Secondary electron emission from boron-doped diamond under ion impact: Applications in single-ion detection

    International Nuclear Information System (INIS)

    Kamiya, T.; Cholewa, M.; Saint, A.; Prawer, S.; Legge, G.J.; Butler, J.E.; Vestyck, D.J. , Jr.

    1997-01-01

    The secondary electron emission from a 2 μm thick boron-doped diamond film under ion (4.6 endash 7.7 MeV He + )impact is reported. The yield under ions impact is found to be remarkably high, stable over a period of many months, and independent of which side of the film (i.e., growth or substrate side) is exposed to the ion flux. By taking advantage of the high secondary-electron yield, the passage of each ion through the film could be detected with an efficiency of close to 100%, which to the best of our knowledge is the highest efficiency recorded to date for any thin-film window. This finding has an immediate application in single-ion irradiation systems where a thin vacuum window is required to allow extraction of an ion beam from the vacuum into air and at the same time offer 100% efficiency for the detection of the passage of the ion through the window. copyright 1997 American Institute of Physics

  18. Potential New Ligand Systems for Binding Uranyl Ions in Seawater Environments

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-12-13

    Work began this quarter on a new project involving a combined computational and biosynthetic approach to selective recognition of uranyl ion in aqueous solution. This project exploits the results of computational studies to discover new ligand classes. Synthetic studies will follow to generate target systems for uranyl binding and determination of binding constants. The process will be iterative, with results from computation informing synthesis, and vice versa. The theme of the ligand classes to be examined initially will be biologically based. New phosphonate-containing α-amino acid N-carboxyanhydride (NCA) monomers were used recently to prepare well-defined phosphonate-containing poly-peptides and block copolypeptides. Our first approach is to utilize these phosphate- and phosphonate-containing NCAs for the coordination of uranyl. The work includes the laboratory-scale preparation of a series of NCAs and the full thermodynamic and spectroscopic characterization of the resulting uranyl complexes. We are also evaluating the sequestering activity in different physiological and environmental conditions of these copolymers as well as their biodegradability.

  19. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.

    Science.gov (United States)

    Edmondson, Andrew C; Song, Daqing; Alvarez, Luis A; Wall, Melisa K; Almond, David; McClellan, David A; Maxwell, Anthony; Nielsen, Brent L

    2005-04-01

    A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.

  20. Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations.

    Science.gov (United States)

    Ratheal, Ian M; Virgin, Gail K; Yu, Haibo; Roux, Benoît; Gatto, Craig; Artigas, Pablo

    2010-10-26

    The Na/K pump is a P-type ATPase that exchanges three intracellular Na(+) ions for two extracellular K(+) ions through the plasmalemma of nearly all animal cells. The mechanisms involved in cation selection by the pump's ion-binding sites (site I and site II bind either Na(+) or K(+); site III binds only Na(+)) are poorly understood. We studied cation selectivity by outward-facing sites (high K(+) affinity) of Na/K pumps expressed in Xenopus oocytes, under voltage clamp. Guanidinium(+), methylguanidinium(+), and aminoguanidinium(+) produced two phenomena possibly reflecting actions at site III: (i) voltage-dependent inhibition (VDI) of outwardly directed pump current at saturating K(+), and (ii) induction of pump-mediated, guanidinium-derivative-carried inward current at negative potentials without Na(+) and K(+). In contrast, formamidinium(+) and acetamidinium(+) induced K(+)-like outward currents. Measurement of ouabain-sensitive ATPase activity and radiolabeled cation uptake confirmed that these cations are external K(+) congeners. Molecular dynamics simulations indicate that bound organic cations induce minor distortion of the binding sites. Among tested metals, only Li(+) induced Na(+)-like VDI, whereas all metals tested except Na(+) induced K(+)-like outward currents. Pump-mediated K(+)-like organic cation transport challenges the concept of rigid structural models in which ion specificity at site I and site II arises from a precise and unique arrangement of coordinating ligands. Furthermore, actions by guanidinium(+) derivatives suggest that Na(+) binds to site III in a hydrated form and that the inward current observed without external Na(+) and K(+) represents cation transport when normal occlusion at sites I and II is impaired. These results provide insights on external ion selectivity at the three binding sites.

  1. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.

    Science.gov (United States)

    Sinha, Kaustubh; Sangani, Sahil S; Kehr, Andrew D; Rule, Gordon S; Jen-Jacobson, Linda

    2016-11-08

    Metal ion cofactors can alter the energetics and specificity of sequence specific protein-DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein-DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg 2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu 3+ or two La 3+ cations bind, and two new crystal structures confirm that Lu 3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1 H- 15 N amide resonances, for 1 H- 13 C Ile-δ-CH 3 resonances, and for stereospecifically assigned Leu-δ-CH 3 and Val-γ-CH 3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex.

  2. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

    Science.gov (United States)

    2016-01-01

    Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

  3. Elucidating the structures and cooperative binding mechanism of cesium salts to the multitopic ion-pair receptor through density functional theory calculations.

    Science.gov (United States)

    Sadhu, Biswajit; Sundararajan, Mahesh; Velmurugan, Gunasekaran; Venuvanalingam, Ponnambalam

    2015-09-21

    Designing new and innovative receptors for the selective binding of radionuclides is central to nuclear waste management processes. Recently, a new multi-topic ion-pair receptor was reported which binds a variety of cesium salts. Due to the large size of the receptor, quantum chemical calculations on the full ion-pair receptors are restricted, thus the binding mechanisms are not well understood at the molecular level. We have assessed the binding strengths of various cesium salts to the recently synthesized multi-topic ion-pair receptor molecule using density functional theory based calculations. Our calculations predict that the binding of cesium salts to the receptor predominantly occurs via the cooperative binding mechanism. Cesium and the anion synergistically assist each other to bind favorably inside the receptor. Energy decomposition analysis on the ion-pair complexes shows that the Cs salts are bound to the receptor mainly through electrostatic interactions with small contribution from covalent interactions for large ionic radius anions. Further, QTAIM analysis characterizes the importance of different inter-molecular interactions between the ions and the receptor inside the ion-pair complexes. The role of the crystallographic solvent molecule contributes significantly by ~10 kcal mol(-1) to the overall binding affinities which is quite significant. Further, unlike the recent molecular mechanics (MM) calculations, our calculated binding affinity trends for various Cs ion-pair complexes (CsF, CsCl and CsNO3) are now in excellent agreement with the experimental binding affinity trends.

  4. Scanning probe microscopy of single Au ion implants in Si

    International Nuclear Information System (INIS)

    Vines, L.; Monakhov, E.; Maknys, K.; Svensson, B.G.; Jensen, J.; Hallen, A.; Kuznetsov, A. Yu.

    2006-01-01

    We have studied 5 MeV Au 2+ ion implantation with fluences between 7 x 10 7 and 2 x 10 8 cm -2 in Si by deep level transient spectroscopy (DLTS) and scanning capacitance microscopy (SCM). The DLTS measurements show formation of electrically active defects such as the two negative charge states of the divacancy (V 2 (=/-) and V 2 (-/0)) and the vacancy-oxygen (VO) center. It is observed that the intensity of the V 2 (=/-) peak is lower compared to that of V 2 (-/0) by a factor of 5. This has been attributed to a highly localized distribution of the defects along the ion tracks, which results in trapping of the carriers at V 2 (-/0) and incomplete occupancy of V 2 (=/-). The SCM measurements obtained in a plan view show a random pattern of regions with a reduced SCM signal for the samples implanted with fluence above 2 x 10 8 cm -2 . The reduced SCM signal is attributed to extra charges associated with acceptor states, such as V 2 (-/0), formed along the ion tracks in the bulk Si. Indeed, the electron emission rate from the V 2 (-/0) state is in the range of 10 kHz at room temperature, which is well below the probing frequency of the SCM measurements, resulting in 'freezing' of electrons at V 2 (-/0)

  5. A simple and rapid method for high-resolution visualization of single-ion tracks

    Directory of Open Access Journals (Sweden)

    Masaaki Omichi

    2014-11-01

    Full Text Available Prompt determination of spatial points of single-ion tracks plays a key role in high-energy particle induced-cancer therapy and gene/plant mutations. In this study, a simple method for the high-resolution visualization of single-ion tracks without etching was developed through the use of polyacrylic acid (PAA-N, N’-methylene bisacrylamide (MBAAm blend films. One of the steps of the proposed method includes exposure of the irradiated films to water vapor for several minutes. Water vapor was found to promote the cross-linking reaction of PAA and MBAAm to form a bulky cross-linked structure; the ion-track scars were detectable at a nanometer scale by atomic force microscopy. This study demonstrated that each scar is easily distinguishable, and the amount of generated radicals of the ion tracks can be estimated by measuring the height of the scars, even in highly dense ion tracks. This method is suitable for the visualization of the penumbra region in a single-ion track with a high spatial resolution of 50 nm, which is sufficiently small to confirm that a single ion hits a cell nucleus with a size ranging between 5 and 20 μm.

  6. Network type sp3 boron-based single-ion conducting polymer electrolytes for lithium ion batteries

    Science.gov (United States)

    Deng, Kuirong; Wang, Shuanjin; Ren, Shan; Han, Dongmei; Xiao, Min; Meng, Yuezhong

    2017-08-01

    Electrolytes play a vital role in modulating lithium ion battery performance. An outstanding electrolyte should possess both high ionic conductivity and unity lithium ion transference number. Here, we present a facile method to fabricate a network type sp3 boron-based single-ion conducting polymer electrolyte (SIPE) with high ionic conductivity and lithium ion transference number approaching unity. The SIPE was synthesized by coupling of lithium bis(allylmalonato)borate (LiBAMB) and pentaerythritol tetrakis(2-mercaptoacetate) (PETMP) via one-step photoinitiated in situ thiol-ene click reaction in plasticizers. Influence of kinds and content of plasticizers was investigated and the optimized electrolytes show both outstanding ionic conductivity (1.47 × 10-3 S cm-1 at 25 °C) and high lithium transference number of 0.89. This ionic conductivity is among the highest ionic conductivity exhibited by SIPEs reported to date. Its electrochemical stability window is up to 5.2 V. More importantly, Li/LiFePO4 cells with the prepared single-ion conducting electrolytes as the electrolyte as well as the separator display highly reversible capacity and excellent rate capacity under room temperature. It also demonstrates excellent long-term stability and reliability as it maintains capacity of 124 mA h g-1 at 1 C rate even after 500 cycles without obvious decay.

  7. The method and equipment for the investigation of ions orienting transmission through thin single crystals

    CERN Document Server

    Soroka, V Y; Maznij, Y O

    2003-01-01

    A new approach is proposed to solve the task of angular distribution measurement of intensity strongly differentiated ions fluxes. Channeling effect makes this problem a regular feature of experimental study of ions orientating transmission through thin single crystals. The approach is based on the use of ions additional scattering by an amorphous (polycrystalline) target after passing through single crystal. The additional target manipulator is joined with the principal target chamber equipment with three-axis goniometer. The manipulator allows to move an additional target in the vicinity of the accelerator beam within the limits of +- 3 sup 0 in all directions and allows to measure the angular distribution of scattered ions with the accuracy of 1 min. The method and equipment were tested at the single ended electrostatic accelerator (EG-5) using a proton beam. At present the measurements have been resumed at the tandem accelerator (EG-10) of the Institute for Nuclear Research of the Academy of Sciences of U...

  8. Combined determination of copper ions and β-amyloid peptide by a single ratiometric electrochemical biosensor.

    Science.gov (United States)

    Yu, Yanyan; Wang, Peng; Zhu, Xiaodan; Peng, Qiwen; Zhou, Yi; Yin, Tianxiao; Liang, Yixin; Yin, Xiaoxing

    2017-12-18

    Copper ions (Cu 2+ ) play a critical role in biological processes and are directly involved in β-amyloid peptide (Aβ) aggregation, which is responsible for the occurrence and development of Alzheimer's disease (AD). Therefore, combined determination of Cu 2+ and Aβ in one analytical system is of great significance to understand the exact nature of the AD event. This work presents a novel ratiometric electrochemical biosensor for the dual determination of Cu 2+ and Aβ 1-42 . This unique sensor is based on a 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulphonate) (ABTS) and poly(diallyldimethylammonium chloride) (PDDA)-bi functionalized single-walled carbon nanotubes (ABTS-PDDA/CNTs) composite. The inclusion of ABTS not only enhanced the sensitivity, but it also acted as an inner reference molecule to improve detection accuracy. The specific recognition of Cu 2+ was realized by neurokinin B (NKB) coatings on the ABTS-PDDA/CNTs surface to form a [Cu II (NKB) 2 ] complex with Cu 2+ . The ABTS-PDDA/CNTs-NKB modified electrode also displayed an excellent electrochemical response toward the Aβ 1-42 monomer, when a certain amount of the Aβ 1-42 monomer was added to Cu 2+ -contained PBS buffer, which was due to the release of Cu 2+ from the [Cu II (NKB) 2 ] complex through Aβ binding to Cu 2+ . Meanwhile, our work showed that Cu 2+ bound Aβ 1-42 was concentration-dependent. Consequently, the presented electrochemical approach was capable of quantifying two important biological species associated with AD by one single biosensor, with the detection limits of 0.04 μM for Cu 2+ and 0.5 ng mL -1 for Aβ 1-42 , respectively. Finally, the ratiometric electrode was successfully applied for monitoring Cu 2+ and Aβ 1-42 variations in plasma and hippocampus of normal and AD rats.

  9. Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

    Science.gov (United States)

    Borodin, Oleg

    2009-09-10

    A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

  10. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity.

    Science.gov (United States)

    Petzold, Christine; Marceau, Aimee H; Miller, Katherine H; Marqusee, Susan; Keck, James L

    2015-06-05

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity*

    Science.gov (United States)

    Petzold, Christine; Marceau, Aimee H.; Miller, Katherine H.; Marqusee, Susan; Keck, James L.

    2015-01-01

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome. PMID:25903123

  12. Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization.

    Science.gov (United States)

    Rivas-Pardo, Jaime Andrés; Alegre-Cebollada, Jorge; Ramírez-Sarmiento, César A; Fernandez, Julio M; Guixé, Victoria

    2015-01-01

    Enzyme-substrate binding is a dynamic process intimately coupled to protein structural changes, which in turn changes the unfolding energy landscape. By the use of single-molecule force spectroscopy (SMFS), we characterize the open-to-closed conformational transition experienced by the hyperthermophilic adenine diphosphate (ADP)-dependent glucokinase from Thermococcus litoralis triggered by the sequential binding of substrates. In the absence of substrates, the mechanical unfolding of TlGK shows an intermediate 1, which is stabilized in the presence of Mg·ADP(-), the first substrate to bind to the enzyme. However, in the presence of this substrate, an additional unfolding event is observed, intermediate 1*. Finally, in the presence of both substrates, the unfolding force of intermediates 1 and 1* increases as a consequence of the domain closure. These results show that SMFS can be used as a powerful experimental tool to investigate binding mechanisms of different enzymes with more than one ligand, expanding the repertoire of protocols traditionally used in enzymology.

  13. Leishmania replication protein A-1 binds in vivo single-stranded telomeric DNA

    International Nuclear Information System (INIS)

    Neto, J.L. Siqueira; Lira, C.B.B.; Giardini, M.A.; Khater, L.; Perez, A.M.; Peroni, L.A.; Reis, J.R.R. dos; Freitas-Junior, L.H.; Ramos, C.H.I.; Cano, M.I.N.

    2007-01-01

    Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in different events of DNA metabolism. In yeast, subunits 1 (RPA-1) and 2 (RPA-2) work also as telomerase recruiters and, in humans, the complex unfolds G-quartet structures formed by the 3' G-rich telomeric strand. In most eukaryotes, RPA-1 and RPA-2 bind DNA using multiple OB fold domains. In trypanosomatids, including Leishmania, RPA-1 has a canonical OB fold and a truncated RFA-1 structural domain. In Leishmania amazonensis, RPA-1 alone can form a complex in vitro with the telomeric G-rich strand. In this work, we show that LaRPA-1 is a nuclear protein that associates in vivo with Leishmania telomeres. We mapped the boundaries of the OB fold DNA-binding domain using deletion mutants. Since Leishmania and other trypanosomatids lack homologues of known telomere end binding proteins, our results raise questions about the function of RPA-1 in parasite telomeres

  14. Most spin-1/2 transition-metal ions do have single ion anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jia; Whangbo, Myung-Hwan, E-mail: hxiang@fudan.edu.cn, E-mail: mike-whangbo@ncsu.edu [Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695 (United States); Koo, Hyun-Joo [Department of Chemistry and Research Institute for Basic Sciences, Kyung Hee University, Seoul 130-701 (Korea, Republic of); Xiang, Hongjun, E-mail: hxiang@fudan.edu.cn, E-mail: mike-whangbo@ncsu.edu [Key Laboratory of Computational Physical Sciences (Ministry of Education), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, Shanghai 200433 (China); Kremer, Reinhard K. [Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, D-70569 Stuttgart (Germany)

    2014-09-28

    The cause for the preferred spin orientation in magnetic systems containing spin-1/2 transition-metal ions was explored by studying the origin of the easy-plane anisotropy of the spin-1/2 Cu{sup 2+} ions in CuCl{sub 2}·2H{sub 2}O, LiCuVO{sub 4}, CuCl{sub 2}, and CuBr{sub 2} on the basis of density functional theory and magnetic dipole-dipole energy calculations as well as a perturbation theory treatment of the spin-orbit coupling. We find that the spin orientation observed for these spin-1/2 ions is not caused by their anisotropic spin exchange interactions, nor by their magnetic dipole-dipole interactions, but by the spin-orbit coupling associated with their crystal-field split d-states. Our study also predicts in-plane anisotropy for the Cu{sup 2+} ions of Bi{sub 2}CuO{sub 4} and Li{sub 2}CuO{sub 2}. The results of our investigations dispel the mistaken belief that magnetic systems with spin-1/2 ions have no magnetic anisotropy induced by spin-orbit coupling.

  15. Single photons, dileptons and hadrons from relativistic heavy ion ...

    Indian Academy of Sciences (India)

    The production of single photons in Pb+Pb collisions at the CERN SPS as measured by the WA98 experiment is analysed. A quark gluon plasma is assumed to be formed initially, which expands, cools, hadronizes, and undergoes freeze-out. A rich hadronic equation of state is used and the transverse expansion of the ...

  16. Single photons, dileptons and hadrons from relativistic heavy ion ...

    Indian Academy of Sciences (India)

    Abstract. The production of single photons in Pb+Pb collisions at the CERN SPS as measured by the WA98 experiment is analysed. A quark gluon plasma is assumed to be formed initially, which expands, cools, hadronizes, and undergoes freeze-out. A rich hadronic equation of state is used and the transverse expansion of ...

  17. Single event simulation for memories using accelerated ions

    International Nuclear Information System (INIS)

    Sakagawa, Y.; Shiono, N.; Mizusawa, T.; Sekiguchi, M.; Sato, K.; Sugai, I.; Hirao, Y.; Nishimura, J.; Hattori, T.

    1987-01-01

    To evaluate the error immunity of the LSI memories from cosmic rays in space, an irradiation test using accelerated heavy ions is performed. The sensitive regions for 64 K DRAM (Dynamic Random Access Memory) and 4 K SRAM (Static Random Access Memory) are determined from the irradiation test results and the design parameters of the devices. The observed errors can be classified into two types. One is the direct ionization type and the other is the recoil produced error type. Sensitive region is determined for the devices. Error rate estimation methods for both types are proposed and applied to those memories used in space. The error rate of direct ionization exceeds the recoil type by 2 or 3 orders. And the direct ionization is susceptible to shield thickness. (author)

  18. Single event effects induced by 15.14 MeV/u 136Xe ions

    International Nuclear Information System (INIS)

    Hou Mingdong; Zhang Qingxiang; Liu Jie; Wang Zhiguang; Jin Yunfan; Zhu Zhiyong; Zhen Honglou; Liu Changlong; Chen Xiaoxi; Wei Xinguo; Zhang Lin; Fan Youcheng; Zhu Zhourong; Zhang Yiting

    2002-01-01

    Single event effects induced by 15.14 MeV/u 136 Xe ions in different batches of 32k x 8 bits static random access memory are studied. The incident angle dependences of the cross sections for single event upset and single event latch up are presented. The SEE cross sections are plotted versus energy loss instead of linear energy transfer value in sensitive region. The depth of sensitive volume and thickness of 'dead' layer above the sensitive volume are estimated

  19. Imaging large cohorts of single ion channels and their activity

    Directory of Open Access Journals (Sweden)

    Katia eHiersemenzel

    2013-09-01

    Full Text Available As calcium is the most important signaling molecule in neurons and secretory cells, amongst many other cell types, it follows that an understanding of calcium channels and their regulation of exocytosis is of vital importance. Calcium imaging using calcium dyes such as Fluo3, or FRET-based dyes that have been used widely has provided invaluable information, which combined with modeling has estimated the sub-types of channels responsible for triggering the exocytotic machinery as well as inferences about the relative distances away from vesicle fusion sites these molecules adopt. Importantly, new super-resolution microscopy techniques, combined with novel Ca2+ indicators and imaginative imaging approaches can now define directly the nanoscale locations of very large cohorts of single channel molecules in relation to single vesicles. With combinations of these techniques the activity of individual channels can be visualized and quantified using novel Ca2+ indicators. Fluorescently labeled specific channel toxins can also be used to localize endogenous assembled channel tetramers. Fluorescence lifetime imaging microscopy and other single-photon-resolution spectroscopic approaches offer the possibility to quantify protein-protein interactions between populations of channels and the SNARE protein machinery for the first time. Together with simultaneous electrophysiology, this battery of quantitative imaging techniques has the potential to provide unprecedented detail describing the locations, dynamic behaviours, interactions and conductance activities of many thousands of channel molecules and vesicles in living cells.

  20. Quantifying metal ions binding onto dissolved organic matter using log-transformed absorbance spectra.

    Science.gov (United States)

    Yan, Mingquan; Wang, Dongsheng; Korshin, Gregory V; Benedetti, Marc F

    2013-05-01

    This study introduces the concept of consistent examination of changes of log-transformed absorbance spectra of dissolved organic matter (DOM) at incrementally increasing concentrations of heavy metal cations such as copper, cadmium, and aluminum at environmentally relevant concentrations. The approach is designed to highlight contributions of low-intensity absorbance features that appear to be especially sensitive to DOM reactions. In accord with this approach, log-transformed absorbance spectra of fractions of DOM from the Suwannee River were acquired at varying pHs and concentrations of copper, cadmium, and aluminum. These log-transformed spectra were processed using the differential approach and used to examine the nature of the observed changes of DOM absorbance and correlate them with the extent of Me-DOM complexation. Two alternative parameters, namely the change of the spectral slope in the range of wavelengths 325-375 nm (DSlope325-375) and differential logarithm of DOM absorbance at 350 nm (DLnA350) were introduced to quantify Cu(II), Cd(II), and Al(III) binding onto DOMs. DLnA350 and DSlope325-375 datasets were compared with the amount of DOM-bound Cu(II), Cd(II), and Al(III) estimated based on NICA-Donnan model calculations. This examination showed that the DLnA350 and DSlope325-375 acquired at various pH values, metal ions concentrations, and DOM types were strongly and unambiguously correlated with the concentration of DOM-bound metal ions. The obtained experimental results and their interpretation indicate that the introduced DSlope325-375 and DLnA35 parameters are predictive of and can be used to quantify in situ metal ions interactions with DOMs. The presented approach can be used to gain more information about DOM-metal interactions and for further optimization of existing formal models of metal-DOM complexation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Assaying the binding strength of G-quadruplex ligands using single-molecule TPM experiments.

    Science.gov (United States)

    Liu, Shih-Wei; Chu, Jen-Fei; Tsai, Cheng-Ting; Fang, Hung-Chih; Chang, Ta-Chau; Li, Hung-Wen

    2013-05-15

    G-quadruplexes are stable secondary structures formed by Hoogsteen base pairing of guanine-rich single-stranded DNA sequences in the presence of monovalent cations (Na(+) or K(+)). Folded G-quadruplex (G4) structures in human telomeres have been proposed as a potential target for cancer therapy. In this study, we used single-molecule tethered particle motion (TPM) experiments to assay the binding strength of possible G4 ligands. We found that individual single-stranded DNA molecules containing the human telomeric sequence d[AGGG(TTAGGG)3] fluctuated between the folded and the unfolded states in a 10 mM Na(+) solution at 37 °C. The durations of folded and unfolded states were single-exponentially distributed, and in return the folding and unfolding rate constants were 1.68 ± 0.01 and 1.63 ± 0.03 (s(-1)), respectively. In the presence of G4 ligands, such as TMPyP4, DODCI, BMVC, and BMVPA, the unfolding rate constant decreased appreciably. In addition, combining the Cu(2+)-induced G4 unfolding and TPM assay, we showed that BMVC and TMPyP4 are better G4 stabilizers than DODCI. The capability of monitoring the fluctuation between the folded and the unfolded state of G4 DNA in real time allows the determination of both kinetic and thermodynamic parameters in a single measurement and offers a simple way to assay binding strength under various conditions. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

  2. Iron ions and haeme modulate the binding properties of complement subcomponent C1q and of immunoglobulins.

    Science.gov (United States)

    Dimitrov, J D; Roumenina, L T; Doltchinkova, V R; Vassilev, T L

    2007-03-01

    The complement system and circulating antibodies play a major role in the defence against infection. They act at the sites of inflammation, where the harsh microenvironment and the oxidative stress lead to the release of free iron ions and haeme. The aim of this study was to analyse the consequences of the exposure of C1q and immunoglobulins to iron ions or haeme. The changes in target recognition by C1q and in the rheumatoid factor activity of the immunoglobulins were investigated. The exposure of C1q to ferrous ions increased its binding to IgG and to IgM. In contrast, haeme inhibited C1q binding to all studied targets, especially to IgG1 and C-reactive protein. Thus, the haeme released as a result of tissue damage and oxidative stress may act as a negative feedback regulator of an inappropriate complement triggering as seen in ischaemia-reperfusion tissue injury. The results also show that iron ions and haeme were able to reveal rheumatoid factor activity of IgG. The modulation of the C1q-target binding as well as the revealing of rheumatoid factor activity of IgG by exposure to redox-active agents released at the sites of inflammation may have important consequences for the understanding of the immunopathological mechanisms of inflammatory and autoimmune diseases.

  3. Laser spectroscopic investigation of singly and doubly charged thorium ions

    Energy Technology Data Exchange (ETDEWEB)

    Thielking, Johannes; Meier, David-Marcel; Glowacki, Przemyslaw; Okhapkin, Maksim V.; Peik, Ekkehard [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany)

    2017-07-01

    The {sup 229}Th isotope possesses a unique, low-energy nuclear isomeric state at about 7.8(5) eV. This fact has stimulated the development of novel ideas in the borderland between atomic and nuclear physics, for example the use as an optical nuclear clock. Since the required precise information on the isomer energy is not yet available, it is intensely searched for using different experimental approaches. For the excitation of the nuclear isomer via electronic bridge or NEET processes, we plan to use two-photon laser excitation of high-lying electronic levels in Th{sup +}. We recently expanded our search range to higher energies and measured 38 previously unknown energy levels in the range from 7.8 eV to 8.7 eV. We also prepare to study the nuclear structure of the isomeric state in cooperation with the Maier-Leibnitz-Laboratorium at LMU Munich, using trapped recoil ions, where the isomeric state is populated via α-decay from {sup 233}U. For this purpose we investigate the hyperfine structure of suitable transitions of Th{sup 2+}.

  4. Transmission of Fast Highly Charged Ions through a Single Glass Macrocapillary and Polycarbonate Nanocapillary Foils

    Science.gov (United States)

    Ayyad, A. M.; Dassanayake, B. S.; Keerthisinghe, D.; DeSilva, G. G.; Elkafrawy, T.; Kayani, N.; Tanis, J. A.

    2012-11-01

    Transmission of 3 MeV protons and 16 MeV O5+ ions through a single glass macrocapillary and a polycarbonate nanocapillary foil has been investigated. Results show that 3 MeV protons transmit through the capillary and the foils with little or no energy loss, while 16 MeV O5+ ions show transmission through the capillary and the foil with energy losses that vary with the tilt angle, and there are also changes in the charge state.

  5. Characterization of strained InGaAs single quantum well structures by ion beam methods

    International Nuclear Information System (INIS)

    Yu, K.M.; Chan, K.T.

    1990-01-01

    We have investigated strained InGaAs single quantum well structures using MeV ion beam methods. The structural properties of these structures, including composition and well size, have been studied. It has been found that the composition obtained by Rutherford backscattering spectrometry and particle-induced x-ray emission techniques agrees very well with that obtained by the ion channeling method

  6. Effect of 120 MeV Ag9+ ion irradiation of YCOB single crystals

    Science.gov (United States)

    Arun Kumar, R.; Dhanasekaran, R.

    2012-09-01

    Single crystals of yttrium calcium oxy borate (YCOB) grown from boron-tri-oxide flux were subjected to swift heavy ion irradiation using silver Ag9+ ions from the 15 UD Pelletron facility at Inter University Accelerator Center, New Delhi. The crystals were irradiated at 1 × 1013, 5 × 1013 and 1 × 1014 ions/cm2 fluences at room temperature and with 5 × 1013 ions/cm2 fluence at liquid nitrogen temperature. The pristine and the irradiated samples were characterized by glancing angle X-ray diffraction, UV-Vis-NIR and photoluminescence studies. From the characterization studies performed on the samples, it is inferred that the crystals irradiated at liquid nitrogen temperature had fewer defects compared to the crystals irradiated at room temperature and the defects increased when the ion fluence was increased at room temperature.

  7. Ion beam synthesis of buried single crystal erbium silicide

    International Nuclear Information System (INIS)

    Golanski, A.; Feenstra, R.; Galloway, M.D.; Park, J.L.; Pennycook, S.J.; Harmon, H.E.; White, C.W.

    1990-01-01

    High doses (10 16 --10 17 /cm 2 ) of 170 keV Er + were implanted into single-crystal left-angle 111 right-angle Si at implantation temperatures between 350 degree C and 520 degree C. Annealing at 800 degree C in vacuum following the implant, the growth and coalescence of ErSi 2 precipitates leads to a buried single crystalline ErSi 2 layer. This has been studied using Rutherford backscattering/channeling, X-ray diffraction, cross-sectional TEM and resistance versus temperature measurements. Samples implanted at 520 degree C using an Er dose of 7 x 10 16 /cm 2 and thermally annealed were subsequently used as seeds for the mesoepitaxial growth of the buried layer during a second implantation and annealing process. Growth occurs meso-epitaxially along both interfaces through beam induced, defect mediated mobility of Er atoms. The crystalline quality of the ErSi 2 layer strongly depends on the temperature during the second implantation. 12 refs., 4 figs

  8. Accuracy of the detection of binding events using 3D single particle tracking.

    Science.gov (United States)

    Carozza, Sara; Culkin, Jamie; van Noort, John

    2017-01-01

    Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D . However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion. This issue is of particular importance in an experiment aiming to quantify dynamic processes. Here, we present simulations and 3D tracking experiments with Gold Nanorods freely diffusing in glycerol solution to establish the best analysis parameters to extract the diffusion coefficient. We applied this knowledge to the detection of a temporary change in diffusion, as it can occur due to the transient binding of a particle to an immobile structure within the cell, and tested its dependence on the magnitude of the change in diffusion and duration of this event. The simulations show that the spatial accuracy of particle tracking generally does not limit the detection of short binding events. Careful analysis of the magnitude of the change in diffusion and the number of frames per binding event is required for accurate quantification of such events.

  9. Quantum ion-acoustic oscillations in single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Khan, S.A. [Kyoto Univ., Katsura (Japan). Graduate School of Engineering; Quaid-i-Azam Univ., Islamabad (Pakistan). National Centre for Physics; Iqbal, Z. [University of Management and Technology, Sialkot (Pakistan); Wazir, Z. [Riphah International Univ., Islamabad (Pakistan). Dept. of Basic Sciences; Rehman, Aman ur [Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad (Pakistan)

    2016-08-01

    Quantum ion-acoustic oscillations in single-walled carbon nanotubes are studied by employing a quantum hydrodynamics model. The dispersion equation is obtained by Fourier transformation, which exhibits the existence of quantum ion-acoustic wave affected by change of density balance due to presence of positive or negative heavy species as stationary ion clusters and wave potential at equilibrium. The numerical results are presented, and the role of quantum degeneracy, nanotube geometry, electron exchange-correlation effects, and concentration and polarity of heavy species on wave dispersion is pointed out for typical systems of interest.

  10. Quantum Ion-Acoustic Oscillations in Single-Walled Carbon Nanotubes

    Science.gov (United States)

    Khan, S. A.; Iqbal, Z.; Wazir, Z.; Aman-ur-Rehman

    2016-05-01

    Quantum ion-acoustic oscillations in single-walled carbon nanotubes are studied by employing a quantum hydrodynamics model. The dispersion equation is obtained by Fourier transformation, which exhibits the existence of quantum ion-acoustic wave affected by change of density balance due to presence of positive or negative heavy species as stationary ion clusters and wave potential at equilibrium. The numerical results are presented, and the role of quantum degeneracy, nanotube geometry, electron exchange-correlation effects, and concentration and polarity of heavy species on wave dispersion is pointed out for typical systems of interest.

  11. The interaction of human serum albumin with selected lanthanide and actinide ions: Binding affinities, protein unfolding and conformational changes.

    Science.gov (United States)

    Ali, Manjoor; Kumar, Amit; Kumar, Mukesh; Pandey, Badri N

    2016-04-01

    Human serum albumin (HSA), the most abundant soluble protein in blood plays critical roles in transportation of biomolecules and maintenance of osmotic pressure. In view of increasing applications of lanthanides- and actinides-based materials in nuclear energy, space, industries and medical applications, the risk of exposure with these metal ions is a growing concern for human health. In present study, binding interaction of actinides/lanthanides [thorium: Th(IV), uranium: U(VI), lanthanum: La(III), cerium: Ce(III) and (IV)] with HSA and its structural consequences have been investigated. Ultraviolet-visible, Fourier transform-infrared, Raman, Fluorescence and Circular dichroism spectroscopic techniques were applied to study the site of metal ions interaction, binding affinity determination and the effect of metal ions on protein unfolding and HSA conformation. Results showed that these metal ions interacted with carbonyl (CO..:)/amide(N..-H) groups and induced exposure of aromatic residues of HSA. The fluorescence analysis indicated that the actinide binding altered the microenvironment around Trp214 in the subdomain IIA. Binding affinity of U(VI) to HSA was slightly higher than that of Th(IV). Actinides and Ce(IV) altered the secondary conformation of HSA with a significant decrease of α-helix and an increase of β-sheet, turn and random coil structures, indicating a partial unfolding of HSA. A correlation was observed between metal ion's ability to alter HSA conformation and protein unfolding. Both cationic effects and coordination ability of metal ions seemed to determine the consequences of their interaction with HSA. Present study improves our understanding about the protein interaction of these heavy ions and their impact on its secondary structure. In addition, binding characteristics may have important implications for the development of rational antidote for the medical management of health effects of actinides and lanthanides. Copyright © 2016 Elsevier

  12. Ultra-fast optical manipulation of single proteins binding to the actin cytoskeleton

    Science.gov (United States)

    Capitanio, Marco; Gardini, Lucia; Pavone, Francesco Saverio

    2014-02-01

    In the last decade, forces and mechanical stresses acting on biological systems are emerging as regulatory factors essential for cell life. Emerging evidences indicate that factors such as applied forces or the rigidity of the extracellular matrix (ECM) determine the shape and function of cells and organisms1. Classically, the regulation of biological systems is described through a series of biochemical signals and enzymatic reactions, which direct the processes and cell fate. However, mechanotransduction, i.e. the conversion of mechanical forces into biochemical and biomolecular signals, is at the basis of many biological processes fundamental for the development and differentiation of cells, for their correct function and for the development of pathologies. We recently developed an in vitro system that allows the investigation of force-dependence of the interaction of proteins binding the actin cytoskeleton, at the single molecule level. Our system displays a delay of only ~10 μs between formation of the molecular bond and application of the force and is capable of detecting interactions as short as 100 μs. Our assay allows direct measurements of load-dependence of lifetimes of single molecular bonds and conformational changes of single proteins and molecular motors. We demonstrate our technique on molecular motors, using myosin II from fast skeletal muscle and on protein-DNA interaction, specifically on Lactose repressor (LacI). The apparatus is stabilized to less than 1 nm with both passive and active stabilization, allowing resolving specific binding regions along the actin filament and DNA molecule. Our technique extends single-molecule force-clamp spectroscopy to molecular complexes that have been inaccessible up to now, opening new perspectives for the investigation of the effects of forces on biological processes.

  13. Feasibility of Observing and Characterizing Single Ion Strikes in Microelectronic Components.

    Energy Technology Data Exchange (ETDEWEB)

    Dingreville, Remi Philippe Michel [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Hattar, Khalid Mikhiel [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Bufford, Daniel Charles [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-11-01

    The transient degradation of semiconductor device performance under irradiation has long been an issue of concern. A single high-energy charged particle can degrade or permanently destroy the microelectronic component, potentially altering the course or function of the systems. Disruption of the the crystalline structure through the introduction of quasi-stable defect structures can change properties from semiconductor to conductor. Typically, the initial defect formation phase is followed by a recovery phase in which defect-defect or defect-dopant interactions modify the characteristics of the damaged structure. In this LDRD Express, in-situ ion irradiation transmission microscopy (TEM) in-situ TEM experiments combined with atomistic simulations have been conducted to determine the feasibility of imaging and characterizing the defect structure resulting from a single cascade in silicon. In-situ TEM experiments have been conducted to demonstrate that a single ion strike can be observed in Si thin films with nanometer resolution in real time using the in-situ ion irradiation transmission electron microscope (I3TEM). Parallel to this experimental effort, ion implantation has been numerically simulated using Molecular Dynamics (MD). This numerical framework provides detailed predictions of the damage and follow the evolution of the damage during the first nanoseconds. The experimental results demonstrate that single ion strike can be observed in prototypical semiconductors.

  14. Single-ion and pair-interaction potentials near simple metal surfaces

    International Nuclear Information System (INIS)

    Barnett, R.N.; Barrera, R.G.; Cleveland, C.L.; Landman, U.

    1983-01-01

    Presented is a model for semi-infinite simple metals which does not require crystalline order or a single species, and thus is applicable to problems of defect energetics near the surface and random-alloy surfaces as well as ideal metal surfaces. The formulation is based on the use of ionic pseudopotentials and linear-response theory. An expression for the total energy is obtained which depends explicitly on ionic species and position. This expression is decomposed into a density-dependent term and single-ion and ionic pair-interaction potential terms. The single-ion potentials oscillate about a constant bulk value, with the magnitude of the oscillation decreasing rapidly away from the surface. The interaction between pairs of ions near the surface is shown to be a noncentral force interaction which differs significantly from the central-force bulk pair potential. The effect of quantum interference in the response of the semi-infinite electron gas to the ions is seen in both the single-ion and the pair-interaction potentials. Results are presented for the simple metals sodium, potassium, and rubidium

  15. Feasibility of Observing and Characterizing Single Ion Strikes in Microelectronic Components

    International Nuclear Information System (INIS)

    Dingreville, Remi Philippe Michel; Hattar, Khalid Mikhiel; Bufford, Daniel Charles

    2015-01-01

    The transient degradation of semiconductor device performance under irradiation has long been an issue of concern. A single high-energy charged particle can degrade or permanently destroy the microelectronic component, potentially altering the course or function of the systems. Disruption of the the crystalline structure through the introduction of quasi-stable defect structures can change properties from semiconductor to conductor. Typically, the initial defect formation phase is followed by a recovery phase in which defect-defect or defect-dopant interactions modify the characteristics of the damaged structure. In this LDRD Express, in-situ ion irradiation transmission microscopy (TEM) in-situ TEM experiments combined with atomistic simulations have been conducted to determine the feasibility of imaging and characterizing the defect structure resulting from a single cascade in silicon. In-situ TEM experiments have been conducted to demonstrate that a single ion strike can be observed in Si thin films with nanometer resolution in real time using the in-situ ion irradiation transmission electron microscope (I 3 TEM). Parallel to this experimental effort, ion implantation has been numerically simulated using Molecular Dynamics (MD). This numerical framework provides detailed predictions of the damage and follow the evolution of the damage during the first nanoseconds. The experimental results demonstrate that single ion strike can be observed in prototypical semiconductors.

  16. Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

    Science.gov (United States)

    Mason, Claire E.; Jergic, Slobodan; Lo, Allen T. Y.; Wang, Yao; Dixon, Nicholas E.; Beck, Jennifer L.

    2013-02-01

    Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)70, one molecule of (dT)35, or two molecules of (dT)35] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

  17. Tight binding simulation study on zigzag single-walled carbon nanotubes

    Science.gov (United States)

    Sharma, Deepa; Jaggi, Neena; Gupta, Vishu

    2018-01-01

    Tight binding simulation studies using the density functional tight binding (DFTB) model have been performed on various zigzag single-walled carbon-nanotubes (SWCNTs) to investigate their electronic properties using DFTB module of the Material Studio Software version 7.0. Various combinations of different eigen-solvers and charge mixing schemes available in the DFTB Module have been tried to chalk out the electronic structure. The analytically deduced values of the bandgap of (9, 0) SWCNT were compared with the experimentally determined value reported in the literature. On comparison, it was found that the tight binding approximations tend to drastically underestimate the bandgap values. However, the combination of Anderson charge mixing method with standard eigensolver when implemented using the smart algorithm was found to produce fairly close results. These optimized model parameters were then used to determine the band structures of various zigzag SWCNTs. (9, 0) Single-walled Nanotube which is extensively being used for sensing NH3, CH4 and NO2 has been picked up as a reference material since its experimental bandgap value has been reported in the literature. It has been found to exhibit a finite energy bandgap in contrast to its expected metallic nature. The study is of utmost significance as it not only probes and validates the simulation route for predicting suitable properties of nanomaterials but also throws light on the comparative efficacy of the different approximation and rationalization quantum mechanical techniques used in simulation studies. Such simulation studies if used intelligently prove to be immensely useful to the material scientists as they not only save time and effort but also pave the way to new experiments by making valuable predictions.

  18. Exchange interaction of strongly anisotropic tripodal erbium single-ion magnets with metallic surfaces

    DEFF Research Database (Denmark)

    Dreiser, Jan; Wäckerlin, Christian; Ali, Md. Ehesan

    2014-01-01

    We present a comprehensive study of Er(trensal) single-ion magnets deposited in ultrahigh vacuum onto metallic surfaces. X-ray photoelectron spectroscopy reveals that the molecular structure is preserved after sublimation, and that the molecules are physisorbed on Au(111) while they are chemisorbed....... Furthermore XMCD indicates a weak antiferromagnetic exchange coupling between the single-ion magnets and the ferromagnetic Ni/Cu(100) substrate. For the latter case, spin-Hamiltonian fits to the XMCD M(H) suggest a significant structural distortion of the molecules. Scanning tunneling microscopy reveals...

  19. Nanometer-size surface modification produced by single, low energy, highly charged ions

    International Nuclear Information System (INIS)

    Stockli, M.P.

    1994-01-01

    Atomically flat surfaces of insulators have been bombarded with low energy, highly charged ions to search for nanometer-size surface modifications. It is expected that the high electron deficiency of highly charged ions will capture and/or remove many of the insulator's localized electrons when impacting on an insulating surface. The resulting local electron deficiency is expected to locally disintegrate the insulator through a open-quotes Coulomb explosionclose quotes forming nanometer-size craters. Xe ions with charge states between 10+ and 45+ and kinetic energies between 0 and 10 keV/q were obtained from the KSU-CRYEBIS, a CRYogenic Electron Beam Ion Source and directed onto various insulating materials. Mica was favored as target material as atomically flat surfaces can be obtained reliably through cleaving. However, the authors observations with an atomic force microscope have shown that mica tends to defoliate locally rather than disintegrate, most likely due to the small binding forces between adjacent layers. So far the authors measurements indicate that each ion produces one blister if the charge state is sufficiently high. The blistering does not seem to depend very much on the kinetic energy of the ions

  20. Xenon gas field ion source from a single-atom tip

    Science.gov (United States)

    Lai, Wei-Chiao; Lin, Chun-Yueh; Chang, Wei-Tse; Li, Po-Chang; Fu, Tsu-Yi; Chang, Chia-Seng; Tsong, T. T.; Hwang, Ing-Shouh

    2017-06-01

    Focused ion beam (FIB) systems have become powerful diagnostic and modification tools for nanoscience and nanotechnology. Gas field ion sources (GFISs) built from atomic-size emitters offer the highest brightness among all ion sources and thus can improve the spatial resolution of FIB systems. Here we show that the Ir/W(111) single-atom tip (SAT) can emit high-brightness Xe+ ion beams with a high current stability. The ion emission current versus extraction voltage was analyzed from 150 K up to 309 K. The optimal emitter temperature for maximum Xe+ ion emission was ˜150 K and the reduced brightness at the Xe gas pressure of 1 × 10-4 torr is two to three orders of magnitude higher than that of a Ga liquid metal ion source, and four to five orders of magnitude higher than that of a Xe inductively coupled plasma ion source. Most surprisingly, the SAT emitter remained stable even when operated at 309 K. Even though the ion current decreased with increasing temperature, the current at room temperature (RT) could still reach over 1 pA when the gas pressure was higher than 1 × 10-3 torr, indicating the feasibility of RT-Xe-GFIS for application to FIB systems. The operation temperature of Xe-SAT-GFIS is considerably higher than the cryogenic temperature required for the helium ion microscope (HIM), which offers great technical advantages because only simple or no cooling schemes can be adopted. Thus, Xe-GFIS-FIB would be easy to implement and may become a powerful tool for nanoscale milling and secondary ion mass spectroscopy.

  1. Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites.

    Science.gov (United States)

    Du, Wenxin; Gao, Jing; Wang, Tingting; Wang, Jinke

    2014-01-01

    In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.

  2. Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface*

    Science.gov (United States)

    Slutzki, Michal; Reshef, Dan; Barak, Yoav; Haimovitz, Rachel; Rotem-Bamberger, Shahar; Lamed, Raphael; Bayer, Edward A.; Schueler-Furman, Ora

    2015-01-01

    Interactions between cohesin and dockerin modules play a crucial role in the assembly of multienzyme cellulosome complexes. Although intraspecies cohesin and dockerin modules bind in general with high affinity but indiscriminately, cross-species binding is rare. Here, we combined ELISA-based experiments with Rosetta-based computational design to evaluate the contribution of distinct residues at the Clostridium thermocellum cohesin-dockerin interface to binding affinity, specificity, and promiscuity. We found that single mutations can show distinct and significant effects on binding affinity and specificity. In particular, mutations at cohesin position Asn37 show dramatic variability in their effect on dockerin binding affinity and specificity: the N37A mutant binds promiscuously both to cognate (C. thermocellum) as well as to non-cognate Clostridium cellulolyticum dockerin. N37L in turn switches binding specificity: compared with the wild-type C. thermocellum cohesin, this mutant shows significantly increased preference for C. cellulolyticum dockerin combined with strongly reduced binding to its cognate C. thermocellum dockerin. The observation that a single mutation can overcome the naturally observed specificity barrier provides insights into the evolutionary dynamics of this system that allows rapid modulation of binding specificity within a high affinity background. PMID:25833947

  3. Targeted regulation of hygroscopicity of soybean antioxidant pentapeptide powder by zinc ions binding to the moisture absorption sites.

    Science.gov (United States)

    Xue, Peiyu; Sun, Na; Li, Yong; Cheng, Sheng; Lin, Songyi

    2018-03-01

    In the present study, a targeted regulation of hygroscopicity of soybean antioxidant pentapeptide (SAP) powder was explored by zinc ions binding to its moisture absorption sites. Scanning electron microscopy, X-ray diffraction analysis, Fourier transform infrared spectroscopy and an energy-dispersive X-ray spectroscope were used to confirm the formation of the SAP-zinc complex. The results showed that morphology of SAP-zinc complex belonged to crystalline nanoparticles. The moisture sorption/desorption kinetics of the SAP-zinc complex changed compared to that of the SAP. In particular, the moisture sorption capacity of the SAP decreased and the distribution of adsorbed water changed after zinc chelation. Based on the binding of zinc ions to the moisture absorption sites, the hygroscopicity of SAP powder could be target regulated. Thus, this study could provide a new method to regulate the hygroscopicity of peptide powder. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Single-photon emission correlated to double-electron capture by bare ions: background processes

    Science.gov (United States)

    Elkafrawy, T.; Warczak, A.; Simon, A.; Tanis, J. A.

    2013-09-01

    Radiative single- and double-electron capture are one-step processes where a single target electron or two target electrons, respectively, are captured to a bound state of a highly charged projectile with the simultaneous emission of a single photon. In ion-atom collisions, several background processes are likely to contribute to these processes and may interfere with the measured x-rays due to radiative single and double capture. In this study, possible contributions from radiative electron capture to the continuum, secondary electron bremsstrahlung, the two-step process of independent double radiative electron capture, as well as radiative- combined with nonradiative-electron capture are taken into account based on our analysis of the data for 2.21 MeV u-1 F9+ ions colliding with a thin carbon foil.

  5. Structural and optical properties of Cd2+ ion on the growth of sulphamic acid single crystals

    Science.gov (United States)

    Rajyalakshmi, S.; Rao, Valluru Srinivasa; Reddy, P. V. S. S. S. N.; Krishna, V. Y. Rama; Samatha, K.; Rao, K. Ramachandra

    2016-05-01

    Transparent single crystals of Cadmium doped Sulphamic acid (SA) was grown by Conventional slow evaporation solution technique (SEST) which had the size of 13 × 8 × 7 mm3. The grown single crystals have been characterized using single crystal X-ray diffraction UV-visible Spectral studies and Second harmonic generation (SHG) efficiency and the results were discussed. The lattice parameters of the grown Cd2+ ion doped SA crystal are confirmed by single crystal X-ray diffraction and belong to orthorhombic system. Optical transmittance of the crystal was recorded using UV-vis NIR spectrophotometer with its lower cut off wavelength around 259nm. SHG measurements indicate that the SHG efficiency of the grown Cd2+ ion doped SA crystal at a fundamental wavelength of 1064 nm is approximately equal to KDP.

  6. Serum albumin forms a lactoferrin-like soluble iron-binding complex in presence of hydrogen carbonate ions.

    Science.gov (United States)

    Ueno, Hiroshi M; Urazono, Hiroshi; Kobayashi, Toshiya

    2014-02-15

    The iron-lactoferrin complex is a common food ingredient because of its iron-solubilizing capability in the presence of hydrogen carbonate ions. However, it is unclear whether the formation of a stable iron-binding complex is limited to lactoferrin. In this study, we investigated the effects of bovine serum albumin (BSA) on iron solubility and iron-catalyzed lipid oxidation in the presence of hydrogen carbonate ions. BSA could solubilize >100-fold molar equivalents of iron at neutral pH, exceeding the specific metal-binding property of BSA. This iron-solubilizing capability of BSA was impaired by thermally denaturing BSA at ≥ 70 °C for 10 min at pH 8.5. The resulting iron-BSA complex inhibited iron-catalyzed oxidation of soybean oil in a water-in-oil emulsion measured using the Rancimat test. Our study is the first to show that BSA, like lactoferrin, forms a soluble iron-binding complex in the presence of hydrogen carbonate ions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Binding selectivity of vitamin K3 based chemosensors towards nickel(II) and copper(II) metal ions

    Science.gov (United States)

    Patil, Amit; Lande, Dipali N.; Nalkar, Archana; Gejji, Shridhar P.; Chakrovorty, Debamitra; Gonnade, Rajesh; Moniz, Tânia; Rangel, Maria; Pereira, Eulália; Salunke-Gawali, Sunita

    2017-09-01

    The vitamin K3 derivatives 2-methyl-3-[(pyridin-2-ylmethyl)-amino]-1,4-naphthoquinone (M-1), 2-methyl-3-[(pyridin-2-ylethyl)-amino]-1,4-naphthoquinone (M-2), 2-methyl-3-((2-(thiophen-2-yl)methyl)amino)naphthalene-1,4-dione (M-3) and 2-methyl-3-((2-(thiophen-2-yl)ethyl)amino)naphthalene-1,4-dione (M-4) have been synthesized, characterized and studied for their chemosensor abilities towards transition metal ions. Crystal structures of M-1 to M-4 revealed a variety of Nsbnd H⋯O, Csbnd H⋯O, Csbnd H⋯π and π⋯π interactions. Minor variations in such interactions by chemical stimuli such as metal ions, results in change in color that can be visualized by naked eyes. It has been shown that electronic structure and 1H NMR, vibrational as well as electronic spectra from the density functional theory agree well with the experiments. The metal ion binding in ethanol, ethanol-water and in mild base triethylamine brings forth recognizing ability of M-1 toward Ni2+ whereas M-2 exhibits large sensing ability for Cu2+ ion. Interestingly M-1 display varying metal ion binding specificity in different solvents with the association constant in ethanol being 11,786 M-1 for Ni2+ compared to 9462 M-1 for the Cu2+. A reversal in preferential binding of M-2 with the respective association constants being 4190 M-1 and 6370 M-1 is discernible.

  8. Study of single and binary ion plasma expansion into laboratory-generated plasma wakes

    International Nuclear Information System (INIS)

    Wright, K.H. Jr.

    1988-02-01

    Plasma expansion into the wake of a large rectangular plate immersed in a collisionless, supersonic plasma was investigated in laboratory experiments. The experimental conditions address both single ion and binary ion plasma flows for the case of a body whose size is large in comparison with the Debye length, when the potential difference between the body and the plasma is relatively small. A new plasma source was developed to generate equi-velocity, binary ion plasma flows, which allows access to new parameter space that have previously been unavailable for laboratory studies. Specifically, the new parameters are the ionic mass ratio and the ionic component density ratio. In a series of experiments, a krypton-neon plasma is employed where the ambient density ratio of neon to krypton is varied more than an order of magnitude. The expansion in both the single ion and binary ion plasma cases is limited to early times, i.e., a few ion plasma periods, by the combination of plasma density, plasma drift speed, and vacuum chamber size, which prevented detailed comparison with self-similar theory

  9. Ion beam induced single phase nanocrystalline TiO{sub 2} formation

    Energy Technology Data Exchange (ETDEWEB)

    Rukade, Deepti A. [Department of Physics, University of Mumbai, Mumbai 400098 (India); Tribedi, L.C. [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005 (India); Bhattacharyya, Varsha, E-mail: varsha.b1.physics@gmail.com [Department of Physics, University of Mumbai, Mumbai 400098 (India)

    2014-06-15

    Single phase TiO{sub 2} nanostructures are fabricated by oxygen ion implantation (60 keV) at fluence ranging from 1×10{sup 16} ions/cm{sup 2} to 1×10{sup 17} ions/cm{sup 2} in titanium thin films deposited on fused silica substrate and subsequent thermal annealing in argon atmosphere. GAXRD and Raman spectroscopy study reveals formation of single rutile phases of TiO{sub 2}. Particle size is found to vary from 29 nm to 35 nm, establishing nanostructure formation. Nanostructure formation is also confirmed by the quantum confinement effect manifested by the blueshift of the UV–vis absorption spectra. Photoluminescence spectra show peaks corresponding to TiO{sub 2} rutile phase and reveal the presence of oxygen defects due to implantation. The controlled synthesis of single phase nanostructure is attributed to ion induced defects and post-implantation annealing. It is observed that the size of the nanostructures formed is strongly dependent on the ion fluence.

  10. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel.

    Science.gov (United States)

    Jalily Hasani, Horia; Ganesan, Aravindhan; Ahmed, Marawan; Barakat, Khaled H

    2018-01-01

    The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel

  11. Ion mass dependence for low energy channeling in single-wall nanotubes

    International Nuclear Information System (INIS)

    An Monte Carlo (MC) simulation program has been used to study ion mass dependence for the low energy channeling of natural- and pseudo-Ar ions in single-wall nanotubes. The MC simulations show that the channeling critical angle Ψ C obeys the (E) -1/2 and the (M 1 ) -1/2 rules, where E is the incident energy and M 1 is the ion mass. The reason for this may be that the motion of the channeled (or de-channeled) ions should be correlated with both the incident energy E and the incident momentum (2M 1 E) 1/2 , in order to obey the conservation of energy and momentum

  12. Heavy doping of CdTe single crystals by Cr ion implantation

    Science.gov (United States)

    Popovych, Volodymyr D.; Böttger, Roman; Heller, Rene; Zhou, Shengqiang; Bester, Mariusz; Cieniek, Bogumil; Mroczka, Robert; Lopucki, Rafal; Sagan, Piotr; Kuzma, Marian

    2018-03-01

    Implantation of bulk CdTe single crystals with high fluences of 500 keV Cr+ ions was performed to achieve Cr concentration above the equilibrium solubility limit of this element in CdTe lattice. The structure and composition of the implanted samples were studied using secondary ion mass spectrometry (SIMS), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis, X-ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS) to characterize the incorporation of chromium into the host lattice and to investigate irradiation-induced damage build-up. It was found that out-diffusion of Cr atoms and sputtering of the targets alter the depth distribution and limit concentration of the projectile ions in the as-implanted samples. Appearance of crystallographically oriented, metallic α-Cr nanoparticles inside CdTe matrix was found after implantation, as well as a strong disorder at the depth far beyond the projected range of the implanted ions.

  13. Magnetic anisotropy of a Co-II single ion magnet with distorted trigonal prismatic coordination

    DEFF Research Database (Denmark)

    Peng, Yan; Bodenstein, Tilmann; Fink, Karin

    2016-01-01

    (methanylylidene)) bis(2-methoxyphenol) coordinates to Co(II) does indeed lead to enhanced single-ion behaviour as has previously been predicted. Synthesis of the compound, structural information, and static as well as dynamic magnetic data are presented along with an analysis using quantum chemical ab initio......The single ion magnetic properties of Co(II) are affected by the details of the coordination geometry of the ion. Here we show that a geometry close to trigonal prismatic which arises when the ligand 6,6'-((1Z)-((piperazine-1,4-diylbis(propane-3,1-diyl)) bis(azanylylidene)) bis...... calculations. Though the complex shows a slight deviation from an ideal trigonal prismatic coordination, the zero-field splitting as well as the g-tensor are strongly axial with D = -41 cm(-1) and E

  14. Development of noise-suppressed detector for single ion hit system

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Takuro; Hamano, Tsuyoshi; Suda, Tamotsu; Hirao, Toshio; Kamiya, Tomihiro [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

    1997-03-01

    A noise-suppressed detector for single ion detection has been developed, and combined with the heavy ion microbeam apparatus. This detector consists of a pair of micro channel plates (MCP`s) and a very thin carbon foil. The detection signal is formed by the coincidence of the signals from these MCP`s, so that this detector and the coincidence measurement unit can reduce miscounting in the circuit. The detection efficiency for 15 MeV heavy ions was evaluated to be comparable to that of a silicon surface-barrier detector (SSD) and the miscounting rate was 4 orders lower than the noise rate of a single MCP. The rise time of the detection signal was also estimated. (author)

  15. Surface structure modification of single crystal graphite after slow, highly charged ion irradiation

    Science.gov (United States)

    Alzaher, I.; Akcöltekin, S.; Ban-d'Etat, B.; Manil, B.; Dey, K. R.; Been, T.; Boduch, P.; Rothard, H.; Schleberger, M.; Lebius, H.

    2018-04-01

    Single crystal graphite was irradiated by slow, highly charged ions. The modification of the surface structure was studied by means of Low-Energy Electron Diffraction. The observed damage cross section increases with the potential energy, i.e. the charge state of the incident ion, at a constant kinetic energy. The potential energy is more efficient for the damage production than the kinetic energy by more than a factor of twenty. Comparison with earlier results hints to a strong link between early electron creation and later target atom rearrangement. With increasing ion fluence, the initially large-scale single crystal is first transformed into μ m-sized crystals, before complete amorphisation takes place.

  16. Production of multi-, oligo- and single-pore membranes using a continuous ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Apel, P.Yu., E-mail: apel@nrmail.jinr.ru [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Dubna International University, Universitetskaya Str. 19, 141980 Dubna (Russian Federation); Ivanov, O.M.; Lizunov, N.E.; Mamonova, T.I.; Nechaev, A.N. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Olejniczak, K. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Faculty of Chemistry, Nicolaus Copernicus University, Gagarina Str. 7, 87-100 Torun (Poland); Vacik, J. [Nuclear Physics Institute, ASCR, v.v.i., 25068 Řež (Czech Republic); Dmitriev, S.N. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation)

    2015-12-15

    Ion track membranes (ITM) have attracted significant interest over the past two decades due to their numerous applications in physical, biological, chemical, biochemical and medical experimental works. A particular feature of ITM technology is the possibility to fabricate samples with a predetermined number of pores, including single-pore membranes. The present report describes a procedure that allowed for the production of multi-, oligo- and single-pore membranes using a continuous ion beam from an IC-100 cyclotron. The beam was scanned over a set of small diaphragms, from 17 to ∼1000 μm in diameter. Ions passed through the apertures and impinged two sandwiched polymer foils, with the total thickness close to the ion range in the polymer. The foils were pulled across the ion beam at a constant speed. The ratio between the transport speed and the scanning frequency determined the distance between irradiation spots. The beam intensity and the aperture diameters were adjusted such that either several, one or no ions passed through the diaphragms during one half-period of scanning. After irradiation, the lower foil was separated from the upper foil and was etched to obtain pores 6–8 μm in diameter. The pores were found using a color chemical reaction between two reagents placed on opposite sides of the foil. The located pores were further confirmed using SEM and optical microscopy. The numbers of tracks in the irradiation spots were consistent with the Poisson statistics. Samples with single or few tracks obtained in this way were employed to study fine phenomena in ion track nanopores.

  17. Potential of electric quadrupole transitions in radium isotopes for single-ion optical frequency standards

    NARCIS (Netherlands)

    Versolato, O. O.; Wansbeek, L. W.; Jungmann, K.; Timmermans, R. G. E.; Willmann, L.; Wilschut, H. W.

    2011-01-01

    We explore the potential of the electric quadrupole transitions 7s (2)S(1/2)-(6)d (2)D(3/2), 6d (2)D(5/2) in radium isotopes as single-ion optical frequency standards. The frequency shifts of the clock transitions due to external fields and the corresponding uncertainties are calculated. Several

  18. Towards a Precise Measurement of Atomic Parity Violation in a Single Ra+ Ion

    NARCIS (Netherlands)

    Jungmann, K.; Giri, G. S.; Versolato, O. O.; Steadman, SG; Stephans, GSF; Taylor, FE

    2012-01-01

    In the singly charged Ra+ ion the contributions of the weak interactions to the atomic level energies are some 50 times larger than in the Cs atom. We report the results of laser spectroscopy experiments on Ra-209-214(+) isotopes in preparation of a precision atomic parity violation experiment.

  19. Dimer self-organization of impurity ytterbium ions in synthetic forsterite single crystals

    Science.gov (United States)

    Tarasov, V. F.; Sukhanov, A. A.; Dudnikova, V. B.; Zharikov, E. V.; Lis, D. A.; Subbotin, K. A.

    2017-07-01

    Paramagnetic centers formed by impurity Yb3+ ions in synthetic forsterite (Mg2SiO4) grown by the Czochralski technique are studied by X-band CW and pulsed EPR spectroscopy. These centers are single ions substituting magnesium in two different crystallographic positions denoted M1 and M2, and dimer associates formed by two Yb3+ ions in nearby positions M1. It is established that there is a pronounced mechanism favoring self-organization of ytterbium ions in dimer associates during the crystal growth, and the mechanism of the spin-spin coupling between ytterbium ions in the associate has predominantly a dipole-dipole character, which makes it possible to control the energy of the spin-spin interaction by changing the orientation of the external magnetic field. The structural computer simulation of cluster ytterbium centers in forsterite crystals is carried out by the method of interatomic potentials using the GULP 4.0.1 code (General Utility Lattice Program). It is established that the formation of dimer associates in the form of a chain parallel to the crystallographic axis consisting of two ytterbium ions with a magnesium vacancy between them is the most energetically favorable for ytterbium ions substituting magnesium in the position M1.

  20. Transport of ions and biomolecules through asymmetric single nanopores fabricated by heavy ion irradiation and chemical etching

    International Nuclear Information System (INIS)

    Neumann, R.; Siwy, Z.; Schiedt, B.; Toimil Molares, M.E.

    2005-01-01

    In the framework of the CRP 'Radiation Synthesis of Stimuli-responsive Membranes, Hydrogels and Adsorbents for Separation Purposes', GSI has worked on the production of polymeric single conical nanopores and the study of the ionic transport through these pores. To produce single-pore membranes, polyethylene teraphthalate (PET) and polyimide (PI) foils were first irradiated with GeV single heavy ions. By subsequent one-side etching, asymmetric nanopores were created. The diameter of the conical pores in PET varied between 4-20 nm at the small opening and several hundred nm at the large opening. In the case of PI, due to the higher bulk etching rate, the large aperture reached a few μm. The current-voltage (I-V) characteristics were measured at symmetric electrolyte conditions of KCl at various concentrations and pH values. It was found that conical nanopores with charged surfaces are cation selective, and show preferential cation flow (i.e. rectification) from the narrow entrance to the wide opening of the cone. Concentration and pH influence the rectification properties for both polymers was studied. The experimental results are in agreement with existing models. The transient transport properties of single PET and PI pores were also investigated. The ion current through PET nanopores fluctuates considerably, the fluctuation depending on the voltage, whereas PI nanopores display a stable current signal for KCl concentrations between 0.1 and 3 M, and pH values between 2 and 8. This different behavior has been attributed to the chemical structure of the two polymers influencing surface characteristics of the resulting nanopores. Finally, the application of polyimide conical nanopores as single-molecule-DNA sensors is being investigated. First results demonstrate their ability to detect individual plasmid DNA molecules. The nanopore sensor is also able to discriminate between DNA fragments of different lengths. (author)

  1. Non-uniform binding of single-stranded DNA binding proteins to hybrids of single-stranded DNA and single-walled carbon nanotubes observed by atomic force microscopy in air and in liquid

    Energy Technology Data Exchange (ETDEWEB)

    Umemura, Kazuo, E-mail: meicun2006@163.com; Ishizaka, Kei; Nii, Daisuke; Izumi, Katsuki

    2016-12-01

    Highlights: • Conjugates of protein, DNA, and SWNTs were observed by AFM in liquid. • Non-uniform binding of proteins was visualized in liquid. • Thickness of DNA molecules on SWNT surfaces was well characterized in liquid. - Abstract: Using atomic force spectroscopy (AFM), we observed hybrids of single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWNTs) with or without protein molecules in air and in an aqueous solution. This is the first report of ssDNA–SWNT hybrids with proteins in solution analyzed by AFM. In the absence of protein, the height of the ssDNA–SWNT hybrids was 1.1 ± 0.3 nm and 2.4 ± 0.6 nm in air and liquid, respectively, suggesting that the ssDNA molecules adopted a flexible structure on the SWNT surface. In the presence of single-stranded DNA binding (SSB) proteins, the heights of the hybrids in air and liquid increased to 6.4 ± 3.1 nm and 10.0 ± 4.5 nm, respectively. The AFM images clearly showed binding of the SSB proteins to the ssDNA–SWNT hybrids. The morphology of the SSB–ssDNA–SWNT hybrids was non-uniform, particularly in aqueous solution. The variance of hybrid height was quantitatively estimated by cross-section analysis along the long-axis of each hybrid. The SSB–ssDNA–SWNT hybrids showed much larger variance than the ssDNA–SWNT hybrids.

  2. Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA

    International Nuclear Information System (INIS)

    Shokri, Leila; Williams, Mark C; Rouzina, Ioulia

    2009-01-01

    Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork

  3. Deep level defects in 4H-SiC introduced by ion implantation: the role of single ion regime.

    Science.gov (United States)

    Pastuović, Željko; Siegele, Rainer; Capan, Ivana; Brodar, Tomislav; Sato, Shin-Ichiro; Ohshima, Takeshi

    2017-11-29

    We characterized intrinsic deep level defects created in ion collision cascades which were produced by patterned implantation of single accelerated 2.0 MeV He and 600 keV H ions into n-type 4H-SiC epitaxial layers using a fast-scanning reduced-rate ion microbeam. The initial deep level transient spectroscopy measurement performed on as-grown material in the temperature range 150-700 K revealed the presence of only two electron traps, Z 1/2 (0.64 eV) and EH 6/7 (1.84 eV) assigned to the two different charge state transitions of the isolated carbon vacancy, V C (=/0) and (0/+). C-V measurements of as-implanted samples revealed the increasing free carrier removal with larger ion fluence values, in particular at depth corresponding to a vicinity of the end of an ion range. The first DLTS measurement of as-implanted samples revealed formation of additional deep level defects labelled as ET1 (0.35 eV), ET2 (0.65 eV) and EH3 (1.06 eV) which were clearly distinguished from the presence of isolated carbon vacancies (Z 1/2 and EH 6/7 defects) in increased concentrations after implantations either by He or H ions. Repeated C-V measurements showed that a partial net free-carrier recovery occurred in as-implanted samples upon the low-temperature annealing following the first DLTS measurement. The second DLTS measurement revealed the almost complete removal of ET2 defect and the partial removal of EH3 defect, while the concentrations of Z 1/2 and EH 6/7 defects increased, due to the low temperature annealing up to 700 K accomplished during the first temperature scan. We concluded that the ET2 and EH3 defects: (i) act as majority carrier removal traps, (ii) exhibit a low thermal stability and (iii) can be related to the simple point-like defects introduced by light ion implantation, namely interstitials and/or complex of interstitials and vacancies in both carbon and silicon sub-lattices.

  4. Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy

    OpenAIRE

    Shishmarev, Dmitry; Wang, Yao; Mason, Claire E.; Su, Xun-Cheng; Oakley, Aaron J.; Graham, Bim; Huber, Thomas; Dixon, Nicholas E.; Otting, Gottfried

    2013-01-01

    Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron den...

  5. Progressing single biomolecule force spectroscopy measurements for the screening of DNA binding agents

    Science.gov (United States)

    Zhang, Wenke; Barbagallo, Romina; Madden, Claire; Roberts, Clive J.; Woolford, Alison; Allen, Stephanie

    2005-10-01

    Recent studies have indicated that the force-extension properties of single molecules of double stranded (ds) DNA are sensitive to the presence of small molecule DNA binding agents, and also to their mode of binding. These observations raise the possibility of using this approach as a highly sensitive tool for the screening of such agents. However, particularly for studies employing the atomic force microscope (AFM), several non-trivial barriers hinder the progress of this approach to the non-specialist arena and hence also the full realization of this possibility. In this paper, we therefore address a series of key reproducibility and metrological issues associated with this type of measurement. Specifically, we present an improved immobilization method that covalently anchors one end (5' end) of a dual labelled (5'-thiol, 3'-biotin) p53 DNA molecule onto a gold substrate via gold-thiol chemistry, whilst the biotinylated 3' end is available for 'pick-up' using a streptavidin modified AFM tip. We also show that co-surface immobilization of DNA with 6-mercapto-1-hexanol (MCH) can also lead to a further increase the measured contour length. We demonstrate the impact of these improved protocols through the observation of the cooperative transition plateau in a DNA fragment of approximately 118 bp, a significantly smaller fragment than previously investigated. The results of a comparative study of the effects of a model minor groove binder (Hoechst 33258) and an intercalating drug (proflavine), alone, as a mixture and under different buffer conditions, are also presented.

  6. Dependence of single-walled carbon nanotube adsorption kinetics on temperature and binding energy.

    Science.gov (United States)

    Rawat, D S; Krungleviciute, V; Heroux, L; Bulut, M; Calbi, M M; Migone, A D

    2008-12-02

    We present results for the isothermal adsorption kinetics of methane, hydrogen, and tetrafluoromethane on closed-ended single-walled carbon nanotubes. In these experiments, we monitor the pressure decrease as a function of time as equilibrium is approached, after a dose of gas is added to the cell containing the nanotubes. The measurements were performed at different fractional coverages limited to the first layer. The results indicate that, for a given coverage and temperature, the equilibration time is an increasing function of E/(k(B)T), where E is the binding energy of the adsorbate and k(B)T is the thermal energy. These findings are consistent with recent theoretical predictions and computer simulations results that we use to interpret the experimental measurements.

  7. Modulation of protein A binding allows single-step purification of mouse bispecific antibodies that retain FcRn binding

    Science.gov (United States)

    Armstrong, Anthony A.; Pardinas, Jose R.; Zheng, Songmao; Brosnan, Kerry; Emmell, Eva; Luo, Jeffrey; Chiu, Mark L.

    2017-01-01

    ABSTRACT The increased number of bispecific antibodies (BsAb) under therapeutic development has resulted in a need for mouse surrogate BsAbs. Here, we describe a one-step method for generating highly pure mouse BsAbs suitable for in vitro and in vivo studies. We identify two mutations in the mouse IgG2a and IgG2b Fc region: one that eliminates protein A binding and one that enhances protein A binding by 8-fold. We show that BsAbs harboring these mutations can be purified from the residual parental monoclonal antibodies in one step using protein A affinity chromatography. The structural basis for the effects of these mutations was analyzed by X-ray crystallography. While the mutation that disrupted protein A binding also inhibited FcRn interaction, a bispecific mutant in which one subunit retained the ability to bind protein A could still interact with FcRn. Pharmacokinetic analysis of the serum half-lives of the mutants showed that the mutant BsAb had a serum half-life comparable to a wild-type Ab. The results describe a rapid method for generating panels of mouse BsAbs that could be used in mouse studies. PMID:28898162

  8. Combining confocal and atomic force microscopy to quantify single-virus binding to mammalian cell surfaces.

    Science.gov (United States)

    Newton, Richard; Delguste, Martin; Koehler, Melanie; Dumitru, Andra C; Laskowski, Pawel R; Müller, Daniel J; Alsteens, David

    2017-11-01

    Over the past five years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool set capable of imaging the surfaces of biological samples ranging from single receptors to membranes and tissues. One of these approaches, force-distance curve-based AFM (FD-based AFM), uses a probing tip functionalized with a ligand to image living cells at high-resolution and simultaneously localize and characterize specific ligand-receptor binding events. Analyzing data from FD-based AFM experiments using appropriate probabilistic models allows quantification of the kinetic and thermodynamic parameters that describe the free-energy landscape of the ligand-receptor bond. We have recently developed an FD-based AFM approach to quantify the binding events of single enveloped viruses to surface receptors of living animal cells while simultaneously observing them by fluorescence microscopy. This approach has provided insights into the early stages of the interaction between a virus and a cell. Applied to a model virus, we probed the specific interaction with cells expressing viral cognate receptors and measured the affinity of the interaction. Furthermore, we observed that the virus rapidly established specific multivalent interactions and found that each bond formed in sequence strengthened the attachment of the virus to the cell. Here we describe detailed procedures for probing the specific interactions of viruses with living cells; these procedures cover tip preparation, cell sample preparation, step-by-step FD-based AFM imaging and data analysis. Experienced microscopists should be able to master the entire set of protocols in 1 month.

  9. Aggregation induced emission enhancement (AIEE) characteristics of quinoline based compound - A versatile fluorescent probe for pH, Fe(III) ion, BSA binding and optical cell imaging

    Science.gov (United States)

    Manikandan, Irulappan; Chang, Chien-Huei; Chen, Chia-Ling; Sathish, Veerasamy; Li, Wen-Shan; Malathi, Mahalingam

    2017-07-01

    Novel benzimidazoquinoline derivative (AVT) was synthesized through a substitution reaction and characterized by various spectral techniques. Analyzing the optical properties of AVT under absorption and emission spectral studies in different environments exclusively with respect to solvents and pH, intriguing characteristics viz. aggregation induced emission enhancement (AIEE) in the THF solvent and 'On-Off' pH sensing were found at neutral pH. Sensing nature of AVT with diverse metal ions and bovine serum albumin (BSA) was also studied. Among the metal ions, Fe3 + ion alone tunes the fluorescence intensity of AVT probe in aqueous medium from ;turn-on; to ;turn-off; through ligand (probe) to metal charge transfer (LMCT) mechanism. The probe AVT in aqueous medium interacts strongly with BSA due to Fluorescence Resonance Energy Transfer (FRET) and the conformational change in BSA was further analyzed using synchronous fluorescence techniques. Docking study of AVT with BSA reveals that the active site of binding is tryptophan residue which is also supported by the experimental results. Interestingly, fluorescent AVT probe in cells was examined through cellular imaging studies using BT-549 and MDA-MB-231 cells. Thus, the single molecule probe based detection of multiple species and stimuli were described.

  10. Interactions of DNA binding proteins with G-Quadruplex structures at the single molecule level

    Science.gov (United States)

    Ray, Sujay

    Guanine-rich nucleic acid (DNA/RNA) sequences can form non-canonical secondary structures, known as G-quadruplex (GQ). Numerous in vivo and in vitro studies have demonstrated formation of these structures in telomeric and non-telomeric regions of the genome. Telomeric GQs protect the chromosome ends whereas non-telomeric GQs either act as road blocks or recognition sites for DNA metabolic machinery. These observations suggest the significance of these structures in regulation of different metabolic processes, such as replication and repair. GQs are typically thermodynamically more stable than the corresponding Watson-Crick base pairing formed by G-rich and C-rich strands, making protein activity a crucial factor for their destabilization. Inside the cell, GQs interact with different proteins and their enzymatic activity is the determining factor for their stability. We studied interactions of several proteins with GQs to understand the underlying principles of protein-GQ interactions using single-molecule FRET and other biophysical techniques. Replication Protein-A (RPA), a single stranded DNA (ssDNA) binding protein, is known to posses GQ unfolding activity. First, we compared the thermal stability of three potentially GQ-forming DNA sequences (PQS) to their stability against RPA-mediated unfolding. One of these sequences is the human telomeric repeat and the other two, located in the promoter region of tyrosine hydroxylase gene, are highly heterogeneous sequences that better represent PQS in the genome. The thermal stability of these structures do not necessarily correlate with their stability against protein-mediated unfolding. We conclude that thermal stability is not necessarily an adequate criterion for predicting the physiological viability of GQ structures. To determine the critical structural factors that influence protein-GQ interactions we studied two groups of GQ structures that have systematically varying loop lengths and number of G-tetrad layers. We

  11. Ion binding by humic and fulvic acids: A computational procedure based on functional site heterogeneity and the physical chemistry of polyelectrolyte solutions

    International Nuclear Information System (INIS)

    Marinsky, J.A.; Reddy, M.M.; Ephraim, J.; Mathuthu, A.

    1988-04-01

    Ion binding equilibria for humic and fulvic acids are examined from the point of view of functional site heterogeneity and the physical chemistry of polyelectrolyte solutions. A detailed explanation of the potentiometric properties of synthetic polyelectrolytes and ion-exchange gels is presented first to provide the basis for a parallel consideration of the potentiometric properties exhibited by humic and fulvic acids. The treatment is then extended to account for functional site heterogeneity. Sample results are presented for analysis of the ion-binding reactions of a standard soil fulvic acid (Armadale Horizons Bh) with this approach to test its capability for anticipation of metal ion removal from solution. The ultimate refined model is shown to be adaptable, after appropriate consideration of the heterogeneity and polyelectrolyte factors, to programming already available for the consideration of ion binding by inorganics in natural waters. (orig.)

  12. Effect of H + ion implantation on structural, morphological, optical and dielectric properties of L-arginine monohydrochloride monohydrate single crystals

    Science.gov (United States)

    Sangeetha, K.; Babu, R. Ramesh; Kumar, P.; Bhagvannarayana, G.; Ramamurthi, K.

    2011-06-01

    L-arginine monohydrochloride monohydrate (LAHCl) single crystals have been implanted with 100 keV H + ions at different ion fluence ranging from 10 12 to 10 15 ions/cm 2. Implanted LAHCl single crystals have been investigated for property changes. Crystal surface and crystalline perfection of the pristine and implanted crystals were analyzed by atomic force microscope and high-resolution X-ray diffraction studies, respectively. Optical absorption bands induced by colour centers, refractive index and birefringence, mechanical stability and dielectric constant of implanted crystals were studied at different ion fluence and compared with that of pristine LAHCl single crystal.

  13. DNA deformability changes of single base pair mutants within CDE binding sites in S. Cerevisiae centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries

    Directory of Open Access Journals (Sweden)

    Marx Kenneth A

    2006-03-01

    Full Text Available Abstract Background The centromeres in yeast (S. cerevisiae are organized by short DNA sequences (125 bp on each chromosome consisting of 2 conserved elements: CDEI and CDEIII spaced by a CDEII region. CDEI and CDEIII are critical sequence specific protein binding sites necessary for correct centromere formation and following assembly with proteins, are positioned near each other on a specialized nucleosome. Hegemann et al. BioEssays 1993, 15: 451–460 reported single base DNA mutants within the critical CDEI and CDEIII binding sites on the centromere of chromosome 6 and quantitated centromere loss of function, which they measured as loss rates for the different chromosome 6 mutants during cell division. Olson et al. Proc Natl Acad Sci USA 1998, 95: 11163–11168 reported the use of protein-DNA crystallography data to produce a DNA dinucleotide protein deformability energetic scale (PD-scale that describes local DNA deformability by sequence specific binding proteins. We have used the PD-scale to investigate the DNA sequence dependence of the yeast chromosome 6 mutants' loss rate data. Each single base mutant changes 2 PD-scale values at that changed base position relative to the wild type. In this study, we have utilized these mutants to demonstrate a correlation between the change in DNA deformability of the CDEI and CDEIII core sites and the overall experimentally measured chromosome loss rates of the chromosome 6 mutants. Results In the CDE I and CDEIII core binding regions an increase in the magnitude of change in deformability of chromosome 6 single base mutants with respect to the wild type correlates to an increase in the measured chromosome loss rate. These correlations were found to be significant relative to 105 Monte Carlo randomizations of the dinucleotide PD-scale applied to the same calculation. A net loss of deformability also tends to increase the loss rate. Binding site position specific, 4 data-point correlations were also

  14. Modification of mechanical properties of single crystal aluminum oxide by ion beam induced structural changes

    International Nuclear Information System (INIS)

    Ensinger, W.; Nowak, R.; Horino, Y.; Baba, K.

    1993-01-01

    The mechanical behaviour of ceramics is essentially determined by their surface qualities. As a surface modification technique, ion implantation provides the possibility to modify the mechanical properties of ceramics. Highly energetic ions are implanted into the near-surface region of a material and modify its composition and structure. Ions of aluminum, oxygen, nickel and tantalum were implanted into single-crystal α-aluminum oxide. Three-point bending tests showed that an increase in flexural strength of up to 30% could be obtained after implantation of aluminum and oxygen. Nickel and tantalum ion implantation increased the fracture toughness. Indentation tests with Knoop and Vickers diamonds and comparison of the lengths of the developed radial cracks showed that ion implantation leads to a reaction in cracking. The observed effects are assigned to radiation induced structural changes of the ceramic. Ion bombardment leads to radiation damage and formation of compressive stress. In case of tantalum implantation, the implanted near-surface zone becomes amorphous. These effects make the ceramic more resistant to fracture. (orig.)

  15. Engineering of electronic properties of single layer graphene by swift heavy ion irradiation

    Science.gov (United States)

    Kumar, Sunil; Kumar, Ashish; Tripathi, Ambuj; Tyagi, Chetna; Avasthi, D. K.

    2018-04-01

    In this work, swift heavy ion irradiation induced effects on the electrical properties of single layer graphene are reported. The modulation in minimum conductivity point in graphene with in-situ electrical measurement during ion irradiation was studied. It is found that the resistance of graphene layer decreases at lower fluences up to 3 × 1011 ions/cm2, which is accompanied by the five-fold increase in electron and hole mobilities. The ion irradiation induced increase in electron and hole mobilities at lower fluence up to 1 × 1011 ions/cm2 is verified by separate Hall measurements on another irradiated graphene sample at the selected fluence. In contrast to the adverse effects of irradiation on the electrical properties of materials, we have found improvement in electrical mobility after irradiation. The increment in mobility is explained by considering the defect annealing in graphene after irradiation at a lower fluence regime. The modification in carrier density after irradiation is also observed. Based on findings of the present work, we suggest ion beam irradiation as a useful tool for tuning of the electrical properties of graphene.

  16. Single Qubit Manipulation in a Microfabricated Surface Electrode Ion Trap (Open Access, Publisher’s Version)

    Science.gov (United States)

    2013-09-13

    electrode ion trap with field compensation using a modulated Raman effect D T C Allcock, J A Sherman, D N Stacey et al. Spatially uniform single-qubit gate...in thermal states of motion G Kirchmair, J Benhelm, F Zähringer et al. Normal modes of trapped ions in the presence of anharmonic trap potentials J P...Qloaded = 280) [35]. New Journal of Physics 15 (2013) 093018 (http://www.njp.org/) 5 2.1 GHz Zeeman = 1.4 MHz/G 36 9. 5 nm HF = 12.6 GHz 171Yb+ 2P 1

  17. Changes in ion channel geometry resolved to sub-angstroem precision via single molecule mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Joseph W F; Kasianowicz, John J; Reiner, Joseph E [Semiconductor Electronics Division, Electronics and Electrical Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States)

    2010-11-17

    The ion channel formed by Staphylococcus aureus alpha-hemolysin switches between multiple open conducting states. We describe a method for precisely estimating the changes in the ion channel geometry that correspond to these different states. Experimentally, we observed that the permeability of a single channel to differently sized poly(ethylene glycol) molecules depends on the magnitude of the open state conductance. A simple theory is proposed for determining changes in channel length of 4.2% and in cross-sectional area of - 0.4%.

  18. Single electron attachment and stripping cross sections for relativistic heavy ions

    International Nuclear Information System (INIS)

    Crawford, H.J.

    1979-06-01

    The results of a Bevalac experiment to measure the single electron attachment and stripping cross sections for relativistic (0.5 1 , and fully stripped, N 0 , ion beams emerging from the targets. Separate counters measured the number of ions in each charge state. The ratios N 1 /N 0 for different target thicknesses were fit to a simple growth curve to yield electron attachment and stripping cross sections. The data are compared to relativistic extrapolations of available theories. Clear evidence for two separate attachment processes, radiative and non-radiative, is found. Data are compared to a recently improved formulation for the stripping cross sections

  19. Single electron attachment and stripping cross sections for relativistic heavy ions

    International Nuclear Information System (INIS)

    Crawford, H.J.

    1979-01-01

    The results of a Bevalac experiment to measure the single electron attachment and stripping cross sections for relativistic (0.5 1 , and fully stripped, N 0 , ion beams emerging from the targets. Separate counters measured the number of ions in each charge state. The ratios N 1 /N 0 for different target thicknesses were fit to a simple growth curve to yield electron attachment and stripping cross sections. The data are compared to relativistic extrapolations of available theories. Clear evidence of two separate attachment processes, radiative and non-radiative, is found. Data are compared to a recently improved formulation for the stripping cross sections

  20. Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose-5-phosphate binding

    DEFF Research Database (Denmark)

    Willemoës, Martin; Nilsson, Dan; Hove-Jensen, Bjarne

    1996-01-01

    The three conserved aspartic acid residues of the 5-phospho-d-ribosyl a-1-diphosphate binding site (213-GRDCVLVDDMIDTGGT-228) of Escherichia coli phosphoribosyl diphosphate synthetase were studied by analysis of the mutant enzymes D220E, D220F, D221A, D224A, and D224S. The mutant enzymes showed...... enzymes were dependent on the metal ion present, suggesting a function of the investigated aspartic acid residues both in the binding of ribose 5-phosphate, possibly via a divalent metal ion, and in the interaction with a divalent metal ion during catalysis....

  1. Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.

    Science.gov (United States)

    Hansen, William A; Khare, Sagar D

    2017-08-01

    The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, symmetric protein recursive ion-cofactor sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model). Using SyPRIS on a curated benchmark set of protein structures with symmetric metal binding sites, we found high recovery of native metal coordinating rotamers: in 65 of the 67 (97.0%) cases, native rotamers featured in the best scoring model while in the remaining cases native rotamers were found within the top three scoring models. In a second test, chelant models were crossmatched against protein structures with identical cyclic symmetry. In addition to recovering all native placements, 10.4% (8939/86013) of the non-native placements, had acceptable geometric compatibility scores. Discrimination between native and non-native metal site placements was further enhanced upon constrained energy minimization using the Rosetta energy function. Upon sequence design of the surrounding first-shell residues, we found further stabilization of native placements and a small but significant (1.7%) number of non-native placement-based sites with favorable Rosetta energies, indicating their designability in existing protein interfaces. The generality of the SyPRIS approach allows design of novel symmetric metal sites including with non-natural amino acid sidechains, and should enable the predictive incorporation of a variety of metal-containing cofactors at symmetric protein interfaces. © 2017 The Protein Society.

  2. Ion binding to natural organic matter : General considerations and the NICA-Donnan model

    NARCIS (Netherlands)

    Koopal, L.K.; Saito, T.; Pinheiro, J.P.; Riemsdijk, van W.H.

    2005-01-01

    The general principles of cation binding to humic matter and the various aspects of modeling used in general-purpose speciation programs are discussed. The discussion will focus on (1) the discrimination between chemical and electrostatic interactions, (2) the binding site heterogeneity, (3) the

  3. The tensile effect on crack formation in single crystal silicon irradiated by intense pulsed ion beam

    Science.gov (United States)

    Liang, Guoying; Shen, Jie; Zhang, Jie; Zhong, Haowen; Cui, Xiaojun; Yan, Sha; Zhang, Xiaofu; Yu, Xiao; Le, Xiaoyun

    2017-10-01

    Improving antifatigue performance of silicon substrate is very important for the development of semiconductor industry. The cracking behavior of silicon under intense pulsed ion beam irradiation was studied by numerical simulation in order to understand the mechanism of induced surface peeling observed by experimental means. Using molecular dynamics simulation based on Stillinger Weber potential, tensile effect on crack growth and propagation in single crystal silicon was investigated. Simulation results reveal that stress-strain curves of single crystal silicon at a constant strain rate can be divided into three stages, which are not similar to metal stress-strain curves; different tensile load velocities induce difference of single silicon crack formation speed; the layered stress results in crack formation in single crystal silicon. It is concluded that the crack growth and propagation is more sensitive to strain rate, tensile load velocity, stress distribution in single crystal silicon.

  4. Damage evolution in Xe-ion irradiated rutile (TiO2) single crystals

    International Nuclear Information System (INIS)

    Li, F.; Sickafus, K.E.; Evans, C.R.; Nastasi, M.

    1999-01-01

    Rutile (TiO 2 ) single crystals with (110) orientation were irradiated with 360 keV Xe 2+ ions at 300 K to fluences ranging from 2 x 10 19 to 1 x 10 20 Xe/m 2 . Irradiated samples were analyzed using: (1) Rutherford backscattering spectroscopy combined with ion channeling analysis (RBS/C); and (2) cross-sectional transmission electron microscopy (XTEM). Upon irradiation to a fluence of 2 x 10 19 Xe/m 2 , the sample thickness penetrated by the implanted ions was observed to consist of three distinct layers: (1) a defect-free layer at the surface (thickness about 12 nm) exhibiting good crystallinity; (2) a second layer with a low density of relatively large-sized defects; and (3) a third layer consisting of a high concentration of small defects. After the fluence was increased to 7 x 10 19 Xe/m 2 , a buried amorphous layer was visible by XTEM. The thickness of the amorphous layer was found to increase with increasing Xe ion fluence. The location of this buried amorphous layer was found to coincide with the measured peak in the Xe concentration (measured by RBS/C), rather than with the theoretical maximum in the displacement damage profile. This observation suggests the implanted Xe ions may serve as nucleation sites for the amorphization transformation. The total thickness of the damaged microstructure due to ion irradiation was always found to be much greater than the projected range of the Xe ions. This is likely due to point defect migration under the high stresses induced by ion implantation

  5. Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64).

    Science.gov (United States)

    Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, Adam; Ożyhar, Andrzej; Dobryszycki, Piotr

    2017-11-01

    Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Dansyl-naphthalimide dyads as molecular probes: effect of spacer group on metal ion binding properties.

    Science.gov (United States)

    Shankar, Balaraman H; Ramaiah, Danaboyina

    2011-11-17

    Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results

  7. Single-column ion chromatography with determination of hydrazoic acid produced in spent nuclear fuel reprocessing

    International Nuclear Information System (INIS)

    Ma Guilan; Tan Shuping

    2006-01-01

    The reaction of hydrazine and its derivative with ammonium metavanadate may produce hydrazoic acid (HN 3 ). A single-column ion chromatography is used for the determination of HN 3 after neutralizing the rest acid in the sample with sodium hydroxide. Chromatography separation of HN 3 is carried out on a 25 cm x 0.46 cm (inside diameter) stainless steel column packed with Vydac IC302 ion Chromatography packing. The eluent is 1 mmol/L o-phthalic acid, and the ion is detected by conductivity detector. The detection limit in the presence chromatography is 5 μg/mL, the linear range is from 5 to 201 μg/mL, the linear correlation coefficient is 0.9994, respectively. The analysis accuracy is 2% for standard sample, and the detection limit is 51 μg/mL for HN 3 in the real sample. (authors)

  8. A Single Rainbow Trout Cobalamin-binding Protein Stands in for Three Human Binders

    DEFF Research Database (Denmark)

    Greibe, Eva Holm; Fedosov, Sergey; Sorensen, Boe S

    2012-01-01

    Cobalamin uptake and transport in mammals are mediated by three cobalamin-binding proteins: haptocorrin, intrinsic factor, and transcobalamin. The nature of cobalamin-binding proteins in lower vertebrates remains to be elucidated. The aim of this study was to characterize the cobalamin......-binding proteins of the rainbow trout (Oncorhynchus mykiss) and to compare their properties with those of the three human cobalamin-binding proteins. High cobalamin-binding capacity was found in trout stomach (210 pmol/g), roe (400 pmol/g), roe fluid (390 nmol/liter), and plasma (2500 nmol/liter). In all cases......, it appeared to be the same protein based on analysis of partial sequences and immunological responses. The trout cobalamin-binding protein was purified from roe fluid, sequenced, and further characterized. Like haptocorrin, the trout cobalamin-binding protein was stable at low pH and had a high binding...

  9. Metal ions-binding T4 lysozyme as an intramolecular protein purification tag compatible with X-ray crystallography.

    Science.gov (United States)

    Boura, Evzen; Baumlova, Adriana; Chalupska, Dominika; Dubankova, Anna; Klima, Martin

    2017-06-01

    Phage T4 lysozyme is a well folded and highly soluble protein that is widely used as an insertion tag to improve solubility and crystallization properties of poorly behaved recombinant proteins. It has been used in the fusion protein strategy to facilitate crystallization of various proteins including multiple G protein-coupled receptors, lipid kinases, or sterol binding proteins. Here, we present a structural and biochemical characterization of its novel, metal ions-binding mutant (mbT4L). We demonstrate that mbT4L can be used as a purification tag in the immobilized-metal affinity chromatography and that, in many respects, it is superior to the conventional hexahistidine tag. In addition, structural characterization of mbT4L suggests that mbT4L can be used as a purification tag compatible with X-ray crystallography. © 2017 The Protein Society.

  10. Sequential binding of calcium ions to the B-repeat domain of SdrD from Staphylococcus aureus.

    Science.gov (United States)

    Roman, Andrei Yu; Devred, François; Lobatchov, Vladimir M; Makarov, Alexander A; Peyrot, Vincent; Kubatiev, Aslan A; Tsvetkov, Philipp O

    2016-02-01

    Biofilms of live bacteria forming on medical devices and implants contribute significantly to bacterial blood dissemination and to the spread of nosocomial infections. Cell surface SdrD protein plays a key role in the attachment of Staphylococcus aureus to the extracellular matrix (ECM) and in the formation of biofilm. SdrD binds calcium ions using its B1-B5 region bearing EF-hand Ca-binding sites, leading to conformational changes in the structure of SdrD. This alters the distance between the bacterial surface and the ECM-interacting domain of SdrD in a spring-like fashion, participating in bacterial attachment. In this study we investigated calcium binding to EF-hand sites of SdrD using isothermal titration calorimetry and determined the impact of this process on SdrD's thermodynamic stability. This allowed us to propose a model of B1-B5 reorganization upon binding of calcium and to get new insight into the molecular mechanism of SdrD's action.

  11. Charging the quantum capacitance of graphene with a single biological ion channel.

    Science.gov (United States)

    Wang, Yung Yu; Pham, Ted D; Zand, Katayoun; Li, Jinfeng; Burke, Peter J

    2014-05-27

    The interaction of cell and organelle membranes (lipid bilayers) with nanoelectronics can enable new technologies to sense and measure electrophysiology in qualitatively new ways. To date, a variety of sensing devices have been demonstrated to measure membrane currents through macroscopic numbers of ion channels. However, nanoelectronic based sensing of single ion channel currents has been a challenge. Here, we report graphene-based field-effect transistors combined with supported lipid bilayers as a platform for measuring, for the first time, individual ion channel activity. We show that the supported lipid bilayers uniformly coat the single layer graphene surface, acting as a biomimetic barrier that insulates (both electrically and chemically) the graphene from the electrolyte environment. Upon introduction of pore-forming membrane proteins such as alamethicin and gramicidin A, current pulses are observed through the lipid bilayers from the graphene to the electrolyte, which charge the quantum capacitance of the graphene. This approach combines nanotechnology with electrophysiology to demonstrate qualitatively new ways of measuring ion channel currents.

  12. The single-ion anisotropy effects in the mixed-spin ternary-alloy

    Science.gov (United States)

    Albayrak, Erhan

    2018-04-01

    The effect of single-ion anisotropy on the thermal properties of the ternary-alloy in the form of ABpC1-p is investigated on the Bethe lattice (BL) in terms of exact recursion relations. The simulation on the BL consists of placing A atoms (spin-1/2) on the odd shells and randomly placing B (spin-3/2) or C (spin-5/2) atoms with concentrations p and 1 - p, respectively, on the even shells. The phase diagrams are calculated in possible planes spanned by the system parameters: temperature, single-ion anisotropy, concentration and ratio of the bilinear interaction parameters for z = 3 corresponding to the honeycomb lattice. It is found that the crystal field drives the system to the lowest possible state therefore reducing the temperatures of the critical lines in agreement with the literature.

  13. Modifying the properties of 4f single-ion magnets by peripheral ligand functionalisation

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Ungur, Liviu; Sigrist, Marc

    2014-01-01

    We study the ligand-field splittings and magnetic properties of three ErIII single-ion magnets which differ in the peripheral ligand sphere but exhibit similar first coordination spheres by inelastic neutron scattering (INS) and SQUID magnetometry. The INS spectra of the three compounds are profo......We study the ligand-field splittings and magnetic properties of three ErIII single-ion magnets which differ in the peripheral ligand sphere but exhibit similar first coordination spheres by inelastic neutron scattering (INS) and SQUID magnetometry. The INS spectra of the three compounds...... allows for the extraction of the sign and magnitude of all symmetry-allowed Stevens parameters. The parameter values and the energy spectrum derived from INS are compared to the results of state-of-the-art ab initio CASSCF calculations. Temperature-dependent alternating current (ac) susceptibility...... measurements suggest that the magnetisation relaxation in the investigated temperature range of 1.9 K

  14. Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

    OpenAIRE

    Wang, Yuliang; Lieberman, Marya; Hang, Qingling; Bernstein, Gary

    2009-01-01

    The surface attachment properties of the Creutz-Taube ion, i.e., [(NH3)5Ru(pyrazine)Ru(NH3)5]5+, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS). The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO2 and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH3 terminated organic SAMs and poly(methylmethacrylate) (PMMA) thin film...

  15. Composite absorbers consisting of inorganic ion-exchangers and polyacrylonitrile binding matrix

    International Nuclear Information System (INIS)

    Sebesta, F.; John, J.; Motl, A.; Peka, V.; Vackova, E.

    1997-01-01

    Both cementation and vitrification was shown by preliminary experiments to be applicable for treatment of the spent composite absorbers with polyacrylonitrile binding matrix for final disposal. Loading of cement mix with composite absorbers up to 5-9% (w/w) were achieved Admixtures of natural clinoptilolite were found to improve compressive strength of the samples. The presence of PAN binding polymer was found not to disqualify the composite absorber tested from final treatment by vitrification. (author)

  16. Investigating change of properties in gallium ion irradiation patterned single-layer graphene

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan, E-mail: wangq@mail.ujs.edu.cn [School of Mechanical Engineering, Jiangsu University, Zhenjiang 212013 (China); Key Laboratory of Nanodevices and Applications, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences (China); Dong, Jinyao; Bai, Bing [School of Mechanical Engineering, Jiangsu University, Zhenjiang 212013 (China); Xie, Guoxin [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China)

    2016-10-14

    Besides its excellent physical properties, graphene promises to play a significant role in electronics with superior properties, which requires patterning of graphene for device integration. Here, we presented the changes in properties of single-layer graphene before and after patterning using gallium ion beam. Combined with Raman spectra of graphene, the scanning capacitance microscopy (SCM) image confirmed that a metal–insulator transition occurred after large doses of gallium ion irradiation. The changes in work function and Raman spectra of graphene indicated that the defect density increased as increasing the dose and a structural transition occurred during gallium ion irradiation. The patterning width of graphene presented an increasing trend due to the scattering influence of the impurities and the substrate. - Highlights: • The scanning capacitance microscopy image confirmed a metal–insulator transition occurred after large doses of gallium ion irradiation. • The changes indicated the defect density increased as increasing the dose and a structural transition occurred during gallium ion irradiation. • The patterning width of graphene presented a increasing trend due to the scattering influence of the impurities and the substrate.

  17. Investigating change of properties in gallium ion irradiation patterned single-layer graphene

    International Nuclear Information System (INIS)

    Wang, Quan; Dong, Jinyao; Bai, Bing; Xie, Guoxin

    2016-01-01

    Besides its excellent physical properties, graphene promises to play a significant role in electronics with superior properties, which requires patterning of graphene for device integration. Here, we presented the changes in properties of single-layer graphene before and after patterning using gallium ion beam. Combined with Raman spectra of graphene, the scanning capacitance microscopy (SCM) image confirmed that a metal–insulator transition occurred after large doses of gallium ion irradiation. The changes in work function and Raman spectra of graphene indicated that the defect density increased as increasing the dose and a structural transition occurred during gallium ion irradiation. The patterning width of graphene presented an increasing trend due to the scattering influence of the impurities and the substrate. - Highlights: • The scanning capacitance microscopy image confirmed a metal–insulator transition occurred after large doses of gallium ion irradiation. • The changes indicated the defect density increased as increasing the dose and a structural transition occurred during gallium ion irradiation. • The patterning width of graphene presented a increasing trend due to the scattering influence of the impurities and the substrate.

  18. Single-crate stand-alone CAMAC control system for a negative ion source test facility

    International Nuclear Information System (INIS)

    Juras, R.C.; Ziegler, N.F.

    1979-01-01

    A single-crate CAMAC system was configured to control a negative ion source development facility at ORNL and control software was written for the crate microcomputer. The software uses inputs from a touch panel and a shaft encoder to control the various operating parameters of the test facility and uses the touch panel to display the operating status. Communication to and from the equipment at ion source potential is accomplished over optical fibers from an ORNL-built CAMAC module. A receiver at ion source potential stores the transmitted data and some of these stored values are then used to control discrete parameters of the ion source (i.e., power supply on or off). Other stored values are sent to a multiplexed digital-to-analog converter to provide analog control signals. A transmitter at ion source potential transmits discrete status information and several channels of analog data from an analog-to-digital converter back to the ground-potential receiver where it is stored to be read and displayed by the software

  19. Impact of temperature on single event upset measurement by heavy ions in SRAM devices

    International Nuclear Information System (INIS)

    Liu Tianqi; Geng Chao; Zhang Zhangang; Gu Song; Tong Teng; Xi Kai; Hou Mingdong; Liu Jie; Zhao Fazhan; Liu Gang; Han Zhengsheng

    2014-01-01

    The temperature dependence of single event upset (SEU) measurement both in commercial bulk and silicon on insulator (SOI) static random access memories (SRAMs) has been investigated by experiment in the Heavy Ion Research Facility in Lanzhou (HIRFL). For commercial bulk SRAM, the SEU cross section measured by 12 C ions is very sensitive to the temperature. The temperature test of SEU in SOI SRAM was conducted by 209 Bi and 12 C ions, respectively, and the SEU cross sections display a remarkable growth with the elevated temperature for 12 C ions but keep constant for 209 Bi ions. The impact of temperature on SEU measurement was analyzed by Monte Carlo simulation. It is revealed that the SEU cross section is significantly affected by the temperature around the threshold linear energy transfer of SEU occurrence. As the SEU occurrence approaches saturation, the SEU cross section gradually exhibits less temperature dependency. Based on this result, the experimental data measured in HIRFL was analyzed, and then a reasonable method of predicting the on-orbit SEU rate was proposed. (semiconductor devices)

  20. Not Only Enthalpy: Large Entropy Contribution to Ion Permeation Barriers in Single-File Channels

    OpenAIRE

    Portella, Guillem; Hub, Jochen S.; Vesper, Martin D.; de Groot, Bert L.

    2008-01-01

    The effect of channel length on the barrier for potassium ion permeation through single-file channels has been studied by means of all-atom molecular dynamics simulations. Using series of peptidic gramicidin-like and simplified ring-structured channels, both embedded in model membranes, we obtained two distinct types of behavior: saturation of the central free energy barriers for peptidic channels and a linear increase in simplified ring-structured channels with increasing channel length. The...

  1. The rise of 3-d single-ion magnets in molecular magnetism: towards materials from molecules?

    Science.gov (United States)

    Frost, Jamie M; Harriman, Katie L M; Murugesu, Muralee

    2016-04-21

    Single-molecule magnets (SMMs) that contain one spin centre (so-called single-ion magnets) theoretically represent the smallest possible unit for spin-based electronic devices. The realisation of this and related technologies, depends on first being able to design systems with sufficiently large energy barriers to magnetisation reversal, U eff , and secondly, on being able to organise these molecules into addressable arrays. In recent years, significant progress has been made towards the former goal - principally as a result of efforts which have been directed towards studying complexes based on highly anisotropic lanthanide ions, such as Tb(iii) and Dy(iii). Since 2013 however, and the remarkable report by Long and co-workers of a linear Fe(i) system exhibiting U eff = 325 K, single-ion systems of transition metals have undergone something of a renaissance in the literature. Not only do they have important lessons to teach us about anisotropy and relaxation dynamics in the quest to enhance U eff , the ability to create strongly coupled spin systems potentially offers access to a whole of host of 1, 2 and 3-dimensional materials with interesting structural and physical properties. This perspective summarises recent progress in this rapidly expanding sub-genre of molecular magnetism from the viewpoint of the synthetic chemist, with a particular focus on the lessons that have so far been learned from single-ion magnets of the d-block, and, the future research directions which we feel are likely to emerge in the coming years.

  2. A generalized Jaynes-Cummings model: The relativistic parametric amplifier and a single trapped ion

    Energy Technology Data Exchange (ETDEWEB)

    Ojeda-Guillén, D., E-mail: dojedag@ipn.mx [Escuela Superior de Cómputo, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz esq. Av. Miguel Othón de Mendizábal, Col. Lindavista, Delegación Gustavo A. Madero, C.P. 07738 Ciudad de México (Mexico); Mota, R. D. [Escuela Superior de Ingeniería Mecánica y Eléctrica, Unidad Culhuacán, Instituto Politécnico Nacional, Av. Santa Ana No. 1000, Col. San Francisco Culhuacán, Delegación Coyoacán, C.P. 04430 Ciudad de México (Mexico); Granados, V. D. [Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Ed. 9, Unidad Profesional Adolfo López Mateos, Delegación Gustavo A. Madero, C.P. 07738 Ciudad de México (Mexico)

    2016-06-15

    We introduce a generalization of the Jaynes-Cummings model and study some of its properties. We obtain the energy spectrum and eigenfunctions of this model by using the tilting transformation and the squeezed number states of the one-dimensional harmonic oscillator. As physical applications, we connect this new model to two important and novelty problems: the relativistic parametric amplifier and the quantum simulation of a single trapped ion.

  3. V79 cell survival after a single lithium ion nuclear traversal

    International Nuclear Information System (INIS)

    Pinto, M.; Buonanno, M.; Campajola, L.; Durante, M.; Grossi, G.; Publiese, G.; Scampoli, P.; Gialanella, G.; Manti, L.

    2003-01-01

    Full text: Biological studies on the effects of low doses of densely ionising radiation are highly influenced by the stochastic character of the energy deposition events. For several end-points, including clonogenic survival, to follow-up individual cells that have undergone an exactly determined number of charged particle traversals is highly desirable. While RBE-LET curves have been measured after conventional 'broad beam' irradiation with several ions of varying energies, the probability of cell survival after a single charged particle traversal has only been determined for accelerated protons and alpha particles, whereas the ability of single particle traversals at higher LET to cause clonogenic death is yet unknown. Recently, low dose studies have also shown phenomena of high interest, such as the hypersensitivity/induced radioresistance(HS/IRR) adaptive responses. However, for particles of high LET, even a single nuclear traversal may deliver an average dose to a single cell that may be beyond the dose region of the HS/IRR response. We ave set up an experimental apparatus for the determination of the inactivation cross section after an exactly known number of accelerated Lithium ions traversals (210 keV/micron when hitting the cell surface). Using a bio-stack approach (Pugliese et al, IJRB Oct;72(4):397-407 1997) LR115 thin nuclear track detectors have been employed for the direct visualisation of Lithium ion traversals in V79 cells nuclei that are labeled with Hoechst 33258. A computer software has been designed and implemented to control micro-meter movements of a motorised Marzhauser stage, mounted on a fluorescent microscope, for the acquisition of individual attached cell coordinates, type of traversal, as well as for re-visiting the registered coordinates for analysis of survivors. The V79 cell survival experiment after exactly known numbers of Lithium ions traversals is in progress, along with a classical 'broad beam' survival assay

  4. Heavy Ion Irradiation Fluence Dependence for Single-Event Upsets of NAND Flash Memory

    Science.gov (United States)

    Chen, Dakai; Wilcox, Edward; Ladbury, Raymond; Kim, Hak; Phan, Anthony; Seidleck, Christina; LaBel, Kenneth

    2016-01-01

    We investigated the single-event effect (SEE) susceptibility of the Micron 16 nm NAND flash, and found the single-event upset (SEU) cross section varied inversely with fluence. The SEU cross section decreased with increasing fluence. We attribute the effect to the variable upset sensitivities of the memory cells. The current test standards and procedures assume that SEU follow a Poisson process and do not take into account the variability in the error rate with fluence. Therefore, heavy ion irradiation of devices with variable upset sensitivity distribution using typical fluence levels may underestimate the cross section and on-orbit event rate.

  5. Anisotropy effect of crater formation on single crystal silicon surface under intense pulsed ion beam irradiation

    Science.gov (United States)

    Shen, Jie; Yu, Xiao; Zhang, Jie; Zhong, Haowen; Cui, Xiaojun; Liang, Guoying; Yu, Xiang; Huang, Wanying; Shahid, Ijaz; Zhang, Xiaofu; Yan, Sha; Le, Xiaoyun

    2018-04-01

    Due to the induced extremely fast thermal and dynamic process, Intense Pulsed Ion Beam (IPIB) is widely applied in material processing, which can bring enhanced material performance and surface craters as well. To investigate the craters' formation mechanism, a specific model was built with Finite Element Methods (FEM) to simulate the thermal field on irradiated single crystal silicon. The direct evidence for the existence of the simulated 6-fold rotational symmetric thermal distribution was provided by electron microscope images obtained on single crystal silicon. The correlation of the experiment and simulation is of great importance to understand the interaction between IPIB and materials.

  6. The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.

    Science.gov (United States)

    Dathan, Nina; Zaccaro, Laura; Esposito, Sabrina; Isernia, Carla; Omichinski, James G; Riccio, Andrea; Pedone, Carlo; Di Blasio, Benedetto; Fattorusso, Roberto; Pedone, Paolo V

    2002-11-15

    The Arabidopsis SUPERMAN (SUP) gene has been shown to be important in maintaining the boundary between stamens and carpels, and is presumed to act by regulating cell proliferation. In this work, we show that the SUP protein, which contains a single Cys2-His2 zinc finger domain including the QALGGH sequence, highly conserved in the plant zinc finger proteins, binds DNA. Using a series of deletion mutants, it was determined that the minimal domain required for specific DNA binding (residues 15-78) includes the single zinc finger and two basic regions located on either side of this motif. Furthermore, amino acid substitutions in the zinc finger or in the basic regions, including a mutation that knocks out the function of the SUP protein in vivo (glycine 63 to aspartate), have been found to abolish the activity of the SUP DNA-binding domain. These results strongly suggest that the SUP protein functions in vivo by acting as a DNA-binding protein, likely involved in transcriptional regulation. The association of both an N-terminal and a C-terminal basic region with a single Cys2-His2 zinc finger represents a novel DNA-binding motif suggesting that the mechanism of DNA recognition adopted by the SUP protein is different from that described so far in other zinc finger proteins.

  7. Towards radiocarbon dating of single foraminifera with a gas ion source

    Science.gov (United States)

    Wacker, L.; Lippold, J.; Molnár, M.; Schulz, H.

    2013-01-01

    Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 μg for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO2 is liberated from 150 to 1150 μg of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO2 is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 μg (50 μg C) typically gives a 12C- ion source current of 10-15 μA over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 μg Cibicides pseudoungerianus test at 14,030 ± 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

  8. Towards radiocarbon dating of single foraminifera with a gas ion source

    International Nuclear Information System (INIS)

    Wacker, L.; Lippold, J.; Molnár, M.; Schulz, H.

    2013-01-01

    Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 μg for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO 2 is liberated from 150 to 1150 μg of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO 2 is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 μg (50 μg C) typically gives a 12 C − ion source current of 10–15 μA over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 μg Cibicides pseudoungerianus test at 14,030 ± 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

  9. Towards radiocarbon dating of single foraminifera with a gas ion source

    Energy Technology Data Exchange (ETDEWEB)

    Wacker, L., E-mail: wacker@phys.ethz.ch [Laboratory of Ion Beam Physics, ETH Zurich, 8093 Zurich (Switzerland); Lippold, J. [Heidelberg Academy of Sciences, 69120 Heidelberg (Germany); Molnar, M. [Laboratory of Ion Beam Physics, ETH Zurich, 8093 Zurich (Switzerland); Institute of Nuclear Research, Hungarian Academy of Sciences, 4026 Debrecen (Hungary); Schulz, H. [Institute for Geosciencies, University of Tuebingen, 72076 Tuebingen (Germany)

    2013-01-15

    Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 {mu}g for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO{sub 2} is liberated from 150 to 1150 {mu}g of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO{sub 2} is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 {mu}g (50 {mu}g C) typically gives a {sup 12}C{sup -} ion source current of 10-15 {mu}A over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 {mu}g Cibicides pseudoungerianus test at 14,030 {+-} 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

  10. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    DEFF Research Database (Denmark)

    Guo, Yang; Kragelund, Birthe Brandt; White, Malcolm F.

    2015-01-01

    encoding proteins of unknown function and forming an operon with ORF207 (gp19). SIRV2 gp17 was found to be a single-stranded DNA (ssDNA) binding protein different in structure from all previously characterized ssDNA binding proteins. Mutagenesis of a few conserved basic residues suggested a U......-shaped binding path for ssDNA. The recombinant gp18 showed an ssDNA annealing activity often associated with helicases and recombinases. To gain insight into the biological role of the entire operon, we characterized SIRV2 gp19 and showed it to possess a 5'→3' ssDNA exonuclease activity, in addition...... for rudiviruses and the close interaction among the ssDNA binding, annealing and nuclease proteins strongly point to a role of the gene operon in genome maturation and/or DNA recombination that may function in viral DNA replication/repair....

  11. Cultivated single stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA binding stains

    DEFF Research Database (Denmark)

    Holmfeldt, Karin; Odic, Dusko; Sullivan, Matthew B.

    2012-01-01

    This is the first description of cultivated icosahedral single stranded DNA (ssDNA) phages isolated on heterotrophic marine bacterioplankton and with Bacteroidetes hosts. None of the 8 phages stained well with DNA binding stains, suggesting that in situ abundances of ssDNA phages are drastically...

  12. No significant effects of single intravenous, single oral and subchronic oral administration of acetylcholinesterase inhibitors on striatal [{sup 123}I]FP-CIT binding in rats

    Energy Technology Data Exchange (ETDEWEB)

    Knol, R.J.J.; Booij, J. [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Center, Amsterdam (Netherlands); Graduate School of Neurosciences, Amsterdam (Netherlands); Bruin, K. de; Eck-Smit, B.L.F. van [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Center, Amsterdam (Netherlands)

    2008-03-15

    [{sup 123}I]FP-CIT SPECT is a valuable diagnostic tool to discriminate Lewy body dementia from Alzheimer's dementia. To date, however, it is uncertain whether the frequently used acetylcholinesterase inhibitors (AChEIs) by demented patients, have an effect on [{sup 123}I]FP-CIT binding to dopamine transporters (DATs). Earlier animal studies showed a decline of DAT availability after acute intravenous injection of AChEIs. The aim of this study was to investigate effects of single intravenous, single oral and subchronic oral administration of AChEIs on DAT availability in the rat brain as measured by [{sup 123}I]FP-CIT. Biodistribution studies were performed in Wistar rats (n = 5-16 per group). Before [{sup 123}I]FP-CIT injection, rats were injected intravenously with a single dose of the AChEI rivastigmine (2.5 mg/kg body weight) or donepezil (0.5 mg/kg), the DAT-blocker methylphenidate (10 mg/kg) or saline. A second group was orally treated with a single dose of rivastigmine or donepezil (2.5 mg/kg), methylphenidate (10 mg/kg) or saline before injection of [{sup 123}I]FP-CIT. Studies were also performed in rats that were orally treated during 14 consecutive days with either rivastigmine (1 mg/kg daily), donepezil (1.5 mg/kg daily), methylphenidate (2.5 mg/kg) or saline. Brain parts were assayed in a gamma counter, and specific striatum/cerebellum ratios were calculated for the [{sup 123}I]FP-CIT binding to DATs. No significant effects of either single intravenous, single oral or subchronic oral administration of AChEIs on striatal FP-CIT binding could be detected. Single pretreatment with methylphenidate resulted in an expected significantly lower striatal FP-CIT binding. We conclude that in rats, single intravenous and single or subchronic oral administration of the tested AChEIs does not lead to an important alteration of [{sup 123}I]FP-CIT binding to striatal DATs. Therefore, it is unlikely that these drugs will induce large effects on the interpretation of

  13. Designing Single-Ion Magnets and Phosphorescent Materials with 1-Methylimidazole-5-carboxylate and Transition-Metal Ions.

    Science.gov (United States)

    García-Valdivia, Antonio A; Seco, Jose M; Cepeda, Javier; Rodríguez-Diéguez, Antonio

    2017-11-20

    Detailed structural, magnetic, and photoluminescence (PL) characterization of four new compounds based on 1-methylimidazole-5-carboxylate (mimc) ligand and transition metal ions, namely [Ni(mimc) 2 (H 2 O) 4 ] (1), [Co(μ-mimc) 2 ] n (2), {[Cu 2 (μ-mimc) 4 (H 2 O)]·2H 2 O} n (3), and [Cd(μ-mimc) 2 (H 2 O)] n (4) is reported. The structural diversity found in the family of compounds derives from the coordination versatility of the ligand, which coordinates as a terminal ligand to give a supramolecular network of monomeric entities in 1 or acts as a bridging linker to build isoreticular 2D coordination polymers (CPs) in 2-4. Magnetic direct-current (dc) susceptibility data have been measured for compounds 1-3 to analyze the exchange interactions among paramagnetic centers, which have been indeed supported by calculations based on broken symmetry (BS) and density functional theory (DFT) methodology. The temperature dependence of susceptibility and magnetization data of 2 are indicative of easy-plane anisotropy (D = +12.9 cm -1 , E = +0.5 cm -1 ) that involves a bistable M s = ±1/2 ground state. Alternating-current (ac) susceptibility curves exhibit field-induced single-ion magnet (SIM) behavior that occurs below 14 K, which is characterized by two spin relaxation processes of distinct nature: fast relaxation of single ions proceeding through multiple mechanisms (U eff = 26 K) and a slow relaxation attributed to interactions along the polymeric crystal building. Exhaustive PL analysis of compound 4 in the solid state confirms low-temperature phosphorescent green emission consisting of radiative lifetimes in the range of 0.25-0.43 s, which explains the afterglow observed during about 1 s after the removal of the UV source. Time-dependent DFT and computational calculations to estimate phosphorescent vertical transitions have been also employed to provide an accurate description of the PL performance of this long-lasting phosphor.

  14. Binding energies and isomerization in metallocene ions from threshold photoelectron photoion coincidence spectroscopy.

    Science.gov (United States)

    Révész, Agnes; Szepes, László; Baer, Tomas; Sztáray, Bálint

    2010-12-22

    Metallocene ions (Cp(2)M(+), M = Cr, Co, Ni) were studied by threshold photoelectron photoion coincidence spectroscopy (TPEPICO) to investigate the mechanism, energetics, and kinetics of the ionic dissociation processes. The examined energy-selected Cp(2)M(+) ions fragment by losing the neutral cyclopentadienyl ligand. In addition, CH and C(2)H(2) losses appear as minor channels, while the cobaltocene ion also loses an H atom. A possible isomerization pathway has also been observed for Cp(2)Ni(+), yielding a complex with pentafulvalene (C(10)H(8)) with a loss of H(2). In order to determine the 0 K appearance energies for the CpM(+) fragment ions, the asymmetric time-of-flight peak shapes and the breakdown diagrams of the energy-selected metallocene ions were modeled by both the rigid activated complex (RAC) Rice-Ramsperger-Kassel-Marcus (RRKM) theory and the simplified statistical adiabatic channel model (SSACM). The following appearance energies were obtained with SSACM, which is more reliable for loose transition states: 10.57 ± 0.14, 11.01 ± 0.13, and 10.18 ± 0.13 eV for M = Cr, Co, and Ni, respectively. These values combined with the corresponding adiabatic ionization energies yield M-Cp bond dissociation energies in Cp(2)M(+) ions of 5.04 ± 0.16, 5.77 ± 0.15, and 3.96 ± 0.15 eV. Density functional calculations at the B3LYP/6-311G(d,p) level of theory were used to determine the structures of these complexes and to provide parameters necessary for the analysis of the experimental data. The trends in the M-Cp bond energies can be related to the electronic structures of the metallocene ions based on a simple molecular orbital picture.

  15. Fast detection of narcotics by single photon ionization mass spectrometry and laser ion mobility spectrometry

    Science.gov (United States)

    Laudien, Robert; Schultze, Rainer; Wieser, Jochen

    2010-10-01

    In this contribution two analytical devices for the fast detection of security-relevant substances like narcotics and explosives are presented. One system is based on an ion trap mass spectrometer (ITMS) with single photon ionization (SPI). This soft ionization technique, unlike electron impact ionization (EI), reduces unwanted fragment ions in the mass spectra allowing the clear determination of characteristic (usually molecular) ions. Their enrichment in the ion trap and identification by tandem MS investigations (MS/MS) enables the detection of the target substances in complex matrices at low concentrations without time-consuming sample preparation. For SPI an electron beam pumped excimer light source of own fabrication (E-Lux) is used. The SPI-ITMS system was characterized by the analytical study of different drugs like cannabis, heroin, cocaine, amphetamines, and some precursors. Additionally, it was successfully tested on-site in a closed illegal drug laboratory, where low quantities of MDMA could be directly detected in samples from floors, walls and lab equipments. The second analytical system is based on an ion mobility (IM) spectrometer with resonant multiphoton ionization (REMPI). With the frequency quadrupled Nd:YAG laser (266 nm), used for ionization, a selective and sensitive detection of aromatic compounds is possible. By application of suited aromatic dopants, in addition, also non-aromatic polar compounds are accessible by ion molecule reactions like proton transfer or complex formation. Selected drug precursors could be successfully detected with this device as well, qualifying it to a lower-priced alternative or useful supplement of the SPI-ITMS system for security analysis.

  16. Competition of dipositive metal ions for Fe (III) binding sites in chelation therapy of Iron Load

    International Nuclear Information System (INIS)

    Rehmani, Fouzia S.

    2005-01-01

    Iron overload is a condition in which excessive iron deposited in the liver, kidney and spleen of human beings in the patients of beta thalassemia and sickle cell anemia. Instead of its importance iron could be toxic when in excess, it damages the tissues. For the treatment of iron overload, a drug desferrioxamine mesylate has been used. It is linear trihydroxamic acid, a natural siderophore produced by streptomyces which removes the extra iron from body. Salicylhydroxamate type siderphore. In present research salicylhydroxamate was used for the complexation with dipositive metal ions which are available in biological environments such as Mn (II), Co (II), Ni (II) and Cu (II). The aim of our work was to study the competition reactions between Fe (III) and other dipositive ions; to calculate the thermodynamic data of chelation of these metal ions complexes with hydroxamate by computer program and comparison with hydroxamate complexes. (author)

  17. Isolation of Panels of Llama Single-Domain Antibody Fragments Binding All Nine Neuraminidase Subtypes of Influenza A Virus

    Directory of Open Access Journals (Sweden)

    Guus Koch

    2013-04-01

    Full Text Available Avian influenza A virus comprises sixteen hemagglutinin (HA and nine neuraminidase (NA subtypes (N1–N9. To isolate llama single-domain antibody fragments (VHHs against all N subtypes, four llamas were immunized with mixtures of influenza viruses. Selections using influenza virus yielded predominantly VHHs binding to the highly immunogenic HA and nucleoprotein. However, selection using enzymatically active recombinant NA (rNA protein enabled us to isolate NA binding VHHs. Some isolated VHHs cross-reacted to other N subtypes. These were subsequently used for the capture of N subtypes that could not be produced as recombinant protein (rN6 or were enzymatically inactive (rN1, rN5 in phage display selection, yielding novel VHHs. In total we isolated 188 NA binding VHHs, 64 of which were expressed in yeast. Most VHHs specifically recognize a single N subtype, but some VHHs cross-react with other N-subtypes. At least one VHH bound to all N subtypes, except N4, identifying a conserved antigenic site. Thus, this work (1 describes methods for isolating NA binding VHHs, (2 illustrates the suitability of llama immunization with multiple antigens for retrieving many binders against different antigens and (3 describes 64 novel NA binding VHHs, including a broadly reactive VHH, which can be used in various assays for influenza virus subtyping, detection or serology.

  18. Effect of swift heavy ion irradiation on single- and multiwalled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Olejniczak, Andrzej, E-mail: aolejnic@chem.uni.torun.pl [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Faculty of Chemistry, Nicolaus Copernicus University, ul. Gagarina 7, 87-100 Toruń (Poland); Skuratov, Vladimir A. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation)

    2014-05-01

    The effect of irradiation with swift heavy ions on the structure and properties of carbon nanotubes was investigated by Raman spectroscopy. It was found that disordering of the system occurred mainly at the surface. No ordering phenomena have been observed over a whole range of both fluences and electronic stopping powers studied. The disorder parameter (i.e., the ratio of the D and G band intensities (I{sub D}/I{sub G})) increases non-linearly with the irradiation dose, showing a tendency to saturate at high fluences. The increase in the disorder parameter upon irradiation was proportional to the square root of the ion fluence. The radiation stability of the few-walled nanotubes was ca. 1.6 higher than that of the single-walled ones. The irradiation with both the Xe and Kr ions leads to essentially the same increase in the I{sub D}/I{sub G} ratio with respect to the deposited electronic energy density. In the case of the Ar ion irradiation, the observed increase in the I{sub D}/I{sub G} ratio is much lower, suggesting that the electronic stopping power threshold for defects creation in carbon nanotubes is lower than that for graphite.

  19. Trapped-ion anomalous diffusion coefficient on the basis of single mode saturation

    International Nuclear Information System (INIS)

    Koshi, Yuji; Hatayama, Akiyoshi; Ogasawara, Masatada.

    1982-03-01

    Expressions of the anomalous diffusion coefficient due to the dissipative trapped ion instability (DTII) are derived for the case with and without the effect of magnetic shear. Derivation is made by taking into account of the single mode saturation of the DTII previously obtained numerically. In the absence of the shear effect, the diffusion coefficient is proportional to #betta#sub(i)a 2 (#betta#sub(i) is the effective collision frequency of the trapped ions and a is the minor radius of a torus) and is much larger than the neoclassical ion heat conductivity. In the presence of the shear effect, the diffusion coefficient is much smaller than the Kadomtsev and Pogutse's value and is the same order of magnitude as the neoclassical ion heat conductivity. Dependences of the diffusion coefficient on the temperature and on the total particle number density are rather complicated due to the additional spectral cut-off, which is introduced to regularize the short wavelength modes in the numerical analysis. (author)

  20. Live cell imaging combined with high-energy single-ion microbeam

    International Nuclear Information System (INIS)

    Guo, Na; Du, Guanghua; Liu, Wenjing; Wu, Ruqun; Wei, Junzhe; Guo, Jinlong; Chen, Hao

    2016-01-01

    DNA strand breaks can lead to cell carcinogenesis or cell death if not repaired rapidly and efficiently. An online live cell imaging system was established at the high energy microbeam facility at the Institute of Modern Physics to study early and fast cellular response to DNA damage after high linear energy transfer ion radiation. The HT1080 cells expressing XRCC1-RFP were irradiated with single high energy nickel ions, and time-lapse images of the irradiated cells were obtained online. The live cell imaging analysis shows that strand-break repair protein XRCC1 was recruited to the ion hit position within 20 s in the cells and formed bright foci in the cell nucleus. The fast recruitment of XRCC1 at the ion hits reached a maximum at about 200 s post-irradiation and then was followed by a slower release into the nucleoplasm. The measured dual-exponential kinetics of XRCC1 protein are consistent with the proposed consecutive reaction model, and the measurements obtained that the reaction rate constant of the XRCC1 recruitment to DNA strand break is 1.2 × 10 −3 s −1 and the reaction rate constant of the XRCC1 release from the break-XRCC1 complex is 1.2 × 10 −2 s −1 .

  1. Live cell imaging combined with high-energy single-ion microbeam

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Na; Du, Guanghua, E-mail: gh-du@impcas.ac.cn; Liu, Wenjing; Wu, Ruqun; Wei, Junzhe [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou (China); Guo, Jinlong [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou (China); Northwest Normal University, Lanzhou (China); Chen, Hao [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou (China); Institute of Nuclear Science and Technology, University of Lanzhou, Lanzhou (China)

    2016-03-15

    DNA strand breaks can lead to cell carcinogenesis or cell death if not repaired rapidly and efficiently. An online live cell imaging system was established at the high energy microbeam facility at the Institute of Modern Physics to study early and fast cellular response to DNA damage after high linear energy transfer ion radiation. The HT1080 cells expressing XRCC1-RFP were irradiated with single high energy nickel ions, and time-lapse images of the irradiated cells were obtained online. The live cell imaging analysis shows that strand-break repair protein XRCC1 was recruited to the ion hit position within 20 s in the cells and formed bright foci in the cell nucleus. The fast recruitment of XRCC1 at the ion hits reached a maximum at about 200 s post-irradiation and then was followed by a slower release into the nucleoplasm. The measured dual-exponential kinetics of XRCC1 protein are consistent with the proposed consecutive reaction model, and the measurements obtained that the reaction rate constant of the XRCC1 recruitment to DNA strand break is 1.2 × 10{sup −3} s{sup −1} and the reaction rate constant of the XRCC1 release from the break-XRCC1 complex is 1.2 × 10{sup −2} s{sup −1}.

  2. Live cell imaging combined with high-energy single-ion microbeam

    Science.gov (United States)

    Guo, Na; Du, Guanghua; Liu, Wenjing; Guo, Jinlong; Wu, Ruqun; Chen, Hao; Wei, Junzhe

    2016-03-01

    DNA strand breaks can lead to cell carcinogenesis or cell death if not repaired rapidly and efficiently. An online live cell imaging system was established at the high energy microbeam facility at the Institute of Modern Physics to study early and fast cellular response to DNA damage after high linear energy transfer ion radiation. The HT1080 cells expressing XRCC1-RFP were irradiated with single high energy nickel ions, and time-lapse images of the irradiated cells were obtained online. The live cell imaging analysis shows that strand-break repair protein XRCC1 was recruited to the ion hit position within 20 s in the cells and formed bright foci in the cell nucleus. The fast recruitment of XRCC1 at the ion hits reached a maximum at about 200 s post-irradiation and then was followed by a slower release into the nucleoplasm. The measured dual-exponential kinetics of XRCC1 protein are consistent with the proposed consecutive reaction model, and the measurements obtained that the reaction rate constant of the XRCC1 recruitment to DNA strand break is 1.2 × 10-3 s-1 and the reaction rate constant of the XRCC1 release from the break-XRCC1 complex is 1.2 × 10-2 s-1.

  3. Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

    International Nuclear Information System (INIS)

    Zoest, J.M. van.

    1986-01-01

    This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

  4. Effects of copper ions on DNA binding and cytotoxic activity of a chiral salicylidene Schiff base.

    Science.gov (United States)

    Fei, Bao-Li; Xu, Wu-Shuang; Tao, Hui-Wen; Li, Wen; Zhang, Yu; Long, Jian-Ying; Liu, Qing-Bo; Xia, Bing; Sun, Wei-Yin

    2014-03-05

    A chiral Schiff base HL N-(5-bromo-salicylaldehyde)dehydroabietylamine (1) and its chiral dinuclear copper complex [Cu2L4]·4DMF (2) have been synthesized and fully characterized. The interactions of 1 and 2 with salmon sperm DNA have been investigated by viscosity measurements, UV, fluorescence and circular dichroism (CD) spectroscopic techniques. Absorption spectral (Kb=3.30 × 10(5)M(-)(1) (1), 6.63 × 10(5)M(-)(1)(2)), emission spectral (Ksv=7.58 × 10(3)M(-)(1) (1), 1.52 × 10(4)M(-)(1) (2)), and viscosity measurements reveal that 1 and 2 interact with DNA through intercalation and 2 exhibits a higher DNA binding ability. In addition, CD study indicates 2 cause a more evident perturbation on the base stacking and helicity of B-DNA upon binding to it. In fluorimetric studies, the enthalpy (ΔH>0) and entropy (ΔS>0) changes of the reactions between the compounds with DNA demonstrate hydrophobic interactions. 1 and 2 were also screened for their cytotoxic ability and 2 demonstrates higher growth inhibition of the selected cancer cells at concentration of 50 μM, this result is identical with their DNA binding ability order. All the experimental results show that the involvement of Cu (II) centers has some interesting effect on DNA binding ability and cytotoxicity of the chiral Schiff base. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. K+ congeners that do not compromise Na+ activation of the Na+,K+-ATPase: hydration of the ion binding cavity likely controls ion selectivity.

    Science.gov (United States)

    Mahmmoud, Yasser A; Kopec, Wojciech; Khandelia, Himanshu

    2015-02-06

    The Na(+),K(+)-ATPase is essential for ionic homeostasis in animal cells. The dephosphoenzyme contains Na(+) selective inward facing sites, whereas the phosphoenzyme contains K(+) selective outward facing sites. Under normal physiological conditions, K(+) inhibits cytoplasmic Na(+) activation of the enzyme. Acetamidinium (Acet(+)) and formamidinium (Form(+)) have been shown to permeate the pump through the outward facing sites. Here, we show that these cations, unlike K(+), are unable to enter the inward facing sites in the dephosphorylated enzyme. Consistently, the organic cations exhibited little to no antagonism to cytoplasmic Na(+) activation. Na(+),K(+)-ATPase structures revealed a previously undescribed rotamer transition of the hydroxymethyl side chain of the absolutely conserved Thr(772) of the α-subunit. The side chain contributes its hydroxyl to Na(+) in site I in the E1 form and rotates to contribute its methyl group toward K(+) in the E2 form. Molecular dynamics simulations to the E1·AlF4 (-)·ADP·3Na(+) structure indicated that 1) bound organic cations differentially distorted the ion binding sites, 2) the hydroxymethyl of Thr(772) rotates to stabilize bound Form(+) through water molecules, and 3) the rotamer transition is mediated by water traffic into the ion binding cavity. Accordingly, dehydration induced by osmotic stress enhanced the interaction of the congeners with the outward facing sites and profoundly modified the organization of membrane domains of the α-subunit. These results assign a catalytic role for water in pump function, and shed light on a backbone-independent but a conformation-dependent switch between H-bond and dispersion contact as part of the catalytic mechanism of the Na(+),K(+)-ATPase. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Characterization of the single stranded DNA binding protein SsbB encoded in the Gonoccocal Genetic Island.

    Directory of Open Access Journals (Sweden)

    Samta Jain

    Full Text Available Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins.In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg(2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity.We propose that these novel SsbBs play an unknown role in the maintenance of genetic islands.

  7. Ion adsorption on oxides : surface charge formation and cadmium binding on rutile and hematite

    NARCIS (Netherlands)

    Fokkink, L.G.J.

    1987-01-01

    The adsorption of charge-determining (H +and OH -) and cadmium ions on rutile (TiO 2 ) and hematite (α-Fe

  8. Binding of nickel and zinc ions with activated carbon prepared from ...

    African Journals Online (AJOL)

    Activated carbon was prepared from sugar cane fibre by carbonizing at 500 oC for 30 minutes. This was followed by activation with ammonium chloride. The activated carbon was characterised in terms of pH, bulk density, ash content, surface area and surface charge. Equilibrium sorption of nickel and zinc ions by the ...

  9. Identification and Characterization of Single-Chain Antibodies that Specifically Bind GI Noroviruses.

    Directory of Open Access Journals (Sweden)

    Amy M Hurwitz

    Full Text Available Norovirus infections commonly lead to outbreaks of acute gastroenteritis and spread quickly, resulting in many health and economic challenges prior to diagnosis. Rapid and reliable diagnostic tests are therefore essential to identify infections and to guide the appropriate clinical responses at the point-of-care. Existing tools, including RT-PCR and enzyme immunoassays, pose several limitations based on the significant time, equipment and expertise required to elicit results. Immunochromatographic assays available for use at the point-of-care have poor sensitivity and specificity, especially for genogroup I noroviruses, thus requiring confirmation of results with more sensitive testing methods. Therefore, there is a clear need for novel reagents to help achieve quick and reliable results. In this study, we have identified two novel single-chain antibodies (scFvs-named NJT-R3-A2 and NJT-R3-A3-that effectively detect GI.1 and GI.7 virus-like particles (VLPs through selection of a phage display library against the P-domain of the GI.1 major capsid protein. The limits of detection by each scFv for GI.1 and GI.7 are 0.1 and 0.2 ng, and 6.25 and 25 ng, respectively. They detect VLPs with strong specificity in multiple diagnostic formats, including ELISAs and membrane-based dot blots, and in the context of norovirus-negative stool suspensions. The scFvs also detect native virions effectively in norovirus-positive clinical stool samples. Purified scFvs bind to GI.1 and GI.7 VLPs with equilibrium constant (KD values of 27 nM and 49 nM, respectively. Overall, the phage-based scFv reagents identified and characterized here show utility for detecting GI.1 and GI.7 noroviruses in multiple diagnostic assay formats with strong specificity and sensitivity, indicating promise for integration into existing point-of-care tests to improve future diagnostics.

  10. Microarray study of single nucleotide polymorphisms and expression of ATP-binding cassette genes in breast tumors

    Science.gov (United States)

    Tsyganov, M. M.; Ibragimova, M. K.; Karabut, I. V.; Freydin, M. B.; Choinzonov, E. L.; Litvyakov, N. V.

    2015-11-01

    Our previous research establishes that changes of expression of the ATP-binding cassette genes family is connected with the neoadjuvant chemotherapy effect. However, the mechanism of regulation of resistance gene expression remains unclear. As many researchers believe, single nucleotide polymorphisms can be involved in this process. Thereupon, microarray analysis is used to study polymorphisms in ATP-binding cassette genes. It is thus found that MDR gene expression is connected with 5 polymorphisms, i.e. rs241432, rs241429, rs241430, rs3784867, rs59409230, which participate in the regulation of expression of own genes.

  11. Electrochemical lithium-ion storage properties of quinone molecules encapsulated in single-walled carbon nanotubes.

    Science.gov (United States)

    Ishii, Yosuke; Tashiro, Kosuke; Hosoe, Kento; Al-Zubaidi, Ayar; Kawasaki, Shinji

    2016-04-21

    We investigated the electrochemical lithium-ion storage properties of 9,10-anthraquinone (AQ) and 9,10-phenanthrenequinone (PhQ) molecules encapsulated in the inner hollow core of single-walled carbon nanotubes (SWCNTs). The structural properties of the obtained encapsulated systems were characterized by electron microscopy, synchrotron powder X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. We found that almost all quinone molecules encapsulated in the SWCNTs can store Li-ions reversibly. Interestingly, the undesired capacity fading, which comes from the dissolution of quinone molecules into the electrolyte, was suppressed by the encapsulation. It was also found that the overpotential of AQ was decreased by the encapsulation, probably due to the high-electric conductivity of SWCNTs.

  12. Swift heavy ion induced modifications of single walled carbon nanotube thin films

    Energy Technology Data Exchange (ETDEWEB)

    Vishalli, E-mail: vishalli_2008@yahoo.com [Department of Physics, Panjab University, Chandigarh 160014 (India); Raina, K.K. [Materials Research Laboratory, School of Physics and Materials Science, Thapar University, P.O. Box 32, Patiala 147004, Punjab (India); Avasthi, D.K. [Materials Science Group, Inter University Accelerator Centre, Aruna Asaf Ali Marg, P.O. Box 10502, New Delhi 110067 (India); Srivastava, Alok [Department of Chemistry, Panjab University, Chandigarh 160014 (India); Dharamvir, Keya [Department of Physics, Panjab University, Chandigarh 160014 (India)

    2016-04-15

    Thin films of single walled carbon nanotubes (SWCNTs) were prepared by Langmuir–Blodgett method and irradiated with swift heavy ions, carbon and nickel each of energy 60 MeV. The ion beams have different electronic energy loss (S{sub e}) values and the samples were exposed to various irradiation doses. The irradiated films were characterized using Raman and optical absorption spectroscopy. Raman spectroscopy results indicate the competing processes of defect creation and healing (annealing) of SWCNTs at lower fluences, while at higher fluences defect creation or damage dominates. In UV–Vis–NIR spectroscopy we find that there is decrease in the intensity of characteristic peaks with every increasing fluence, indicating decrease in the optically active states with irradiation.

  13. Investigation on optical absorption properties of ion irradiated single walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Vishalli,, E-mail: vishalli-2008@yahoo.com; Dharamvir, Keya, E-mail: keya@pu.ac.in [Department of Physics, Panjab University, Chandigarh (India); Kaur, Ramneek; Raina, K. K. [Materials Research Laboratory, School of Physics and Materials Science, Thapar University, Patiala (India); Avasthi, D. K. [Materials Science Group, Inter University Accelerator Centre, ArunaAsaf Ali Marg, NewDelhi (India); Jeet, Kiran [Electron Microscopy and Nanoscience laboratory, Punjab Agriculture University, Ludhiana (India)

    2015-08-28

    In the present study change in the optical absorption properties of single walled carbon nanotubes (SWCNTs) under nickel ion (60 MeV) irradiation at various fluences has been investigated. Langmuir Blodgett technique is used to deposit SWCNT thin film of uniform thickness. AFM analysis shows a network of interconnected bundles of nanotubes. UV-Vis-NIR absorption spectra indicate that the sample mainly contain SWCNTs of semiconducting nature. It has been found in absorption spectra that there is decrease in the intensity of the characteristic SWCNT peaks with increase in fluence. At fluence value 1×10{sup 14} ions/cm{sup 2} there is almost complete suppression of the characteristic SWCNTs peaks.The decrease in the optical absorption with increase in fluence is due to the increase in the disorder in the system which leads to the decrease in optically active states.

  14. Energy transduction and signal averaging of fluctuating electric fields by a single protein ion channel.

    Science.gov (United States)

    Verdia-Baguena, C; Gomez, V; Cervera, J; Ramirez, P; Mafe, S

    2016-12-21

    We demonstrate the electrical rectification and signal averaging of fluctuating signals using a biological nanostructure in aqueous solution: a single protein ion channel inserted in the lipid bilayer characteristic of cell membranes. The conversion of oscillating, zero time-average potentials into directional currents permits charging of a load capacitor to significant steady-state voltages within a few minutes in the case of the outer membrane porin F (OmpF) protein, a bacterial channel of Escherichia coli. The experiments and simulations show signal averaging effects at a more fundamental level than the traditional cell and tissue scales, which are characterized by ensembles of many ion channels operating simultaneously. The results also suggest signal transduction schemes with bio-electronic interfaces and ionic circuits where soft matter nanodiodes can be coupled to conventional electronic elements.

  15. Analysis of single particle diffusion with transient binding using particle filtering.

    Science.gov (United States)

    Bernstein, Jason; Fricks, John

    2016-07-21

    Diffusion with transient binding occurs in a variety of biophysical processes, including movement of transmembrane proteins, T cell adhesion, and caging in colloidal fluids. We model diffusion with transient binding as a Brownian particle undergoing Markovian switching between free diffusion when unbound and diffusion in a quadratic potential centered around a binding site when bound. Assuming the binding site is the last position of the particle in the unbound state and Gaussian observational error obscures the true position of the particle, we use particle filtering to predict when the particle is bound and to locate the binding sites. Maximum likelihood estimators of diffusion coefficients, state transition probabilities, and the spring constant in the bound state are computed with a stochastic Expectation-Maximization (EM) algorithm. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. An efficient single-step scheme for manipulating quantum information of two trapped ions beyond the Lamb-Dicke limit

    International Nuclear Information System (INIS)

    Wei, L.F.; Nori, Franco

    2003-01-01

    Based on the exact conditional quantum dynamics for a two-ion system, we propose an efficient single-step scheme for coherently manipulating quantum information of two trapped cold ions by using a pair of synchronous laser pulses. Neither the auxiliary atomic level nor the Lamb-Dicke approximation are needed

  17. Effects of soil salinity on the content, composition, and ion binding capacity of glomalin-related soil protein (GRSP).

    Science.gov (United States)

    Zhang, Zhonghua; Wang, Qiong; Wang, Hua; Nie, Siming; Liang, Zhengwei

    2017-03-01

    Soil aggregation, an ecosystem function correlated with the concentration of glomalin-related soil protein (GRSP), is highly disturbed in saline soil. However, few studies have focused on differences in amount, composition, and ion binding capacity of GRSP in typical sodic-saline soils. In this study, a field study was performed in Songnen Plain. Combined indicators of soil salinity (Q value) were significant negatively correlated with GRSP concentration by Principal Component Analysis. Multiple linear regression models showed that soil salinity might account for 46%, 25% and 44% variation in total GRSP (T-GRSP), easily-extractable GRSP (EE-GRSP) and difficultly-extractable GRSP (DE-GRSP), respectively. Soil bulk density had most important impact on GRSP concentration, followed by the pH, soil EC had the weak influence. Comparative analysis was carried out between low-salinity and high-salinity soil. Purified T-GRSP of high-saline soil contained higher N content (13.13%), lower C content (43.41%) and lower functional groups relative content (e.g. CO and SiOSi). Purified T-GRSP of high-salinity soil had a greater binding capacity with calcium and phosphorus, the binding capacity could compensate the GRSP loss about 29.8% and 14.1%, respectively. Our findings suggested that sodic salinization of the soil led to a decrease in GRSP concentration and a change in the component percentages. This change in composition might be related to adaptation of fungi-plant systems to varied environments. The calcium and phosphorus binding capacity had a positive dependent of soil salinization, which was possible to develop ecological management or recovery technology in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Numerical simulation study into the effect of a single heavy ion on a sub-micron CMOS device

    International Nuclear Information System (INIS)

    Detcheverry, C.; Lorfevre, E.; Bruguier, G.; Palau, J.M.; Gasiot, J.; Ecoffet, R.

    1997-01-01

    This article discusses coupling between the MEDICI component simulator and the SPICE circuit simulator to study single-event-upset phenomena caused by a single ion on a 0.6 μm CMOS device. Results conforming closely to experimental values were obtained by adopting an appropriate mesh size, a hydrodynamic charge transport model (rather than a diffusion-conduction model), and realistic simulation of photon-induced carrier generation, to accurately model the ion passage and trajectory. (authors)

  19. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

    Science.gov (United States)

    Yang, Haozhe; Mei, Hui; Seela, Frank

    2015-07-06

    Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. All three Ca[superscript 2+]-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Lu; Vysotski, Eugene S.; Markova, Svetlana V.; Liu, Zhi-Jie; Lee, John; Rose, John; Wang, Bi-Cheng (Georgia)

    2010-07-13

    The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 {angstrom} and 2.2 {angstrom}, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca{sup 2+}-discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca{sup 2+} concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.

  1. Single-Qubit-Gate Error below 0.0001 in a Trapped Ion

    Science.gov (United States)

    2011-01-01

    nuclear spins in liquid-state nuclear-magnetic resonance experiments [6] and with neutral atoms confined in optical lattices [7]; here we demonstrate...Single trapped ion 2.0(2)×10−5 Reference [6] (2009) Nuclear magnetic resonance 1.3(1)×10−4 Reference [7] (2010) Atoms in an optical lattice 1.4(1)×10...determined by comparing the qubit frequency measured in a Ramsey experiment with that of a Rabi experiment. Such back-to-back comparisons yielded values

  2. Machining with micro-size single crystalline diamond tools fabricated by a focused ion beam

    International Nuclear Information System (INIS)

    Ding, X; Butler, D L; Lim, G C; Shaw, K C; Liu, K; Fong, W S; Zheng, H Y; Cheng, C K

    2009-01-01

    A study was carried out to understand the physics of micro-scale mechanical machining (henceforth referred to as 'micro-machining') with a micro-size tool using a five-axis ultra-precision machine. A micro-size single crystalline diamond (SCD) tool with sharp cutting edges fabricated by a focused ion beam (FIB) was employed to orthogonal-machine four materials (three polycrystalline metals with various grain sizes and one amorphous metal plating material). Since the wealth of knowledge of macro-machining cannot be successfully used in micro-machining, this study contributes to the understanding of the physics of mechanical machining with micro-size tools

  3. Rational Design of Lanthanoid Single-Ion Magnets: Predictive Power of the Theoretical Models.

    Science.gov (United States)

    Baldoví, José J; Duan, Yan; Morales, Roser; Gaita-Ariño, Alejandro; Ruiz, Eliseo; Coronado, Eugenio

    2016-09-12

    We report two new single-ion magnets (SIMs) of a family of oxydiacetate lanthanide complexes with D3 symmetry to test the predictive capabilities of complete active space ab initio methods (CASSCF and CASPT2) and the semiempirical radial effective charge (REC) model. Comparison of the theoretical predictions of the energy levels, wave functions and magnetic properties with detailed spectroscopic and magnetic characterisation is used to critically discuss the limitations of these theoretical approaches. The need for spectroscopic information for a reliable description of the properties of lanthanide SIMs is emphasised. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Subattoampere current induced by single ions in silicon oxide layers of nonvolatile memory cells

    International Nuclear Information System (INIS)

    Cellere, G.; Paccagnella, A.; Larcher, L.; Visconti, A.; Bonanomi, M.

    2006-01-01

    A single ion impinging on a thin silicon dioxide layer generates a number of electron/hole pairs proportional to its linear energy transfer coefficient. Defects generated by recombination can act as a conductive path for electrons that cross the oxide barrier, thanks to a multitrap-assisted mechanism. We present data on the dependence of this phenomenon on the oxide thickness by using floating gate memory arrays. The tiny number of excess electrons stored in these devices allows for extremely high sensitivity, impossible with any direct measurement of oxide leakage current. Results are of particular interest for next generation devices

  5. Fracture analysis of surface exfoliation on single crystal silicon irradiated by intense pulsed ion beam

    Science.gov (United States)

    Shen, Jie; Shahid, Ijaz; Yu, Xiao; Zhang, Jie; Zhong, Haowen; Cui, Xiaojun; Liang, Guoying; Yu, Xiang; Huang, Wanying; Yan, Sha; Zhang, Gaolong; Zhang, Xiaofu; Le, Xiaoyun

    2017-12-01

    Surface exfoliation was observed on single crystal silicon surface irradiated by Intense Pulsed Ion Beam (IPIB). As the strong transient thermal stress impact induced by IPIB was mainly attributed to the exfoliation, a micro scale model combined with thermal conduction and linear elastic fracture mechanics was built to analyze the thermal stress distribution along the energy deposition process. After computation with finite element method, J integral parameter was applied as the criterion for crack development. It was demonstrated that the exfoliation initiation calls for specific material, crack depth and IPIB parameter. The results are potentially valuable for beam/target selection and IPIB parameter optimization.

  6. Measurement of Cadmium Ion in the Presence of Metal-Binding Biopolymers in Aqueous Sample

    Directory of Open Access Journals (Sweden)

    Jian Pu

    2013-01-01

    Full Text Available In aqueous environment, water-soluble polymers are effectively used to separate free metal ions from metal-polymer complexes. The feasibilities of four different analytical techniques, cadmium ion-selective electrode, dialysis sack, chelate disk cartridge, and ultrafiltration, in distinguishing biopolymer-bound and nonbound cadmium in aqueous samples were investigated. And two different biopolymers were used, including bovine serum albumin (BSA and biopolymer solution extracted from cultivated activated sludge (ASBP. The ISE method requires relatively large amount of sample and contaminates sample during the pretreatment. After the long reaction time of dialysis, the equilibrium of cadmium in the dialysis sack would be shifted. Due to the sample nature, chelate disk cartridge could not filter within recommended time, which makes it unavailable for biopolymer use. Ultrafiltration method would not experience the difficulties mentioned above. Ultrafiltration method measuring both weakly and strongly bound cadmium was included in nominally biopolymer-cadmium complex. It had significant correlation with the Ion-selective electrode (ISE method (R2=0.989 for BSA, 0.985 for ASBP.

  7. A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors

    Energy Technology Data Exchange (ETDEWEB)

    de Vries, Robert P.; Tzarum, Netanel; Peng, Wenjie; Thompson, Andrew J.; Ambepitiya Wickramasinghe, Iresha N.; de la Pena, Alba T. Torrents; van Breemen, Marielle J.; Bouwman, Kim M.; Zhu, Xueyong; McBride, Ryan; Yu, Wenli; Sanders, Rogier W.; Verheije, Monique H.; Wilson, Ian A.; Paulson, James C.

    2017-07-10

    In June 2013, the first case of human infection with an avian H6N1 virus was reported in a Taiwanese woman. Although this was a single non-fatal case, the virus continues to circulate in Taiwanese poultry. As with any emerging avian virus that infects humans, there is concern that acquisition of human-type receptor specificity could enable transmission in the human population. Despite mutations in the receptor-binding pocket of the human H6N1 isolate, it has retained avian-type (NeuAcα2-3Gal) receptor specificity. However, we show here that a single nucleotide substitution, resulting in a change from Gly to Asp at position 225 (G225D), completely switches specificity to human-type (NeuAcα2-6Gal) receptors. Significantly, G225D H6 loses binding to chicken trachea epithelium and is now able to bind to human tracheal tissue. Structural analysis reveals that Asp225 directly interacts with the penultimate Gal of the human-type receptor, stabilizing human receptor binding.

  8. Electron paramagnetic resonance and optical absorption of uranium ions diluted in CdF2 single crystals

    International Nuclear Information System (INIS)

    Pereira, J.J.C.R.

    1976-08-01

    The electron paramagnetic resonance (EPR) has been studied in conection with the optical absortion spectra of Uranium ions diluted in CdF 2 single crystals. Analyses of the EPR and optical absorption spectra obtained experimentally, and a comparison with known results in the isomorfic CaF 2 , SrF 2 and BaF 2 , allowed the identification of two paramagnetic centers associated with Uranium ions. These are the U(2+) ion in cubic symmetry having the triplet γ 5 as ground state, and the U(3+) ion in cubic symmetry having the dublet γ 6 as ground state. (Author) [pt

  9. Numerical Simulations of Calcium Ions Spiral Wave in Single Cardiac Myocyte

    Science.gov (United States)

    Bai, Yong-Qiang; Zhu, Xing

    2010-04-01

    The calcium ions (Ca2+) spark is an elementary Ca2+ release event in cardiac myocytes. It is believed to buildup cell-wide Ca2+ signals, such as Ca2+ transient and Ca2+ wave, through a Ca2+-induced Ca2+ release (CICR) mechanism. Here the excitability of the Ca2+ wave in a single cardiac myocyte is simulated by employing the fire-diffuse-fire model. By modulating the dynamic parameters of Ca2+ release and re-uptake channels, we find three Ca2+ signaling states in a single cardiac myocyte: no wave, plane wave, and spiral wave. The period of a spiral wave is variable in the different regimes. This study indicates that the spiral wave or the excitability of the system can be controlled through micro-modulation in a living excitable medium.

  10. Experimental Verification of a Jarzynski-Related Information-Theoretic Equality by a Single Trapped Ion

    Science.gov (United States)

    Xiong, T. P.; Yan, L. L.; Zhou, F.; Rehan, K.; Liang, D. F.; Chen, L.; Yang, W. L.; Ma, Z. H.; Feng, M.; Vedral, V.

    2018-01-01

    Most nonequilibrium processes in thermodynamics are quantified only by inequalities; however, the Jarzynski relation presents a remarkably simple and general equality relating nonequilibrium quantities with the equilibrium free energy, and this equality holds in both the classical and quantum regimes. We report a single-spin test and confirmation of the Jarzynski relation in the quantum regime using a single ultracold Ca40 + ion trapped in a harmonic potential, based on a general information-theoretic equality for a temporal evolution of the system sandwiched between two projective measurements. By considering both initially pure and mixed states, respectively, we verify, in an exact and fundamental fashion, the nonequilibrium quantum thermodynamics relevant to the mutual information and Jarzynski equality.

  11. High-fidelity state detection and tomography of a single-ion Zeeman qubit

    International Nuclear Information System (INIS)

    Keselman, A; Glickman, Y; Akerman, N; Kotler, S; Ozeri, R

    2011-01-01

    We demonstrate high-fidelity Zeeman qubit state detection in a single trapped 88 Sr + ion. Qubit readout is performed by shelving one of the qubit states to a metastable level using a narrow linewidth diode laser at 674 nm, followed by state-selective fluorescence detection. The average fidelity reached for the readout of the qubit state is 0.9989(1). We then measure the fidelity of state tomography, averaged over all possible single-qubit states, which is 0.9979(2). We also fully characterize the detection process using quantum process tomography. This readout fidelity is compatible with recent estimates of the detection error threshold required for fault-tolerant computation, whereas high-fidelity state tomography opens the way for high-precision quantum process tomography.

  12. High-fidelity state detection and tomography of a single-ion Zeeman qubit

    Energy Technology Data Exchange (ETDEWEB)

    Keselman, A; Glickman, Y; Akerman, N; Kotler, S; Ozeri, R, E-mail: ozeri@weizmann.ac.il [Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100 (Israel)

    2011-07-15

    We demonstrate high-fidelity Zeeman qubit state detection in a single trapped {sup 88}Sr{sup +} ion. Qubit readout is performed by shelving one of the qubit states to a metastable level using a narrow linewidth diode laser at 674 nm, followed by state-selective fluorescence detection. The average fidelity reached for the readout of the qubit state is 0.9989(1). We then measure the fidelity of state tomography, averaged over all possible single-qubit states, which is 0.9979(2). We also fully characterize the detection process using quantum process tomography. This readout fidelity is compatible with recent estimates of the detection error threshold required for fault-tolerant computation, whereas high-fidelity state tomography opens the way for high-precision quantum process tomography.

  13. Conductometric determination of single pores in polyethyleneterephthalate irradiated by heavy ions

    International Nuclear Information System (INIS)

    Oganesyan, V.R.; Trofimov, V.V.; Doerschel, B.; Hermsdorf, D.; Vetter, J.; Danziger, M.

    2002-01-01

    Most of the previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7·10 3 ions/cm 2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20μm was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation, we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed model. Thus, the developed 'track-by-track' method can be used effectively for description of the sequential appearance of individual pores in an electrolytic etching process

  14. Nanomechanical investigation of ion implanted single crystals - Challenges, possibilities and pitfall traps related to nanoindentation

    Science.gov (United States)

    Kurpaska, Lukasz

    2017-10-01

    Nanoindentation technique have developed considerably over last thirty years. Nowadays, commercially available systems offer very precise measurement in nano- and microscale, environmental noise cancelling (or at least noise suppressing), in situ high temperature indentation in controlled atmosphere and vacuum conditions and different additional options, among them dedicated indentation is one of the most popular. Due to its high precision, and ability to measure mechanical properties from very small depths (tens of nm), this technique become quite popular in the nuclear society. It is known that ion implantation (to some extent) can simulate the influence of neutron flux. However, depth of the material damage is very limited resulting in creation of thin layer of modified material over unmodified bulk. Therefore, only very precise technique, offering possibility to control depth of the measurement can be used to study functional properties of the material. For this reason, nanoindentation technique seems to be a perfect tool to investigate mechanical properties of ion implanted specimens. However, conducting correct nanomechanical experiment and extracting valuable mechanical parameters is not an easy task. In this paper a discussion about the nanoindentation tests performed on ion irradiated YSZ single crystal is presented. The goal of this paper is to discuss possible traps when studying mechanical properties of such materials and thin coatings.

  15. An investigation of electron paramagnetic resonance spectra of Mn+2 ion in silver nitrate single crystals

    International Nuclear Information System (INIS)

    Korkmaz, M.

    1974-01-01

    X-band EPR spectra of Mn +2 ion in AgNO 3 single crystals have been investigated as a function of temperature. Because of the small size of the fine structure constant 'a' and the large size of the hyperfine constant 'A' in this crystal, all electronic transitions are superimposed. For this reason, spectra consist of a group of six hyperfine components. The spectra appeared to be isotropic, although the symmetry of the host lattice is orthoromibc. This shows that the local symmetry of the paramagnetic ions is of cubic type. EPR signal disappears completely at -40 0 C. As the temperature is increased from this value the signal intensity increases steadily and reaches a maximum value at +40 0 C. If the temperature is raised further the signal tends to decrease. In other words in this crystal Mn +2 ion shows antiferromagnetic property below +40 0 C and paramagnetic property above +40 0 C. We also found that, in the antiferromagnetic region, the line width increases as the temperature is decreased. In the paramagnetic region the line width increases as the temperature is increased. Other spectral parameters A and g do not change with the temperature. Spectra obtained at room temperature and at different temperatures are also discussed. (Korkmaz, M.)

  16. Diode-like single-ion track membrane prepared by electro-stopping

    International Nuclear Information System (INIS)

    Apel, P.Yu.; Korchev, Yu.E.; Siwy, Z.; Spohr, R.; Yoshida, M.

    2001-01-01

    The preparation of an asymmetric membrane in poly(ethylene terephthalate) (PET) is described, using a combination of chemical and electro-stopping. For this purpose, a single-ion-irradiated PET film is inserted into an electrolytic cell and etched from one side in 9 M sodium hydroxide while bathing the other side in a mixture of 2 M KCl and 2 M HCOOH (1:1 by volume), electrically retracting the OH - ions from the tip of the etch pit during pore break-through. When a preset current has been reached, the etch process is interrupted by replacing the etching solution with acidic 1 M potassium chloride solution. After etching, the current-voltage (I-V) characteristic is determined under symmetric bathing conditions, immersing both sides of the membrane in KCl solutions of identical concentration (0.01-1 M) and pH (3-8). The I-V characteristic is strongly non-linear, comparable to that of an electrical diode. If the polarity during etching is reversed, pushing the OH - ions into the tip of the etch pit, the resulting pores are larger and the degree of asymmetry smaller. The importance of electro-stopping is compared with chemical stopping

  17. Conductometric determination of single pores in polyethyleneterephthalate irradiated by heavy ions

    CERN Document Server

    Oganesyan, V R; Dörschel, B; Hermsdorf, D; Trofimov, V V; Vetter, J

    2002-01-01

    Most of the previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7 centre dot 10 sup 3 ions/cm sup 2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20 mu m was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation, we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed...

  18. Conductometric Determination of Single Pores in Polyethyleneterephthalate Irradiated by Heavy Ions

    CERN Document Server

    Oganesyan, V R; Dörschel, B; Vetter, J E; Danziger, M; Hermsdorf, D

    2002-01-01

    Most of previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7\\cdot 10^{3} ions/cm^2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20 m was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed model. Thus, the de...

  19. Development of the IFJ single ion hit facility for cells irradiation

    International Nuclear Information System (INIS)

    Veselov, O.; Polak, W.; Ugenskiene, R.; Hajduk, R.; Lebed, K.; Lekki, J.; Horwacik, T.; Dutkiewicz, E.M.; Maranda, S.; Pieprzyca, T.; Sarnecki, C.; Stachura, Z.; Szklarz, Z.; Styczen, J.

    2005-12-01

    In recent years a single ion hit facility (SIHF) has been constructed at the IFJ ion microprobe. The setup is used for the precise irradiations of living cells by a controlled number of ions. The facility allows investigations in various aspects of biomedical research, such as adaptive response, bystander effect, inverse dose-rate effect, low-dose hypersensitivity, etc. Those investigations have two very important requirements: (i) cells must be examined in their natural state and environment, i.e. without previously being killed, and preferentially, neither fixed nor stained, and (ii) a possibility of automatic irradiation of large number of cells with a computer recognition of their positions must be provided. This work presents some of the crucial features of the off-line and on-line optical systems, including self-developed software responsible for the automatic cell recognition. We also show several tests carried out to determine the efficiency of the whole setup and some segments. In conclusion, the results of our first irradiation measurements performed with living cells are demonstrated. (author)

  20. Designing Artificial Solid-Electrolyte Interphases for Single-Ion and High-Efficiency Transport in Batteries

    KAUST Repository

    Tu, Zhengyuan

    2017-09-21

    Substrates able to rectify transport of ions based on charge and/or size are ubiquitous in biological systems. Electrolytes and interphases that selectively transport electrochemically active ions are likewise of broad interest in all electrical energy storage technologies. In lithium-ion batteries, electrolytes with single- or near-single-ion conductivity reduce losses caused by ion polarization. In emergent lithium or sodium metal batteries, they maintain high conductivity at the anode and stabilize metal deposition by fundamental mechanisms. We report that 20- to 300-nm-thick, single-ion-conducting membranes deposited at the anode enable electrolytes with the highest combination of cation transference number, ionic conductivity, and electrochemical stability reported. By means of direct visualization we find that single-ion membranes also reduce dendritic deposition of Li in liquids. Galvanostatic measurements further show that the electrolytes facilitate long (3 mAh) recharge of full Li/LiNi0.8Co0.15Al0.05O2 (NCA) cells with high cathode loadings (3 mAh cm−2/19.9 mg cm−2) and at high current densities (3 mA cm−2).

  1. Selective binding and reverse transcription inhibition of single-strand poly(A) RNA by metal TMPyP complexes.

    Science.gov (United States)

    Zhou, Zhu-Xin; Gao, Feng; Chen, Xing; Tian, Xiang-Jing; Ji, Liang-Nian

    2014-10-06

    Ni-, Cu-, and Zn-TMPyP are capable of binding to single-strand poly(A) RNA with high preference and affinity and inhibiting the reverse transcription of RNA by both M-MuLV and HIV-1 reverse transcriptase. With 10 nM azidothymidine, the IC50 value of M-TMPyP could be lowered to 10(-1) μM order.

  2. Persistent photoconductivity in hydrogen ion-implanted KNbO3 bulk single crystal

    Science.gov (United States)

    Tsuruoka, R.; Shinkawa, A.; Nishimura, T.; Tanuma, C.; Kuriyama, K.; Kushida, K.

    2017-06-01

    Persistent Photoconductivity (PPC) in hydorogen-ion implanted (001) oriented KNbO3 bulk single crystals (perovskite structure at room temperature; ferroelectric with a band gap of 3.16 eV) is studied in air at room temperature to prevent the crystallinity degradation caused by the phase transition. Hydrogen is implanted into KNbO3 bulk single crystals using the energy (the peak ion fluence) of 500 keV (5.0 × 1015 cm-2). The resistivity varies from ∼108 Ω/□ for an un-implanted KNbO3 sample to 2.3 × 105 Ω/□ for as-implanted one. suggesting the presence of donors consisting of hydrogen interstitial and oxygen vacancy. The PPC is clearly observed with ultraviolet and blue LEDs illumination rather than green and infrared, suggesting the release of electrons from the metastable conductive state below the conduction band relating to the charge states of the oxygen vacancy as observed in electron irradiated ZnO.

  3. Lanthanide ion containing polymers; investigation of the ion binding properties of tactic poly (methacrylic acid) and degradation of polymers by γ-irradiation using Tb3+ ion as a fluorescent probe

    International Nuclear Information System (INIS)

    Okamoto, Yoshiyuki; Lujan, H.; Cho, Myung D.

    1994-01-01

    Fluorescence properties of lanthanide ions, such as Tb 3+ and Eu 3+ , are extremely sensitive to their environment. Thus, the authors have studied ionomer structure and the ion binding properties of synthetic polyelectrolytes using a Tb 3+ fluorescence probe. They observed that the fluorescence intensity of the isotactic poly (methacrylic acid)-Tb 3+ complex was much larger than that of the syndiotactic poly (methacrylic acid)-Tb 3+ complex. The results indicated that isotactic PMA is bound more strongly with Tb 3+ ion than syndiotactic PMA. They have also investigated the degradation of various polymers in aqueous solution and in the solid state using Tb 3+ fluorescence probe. When poly(ethylene oxide) blended with TbCl 3 films were irradiated with γ-irradiation in air, the fluorescence intensity of Tb 3+ was found to be greatly increased. This result suggests that radiolysis caused chain degradation of PEO and produced carbonyl groups (aldehyde moiety) at the end of the cleaved polymer chain. The chromophore moiety produced transfers energy to the Tb 3+ ion sited within the non-radiative energy transfer distance. It is suggested that blended films of PEO with Tb 3+ may used as convenient and fast detectors of γ-irradiation doses

  4. Comb-shaped single ion conductors based on polyacrylate ethers and lithium alkyl sulfonate

    International Nuclear Information System (INIS)

    Sun Xiaoguang; Hou Jun; Kerr, John B.

    2005-01-01

    Comb-shaped single ion conductors have been synthesized by (1) sulfonation of small molecule chloroethyleneglycols, which, after ion exchange to the Li + salt were then converted to the acrylate by reaction with acryloyl chloride and copolymerized with polyethylene glycol monomethyl ether acrylate (Mn = 454, n = 8) (PAE 8 -co-E 3 SO 3 Li); (2) sulfonation of chloride end groups grafted on to prepolymers of polyacrylate ethers (PAE 8 -g-E n SO 3 Li, n = 2, 3). The highest conductivity at 25 deg. C of 2.0 x 10 -7 S cm -1 was obtained for the PAE 8 -co-E 3 SO 3 Li with a salt concentration of EO/Li = 40. The conductivity of PAE 8 -g-E 3 SO 3 Li is lower than that of PAE 8 -co-E 3 SO 3 Li at similar salt concentrations, which is related to the incomplete sulfonation of the grafted polymer that leads to a lower concentration of Li + . The addition of 50 wt.% of plasticizer, PC/EMC (1/1, v/v), to PAE 8 -g-E 2 SO 3 Li increases the ambient conductivity by three orders of magnitude, which is due to the increased ion mobility in a micro-liquid environment and an increase concentration of free ions as a result of the higher dielectric constant of the solvent. A symmetrical Li/Li cell with an electrolyte membrane consisting of 75 wt.% PC/EMC (1/1, v/v) was cycled at a current density of 100 μA cm -2 at 85 deg. C. The cycling profile showed no concentration polarization after a break-in period during the first few cycles, which was apparently due to reaction of the solvent at the lithium metal surface that reacted with lithium metal to form a stable SEI layer

  5. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Soumadwip; Dixit, Himanshu; Chakrabarti, Rajarshi, E-mail: rajarshi@chem.iitb.ac.in

    2015-09-28

    Highlights: • The dynamics of a single-stranded DNA in presence of different concentrations of Mg{sup 2+} is investigated. • The initial DNA chain collapse is characterized by the formation of non-sequentially stacked base pairs. • The DNA chain re-swells at high concentrations of Mg{sup 2+} as a consequence of overcharging. - Abstract: The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counterions. It is well known that the structural collapse of DNA is favoured in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl{sub 2}) single stranded DNA with base sequence 5′-CGCGAATTCGCG-3′ (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

  6. Ion-Regulated Allosteric Binding of Fullerenes (C-60 and C-70) by Tetrathiafulvalene-Calix[4]pyrroles

    DEFF Research Database (Denmark)

    Davis, C. M.; Lim, J. M.; Larsen, K. R.

    2014-01-01

    The effect of ionic species on the binding of fullerenes (C-60 and C-70) by tetrathiafulvalene-calix[4]pyrrole (TTF-C4P) receptors and the nature of the resulting supramolecular complexes (TTF-C4P + fullerene + halide anion + tetraalkylammonium cation) was studied in the solid state through single...... of the C4P in a ball-and-socket binding mode. The interactions between the TTF-C4P receptors and the fullerene guests are highly influenced by both the nature of halide anions and their counter tetraalkylammonium cations. Three halides (F-, Cl-, and Br-) were studied. All three potentiate the binding...... of the two test fullerenes by inducing a conformational change from the 1,3-alternate to the cone conformer of the TTF-C4Ps, thus acting as positive heterotropic allosteric effectors. For a particular halide anion, the choice of tetraalkylammonium salts serves to modulate the strength of the TTF-C4P...

  7. Density functional theory investigations on the binding modes of amidoximes with uranyl ions.

    Science.gov (United States)

    Yang, Chuting; Pei, Shuqi; Chen, Baihua; Ye, Lina; Yu, Haizhu; Hu, Sheng

    2016-02-21

    Density functional theory (DFT) calculations have been carried out to examine the relative facilities of different coordination modes of aromatic amidoximes (AOs) with UO2(NO3)2. Various η(1)-, η(2)- and chelated κ(2)-coordination modes of the possible neutral AO, tautomerized neutral (TAO, with the hydroxylic hydrogen transferring to the oximic nitrogen atom) and anionic amidoxime (AAO, formed by the deprotonation of AO) were examined. The results indicate that η(1)-O of the TAO and η(1)-O/η(2)-NO of AAO are the most plausible coordination modes. Three types of uranyl complexes, i.e. UO2(NO3)2(TAO)(AAO), UO2(NO3)2(AAO)2 and UO2(EtOH)2(AAO)2 are the predominant binding structures. The good consistency between the calculation results and the experimental observations verifies the proposed conclusions.

  8. Application of equilibrium binding model for analysis of conformational transitions in poly(rA)poly(rU) complexes with metal ions

    OpenAIRE

    Sorokin V. A.; Gladchenko G. O.; Usenko E. L.; Egupov S. A.; Blagoi Yu. P.

    2010-01-01

    Aim. The study is aimed at generalization of the previous experimental results on the metal ion (Mg2+, Ni2+, Cd2+) effects on conformation transitions in poly(rA)·poly(rU). The objective was to find out how the type of a metal ion-polynucleotide complex influences the phase transitions and to estimate the constants (K) of ions binding to polymers of different structures. Methods. The K values were obtained upon theoretical and experimental transition temperature fitting by the least-square me...

  9. Single protein omission reconstitution studies of tetracycline binding to the 30S subunit of Escherichia coli ribosomes

    International Nuclear Information System (INIS)

    Buck, M.; Cooperman, B.S.

    1990-01-01

    In previous work the authors showed that on photolysis of Escherichia coli ribosomes in the presence of [ 3 H]tetracycline (TC) the major protein labeled is S7, and they presented strong evidence that such labeling takes place from a high-affinity site related to the inhibitory action of TC. In this work they use single protein omission reconstitution (SPORE) experiments to identify those proteins that are important for high-affinity TC binding to the 30S subunit, as measured by both cosedimentation and filter binding assays. With respect to both sedimentation coefficients and relative Phe-tRNA Phe binding, the properties of the SPORE particles they obtain parallel very closely those measured earlier, with the exception of the SPORE particle lacking S13. A total of five proteins, S3, S7, S8, S14, and S19, are shown to be important for TC binding, with the largest effects seen on omission of proteins S7 and S14. Determination of the protein compositions of the corresponding SPORE particles demonstrates that the observed effects are, for the most part, directly attributable to the omission of the given protein rather than reflecting an indirect effect of omitting one protein on the uptake of another. A large body of evidence supports the notion that four of these proteins, S3, S7, S14, and S19, are included, along with 16S rRNA bases 920-1,396, in one of the major domains of the 30S subunit. The results support the conclusion that the structure of this domain is important for the binding of TC and that, within this domain, TC binds directly to S7

  10. Mechanism of DNA–binding loss upon single-point mutation in p53

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Despite our current understanding of protein−DNA recognition, the mechanism(s) underlying the loss in protein−DNA binding affinity/ ... Keywords. p53 mutants; protein-DNA interactions; molecular dynamics simulations; free energy decomposition. Abbreviations ... of the salt–bridge with Asp 281, resulting in the loss of DNA.

  11. Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations.

    Science.gov (United States)

    Winter, Bernd; Weber, Ramona; Hertel, Ingolf V; Faubel, Manfred; Jungwirth, Pavel; Brown, Eric C; Bradforth, Stephen E

    2005-05-18

    Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.

  12. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity

    Energy Technology Data Exchange (ETDEWEB)

    Petzold, Christine; Marceau, Aimee H.; Miller, Katherine H.; Marqusee, Susan; Keck, James L. (UW-MED); (UCB)

    2015-04-22

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome.

  13. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions.

    Science.gov (United States)

    Bryan, Louise C; Weilandt, Daniel R; Bachmann, Andreas L; Kilic, Sinan; Lechner, Carolin C; Odermatt, Pascal D; Fantner, Georg E; Georgeon, Sandrine; Hantschel, Oliver; Hatzimanikatis, Vassily; Fierz, Beat

    2017-10-13

    Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. A camelid single-domain antibody neutralizes botulinum neurotoxin A by blocking host receptor binding

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Guorui; Lam, Kwok-ho; Weisemann, Jasmin; Peng, Lisheng; Krez, Nadja; Perry, Kay; Shoemaker, Charles B.; Dong, Min; Rummel, Andreas; Jin, Rongsheng (BCH); (Cornell); (Tufts CTSI); (UCI); (MHH)

    2017-08-07

    Antibody treatment is currently the only available countermeasure for botulism, a fatal illness caused by flaccid paralysis of muscles due to botulinum neurotoxin (BoNT) intoxication. Among the seven major serotypes of BoNT/A-G, BoNT/A poses the most serious threat to humans because of its high potency and long duration of action. Prior to entering neurons and blocking neurotransmitter release, BoNT/A recognizes motoneurons via a dual-receptor binding process in which it engages both the neuron surface polysialoganglioside (PSG) and synaptic vesicle glycoprotein 2 (SV2). Previously, we identified a potent neutralizing antitoxin against BoNT/A1 termed ciA-C2, derived from a camelid heavy-chain-only antibody (VHH). In this study, we demonstrate that ciA-C2 prevents BoNT/A1 intoxication by inhibiting its binding to neuronal receptor SV2. Furthermore, we determined the crystal structure of ciA-C2 in complex with the receptor-binding domain of BoNT/A1 (HCA1) at 1.68 Å resolution. The structure revealed that ciA-C2 partially occupies the SV2-binding site on HCA1, causing direct interference of HCA1 interaction with both the N-glycan and peptide-moiety of SV2. Interestingly, this neutralization mechanism is similar to that of a monoclonal antibody in clinical trials, despite that ciA-C2 is more than 10-times smaller. Taken together, these results enlighten our understanding of BoNT/A1 interactions with its neuronal receptor, and further demonstrate that inhibiting toxin binding to the host receptor is an efficient countermeasure strategy.

  15. Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

    International Nuclear Information System (INIS)

    Ishii, Takaaki; Murayama, Yoshihiro; Katano, Atsuto; Maki, Kosuke; Kuwajima, Kunihiro; Sano, Masaki

    2008-01-01

    Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics

  16. Verifying Heisenberg's error-disturbance relation using a single trapped ion.

    Science.gov (United States)

    Zhou, Fei; Yan, Leilei; Gong, Shijie; Ma, Zhihao; He, Jiuzhou; Xiong, Taiping; Chen, Liang; Yang, Wanli; Feng, Mang; Vedral, Vlatko

    2016-10-01

    Heisenberg's uncertainty relations have played an essential role in quantum physics since its very beginning. The uncertainty relations in the modern quantum formalism have become a fundamental limitation on the joint measurements of general quantum mechanical observables, going much beyond the original discussion of the trade-off between knowing a particle's position and momentum. Recently, the uncertainty relations have generated a considerable amount of lively debate as a result of the new inequalities proposed as extensions of the original uncertainty relations. We report an experimental test of one of the new Heisenberg's uncertainty relations using a single 40 Ca + ion trapped in a harmonic potential. By performing unitary operations under carrier transitions, we verify the uncertainty relation proposed by Busch, Lahti, and Werner (BLW) based on a general error-trade-off relation for joint measurements on two compatible observables. The positive operator-valued measure, required by the compatible observables, is constructed by single-qubit operations, and the lower bound of the uncertainty, as observed, is satisfied in a state-independent manner. Our results provide the first evidence confirming the BLW-formulated uncertainty at a single-spin level and will stimulate broad interests in various fields associated with quantum mechanics.

  17. Verifying Heisenberg’s error-disturbance relation using a single trapped ion

    Science.gov (United States)

    Zhou, Fei; Yan, Leilei; Gong, Shijie; Ma, Zhihao; He, Jiuzhou; Xiong, Taiping; Chen, Liang; Yang, Wanli; Feng, Mang; Vedral, Vlatko

    2016-01-01

    Heisenberg’s uncertainty relations have played an essential role in quantum physics since its very beginning. The uncertainty relations in the modern quantum formalism have become a fundamental limitation on the joint measurements of general quantum mechanical observables, going much beyond the original discussion of the trade-off between knowing a particle’s position and momentum. Recently, the uncertainty relations have generated a considerable amount of lively debate as a result of the new inequalities proposed as extensions of the original uncertainty relations. We report an experimental test of one of the new Heisenberg’s uncertainty relations using a single 40Ca+ ion trapped in a harmonic potential. By performing unitary operations under carrier transitions, we verify the uncertainty relation proposed by Busch, Lahti, and Werner (BLW) based on a general error–trade-off relation for joint measurements on two compatible observables. The positive operator-valued measure, required by the compatible observables, is constructed by single-qubit operations, and the lower bound of the uncertainty, as observed, is satisfied in a state-independent manner. Our results provide the first evidence confirming the BLW-formulated uncertainty at a single-spin level and will stimulate broad interests in various fields associated with quantum mechanics. PMID:28861461

  18. How to resolve microsecond current fluctuations in single ion channels: The power of beta distributions

    Science.gov (United States)

    Schroeder, Indra

    2015-01-01

    Abstract A main ingredient for the understanding of structure/function correlates of ion channels is the quantitative description of single-channel gating and conductance. However, a wealth of information provided from fast current fluctuations beyond the temporal resolution of the recording system is often ignored, even though it is close to the time window accessible to molecular dynamics simulations. This kind of current fluctuations provide a special technical challenge, because individual opening/closing or blocking/unblocking events cannot be resolved, and the resulting averaging over undetected events decreases the single-channel current. Here, I briefly summarize the history of fast-current fluctuation analysis and focus on the so-called “beta distributions.” This tool exploits characteristics of current fluctuation-induced excess noise on the current amplitude histograms to reconstruct the true single-channel current and kinetic parameters. A guideline for the analysis and recent applications demonstrate that a construction of theoretical beta distributions by Markov Model simulations offers maximum flexibility as compared to analytical solutions. PMID:26368656

  19. Electron Ion Collider: The Next QCD Frontier - Understanding the glue that binds us all

    CERN Document Server

    Accardi, A.; Anselmino, M.; Armesto, N.; Aschenauer, E.C.; Bacchetta, A.; Boer, D.; Brooks, W.K.; Burton, T.; Chang, N.B.; Deng, W.T.; Deshpande, A.; Diehl, M.; Dumitru, A.; Dupré, R.; Ent, R.; Fazio, S.; Gao, H.; Guzey, V.; Hakobyan, H.; Hao, Y.; Hasch, D.; Holt, R.; Horn, T.; Huang, M.; Hutton, A.; Hyde, C.; Jalilian-Marian, J.; Klein, S.; Kopeliovich, B.; Kovchegov, Y.; Kumar, K.; Kumerički, K.; Lamont, M.A.C.; Lappi, T.; Lee, J.H.; Lee, Y.; Levin, E.M.; Lin, F.L.; Litvinenko, V.; Ludlam, T.W.; Marquet, C.; Meziani, Z.E.; McKeown, R.; Metz, A.; Milner, R.; Morozov, V.S.; Mueller, A.H.; Müller, B.; Müller, Dieter; Nadel-Turonski, P.; Paukkunen, H.; Prokudin, A.; Ptitsyn, V.; Qian, X.; Qiu, J.W.; Ramsey-Musolf, M.; Roser, T.; Sabatié, F.; Sassot, R.; Schnell, G.; Schweitzer, P.; Sichtermann, E.; Stratmann, M.; Strikman, M.; Sullivan, M.; Taneja, S.; Toll, T.; Trbojevic, D.; Ullrich, T.; Venugopalan, R.; Vigdor, S.; Vogelsang, W.; Weiss, C.; Xiao, B.W.; Yuan, F.; Zhang, Y.H.; Zheng, L.

    2016-01-01

    This White Paper presents the science case of an Electron-Ion Collider (EIC), focused on the structure and interactions of gluon-dominated matter, with the intent to articulate it to the broader nuclear science community. It was commissioned by the managements of Brookhaven National Laboratory (BNL) and Thomas Jefferson National Accelerator Facility (JLab) with the objective of presenting a summary of scientific opportunities and goals of the EIC as a follow-up to the 2007 NSAC Long Range plan. This document is a culmination of a community-wide effort in nuclear science following a series of workshops on EIC physics and, in particular, the focused ten-week program on "Gluons and quark sea at high energies" at the Institute for Nuclear Theory in Fall 2010. It contains a brief description of a few golden physics measurements along with accelerator and detector concepts required to achieve them, and it benefited from inputs from the users' communities of BNL and JLab. This White Paper offers the promise to prope...

  20. Antiviral activity and metal ion-binding properties of some 2-hydroxy-3-methoxyphenyl acylhydrazones.

    Science.gov (United States)

    Carcelli, M; Fisicaro, E; Compari, C; Contardi, L; Rogolino, D; Solinas, C; Stevaert, A; Naesens, L

    2018-02-01

    Here we report on the results obtained from an antiviral screening, including herpes simplex virus, vaccinia virus, vesicular stomatitis virus, Coxsackie B4 virus or respiratory syncytial virus, parainfluenza-3 virus, reovirus-1 and Punta Toro virus, of three 2-hydroxy-3-methoxyphenyl acylhydrazone compounds in three cell lines (i.e. human embryonic lung fibroblast cells, human cervix carcinoma cells, and African Green monkey kidney cells). Interesting antiviral EC 50 values are obtained against herpes simplex virus-1 and vaccinia virus. The biological activity of acylhydrazones is often attributed to their metal coordinating abilities, so potentiometric and microcalorimetric studies are here discussed to unravel the behavior of the three 2-hydroxy-3-methoxyphenyl compounds in solution. It is worth of note that the acylhydrazone with the higher affinity for Cu(II) ions shows the best antiviral activity against herpes simplex and vaccinia virus (EC 50  ~ 1.5 µM, minimal cytotoxic concentration = 60 µM, selectivity index = 40).

  1. Dependence of the structure of ion-modified NiTi single crystal layers on the orientation of irradiated surface

    Science.gov (United States)

    Poletika, T. M.; Meisner, L. L.; Girsova, S. L.; Tverdokhlebova, A. V.; Meisner, S. N.

    2017-07-01

    The composition and structure of Si layers implanted into titanium nickelide single crystals with different orientations relative to the ion beam propagation direction have been studied using Auger electron spectroscopy and transmission electron microscopy. The role of the "soft" [111]B2 and "hard" [001]B2 NiTi orientations in the formation of the structure of ion-modified surface layer, as well as the defect structure of the surface layers of the single crystals, has been revealed. Orientation effects of selective sputtering and channeling of ions, which control the composition and thickness of the oxide and amorphous layers being formed, ion and impurity penetration depth, as well as the concentration profile of the Ni distribution over the surface, have been detected.

  2. Coherent manipulation of three-qubit states in a molecular single-ion magnet

    Science.gov (United States)

    Jenkins, M. D.; Duan, Y.; Diosdado, B.; García-Ripoll, J. J.; Gaita-Ariño, A.; Giménez-Saiz, C.; Alonso, P. J.; Coronado, E.; Luis, F.

    2017-02-01

    We study the quantum spin dynamics of nearly isotropic Gd3 + ions entrapped in polyoxometalate molecules and diluted in crystals of a diamagnetic Y3 + derivative. The full energy-level spectrum and the orientations of the magnetic anisotropy axes have been determined by means of continuous-wave electron paramagnetic resonance experiments, using X-band (9-10 GHz) cavities and on-chip superconducting waveguides and 1.5-GHz resonators. The results show that seven allowed transitions between the 2 S +1 spin states can be separately addressed. Spin coherence T2 and spin-lattice relaxation T1 rates have been measured for each of these transitions in properly oriented single crystals. The results suggest that quantum spin coherence is limited by residual dipolar interactions with neighbor electronic spins. Coherent Rabi oscillations have been observed for all transitions. The Rabi frequencies increase with microwave power and agree quantitatively with predictions based on the spin Hamiltonian of the molecular spin. We argue that the spin states of each Gd3 + ion can be mapped onto the states of three addressable qubits (or, alternatively, of a d =8 -level "qudit"), for which the seven allowed transitions form a universal set of operations. Within this scheme, one of the coherent oscillations observed experimentally provides an implementation of a controlled-controlled-NOT (or Toffoli) three-qubit gate.

  3. The effect of Cu{sup II} ions in L-asparagine single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Santana, Ricardo C., E-mail: santana@ufg.br; Gontijo, Henrique O.; Menezes, Arthur F.; Martins, José A.; Carvalho, Jesiel F., E-mail: carvalho@ufg.br

    2016-11-15

    We report the synthesis, crystal growth, and spectroscopic characterization of L-asparagine monohydrate (LAM) single crystals doped with CuII. The crystals were successfully grown by slow cooling from a supersaturated aqueous solution up to size of 16×12×2 mm{sup 3};the effect of copper impurities in the crystals morphology was discussed. Electron Paramagnetic Resonance (EPR) was used to calculate the g and hyperfine coupling (A) tensors of the CuII ions (g{sub 1}=2.044, g{sub 2}=2.105, g{sub 3}=2.383and A{sub 1}≈0, A{sub 2}=35, A{sub 3}=108 Gauss). The EPR spectra for certain orientations of the magnetic field suggest that CuII ions are coordinated to two {sup 14}N atoms. Correlating the EPR and optical absorption results, the crystal field and the Cu{sup II} orbital bond parameters were calculated. The results indicate that the paramagnetic center occupies interstitial rhombic distorted site and the ground orbital state for the unpaired electron is the d(x{sup 2}-y{sup 2}).

  4. Non-destructive single-pass low-noise detection of ions in a beamline

    Science.gov (United States)

    Schmidt, Stefan; Murböck, Tobias; Andelkovic, Zoran; Birkl, Gerhard; Nörtershäuser, Wilfried; Stahl, Stefan; Vogel, Manuel

    2015-11-01

    We have conceived, built, and operated a device for the non-destructive single-pass detection of charged particles in a beamline. The detector is based on the non-resonant pick-up and subsequent low-noise amplification of the image charges induced in a cylindrical electrode surrounding the particles' beam path. The first stage of the amplification electronics is designed to be operated from room temperature down to liquid helium temperature. The device represents a non-destructive charge counter as well as a sensitive timing circuit. We present the concept and design details of the device. We have characterized its performance and show measurements with low-energy highly charged ions (such as Ar13+) passing through one of the electrodes of a cylindrical Penning trap. This work demonstrates a novel approach of non-destructive, low noise detection of charged particles which is, depending on the bunch structure, suitable, e.g., for ion traps, low-energy beamlines or accelerator transfer sections.

  5. Luminescent single-ion magnets from Lanthanoid(III) complexes with monodentate ketone ligands

    Energy Technology Data Exchange (ETDEWEB)

    Kanetomo, Takuya; Ishida, Takayuki, E-mail: takayuki.ishida@uec.ac.jp [Department of Engineering Science, The University of Electro-Communications, Tokyo (Japan)

    2016-02-01

    We synthesized [Ln{sup III}(hfac){sub 3}(H{sub 2}O)(L)] (abbreviated as Ln-L; Ln = Gd, Tb, Eu; L = DTBK (di-t-butyl ketone), BP (benzophenone)), in which the carbonyl oxygen atom was coordinated to the Ln ion center, despite of such bulky substituents. Their crystal structures were determined by means of X-ray diffraction study. Gd-DTBK is completely isomorphous to the di-t-butyl nitroxide derivative and accordingly can be regarded as a model with the ligand spin masked. The ac magnetic susceptibility measurements on Tb-DTBK and -BP showed frequency dependence, characteristic of single-ion magnets. They also displayed photoluminescence in the solid state at room temperature. The quantum yields of the luminescence of Tb-DTBK and -BP (λ{sub ex} = 360 nm) were improved to 57 and 35%, respectively, from that of the starting material [TbI{sup III}(hfac){sub 3}(H{sub 2}O){sub 2}] (28% at λ{sub ex} = 370 nm). Similarly, the quantum yields for Eu-DTBK and -BP were 8 and 15%, respectively, with λ{sub ex} = 400 nm, while that of the starting material [EuI{sup III}(hfac){sub 3}(H{sub 2}O){sub 2}] was 4% at λ{sub ex}=400 nm.

  6. Luminescent single-ion magnets from Lanthanoid(III) complexes with monodentate ketone ligands

    Science.gov (United States)

    Kanetomo, Takuya; Ishida, Takayuki

    2016-02-01

    We synthesized [LnIII(hfac)3(H2O)(L)] (abbreviated as Ln-L; Ln = Gd, Tb, Eu; L = DTBK (di-t-butyl ketone), BP (benzophenone)), in which the carbonyl oxygen atom was coordinated to the Ln ion center, despite of such bulky substituents. Their crystal structures were determined by means of X-ray diffraction study. Gd-DTBK is completely isomorphous to the di-t-butyl nitroxide derivative and accordingly can be regarded as a model with the ligand spin masked. The ac magnetic susceptibility measurements on Tb-DTBK and -BP showed frequency dependence, characteristic of single-ion magnets. They also displayed photoluminescence in the solid state at room temperature. The quantum yields of the luminescence of Tb-DTBK and -BP (λex = 360 nm) were improved to 57 and 35%, respectively, from that of the starting material [TbIIII(hfac)3(H2O)2] (28% at λex = 370 nm). Similarly, the quantum yields for Eu-DTBK and -BP were 8 and 15%, respectively, with λex = 400 nm, while that of the starting material [EuIIII(hfac)3(H2O)2] was 4% at λex=400 nm.

  7. Single Ion transient-IBIC analyses of semiconductor devices using a cryogenic temperature stage

    International Nuclear Information System (INIS)

    Laird, J.S.; Bardos, R.; Legge, G.J.F.; Jagadish, C.

    1998-01-01

    A new Transient - IBIC data acquisition and analysis system at MARC is described. A discussion on the need for single ion control and temperature control is also given. The recorded signal is used as the trigger for beam pulsing. The new cryostatic temperature control stage is introduced. Data is presented on line profiles across the edge of a Au-Si junction collected over the temperature range of 25-300K using a developed C-V and I-V variable temperature stage incorporating a liquid helium cryostat. It demonstrates the potential improvements in spatial resolution in materials of long lifetime by mapping on timing windows around the prompt charge component in the charge transient

  8. A diode laser stabilization scheme for 40Ca+ single-ion spectroscopy

    Science.gov (United States)

    Rohde, F.; Almendros, M.; Schuck, C.; Huwer, J.; Hennrich, M.; Eschner, J.

    2010-06-01

    We present a scheme for stabilizing multiple lasers at wavelengths between 795 and 866 nm to the same atomic reference line. A reference laser at 852 nm is stabilized to the Cs D2 line using a Doppler-free frequency modulation technique. Through transfer cavities, four lasers are stabilized to the relevant atomic transitions in 40Ca+. The rms linewidth of a transfer-locked laser is measured to be 123 kHz over 200 ms with respect to an independent atomic reference, the Rb D1 line. This stability is confirmed by the comparison of an excitation spectrum of a single 40Ca+ ion to an eight-level Bloch equation model. The long-term stability with respect to the same reference is measured to be 130 kHz over a period of 2 h. The high degree of stability is demonstrated by the measured Allan deviation around 10-11 between 1 and 100 s.

  9. A diode laser stabilization scheme for 40Ca+ single-ion spectroscopy

    International Nuclear Information System (INIS)

    Rohde, F; Almendros, M; Schuck, C; Huwer, J; Hennrich, M; Eschner, J

    2010-01-01

    We present a scheme for stabilizing multiple lasers at wavelengths between 795 and 866 nm to the same atomic reference line. A reference laser at 852 nm is stabilized to the Cs D 2 line using a Doppler-free frequency modulation technique. Through transfer cavities, four lasers are stabilized to the relevant atomic transitions in 40 Ca + . The rms linewidth of a transfer-locked laser is measured to be 123 kHz over 200 ms with respect to an independent atomic reference, the Rb D 1 line. This stability is confirmed by the comparison of an excitation spectrum of a single 40 Ca + ion to an eight-level Bloch equation model. The long-term stability with respect to the same reference is measured to be 130 kHz over a period of 2 h. The high degree of stability is demonstrated by the measured Allan deviation around 10 -11 between 1 and 100 s.

  10. Single Ion transient-IBIC analyses of semiconductor devices using a cryogenic temperature stage

    Energy Technology Data Exchange (ETDEWEB)

    Laird, J.S.; Bardos, R.; Legge, G.J.F. [Melbourne Univ., Parkville, VIC (Australia). School of Physics; Jagadish, C. [Australian National Univ., Canberra, ACT (Australia). School of Physics, Electronic Materials Engineering

    1998-06-01

    A new Transient - IBIC data acquisition and analysis system at MARC is described. A discussion on the need for single ion control and temperature control is also given. The recorded signal is used as the trigger for beam pulsing. The new cryostatic temperature control stage is introduced. Data is presented on line profiles across the edge of a Au-Si junction collected over the temperature range of 25-300K using a developed C-V and I-V variable temperature stage incorporating a liquid helium cryostat. It demonstrates the potential improvements in spatial resolution in materials of long lifetime by mapping on timing windows around the prompt charge component in the charge transient. 2 figs.

  11. Dynamics of a single ion in a perturbed Penning trap: Octupolar perturbation

    International Nuclear Information System (INIS)

    Lara, Martin; Salas, J. Pablo

    2004-01-01

    Imperfections in the design or implementation of Penning traps may give rise to electrostatic perturbations that introduce nonlinearities in the dynamics. In this paper we investigate, from the point of view of classical mechanics, the dynamics of a single ion trapped in a Penning trap perturbed by an octupolar perturbation. Because of the axial symmetry of the problem, the system has two degrees of freedom. Hence, this model is ideal to be managed by numerical techniques like continuation of families of periodic orbits and Poincare surfaces of section. We find that, through the variation of the two parameters controlling the dynamics, several periodic orbits emanate from two fundamental periodic orbits. This process produces important changes (bifurcations) in the phase space structure leading to chaotic behavior

  12. Focused ion beam milling of nanocavities in single colloidal particles and self-assembled opals

    International Nuclear Information System (INIS)

    Woldering, Leon A; Otter, A M; Husken, Bart H; Vos, Willem L

    2006-01-01

    We present a new method of realizing single nanocavities in individual colloidal particles on the surface of silicon dioxide artificial opals using a focused ion beam milling technique. We show that both the radius and the position of the nanocavity can be controlled with nanometre precision, to radii as small as 40 nm. The relation between the defect size and the milling time has been established. We confirmed that milling not only occurs on the surface of the spheres, but into and through them as well. We also show that an array of nanocavities can be fashioned. Structurally modified colloids have interesting potential applications in nanolithography, as well as in chemical sensing and solar cells, and as photonic crystal cavities

  13. Angle-resolved imaging of single-crystal materials with MeV helium ions

    International Nuclear Information System (INIS)

    Strathman, M.D.; Baumann, S.

    1992-01-01

    The simplest form of angle-resolved mapping for single-crystal materials is the creation of a channeling angular scan. Several laboratories have expanded this simple procedure to include mapping as a function of two independent tilts. These angle-resolved images are particularly suited to the assessment of crystal parameters including disorder, lattice location of impurities, and lattice stress. This paper will describe the use of the Charles Evans and Associates RBS-400 scattering chamber for acquisition, display, and analysis of angle-resolved images obtained from backscattered helium ions. Typical data acquisition times are 20 min for a ±2deg X-Y tilt scan with 2500 pixels (8/100deg resolution), and 10 nC per pixel. In addition, we will present a method for automatically aligning crystals for channeling measurements based on this imaging technology. (orig.)

  14. On the calculation of single ion activity coefficients in homogeneous ionic systems by application of the grand canonical ensemble

    DEFF Research Database (Denmark)

    Sloth, Peter

    1993-01-01

    The grand canonical ensemble has been used to study the evaluation of single ion activity coefficients in homogeneous ionic fluids. In this work, the Coulombic interactions are truncated according to the minimum image approximation, and the ions are assumed to be placed in a structureless...... of the individual ionic activity coefficients with respect to the total ionic concentration. This formula has previously been proposed on the basis of somewhat different considerations....

  15. Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

    Directory of Open Access Journals (Sweden)

    Joel Raborn

    Full Text Available The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala(252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala(252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion.

  16. Improved estimation of receptor density and binding rate constants using a single tracer injection and displacement

    International Nuclear Information System (INIS)

    Syrota, A.; Delforge, J.; Mazoyer, B.M.

    1988-01-01

    The possibility of improving receptor model parameter estimation using a displacement experiment in which an excess of an unlabeled ligand (J) is injected after a delay (t D ) following injection of trace amounts of the β + - labeled ligand (J*) is investigated. The effects of varying t D and J/J* on parameter uncertainties are studied in the case of 11 C-MQNB binding to myocardial acetycholine receptor using parameters identified in a dog experiment

  17. Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis.

    Science.gov (United States)

    Olszewski, Marcin; Nowak, Marta; Cyranka-Czaja, Anna; Kur, Józef

    2014-01-01

    Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNA replication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-like gene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoalteromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism. PhaSSB possesses a high sequence similarity to Escherichia coli SSB (48% identity and 57% similarity) and has the longest amino acid sequence (244 amino acid residues) of all the known bacterial SSBs with one OB-fold per monomer. An analysis of purified PhaSSB by means of chemical cross-linking experiments, sedimentation analysis and size exclusion chromatography revealed a stable tetramer in solution. Using EMSA, we characterized the stoichiometry of PhaSSB complexed with a series of ssDNA homopolymers, and the size of the binding site was determined as being approximately 35 nucleotides long. In fluorescence titrations, the occluded site size of PhaSSB on poly(dT) is 34 nucleotides per tetramer under low-salt conditions (2mM NaCl), but increases to 54-64 nucleotides at higher-salt conditions (100-300mM NaCl). This suggests that PhaSSB undergoes a transition between ssDNA binding modes, which is observed for EcoSSB. The binding properties of PhaSSB investigated using SPR technology revealed that the affinity of PhaSSB to ssDNA is typical of SSB proteins. The only difference in the binding mode of PhaSSB to ssDNA is a faster association phase, when compared to EcoSSB, though compensated by faster dissociation rate. When analyzed by differential scanning calorimetry (DSC), the melting temperature (Tm) was determined as 63 °C, which is only a few degrees lower than for EcoSSB. Copyright © 2013 Elsevier GmbH. All rights reserved.

  18. Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii.

    Science.gov (United States)

    Stroud, Amy; Liddell, Susan; Allers, Thorsten

    2012-01-01

    Single-stranded DNA (ssDNA)-binding proteins play an essential role in DNA replication and repair. They use oligonucleotide/oligosaccharide-binding (OB)-folds, a five-stranded β-sheet coiled into a closed barrel, to bind to ssDNA thereby protecting and stabilizing the DNA. In eukaryotes the ssDNA-binding protein (SSB) is known as replication protein A (RPA) and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3) exist in operons with a novel gene specific to Euryarchaeota; this gene encodes a protein that we have termed RPA-associated protein (rpap). The rpap genes encode proteins belonging to COG3390 group and feature OB-folds, suggesting that they might cooperate with RPA in binding to ssDNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only Δrpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins (RPAPs). We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA-binding complex that is unique to Euryarchaeota.

  19. Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors.

    Science.gov (United States)

    Karas, M; Glückmann, M; Schäfer, J

    2000-01-01

    A new model for the ionization processes in UV matrix-assisted laser desorption/ionization (MALDI) which accounts for the major phenomena observed is presented and discussed. The model retains elements of earlier approaches, such as photoionization and photochemical reactions, but it redefines these in the light of new working questions, most importantly why only singly charged ions are detected. Based on experimental evidence, the formation of singly and multiply charged clusters by a deficiency/excess of ions and also by photoionization and subsequent photochemical processes is pointed out to be the major ionization processes, which typically occur in parallel. The generation of electrons and their partial loss into the surrounding vacuum and solid, on the one hand, results in a positively charged ion-neutral plume facilitating a high overall ionization yield. On the other hand, these electrons, and also the large excess of protonated matrix ions in the negative ion mode, induce effective ion reneutralization in the plume. These neutralization processes are most effective for the highly charged cluster ions initially formed. Their fragmentation behaviour is evidenced in fast metastable fragmentation characteristics and agrees well with an electron capture dissociation mechanism and the enthalpy transfer upon neutralization forms the rationale for the prominent fragmentation and intense chemical noise accompanying successful MALDI. Within the course of the paper, cross-correlations with other desorption/ionization techniques and with earlier discussions on their mechanisms are drawn. Copyright 2000 John Wiley & Sons, Ltd.

  20. Spectroscopy of single Pr3+ ion in LaF3 crystal at 1.5 K.

    Science.gov (United States)

    Nakamura, Ippei; Yoshihiro, Tatsuya; Inagawa, Hironori; Fujiyoshi, Satoru; Matsushita, Michio

    2014-12-08

    Optical read-out and manipulation of the nuclear spin state of single rare-earth ions doped in a crystal enable the large-scale storage and the transport of quantum information. Here, we report the photo-luminescence excitation spectroscopy results of single Pr(3+) ions in a bulk crystal of LaF3 at 1.5 K. In a bulk sample, the signal from a single ion at the focus is often hidden under the background signal originating from numerous out-of-focus ions in the entire sample. To combine with a homemade cryogenic confocal microscope, we developed a reflecting objective that works in superfluid helium with a numerical aperture of 0.99, which increases the signal by increasing the solid angle of collection to 1.16π and reduces the background by decreasing the focal volume. The photo-luminescence excitation spectrum of single Pr(3+) was measured at a wing of the spectral line of the (3)H4 → (3)P0 transition at 627.33 THz (477.89 nm). The spectrum of individual Pr(3+) ions appears on top of the background of 60 cps as isolated peaks with intensities of 20-30 cps and full-width at half-maximum widths of approximately 3 MHz at an excitation intensity of 80 W cm(-2).

  1. Effect of giant plasmon excitations in single and double ionization of C60 in fast heavy-ion collisions

    Science.gov (United States)

    Kadhane, Umesh; Kelkar, A.; Misra, D.; Kumar, Ajay; Tribedi, Lokesh C.

    2007-04-01

    Single and multiple ionization of C60 in collisions with highly charged fast oxygen ions have been studied using the recoil-ion time-of-flight technique. The dependence of multiple-ionization cross sections on projectile charge state (qp) was found to be drastically different from those for an atomic target, such as Ne. A model based on the giant dipole plasmon resonance explains quite well the observed qp dependence for the single- and-double-ionization cross sections. But the same model deviates for triple and quadruple ionizations.

  2. Single-electron capture collisions of ground and metastable Ne2+ ions with molecular gases

    Science.gov (United States)

    Hasan, A.; Abu-Haija, O.; Harris, J.; Elkafrawy, T.; Kayani, A.; Kamber, E. Y.

    2013-09-01

    Using the translational energy-gain spectroscopy technique, we have measured the energy-gain spectra and absolute total cross sections for single-electron capture in collisions of Ne2+ with N2, CO2 and H2O at laboratory impact energies between 50 and 400 eV and 0° scattering angles. In all the collision systems studied here, reaction channels have been observed which indicate the presence of the long-lived metastable states of (2s2 2p4 1D and 1S) in the Ne2+ incident beam. These measurements also indicate that capture from the metastable states into excited states of the projectile product ions is the most important inelastic process. Contributions from capture accompanied by the excitation and ionization of the target product are also detected. In addition, the energy dependence of the total single-electron capture cross sections is studied and found to slowly increase with increasing impact energy. The present data are compared with the theoretical calculations of the classical over the barrier, extended classical over the barrier and Landau-Zener models.

  3. Detection of isolated protein-bound metal ions by single-particle cryo-STEM.

    Science.gov (United States)

    Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

    2017-10-17

    Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.

  4. Optical spectroscopy of Eu3+ ions doped in KLu(WO4)2 single crystals

    International Nuclear Information System (INIS)

    Koubaa, T.; Dammak, M.; Pujol, M.C.; Aguiló, M.; Díaz, F.

    2015-01-01

    Europium single doped potassium lutetium tungstate Eu 3+ :KLu(WO 4 ) 2 single crystals have been grown with the top seeded solution growth slow cooling method. Their absorption spectra are studied in detail for principal light polarizations, E||N p , N m and N g at room and low temperatures. The absorption oscillator strengths parameters are calculated by means of the theory of f–f transition intensities for systems with anomalously strong configuration interaction and by Judd–Ofelt theory. The Ω t (t=2, 4, 6) intensity parameters, and the {O dk , O ck , Δ d , Δ c1 and Δ c2 } (k=1, 2, 3) ASCI parameters are calculated. The radiative transition rates A R , radiative lifetimes τ R , and fluorescent branching ratios β R associated with 5 D 0 – 7 F J transitions of Eu 3+ were determined. The calculated decay times are discussed and compared with experimental values. - Highlights: • Absorption spectra of Eu:KLuW are investigated with respect to principal light polarizations. • Spectroscopic properties of Eu:KLuW are modeled within conventional Judd–Ofelt and (ASCI) theories. • 5 D 0 multiplet shows the contribution of a NR processes and an ET between the Eu 3+ ions. • It is suggested that the Eu 3+ :KLuW is a potential host material for optical applications.

  5. Sequential water molecule binding enthalpies for aqueous nanodrops containing a mono-, di- or trivalent ion and between 20 and 500 water molecules.

    Science.gov (United States)

    Heiles, Sven; Cooper, Richard J; DiTucci, Matthew J; Williams, Evan R

    2017-04-01

    Sequential water molecule binding enthalpies, Δ H n , n -1 , are important for a detailed understanding of competitive interactions between ions, water and solute molecules, and how these interactions affect physical properties of ion-containing nanodrops that are important in aerosol chemistry. Water molecule binding enthalpies have been measured for small clusters of many different ions, but these values for ion-containing nanodrops containing more than 20 water molecules are scarce. Here, Δ H n , n -1 values are deduced from high-precision ultraviolet photodissociation (UVPD) measurements as a function of ion identity, charge state and cluster size between 20-500 water molecules and for ions with +1, +2 and +3 charges. The Δ H n , n -1 values are obtained from the number of water molecules lost upon photoexcitation at a known wavelength, and modeling of the release of energy into the translational, rotational and vibrational motions of the products. The Δ H n , n -1 values range from 36.82 to 50.21 kJ mol -1 . For clusters containing more than ∼250 water molecules, the binding enthalpies are between the bulk heat of vaporization (44.8 kJ mol -1 ) and the sublimation enthalpy of bulk ice (51.0 kJ mol -1 ). These values depend on ion charge state for clusters with fewer than 150 water molecules, but there is a negligible dependence at larger size. There is a minimum in the Δ H n , n -1 values that depends on the cluster size and ion charge state, which can be attributed to the competing effects of ion solvation and surface energy. The experimental Δ H n , n -1 values can be fit to the Thomson liquid drop model (TLDM) using bulk ice parameters. By optimizing the surface tension and temperature change of the logarithmic partial pressure for the TLDM, the experimental sequential water molecule binding enthalpies can be fit with an accuracy of ±3.3 kJ mol -1 over the entire range of cluster sizes.

  6. A laser desorption-electron impact ionization ion trap mass spectrometer for real-time analysis of single atmospheric particles

    Science.gov (United States)

    Simpson, E. A.; Campuzano-Jost, P.; Hanna, S. J.; Robb, D. B.; Hepburn, J. H.; Blades, M. W.; Bertram, A. K.

    2009-04-01

    A novel aerosol ion trap mass spectrometer combining pulsed IR laser desorption with electron impact (EI) ionization for single particle studies is described. The strengths of this instrument include a two-step desorption and ionization process to minimize matrix effects; electron impact ionization, a universal and well-characterized ionization technique; vaporization and ionization inside the ion trap to improve sensitivity; and an ion trap mass spectrometer for MSn experiments. The instrument has been used for mass spectral identification of laboratory generated pure aerosols in the 600 nm-1.1 [mu]m geometric diameter range of a variety of aromatic and aliphatic compounds, as well as for tandem mass spectrometry studies (up to MS3) of single caffeine particles. We investigate the effect of various operational parameters on the mass spectrum and fragmentation patterns. The single particle detection limit of the instrument was found to be a 325 nm geometric diameter particle (8.7 × 107 molecules or 22 fg) for 2,4-dihydroxybenzoic acid. Lower single particle detection limits are predicted to be attainable by modifying the EI pulse. The use of laser desorption-electron impact (LD-EI) in an ion trap is a promising technique for determining the size and chemical composition of single aerosol particles in real time.

  7. Single-stranded DNA-binding protein recruits DNA polymerase V to primer termini on RecA-coated DNA.

    Science.gov (United States)

    Arad, Gali; Hendel, Ayal; Urbanke, Claus; Curth, Ute; Livneh, Zvi

    2008-03-28

    Translesion DNA synthesis (TLS) by DNA polymerase V (polV) in Escherichia coli involves accessory proteins, including RecA and single-stranded DNA-binding protein (SSB). To elucidate the role of SSB in TLS we used an in vitro exonuclease protection assay and found that SSB increases the accessibility of 3' primer termini located at abasic sites in RecA-coated gapped DNA. The mutant SSB-113 protein, which is defective in protein-protein interactions, but not in DNA binding, was as effective as wild-type SSB in increasing primer termini accessibility, but deficient in supporting polV-catalyzed TLS. Consistently, the heterologous SSB proteins gp32, encoded by phage T4, and ICP8, encoded by herpes simplex virus 1, could replace E. coli SSB in the TLS reaction, albeit with lower efficiency. Immunoprecipitation experiments indicated that polV directly interacts with SSB and that this interaction is disrupted by the SSB-113 mutation. Taken together our results suggest that SSB functions to recruit polV to primer termini on RecA-coated DNA, operating by two mechanisms: 1) increasing the accessibility of 3' primer termini caused by binding of SSB to DNA and 2) a direct SSB-polV interaction mediated by the C terminus of SSB.

  8. Correlation of precursor and product ions in single-stage high resolution mass spectrometry. A tool for detecting diagnostic ions and improving the precursor elemental composition elucidation

    Energy Technology Data Exchange (ETDEWEB)

    Borràs, S. [Departament de Química Analítica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain); Kaufmann, A., E-mail: anton.kaufmann@klzh.ch [Official Food Control Authority, Fehrenstrasse 15, 8032 Zürich (Switzerland); Companyó, R. [Departament de Química Analítica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)

    2013-04-15

    Highlights: ► We are describing a technique to spot ions which are derived from each other. ► Single stage high resolution data is used. ► This “in silicon” technique is compared to conventional precursor scan. ► Some applications for this technique are presented. -- Abstract: Monitoring of common diagnostic fragments is essential for recognizing molecules which are members of a particular compound class. Up to now, unit resolving tandem quadrupole mass spectrometers, operating in the precursor ion scan mode, have been typically used to perform such analysis. By means of high-resolution mass spectrometry (HRMS) a much more sensitive and selective detection can be achieved. However, using a single-stage HRMS instrument, there is no unequivocal link to the corresponding precursor ion, since such instrumentation does not permit a previous precursor selection. Thus, to address this limitation, an in silico approach to locate precursor ions, based on diagnostic fragments, was developed. Implemented as an Excel macro, the algorithm rapidly assembles and surveys exact mass data to provide a list of feasible precursor candidates according to the correlation of the chromatographic peak shape profile and other additional filtering criteria (e.g. neutral losses and isotopes). The macro was tested with two families of veterinary drugs, sulfonamides and penicillins, which are known to yield diagnostic product ions when fragmented. Data sets obtained from different food matrices (fish and liver), both at high and low concentration of the target compounds, were investigated in order to evaluate the capabilities and limitations of the reported approach. Finally, other possible applications of this technique, such as the elucidation of elemental compositions based on product ions and corresponding neutral losses, were also presented and discussed.

  9. Structural and optical properties of Cd{sup 2+} ion on the growth of sulphamic acid single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Rajyalakshmi, S.; Samatha, K. [Department of Physics, Andhra University, Visakhapatnam-530003 (India); Rao, Valluru Srinivasa; Reddy, P. V. S. S. S. N.; Rao, K. Ramachandra, E-mail: drkrcr@gmail.com [Crystal Growth & Nano Science Research Center, Department of Physics, Govt. College (A), Rajahmundry-533 105 (India); Krishna, V. Y. Rama [Department of Engg. Physics, Andhra University, Visakhapatnam-530003 (India)

    2016-05-06

    Transparent single crystals of Cadmium doped Sulphamic acid (SA) was grown by Conventional slow evaporation solution technique (SEST) which had the size of 13 × 8 × 7 mm{sup 3}. The grown single crystals have been characterized using single crystal X-ray diffraction UV-visible Spectral studies and Second harmonic generation (SHG) efficiency and the results were discussed. The lattice parameters of the grown Cd{sup 2+} ion doped SA crystal are confirmed by single crystal X-ray diffraction and belong to orthorhombic system. Optical transmittance of the crystal was recorded using UV-vis NIR spectrophotometer with its lower cut off wavelength around 259nm. SHG measurements indicate that the SHG efficiency of the grown Cd{sup 2+} ion doped SA crystal at a fundamental wavelength of 1064 nm is approximately equal to KDP.

  10. [(3)H]chlorpromazine photolabeling of the torpedo nicotinic acetylcholine receptor identifies two state-dependent binding sites in the ion channel.

    Science.gov (United States)

    Chiara, David C; Hamouda, Ayman K; Ziebell, Michael R; Mejia, Luis A; Garcia, Galo; Cohen, Jonathan B

    2009-10-27

    Chlorpromazine (CPZ), a potent nicotinic acetylcholine receptor (nAChR) noncompetitive antagonist, binds with higher affinity in the ion channel in the desensitized state than in the closed channel state and with low affinity to additional sites in nAChR-rich membranes. For nAChR equilibrated with agonist, we confirm previous reports that [(3)H]CPZ occupies a site near the cytoplasmic end of the M2 ion channel domain, photolabeling positions M2-2, M2-6, and/or M2-9 in each subunit. We find that [(3)H]CPZ also binds at the extracellular end of the channel, photolabeling amino acids at positions M2-16 (alpha,gamma), M2-17 (alpha,beta,delta), and M2-20 (alpha,beta,delta). The photolabeling at the cytoplasmic end of the channel is fully inhibitable by phencyclidine or proadifen, whereas neither drug inhibits [(3)H]CPZ photolabeling at the extracellular end, establishing that positively charged drugs can bind simultaneously at the cytoplasmic and extracellular ends of the ion channel. [(3)H]CPZ photolabeling is not detected in the transmembrane domain outside the ion channel, but it photolabels alphaMet-386 and alphaSer-393 in the cytoplasmic alphaMA helix. In the nAChR equilibrated with alpha-bungarotoxin to stabilize the nAChR in a closed state, [(3)H]CPZ photolabels amino acids at M2-5 (alpha), M2-6 (alpha,beta,delta), and M2-9 (beta,delta), with no labeling at M2-2. These results provide novel information about the modes of drug binding within the nAChR ion channel and indicate that within the nAChR transmembrane domain, the binding of cationic aromatic amine antagonists can be restricted to the ion channel domain, in contrast to the uncharged, allosteric potentiators and inhibitors that also bind within the delta subunit helix bundle and at subunit interfaces.

  11. Thermodynamic Studies of Cu(I) and Other d10 Metal Ions Binding to Proteins in the Copper Homeostasis Pathway and the Organomercurial Detoxification Pathway

    Science.gov (United States)

    Stevenson, Michael James

    Copper(I) is the predominant oxidation state of this essential metal in living cells due to reducing intracellular conditions. Because of deleterious copper-mediated Fenton chemistry, intracellular copper trafficking pathways involve strict regulation by metallochaperone proteins. Previous studies of the 68-residue metallochaperone, HAH1, have shown that it coordinates Cu(I) with two cysteines for transport from Ctr1 in the cell membrane to ATPases in the Golgi network. Using isothermal titration calorimetry (ITC), and methods to suppress oxidation and disproportionation of Cu(I), the thermodynamics of Cu(I), as well as other metal ions, binding to HAH1 have been accurately quantified. During the course of this study, the Cu(I) binding thermodynamics with the stabilizing ligand hexamethyltrien were determined in order to accurately quantify the Cu(I) binding thermodynamics with proteins, and revealed an unexpected Cu(I) coordination chemistry with this ligand. In addition, HAH1 binding the Cu(I) analogue Ag(I), the abundant cellular metal ion Zn(II), and the thiophilic toxic metal ion Hg(II), have been quantified. The binding thermodynamics of these metal ions were also determined in the presence of glutathione to more accurately model physiological conditions. HAH1 has a high affinity for Cu(I), which is both enthalpically and entropically favorable. It has a substantially lower affinity for Zn(II), which is entropically favored, suggesting that Zn(II) is not able to compete with Cu(I) for HAH1 in vivo. However, HAH1 has an exceptionally high affinity for Hg(II), with its larger thiophilicity, and it will displace Cu(I). Mercury(II) and particularly organomercurial compounds are very toxic, yet proteins from the bacterial mer operon provide resistance to this toxicity. In particular, the organomercurial lyase MerB, whose only known structural homologue is a putative copper metallochaperone, is responsible for cleavage of the carbon-mercury bond of MeHg(II) and

  12. Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L.

    Science.gov (United States)

    Lartigue, Audrey; Gruez, Arnaud; Briand, Loïc; Blon, Florence; Bézirard, Valérie; Walsh, Martin; Pernollet, Jean-Claude; Tegoni, Mariella; Cambillau, Christian

    2004-02-06

    Pheromone binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in several sensory organs from moth and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors. We report here the crystal structure of a PBP (Amel-ASP1) originating from the honey-bee (Apis mellifera) antennae and expressed as recombinant protein in the yeast Pichia pastoris. Crystals of Amel-ASP1 were obtained at pH 5.5 using the nano-drops technique of crystallization with a novel optimization procedure, and the structure was solved initially with the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion. The structure of Amel-ASP1 has been refined at 1.6-A resolution. Its fold is roughly similar to that of other PBP/odorant binding proteins, presenting six helices and three disulfide bridges. Contrary to the PBPs from Bombyx mori (Sandler, B. H., Nikonova, L., Leal, W. S., and Clardy, J. (2000) Chem. Biol. 7, 143-151) and Leucophea maderae (Lartigue, A., Gruez, A., Spinelli, S., Riviere, S., Brossut, R., Tegoni, M., and Cambillau, C. (2003) J. Biol. Chem. 278, 30213-30218), the extended C terminus folds into the protein and forms a wall of the internal hydrophobic cavity. Its backbone groups establish two hydrogen bonds with a serendipitous ligand, n-butyl-benzene-sulfonamide, an additive used in plastics. This mode of binding might, however, mimic that used by one of the pheromonal blend components and illustrates the binding versatility of PBPs.

  13. Characterization of the single-stranded DNA binding protein pV(VGJΦ) of VGJΦ phage from Vibrio cholerae.

    Science.gov (United States)

    Falero, Alina; Caballero, Andy; Trigueros, Sonia; Pérez, Celso; Campos, Javier; Marrero, Karen; Fando, Rafael

    2011-09-01

    pV(VGJΦ), a single-stranded DNA binding protein of the vibriophage VGJΦ was subject to biochemical analysis. Here, we show that this protein has a general affinity for single-stranded DNA (ssDNA) as documented by Electrophoretic Mobility Shift Assay (EMSA). The apparent molecular weight of the monomer is about 12.7kDa as measured by HPLC-SEC. Moreover, isoelectrofocusing showed an isoelectric point for pV(VGJΦ) of 6.82 pH units. Size exclusion chromatography in 150mM NaCl, 50mM sodium phosphate buffer, pH 7.0 revealed a major protein species of 27.0kDa, suggesting homodimeric protein architecture. Furthermore, pV(VGJΦ) binds ssDNA at extreme temperatures and the complex was stable after extended incubation times. Upon frozen storage at -20°C for a year the protein retained its integrity, biological activity and oligomericity. On the other hand, bioinformatics analysis predicted that pV(VGJΦ) protein has a disordered C-terminal, which might be involved in its functional activity. All the aforementioned features make pV(VGJΦ) interesting for biotechnological applications. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. A single amino acid substitution in the group 1 Trypanosoma brucei gambiense haptoglobin-hemoglobin receptor abolishes TLF-1 binding.

    Directory of Open Access Journals (Sweden)

    E DeJesus

    Full Text Available Critical to human innate immunity against African trypanosomes is a minor subclass of human high-density lipoproteins, termed Trypanosome Lytic Factor-1 (TLF-1. This primate-specific molecule binds to a haptoglobin-hemoglobin receptor (HpHbR on the surface of susceptible trypanosomes, initiating a lytic pathway. Group 1 Trypanosoma brucei gambiense causes human African Trypanosomiasis (HAT, escaping TLF-1 killing due to reduced uptake. Previously, we found that group 1 T. b. gambiense HpHbR (TbgHpHbR mRNA levels were greatly reduced and the gene contained substitutions within the open reading frame. Here we show that a single, highly conserved amino acid in the TbgHpHbR ablates high affinity TLF-1 binding and subsequent endocytosis, thus evading TLF-1 killing. In addition, we show that over-expression of TbgHpHbR failed to rescue TLF-1 susceptibility. These findings suggest that the single substitution present in the TbgHpHbR directly contributes to the reduced uptake and resistance to TLF-1 seen in these important human pathogens.

  15. Synchrotron Topographic and Diffractometer Studies of Buried Layered Structures Obtained by Implantation with Swift Heavy Ions in Silicon Single Crystals

    International Nuclear Information System (INIS)

    Wierzchowski, W.; Wieteska, K.; Zymierska, D.; Graeff, W.; Czosnyka, T.; Choinski, J.

    2006-01-01

    A distribution of crystallographic defects and deformation in silicon crystals subjected to deep implantation (20-50 μm) with ions of the energy of a few MeV/amu is studied. Three different buried layered structures (single layer, binary buried structure and triple buried structure) were obtained by implantation of silicon single crystals with 184 MeV argon ions, 29.7 MeV boron ions, and 140 MeV argon ions, each implantation at a fluency of 1x10 14 ions cm -2 . The implanted samples were examined by means of white beam X-ray section and projection topography, monochromatic beam topography and by recording local rocking curves with the beam restricted to 50 x 50 μm 2 . The experiment pointed to a very low level of implantation-induced strain (below 10 -5 ). The white beam Bragg case section experiment revealed a layer producing district black contrast located at a depth of the expected mean ion range. The presence of these buried layered structures in studied silicon crystals strongly affected the fringe pattern caused by curvature of the samples. In case of white beam projection and monochromatic beam topographs the implanted areas were revealed as darker regions with a very tiny grain like structure. One may interpret these results as the effect of considerable heating causing annihilation of point defects and formation of dislocation loops connected with point defect clusters. (author)

  16. Irradiation of zinc single crystal with 500 keV singly-charged carbon ions: surface morphology, structure, hardness, and chemical modifications

    Science.gov (United States)

    Waqas Khaliq, M.; Butt, M. Z.; Saleem, Murtaza

    2017-07-01

    Cylindrical specimens of (1 0 4) oriented zinc single crystal (diameter  =  6 mm and length  =  5 mm) were irradiated with 500 keV C+1 ions with the help of a Pelletron accelerator. Six specimens were irradiated in an ultra-high vacuum (~10‒8 Torr) with different ion doses, namely 3.94  ×  1014, 3.24  ×  1015, 5.33  ×  1015, 7.52  ×  1015, 1.06  ×  1016, and 1.30  ×  1016 ions cm-2. A field emission scanning electron microscope (FESEM) was utilized for the morphological study of the irradiated specimens. Formation of nano- and sub-micron size rods, clusters, flower- and fork-like structures, etc, was observed. Surface roughness of the irradiated specimens showed an increasing trend with the ions dose. Energy dispersive x-ray spectroscopy (EDX) helped to determine chemical modifications in the specimens. It was found that carbon content varied in the range 22.86-31.20 wt.% and that oxygen content was almost constant, with an average value of 10.16 wt.%. The balance content was zinc. Structural parameters, i.e. crystallite size and lattice strain, were determined by Williamson-Hall analysis using x-ray diffraction (XRD) patterns of the irradiated specimens. Both crystallite size and lattice strain showed a decreasing trend with the increasing ions dose. A good linear relationship between crystallite size and lattice strain was observed. Surface hardness depicted a decreasing trend with the ions dose and followed an inverse Hall-Petch relation. FTIR spectra of the specimens revealed that absorption bands gradually diminish as the dose of singly-charged carbon ions is increased from 3.94  ×  1014 ions cm-1 to 1.30  ×  1016 ions cm-1. This indicates progressive deterioration of chemical bonds with the increase in ion dose.

  17. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana.

    Science.gov (United States)

    Olszewski, Marcin; Grot, Anna; Wojciechowski, Marek; Nowak, Marta; Mickiewicz, Małgorzata; Kur, Józef

    2010-10-15

    In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR).

  18. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana

    Directory of Open Access Journals (Sweden)

    Mickiewicz Małgorzata

    2010-10-01

    Full Text Available Abstract Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs from the thermophilic bacteria Thermotoga maritima (TmaSSB and Thermotoga neapolitana (TneSSB. They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively. They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC the melting temperature (Tm was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR.

  19. MeV single-ion beam irradiation of mammalian cells using the Surrey vertical nanobeam, compared with broad proton beam and X-ray irradiations

    Science.gov (United States)

    Prakrajang, K.; Jeynes, J. C. G.; Merchant, M. J.; Kirkby, K.; Kirkby, N.; Thopan, P.; Yu, L. D.

    2013-07-01

    As a part of a systematic study on mechanisms involved in physical cancer therapies, this work investigated response of mammalian cells to ultra-low-dose ion beam irradiation. The ion beam irradiation was performed using the recently completed nanobeam facility at the Surrey Ion Beam Centre. A scanning focused vertical ion nano-beam was applied to irradiate Chinese hamster V79 cells. The V79 cells were irradiated in two different beam modes, namely, focused single ion beam and defocused scanning broad ion beam of 3.8-MeV protons. The single ion beam was capable of irradiating a single cell with a precisely controlled number of the ions to extremely low doses. After irradiation and cell incubation, the number of surviving colonies as a function of the number of the irradiating ions was measured for the cell survival fraction curve. A lower survival for the single ion beam irradiation than that of the broad beam case implied the hypersensitivity and bystander effect. The ion-beam-induced cell survival curves were compared with that from 300-kV X-ray irradiation. Theoretical studies indicated that the cell death in single ion irradiation mainly occurred in the cell cycle phases of cell division and intervals between the cell division and the DNA replication. The success in the experiment demonstrated the Surrey vertical nanobeam successfully completed.

  20. Maturation of Shark Single-Domain (IgNAR) Antibodies: Evidence for Induced-Fit Binding

    Energy Technology Data Exchange (ETDEWEB)

    Stanfield, R.L.; Dooley, H.; Verdino, P.; Flajnik, M.F.; Wilson, I.A.; /Scripps Res. Inst. /Maryland U.

    2007-07-13

    Sharks express an unusual heavy-chain isotype called IgNAR, whose variable regions bind antigen as independent soluble domains. To further probe affinity maturation of the IgNAR response, we structurally characterized the germline and somatically matured versions of a type II variable (V) region, both in the presence and absence of its antigen, hen egg-white lysozyme. Despite a disulfide bond linking complementarity determining regions (CDRs) 1 and 3, both germline and somatically matured V regions displayed significant structural changes in these CDRs upon complex formation with antigen. Somatic mutations in the IgNAR V region serve to increase the number of contacts with antigen, as reflected by a tenfold increase in affinity, and one of these mutations appears to stabilize the CDR3 region. In addition, a residue in the HV4 loop plays an important role in antibody-antigen interaction, consistent with the high rate of somatic mutations in this non-CDR loop.

  1. Water softening by single-bowl ion exchange filter efficiency estimate and improvement

    OpenAIRE

    Kostygin, V. A.; Stolyarenko, G. S.; Kochetov, G. M.; Tugay, A. M.; Vashchenko, V. N.

    2014-01-01

    The article presents results of experimental investigations of the water softener in a laboratory installation of uninterruptible countercurrent ion exchange filter, which has a movable layer of ion exchange material. The installation provides for two simultaneous processes: counter ion sorption and regeneration of the sorbent with the processing capability of the sorbent in the regeneration zone by ultrasonic radiation.

  2. Electrode property of single-walled carbon nanotubes in all-solid-state lithium ion battery using polymer electrolyte

    Energy Technology Data Exchange (ETDEWEB)

    Sakamoto, Y.; Ishii, Y.; Kawasaki, S., E-mail: kawasaki.shinji@nitech.ac.jp [Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi (Japan)

    2016-07-06

    Electrode properties of single-walled carbon nanotubes (SWCNTs) in an all-solid-state lithium ion battery were investigated using poly-ethylene oxide (PEO) solid electrolyte. Charge-discharge curves of SWCNTs in the solid electrolyte cell were successfully observed. It was found that PEO electrolyte decomposes on the surface of SWCNTs.

  3. Possible wave formation and martensitic transformation of iron particles in copper single crystals during argon ion bombardment

    DEFF Research Database (Denmark)

    Thölén, Anders Ragnar; Li, Chang-Hai; Easterling, K.E.

    1983-01-01

    Thin single crystal copper specimens (thickness ~250 nm) containing coherent iron particles (diameter 40–50 nm) have been bombarded with argon ions (5, 80, and 330 keV). During this process some of the iron particles transform to martensite. The transformation was observed near the exposed surface...

  4. MeV single-ion beam irradiation of mammalian cells using the Surrey vertical nanobeam, compared with broad proton beam and X-ray irradiations

    Energy Technology Data Exchange (ETDEWEB)

    Prakrajang, K. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Faculty of Science, Maejo University, Chiang Mai 50290 (Thailand); Jeynes, J.C.G.; Merchant, M.J.; Kirkby, K.; Kirkby, N. [Surrey Ion Beam Center, Faculty of Engineering and Physical Science, University of Surrey, Guildford Surrey, GU2 7XH (United Kingdom); Thopan, P. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Yu, L.D., E-mail: yuld@fnrf.science.cmu.ac.th [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand)

    2013-07-15

    Highlights: •Recently completed nanobeam at the Surrey Ion Beam Centre was used. •3.8-MeV single and broad proton beams irradiated Chinese hamster cells. •Cell survival curves were measured and compared with 300-kV X-ray irradiation. •Single ion irradiation had a lower survival part at ultra-low dose. •It implies hypersensitivity, bystander effect and cell cycle phase of cell death. -- Abstract: As a part of a systematic study on mechanisms involved in physical cancer therapies, this work investigated response of mammalian cells to ultra-low-dose ion beam irradiation. The ion beam irradiation was performed using the recently completed nanobeam facility at the Surrey Ion Beam Centre. A scanning focused vertical ion nano-beam was applied to irradiate Chinese hamster V79 cells. The V79 cells were irradiated in two different beam modes, namely, focused single ion beam and defocused scanning broad ion beam of 3.8-MeV protons. The single ion beam was capable of irradiating a single cell with a precisely controlled number of the ions to extremely low doses. After irradiation and cell incubation, the number of surviving colonies as a function of the number of the irradiating ions was measured for the cell survival fraction curve. A lower survival for the single ion beam irradiation than that of the broad beam case implied the hypersensitivity and bystander effect. The ion-beam-induced cell survival curves were compared with that from 300-kV X-ray irradiation. Theoretical studies indicated that the cell death in single ion irradiation mainly occurred in the cell cycle phases of cell division and intervals between the cell division and the DNA replication. The success in the experiment demonstrated the Surrey vertical nanobeam successfully completed.

  5. Rational design of single-ion magnets and spin qubits based on mononuclear lanthanoid complexes.

    Science.gov (United States)

    Baldoví, José J; Cardona-Serra, Salvador; Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro; Palii, Andrew

    2012-11-19

    Here we develop a general approach to calculating the energy spectrum and the wave functions of the low-lying magnetic levels of a lanthanoid ion submitted to the crystal field created by the surrounding ligands. This model allows us to propose general criteria for the rational design of new mononuclear lanthanoid complexes behaving as single-molecule magnets (SMMs) or acting as robust spin qubits. Three typical environments exhibited by these metal complexes are considered, namely, (a) square antiprism, (b) triangular dodecahedron, and (c) trigonal prism. The developed model is used to explain the properties of some representative examples showing these geometries. Key questions in this area, such as the chemical tailoring of the superparamagnetic energy barrier, tunneling gap, or spin relaxation time, are discussed. Finally, in order to take into account delocalization and/or covalent effects of the ligands, this point-charge model is complemented with ab initio calculations, which provide accurate information on the charge distribution around the metal, allowing for an explanation of the SMM behavior displayed by some sandwich-type organometallic compounds.

  6. A diode laser stabilization scheme for {sup 40}Ca{sup +} single-ion spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rohde, F; Almendros, M; Schuck, C; Huwer, J; Hennrich, M; Eschner, J, E-mail: felix.rohde@icfo.e [ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, E-08860 Castelldefels, Barcelona (Spain)

    2010-06-14

    We present a scheme for stabilizing multiple lasers at wavelengths between 795 and 866 nm to the same atomic reference line. A reference laser at 852 nm is stabilized to the Cs D{sub 2} line using a Doppler-free frequency modulation technique. Through transfer cavities, four lasers are stabilized to the relevant atomic transitions in {sup 40}Ca{sup +}. The rms linewidth of a transfer-locked laser is measured to be 123 kHz over 200 ms with respect to an independent atomic reference, the Rb D{sub 1} line. This stability is confirmed by the comparison of an excitation spectrum of a single {sup 40}Ca{sup +} ion to an eight-level Bloch equation model. The long-term stability with respect to the same reference is measured to be 130 kHz over a period of 2 h. The high degree of stability is demonstrated by the measured Allan deviation around 10{sup -11} between 1 and 100 s.

  7. Role of ICAM-1 polymorphisms (G241R, K469E) in mediating its single-molecule binding ability: Atomic force microscopy measurements on living cells

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Rui [Chinese (301) General Hospital, 28 Fuxing Road, Haidian District, Beijing 100853 (China); Yi, Shaoqiong [Beijing Institute of Biotechnology, 20 Dongdajie, Fengtai, Beijing 100071 (China); Zhang, Xuejie [Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry Chinese Academy of Sciences, 2 Zhongguancun North 1st Street, Beijing 100190 (China); Liu, Huiliang, E-mail: lhl518@vip.sina.com [Department of Cardiology, The General Hospital of Chinese People’s Armed Police Forces, Beijing 100039 (China); Fang, Xiaohong, E-mail: xfang@iccas.ac.cn [Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry Chinese Academy of Sciences, 2 Zhongguancun North 1st Street, Beijing 100190 (China)

    2014-06-13

    Highlights: • We evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations. • AFM was used to measure single-molecule binding ability on living cells. • The SNP of ICAM-1 may induce changes in expressions rather than single-molecule binding ability. - Abstract: Atherosclerosis (As) is characterized by chronic inflammation and is a major cause of human mortality. ICAM-1-mediated adhesion of leukocytes in vessel walls plays an important role in the pathogenesis of atherosclerosis. Two single nucleotide polymorphisms (SNPs) of human intercellular adhesion molecule-1 (ICAM-1), G241R and K469E, are associated with a number of inflammatory diseases. SNP induced changes in ICAM-1 function rely not only on the expression level but also on the single-molecule binding ability which may be affected by single molecule conformation variations such as protein splicing and folding. Previous studies have shown associations between G241R/K469E polymorphisms and ICAM-1 gene expression. Nevertheless, few studies have been done that focus on the single-molecule forces of the above SNPs and their ligands. In the current study, we evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations – GK (G241/K469), GE (G241/E469), RK (R241/K469) and RE (R241/E469). No difference in adhesion ability was observed via cell adhesion assay or atomic force microscopy (AFM) measurement when comparing the GK, GE, RK, or RE genotypes of ICAM-1 to each other. On the other hand, flow cytometry suggested that there was significantly higher expression of GE genotype of ICAM-1 on transfected CHO cells. Thus, we concluded that genetic susceptibility to diseases related to ICAM-1 polymorphisms, G241R or K469E, might be due to the different expressions of ICAM-1 variants rather than to the single-molecule binding ability of ICAM-1.

  8. Core-satellites assembly of silver nanoparticles on a single gold nanoparticle via metal ion-mediated complex.

    Science.gov (United States)

    Choi, Inhee; Song, Hyeon Don; Lee, Suseung; Yang, Young In; Kang, Taewook; Yi, Jongheop

    2012-07-25

    We report core-satellites (Au-Ag) coupled plasmonic nanoassemblies based on bottom-up, high-density assembly of molecular-scale silver nanoparticles on a single gold nanoparticle surface, and demonstrate direct observation and quantification of enhanced plasmon coupling (i.e., intensity amplification and apparent spectra shift) in a single particle level. We also explore metal ion sensing capability based on our coupled plasmonic core-satellites, which enabled at least 1000 times better detection limit as compared to that of a single plasmonic nanoparticle. Our results demonstrate and suggest substantial promise for the development of coupled plasmonic nanostructures for ultrasensitive detection of various biological and chemical analytes.

  9. Single event effects induced by 15.14 MeV/u sup 1 sup 3 sup 6 Xe ions

    CERN Document Server

    Hou Ming Dong; LiuJie; Wang Zhi Guang; Jin Yun Fan; Zhu Zhi Yong; Zhen Hong Lou; Liu Chang Long; Chen Xiao Xi; Wei Xin Guo; Zhang Li; Fan You Cheng; Zhu Zhou Rong; Zhang Yiting

    2002-01-01

    Single event effects induced by 15.14 MeV/u sup 1 sup 3 sup 6 Xe ions in different batches of 32k x 8 bits static random access memory are studied. The incident angle dependences of the cross sections for single event upset and single event latch up are presented. The SEE cross sections are plotted versus energy loss instead of linear energy transfer value in sensitive region. The depth of sensitive volume and thickness of 'dead' layer above the sensitive volume are estimated

  10. Effects of metal ions on stability and activity of hyperthermophilic pyrolysin and further stabilization of this enzyme by modification of a Ca2+-binding site.

    Science.gov (United States)

    Zeng, Jing; Gao, Xiaowei; Dai, Zheng; Tang, Bing; Tang, Xiao-Feng

    2014-05-01

    Pyrolysin is an extracellular subtilase produced by the marine hyperthermophilic archaeon Pyrococcus furiosus. This enzyme functions at high temperatures in seawater, but little is known about the effects of metal ions on the properties of pyrolysin. Here, we report that the supplementation of Na(+), Ca(2+), or Mg(2+) salts at concentrations similar to those in seawater destabilizes recombinant pyrolysin but leads to an increase in enzyme activity. The destabilizing effect of metal ions on pyrolysin appears to be related to the disturbance of surface electrostatic interactions of the enzyme. In addition, mutational analysis of two predicted high-affinity Ca(2+)-binding sites (Ca1 and Ca2) revealed that the binding of Ca(2+) is important for the stabilization of this enzyme. Interestingly, Asn substitutions at residues Asp818 and Asp820 of the Ca2 site, which is located in the C-terminal extension of pyrolysin, resulted in improvements in both enzyme thermostability and activity without affecting Ca(2+)-binding affinity. These effects were most likely due to the elimination of unfavorable electrostatic repulsion at the Ca2 site. Together, these results suggest that metal ions play important roles in modulating the stability and activity of pyrolysin.

  11. Effects of Metal Ions on Stability and Activity of Hyperthermophilic Pyrolysin and Further Stabilization of This Enzyme by Modification of a Ca2+-Binding Site

    Science.gov (United States)

    Zeng, Jing; Gao, Xiaowei; Dai, Zheng; Tang, Bing

    2014-01-01

    Pyrolysin is an extracellular subtilase produced by the marine hyperthermophilic archaeon Pyrococcus furiosus. This enzyme functions at high temperatures in seawater, but little is known about the effects of metal ions on the properties of pyrolysin. Here, we report that the supplementation of Na+, Ca2+, or Mg2+ salts at concentrations similar to those in seawater destabilizes recombinant pyrolysin but leads to an increase in enzyme activity. The destabilizing effect of metal ions on pyrolysin appears to be related to the disturbance of surface electrostatic interactions of the enzyme. In addition, mutational analysis of two predicted high-affinity Ca2+-binding sites (Ca1 and Ca2) revealed that the binding of Ca2+ is important for the stabilization of this enzyme. Interestingly, Asn substitutions at residues Asp818 and Asp820 of the Ca2 site, which is located in the C-terminal extension of pyrolysin, resulted in improvements in both enzyme thermostability and activity without affecting Ca2+-binding affinity. These effects were most likely due to the elimination of unfavorable electrostatic repulsion at the Ca2 site. Together, these results suggest that metal ions play important roles in modulating the stability and activity of pyrolysin. PMID:24561589

  12. Binding Affinity of a Highly Sensitive Au/Ag/Au/Chitosan-Graphene Oxide Sensor Based on Direct Detection of Pb2+ and Hg2+ Ions

    Directory of Open Access Journals (Sweden)

    Nur Hasiba Kamaruddin

    2017-10-01

    Full Text Available The study of binding affinity is essential in surface plasmon resonance (SPR sensing because it allows researchers to quantify the affinity between the analyte and immobilised ligands of an SPR sensor. In this study, we demonstrate the derivation of the binding affinity constant, K, for Pb2+ and Hg2+ ions according to their SPR response using a gold/silver/gold/chitosan–graphene oxide (Au/Ag/Au/CS–GO sensor for the concentration range of 0.1–5 ppm. The higher affinity of Pb2+ to binding with the CS–GO sensor explains the outstanding sensitivity of 2.05 °ppm−1 against 1.66 °ppm−1 of Hg2+. The maximum signal-to-noise ratio (SNR upon detection of Pb2+ is 1.53, and exceeds the suggested logical criterion of an SNR. The Au/Ag/Au/CS–GO SPR sensor also exhibits excellent repeatability in Pb2+ due to the strong bond between its functional groups and this cation. The adsorption data of Pb2+ and Hg2+ on the CS–GO sensor fits well with the Langmuir isotherm model where the affinity constant, K, of Pb2+ and Hg2+ ions is computed. The affinity of Pb2+ ions to the Au/Ag/Au/CS–GO sensor is significantly higher than that of Hg2+ based on the value of K, 7 × 105 M−1 and 4 × 105 M−1, respectively. The higher shift in SPR angles due to Pb2+ and Hg2+ compared to Cr3+, Cu2+ and Zn2+ ions also reveals the greater affinity of the CS–GO SPR sensor to them, thus supporting the rationale for obtaining K for these two heavy metals. This study provides a better understanding on the sensing performance of such sensors in detecting heavy metal ions.

  13. Importance of the alphaC-helix in the cyclic nucleotide binding domain for the stable channel regulation and function of cyclic nucleotide gated ion channels in Arabidopsis.

    Science.gov (United States)

    Chin, Kimberley; Moeder, Wolfgang; Abdel-Hamid, Huda; Shahinas, Dea; Gupta, Deepali; Yoshioka, Keiko

    2010-05-01

    The involvement of cyclic nucleotide gated ion channels (CNGCs) in the signal transduction of animal light and odorant perception is well documented. Although plant CNGCs have recently been revealed to mediate multiple stress responses and developmental pathways, studies that aim to elucidate their structural and regulatory properties are still very much in their infancy. The structure-function relationship of plant CNGCs was investigated here by using the chimeric Arabidopsis AtCNGC11/12 gene that induces multiple defence responses in the Arabidopsis mutant constitutive expresser of PR genes 22 (cpr22) for the identification of functionally essential residues. A genetic screen for mutants that suppress cpr22-conferred phenotypes identified over 20 novel mutant alleles in AtCNGC11/12. One of these mutants, suppressor S58 possesses a single amino acid substitution, arginine 557 to cysteine, in the alphaC-helix of the cyclic nucleotide-binding domain (CNBD). The suppressor S58 lost all cpr22 related phenotypes, such as spontaneous cell death formation under ambient temperature conditions. However, these phenotypes were recovered at 16 degrees C suggesting that the stability of channel function is affected by temperature. In silico modelling and site-directed mutagenesis analyses suggest that arginine 557 in the alphaC-helix of the CNBD is important for channel regulation, but not for basic function. Furthermore, another suppressor mutant, S136 that lacks the entire alphaC-helix due to a premature stop codon, lost channel function completely. Our data presented here indicate that the alphaC-helix is functionally important in plant CNGCs.

  14. Diagnostics and Degradation Investigations of Li-Ion Battery Electrodes using Single Nanowire Electrochemical Cells

    Science.gov (United States)

    Palapati, Naveen Kumar Reddy

    Portable energy storage devices, which drive advanced technological devices, are improving the productivity and quality of our everyday lives. In order to meet the growing needs for energy storage in transportation applications, the current lithium-ion (Li-ion) battery technology requires new electrode materials with performance improvements in multiple aspects: (1) energy and power densities, (2) safety, and (3) performance lifetime. While a number of interesting nanomaterials have been synthesized in recent years with promising performance, accurate capabilities to probe the intrinsic performance of these high-performance materials within a battery environment are lacking. Most studies on electrode nanomaterials have so far used traditional, bulk-scale techniques such as cyclic voltammetry, electrochemical impedance spectroscopy, and Raman spectroscopy. These approaches give an ensemble-average estimation of the electrochemical properties of a battery electrode and does not provide a true indication of the performance that is intrinsic to its material system. Thus, new techniques are essential to understand the changes happening at a single particle level during the operation of a battery. The results from this thesis solve this need and study the electrical, mechanical and size changes that take place in a battery electrode at a single particle level. Single nanowire lithium cells are built by depositing nanowires in carefully designed device regions of a silicon chip using Dielectrophoresis (DEP). This work has demonstrated the assembly of several NW cathode materials like LiFePO 4, pristine and acid-leached alpha-MnO2, todorokite - MnO2, acid and nonacid-leached Na0.44MnO2. Within these materials, alpha-MnO2 was chosen as the model material system for electrochemical experiments. Electrochemical lithiation of pristine alpha-MnO 2 was performed inside a glove box. The volume, elasticity and conductivity changes were measured at each state-of-charge (SOC) to

  15. Novel single-cell mega-size chambers for electrochemical etching of panorama position-sensitive polycarbonate ion image detectors

    Science.gov (United States)

    Sohrabi, Mehdi

    2017-11-01

    A novel development is made here by inventing panorama single-cell mega-size electrochemical etching (MS-ECE) chamber systems for processing panorama position-sensitive mega-size polycarbonate ion image detectors (MS-PCIDs) of potential for many neutron and ion detection applications in particular hydrogen ions or proton tracks and images detected for the first time in polycarbonates in this study. The MS-PCID is simply a large polycarbonate sheet of a desired size. The single-cell MS-ECE invented consists of two large equally sized transparent Plexiglas sheets as chamber walls holding a MS-PCID and the ECE chamber components tightly together. One wall has a large flat stainless steel electrode (dry cell) attached to it which is directly in contact with the MS-PCID and the other wall has a rod electrode with two holes to facilitate feeding and draining out the etching solution from the wet cell. A silicon rubber washer plays the role of the wet cell to hold the etchant and the electrical insulator to isolate the dry cell from the wet cell. A simple 50 Hz-HV home-made generator provides an adequate field strength through the two electrodes across the MS-ECE chamber. Two panorama single-cell MS-ECE chamber systems (circular and rectangular shapes) constructed were efficiently applied to processing the MS-PCIDs for 4π ion emission image detection of different gases in particular hydrogen ions or protons in a 3.5 kJ plasma focus device (PFD as uniquely observed by the unaided eyes). The panorama MS-PCID/MS-ECE image detection systems invented are novel with high potential for many applications in particular as applied to 4π panorama ion emission angular distribution image detection studies in PFD space, some results of which are presented and discussed.

  16. Effect of H{sup +} ion implantation on structural, morphological, optical and dielectric properties of L-arginine monohydrochloride monohydrate single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sangeetha, K. [Crystal Growth and Thin film Laboratory, Department of Physics, School of Physics, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu (India); Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in [Crystal Growth and Thin film Laboratory, Department of Physics, School of Physics, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu (India); Kumar, P. [Inter-University Accelerator Centre, P.O. Box 10502, Aruna Asaf Ali Marg, New Delhi 110067 (India); Bhagvannarayana, G. [Materials Characterization Division, National Physical Laboratory, New Delhi 110012 (India); Ramamurthi, K. [Crystal Growth and Thin film Laboratory, Department of Physics, School of Physics, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu (India)

    2011-06-15

    L-arginine monohydrochloride monohydrate (LAHCl) single crystals have been implanted with 100 keV H{sup +} ions at different ion fluence ranging from 10{sup 12} to 10{sup 15} ions/cm{sup 2}. Implanted LAHCl single crystals have been investigated for property changes. Crystal surface and crystalline perfection of the pristine and implanted crystals were analyzed by atomic force microscope and high-resolution X-ray diffraction studies, respectively. Optical absorption bands induced by colour centers, refractive index and birefringence, mechanical stability and dielectric constant of implanted crystals were studied at different ion fluence and compared with that of pristine LAHCl single crystal.

  17. Interpretation with a Donnan-based concept of the influence of simple salt concentration on the apparent binding of divalent ions to the polyelectrolytes polystyrenesulfonate and dextran sulfate

    Science.gov (United States)

    Marinsky, J.A.; Baldwin, Robert F.; Reddy, M.M.

    1985-01-01

    It has been shown that the apparent enhancement of divalent metal ion binding to polyions such as polystyrenesulfonate (PSS) and dextran sulfate (DS) by decreasing the ionic strength of these mixed counterion systems (M2+, M+, X-, polyion) can be anticipated with the Donnan-based model developed by one of us (J.A.M.). Ion-exchange distribution methods have been employed to measure the removal by the polyion of trace divalent metal ion from simple salt (NaClO4)-polyion (NaPSS) mixtures. These data and polyion interaction data published earlier by Mattai and Kwak for the mixed counterion systems MgCl2-LiCl-DS and MgCl2-CsCl-DS have been shown to be amenable to rather precise analysis by this model. ?? 1985 American Chemical Society.

  18. Water-soluble metal-binding polymers with ultrafiltration: A technology for the removal, concentration, and recovery of metal ions from aqueous streams

    International Nuclear Information System (INIS)

    Smith, B.F.; Robison, T.W.; Jarvinen, G.D.

    1997-01-01

    The use of water-soluble metal-binding polymers coupled with ultrafiltration (UF) is a technology under development to selectively concentrate and recover valuable or regulated metal-ions from dilute process or waste waters. The polymers have a sufficiently large molecular size that they can be separated and concentrated using commercially available UF technology. The polymers can then be reused by changing the solution conditions to release the metal-ions, which are recovered in a concentrated form for recycle or disposal. Pilot-scale demonstrations have been completed for a variety of waste streams containing low concentrations of metal ions including electroplating wastes (zinc and nickel) and nuclear waste streams (plutonium and americium). Many other potential commercial applications exist including remediation of contaminated solids. An overview of both the pilot-scale demonstrated applications and small scale testing of this technology are presented

  19. Water-soluble metal-binding polymers with ultrafiltration: A technology for the removal, concentration, and recovery of metal ions from aqueous streams

    Energy Technology Data Exchange (ETDEWEB)

    Smith, B.F.; Robison, T.W.; Jarvinen, G.D.

    1997-12-31

    The use of water-soluble metal-binding polymers coupled with ultrafiltration (UF) is a technology under development to selectively concentrate and recover valuable or regulated metal-ions from dilute process or waste waters. The polymers have a sufficiently large molecular size that they can be separated and concentrated using commercially available UF technology. The polymers can then be reused by changing the solution conditions to release the metal-ions, which are recovered in a concentrated form for recycle or disposal. Pilot-scale demonstrations have been completed for a variety of waste streams containing low concentrations of metal ions including electroplating wastes (zinc and nickel) and nuclear waste streams (plutonium and americium). Many other potential commercial applications exist including remediation of contaminated solids. An overview of both the pilot-scale demonstrated applications and small scale testing of this technology are presented.

  20. The single-strand DNA binding activity of human PC4 preventsmutagenesis and killing by oxidative DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jen-Yeu; Sarker, Altaf Hossain; Cooper, Priscilla K.; Volkert, Michael R.

    2004-02-01

    Human positive cofactor 4 (PC4) is a transcriptional coactivator with a highly conserved single-strand DNA (ssDNA) binding domain of unknown function. We identified PC4 as a suppressor of the oxidative mutator phenotype of the Escherichia coli fpg mutY mutant and demonstrate that this suppression requires its ssDNA binding activity. Yeast mutants lacking their PC4 ortholog Sub1 are sensitive to hydrogen peroxide and exhibit spontaneous and peroxide induced hypermutability. PC4 expression suppresses the peroxide sensitivity of the yeast sub l{Delta} mutant, suggesting that the human protein has a similar function. A role for yeast and human proteins in DNA repair is suggested by the demonstration that Sub1 acts in a peroxide-resistance pathway involving Rad2 and by the physical interaction of PC4 with the human Rad2 homolog XPG. We show XPG recruits PC4 to a bubble-containing DNA substrate with resulting displacement of XPG and formation of a PC4-DNA complex. We discuss the possible requirement for PC4 in either global or transcription-coupled repair of oxidative DNA damage to mediate the release of XPG bound to its substrate.

  1. Changes in ion channel geometry resolved to sub-ångström precision via single molecule mass spectrometry

    Science.gov (United States)

    Robertson, Joseph W. F.; Kasianowicz, John J.; Reiner, Joseph E.

    2010-11-01

    The ion channel formed by Staphylococcus aureus alpha-hemolysin switches between multiple open conducting states. We describe a method for precisely estimating the changes in the ion channel geometry that correspond to these different states. Experimentally, we observed that the permeability of a single channel to differently sized poly(ethylene glycol) molecules depends on the magnitude of the open state conductance. A simple theory is proposed for determining changes in channel length of 4.2% and in cross-sectional area of - 0.4%.

  2. Strong coupling between a single nitrogen-vacancy spin and the rotational mode of diamonds levitating in an ion trap

    Science.gov (United States)

    Delord, T.; Nicolas, L.; Chassagneux, Y.; Hétet, G.

    2017-12-01

    A scheme for strong coupling between a single atomic spin and the rotational mode of levitating nanoparticles is proposed. The idea is based on spin readout of nitrogen-vacancy centers embedded in aspherical nanodiamonds levitating in an ion trap. We show that the asymmetry of the diamond induces a rotational confinement in the ion trap. Using a weak homogeneous magnetic field and a strong microwave driving we then demonstrate that the spin of the nitrogen-vacancy center can be strongly coupled to the rotational mode of the diamond.

  3. Aptamer based voltammetric determination of ampicillin using a single-stranded DNA binding protein and DNA functionalized gold nanoparticles.

    Science.gov (United States)

    Wang, Jun; Ma, Kui; Yin, Huanshun; Zhou, Yunlei; Ai, Shiyun

    2017-12-20

    An aptamer based method is described for the electrochemical determination of ampicillin. It is based on the use of DNA aptamer, DNA functionalized gold nanoparticles (DNA-AuNPs), and single-stranded DNA binding protein (ssDNA-BP). When the aptamer hybridizes with the target DNA on the AuNPs, the ssDNA-BP is captured on the electrode surface via its specific interaction with ss-DNA. This results in a decreased electrochemical signal of the redox probe Fe(CN) 6 3- which is measured best at a voltage of 0.188 mV (vs. reference electrode). In the presence of ampicillin, the formation of aptamer-ampicillin conjugate blocks the further immobilization of DNA-AuNPs and ssDNA-BP, and this leads to an increased response. The method has a linear reposne that convers the 1 pM to 5 nM ampicillin concentration range, with a 0.38 pM detection limit (at an S/N ratio of 3). The assay is selective, stable and reproducible. It was applied to the determination of ampicillin in spiked milk samples where it gave recoveries ranging from 95.5 to 105.5%. Graphical abstract Schematic of a simple and sensitive electrochemical apta-biosensor for ampicillin detection. It is based on the use of gold nanoparticles (AuNPs), DNA aptamer, DNA functionalized AuNPs (DNA-AuNPs), and single-strand DNA binding protein (SSBP).

  4. Productivity Improvement for the SHX--SEN's Single-Wafer High-Current Ion Implanter

    International Nuclear Information System (INIS)

    Ninomiya, Shiro; Ochi, Akihiro; Kimura, Yasuhiko; Yumiyama, Toshio; Kudo, Tetsuya; Kurose, Takeshi; Kariya, Hiroyuki; Tsukihara, Mitsukuni; Ishikawa, Koji; Ueno, Kazuyoshi

    2011-01-01

    Equipment productivity is a critical issue for device fabrication. For ion implantation, productivity is determined both by ion current at the wafer and by utilization efficiency of the ion beam. Such improvements not only result in higher fabrication efficiency but also reduce consumption of both electrical power and process gases. For high-current ion implanters, reduction of implant area is a key factor to increase efficiency. SEN has developed the SAVING system (Scanning Area Variation Implantation with Narrower Geometrical pattern) to address this opportunity. In this paper, three variations of the SAVING system are introduced along with discussion of their effects on fab productivity.

  5. Single amino acids in the carboxyl terminal domain of aquaporin-1 contribute to cGMP-dependent ion channel activation

    Directory of Open Access Journals (Sweden)

    Yool Andrea J

    2003-10-01

    Full Text Available Abstract Background Aquaporin-1 (AQP1 functions as an osmotic water channel and a gated cation channel. Activation of the AQP1 ion conductance by intracellular cGMP was hypothesized to involve the carboxyl (C- terminus, based on amino acid sequence alignments with cyclic-nucleotide-gated channels and cGMP-selective phosphodiesterases. Results Voltage clamp analyses of human AQP1 channels expressed in Xenopus oocytes demonstrated that the nitric oxide donor, sodium nitroprusside (SNP; 3–14 mM activated the ionic conductance response in a dose-dependent manner. Block of soluble guanylate cyclase prevented the response. Enzyme immunoassays confirmed a linear dose-dependent relationship between SNP and the resulting intracellular cGMP levels (up to 1700 fmol cGMP /oocyte at 14 mM SNP. Results here are the first to show that the efficacy of ion channel activation is decreased by mutations of AQP1 at conserved residues in the C-terminal domain (aspartate D237 and lysine K243. Conclusions These data support the idea that the limited amino acid sequence similarities found between three diverse classes of cGMP-binding proteins are significant to the function of AQP1 as a cGMP-gated ion channel, and provide direct evidence for the involvement of the AQP1 C-terminal domain in cGMP-mediated ion channel activation.

  6. ions

    African Journals Online (AJOL)

    (MP2 B2). In order to draw the final conclusion about the content of the isomers of pentaatomic ions in saturated vapor over cesium chloride, we have taken into account the entropy factor. We considered the isomerization reactions which are given below: Cs3Cl2. + (V-shaped) = Cs3Cl2. + (cyclic or bipyramidal). (1). Cs2Cl3.

  7. Single potential electrodeposition of nanostructured battery materials for lithium-ion batteries

    Science.gov (United States)

    Mosby, James Matthew

    The increasing reliance on portable electronics is continuing to fuel research in the area of low power lithium-ion batteries, while a new surge in research for high power lithium-ion batteries has been sparked by the demand for plug-in hybrid electric vehicles (PHEV) and plug-in electric vehicles (PEV). To compete with current lead-acid battery chemistry, a few of the shortcomings of lithium-ion battery chemistry need to be addressed. The three main drawbacks of lithium-ion batteries for this application are: (1) low power density, (2) safety, and (3) the high cost of manufacturing. This dissertation covers the development of a low cost fabrication technique for an alternative anode material with high surface area geometries. The anode material is safer than the conventional anode material in lithium-ion batteries and the high surface area geometries permit higher power densities to be achieved. Electrodeposition is an inexpensive alternative method for synthesizing materials for electronics, energy conversion and energy storage applications relative to traditional solid state techniques. These techniques led to expensive device fabrication. Unlike most solid state synthesis routes, electrodeposition can usually be performed from common solutions and at moderate conditions. Three other benefits of using electrodeposition are: (1) it allows precise control of composition and crystallinity, (2) it provides the ability to deposit on complex shapes, and (3) it can deposit materials with nanoscale dimensions. The use of electrodeposition for alternative anode materials results in the deposition of the material directly onto the current collector that is used for the battery testing and applications without the need of additional binders and with excellent electrical contact. While this improves the characterization of the material and lowers the weight of the non-active materials within a battery, it also allows the anode to be deposited onto current collectors with

  8. Determination of trace inorganic anions in weak acids by single-pump column-switching ion chromatography.

    Science.gov (United States)

    Zhu, Haibao; Chen, Huadong; Zhong, Yingying; Ren, Dandan; Qian, Yaling; Tang, Hongfang; Zhu, Yan

    2010-08-01

    Ion chromatography has been proposed for the determination of three common inorganic anions (chloride, nitrate, and sulfate) in nine weak acids (tartaric acid, citric acid, formic acid, acetic acid, metacetonic acid, butyric acid, butanedioic acid, hexafluorophosphoric acid, and salicylic acid) using a single pump, two valves, a single eluent, and a single conductivity detector. The present system uses ion exclusion, concentrator, and anion-exchange columns connected in series via 6-port and 10-port valves in a Dionex ICS-2100 ion chromatograph. The valves were switched for the determination of three inorganic anions from weak acids in a single chromatographic run. Sample matrices of weak acids with a series of concentrations can be investigated. Complete separations of the previously mentioned anions are demonstrated within 40 min. Under the optimum conditions, the relative standard deviation values ranged from 1.3 to 3.8%. The detection limits of the three inorganic anions (S/N = 3) were in the range of 0.3-1.7 microg/L. The recoveries were in the range of 75.2-117.6%. With this system, automation for routine analysis, short analysis time, and low cost can be achieved.

  9. Cationized phenylalanine conformations characterized by IRMPD and computation for singly and doubly charged ions

    NARCIS (Netherlands)

    Dunbar, R. C.; Steill, J. D.; Oomens, J.

    2010-01-01

    Electrospray ionization produces phenylalanine (Phe) complexes of the alkali metal ion series, plus Ag+ and Ba2+. Infrared multiple photon dissociation (IRMPD) spectroscopy using the FELIX free electron laser light source is used to characterize the conformations of the ions, in conjunction with

  10. Early Stage of Deformation under Nanoindenter Tip of Ion-irradiated Single Crystals

    International Nuclear Information System (INIS)

    Shin, Chan Sun; Jin, Hyung Ha; Kwon, Jun Hyun

    2010-01-01

    Ion irradiation has been used for almost 40 years to emulate the effect of neutrons. Ion irradiation has a number of advantages in terms of time and expenses compared to neutron irradiation. Ion irradiation is expected to greatly contribute to the development of Fusion and Gen IV materials. Ions have short penetration depth, and they induce continuously varying dose rate over the penetration depth. Although it depends on the energy and species of incident ions, the depth of ion-irradiated region is in general on the order of a few micron meters. Depth controlled probing technique is required to measure the mechanical properties of ion-irradiated layer, and nanoindentation is widely used. During nanoindentation, a hard tip with known properties is pressed into a material which has unknown properties. The depth of penetration and load on the indenter are recorded during loading and unloading. The initial Loading depth curve follows the Hertzian elastic solution, and at a certain load, a sudden displacement excursion occurs in indenter depth and then hardening follows. This is called 'Pop-in' event, and since residual impression can be found only after pop-ins, the pop-in is regarded as the onset of plasticity. The objectives of this research are to investigate the effects of ion irradiation on popins, and to examine dislocation nucleation and propagation at the onset of plasticity by using MD simulations

  11. Early Stage of Deformation under Nanoindenter Tip of Ion-irradiated Single Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Chan Sun; Jin, Hyung Ha; Kwon, Jun Hyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2010-10-15

    Ion irradiation has been used for almost 40 years to emulate the effect of neutrons. Ion irradiation has a number of advantages in terms of time and expenses compared to neutron irradiation. Ion irradiation is expected to greatly contribute to the development of Fusion and Gen IV materials. Ions have short penetration depth, and they induce continuously varying dose rate over the penetration depth. Although it depends on the energy and species of incident ions, the depth of ion-irradiated region is in general on the order of a few micron meters. Depth controlled probing technique is required to measure the mechanical properties of ion-irradiated layer, and nanoindentation is widely used. During nanoindentation, a hard tip with known properties is pressed into a material which has unknown properties. The depth of penetration and load on the indenter are recorded during loading and unloading. The initial Loading depth curve follows the Hertzian elastic solution, and at a certain load, a sudden displacement excursion occurs in indenter depth and then hardening follows. This is called 'Pop-in' event, and since residual impression can be found only after pop-ins, the pop-in is regarded as the onset of plasticity. The objectives of this research are to investigate the effects of ion irradiation on popins, and to examine dislocation nucleation and propagation at the onset of plasticity by using MD simulations

  12. Potent neutralization of influenza A virus by a single-domain antibody blocking M2 ion channel protein.

    Directory of Open Access Journals (Sweden)

    Guowei Wei

    Full Text Available Influenza A virus poses serious health threat to humans. Neutralizing antibodies against the highly conserved M2 ion channel is thought to offer broad protection against influenza A viruses. Here, we screened synthetic Camel single-domain antibody (VHH libraries against native M2 ion channel protein. One of the isolated VHHs, M2-7A, specifically bound to M2-expressed cell membrane as well as influenza A virion, inhibited replication of both amantadine-sensitive and resistant influenza A viruses in vitro, and protected mice from a lethal influenza virus challenge. Moreover, M2-7A showed blocking activity for proton influx through M2 ion channel. These pieces of evidence collectively demonstrate for the first time that a neutralizing antibody against M2 with broad specificity is achievable, and M2-7A may have potential for cross protection against a number of variants and subtypes of influenza A viruses.

  13. Bacillus subtilis single-stranded DNA-binding protein SsbA is phosphorylated at threonine 38 by the serine/threonine kinase YabT

    DEFF Research Database (Denmark)

    Derouiche, Abderahmane; Petranovic, Dina; Macek, Boris

    2016-01-01

    Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. B. subtilis single-stranded DNA-binding pro......Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. B. subtilis single-stranded DNA...... assays.Results: In addition to the known tyrosine phosphorylation of SsbA on tyrosine 82, we identified a new phosphorylation site: threonine 38. The in vitro assays demonstrated that SsbA is preferentially phosphorylated by the B. subtilis Hanks-type kinase YabT, and phosphorylation of threonine 38...... leads to enhanced cooperative binding to DNA.Conclusions: Our findings contribute to the emerging picture that bacterial proteins, exemplified here by SsbA, undergo phosphorylation at multiple residues. This results in a complex regulation of cellular functions, and suggests that the complexity...

  14. Calcium carbonate phosphate binding ion exchange filtration and accelerated denitrification improve public health standards and combat eutrophication in aquatic ecosystems.

    Science.gov (United States)

    Yanamadala, Vijay

    2005-01-01

    Hektoen agar. Initial analyses suggest a strong correlation between phosphate concentrations and bacterial populations; a 66% decrease in phosphate resulted in a 35% reduction in bacterial populations and a 45% reduction in enteropathogenic populations. Likewise, a strong correlation was shown between calcium carbonate concentrations and bacterial reduction greater than that which can be attributed to the phosphate reduction alone. This was followed by the construction of various phosphate binding calcium carbonate filters, which used the ion exchange principle, including a spring loading filter, PVC pipe filter, and a galvanized filter. All were tested with the aid of Stoke's law formulation. The experiment was extremely successful in designing a working phosphate-binding and ammonia-reducing filter, and a large-scale agitator-clarifier filter system is currently being planned for construction in Madrona Marsh; this filter will reduce phosphate and ammonia levels substantially in the following years, bringing ecological, economical, and health-related improvements to the overall ecosystem and habitat.

  15. Specific binding of (/sup 3/H)substance P to the rat submaxillary gland. The effects of ions and guanine nucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Bahouth, S.W.; Musacchio, J.M.

    1985-08-01

    (/sup 3/H)Substance P ((/sup 3/H)SP), in a high ionic strength incubation medium, binds to a single class of saturable, noninteracting binding sites on rat submaxillary gland membranes with a KD = 2.8 +/- 0.34 nM and maximum binding (Bmax) = 220 +/- 31 fmol/mg of protein. The rank order of potency of various tachykinins, SP fragments and analogs to compete against (/sup 3/H)SP is correlated with their potency to induce salivation. These findings indicate that, under the conditions described, (/sup 3/H)SP binds to a physiologically relevant tachykinin receptor of the SP-P subtype. (/sup 3/H)SP binding increases by 35% in the presence of optimal concentrations of Mn++ and Mg++ whereas guanine nucleotides reduce (/sup 3/H)SP binding. The effect produced by either divalent cations or guanine nucleotides is due to increasing or decreasing the Bmax, respectively, without changing the affinity of (/sup 3/H)SP. Guanine nucleotides reduce the Bmax of (/sup 3/H)SP to the same level in the presence or absence of divalent cations, indicating that divalent cations increase the population of SP receptors that are sensitive to guanine nucleotides. In low ionic strength media, and when the nonspecific binding is defined by 1 microM SP, (/sup 3/H)SP binds to two sites: a high affinity site with a KD of 0.14 nM and a Bmax of 370 fmol/mg of protein and a low affinity high capacity site. When the nonspecific binding is defined by 1 microM physalaemin, the high affinity is the only detectable site. However, in low ionic strength media, physalaemin has about one-fiftieth the potency of SP in competing with (/sup 3/H)SP.

  16. Novel molecular-level evidence of iodine binding to natural organic matter from Fourier transform ion cyclotron resonance mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Chen, E-mail: xuchen66@tamu.edu [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States); Chen, Hongmei [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); Sugiyama, Yuko [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); University of Hyogo, 1-1-12, Shinzaike-honcho, Himeji, Hyogo 670-0092 (Japan); Zhang, Saijin; Li, Hsiu-Ping; Ho, Yi-Fang; Chuang, Chia-ying; Schwehr, Kathleen A. [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States); Kaplan, Daniel I. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Yeager, Chris [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Roberts, Kimberly A. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Hatcher, Patrick G. [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); Santschi, Peter H. [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States)

    2013-04-01

    Major fractions of radioiodine ({sup 129}I) are associated with natural organic matter (NOM) in the groundwater and surface soils of the Savannah River Site (SRS). Electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) was applied to elucidate the interactions between inorganic iodine species (iodide and iodate) and a fulvic acid (FA) extracted from a SRS surface soil. Iodate is likely reduced to reactive iodine species by the lignin- and tannin-like compounds or the carboxylic-rich alicyclic molecules (CRAM), during which condensed aromatics and lignin-like compounds were generated. Iodide is catalytically oxidized into reactive iodine species by peroxides, while FA is oxidized by peroxides into more aliphatic and less aromatic compounds. Only 9% of the total identified organo-iodine compounds derived from molecules originally present in the FA, whereas most were iodine binding to newly-produced compounds. The resulting iodinated molecules were distributed in three regions in the van Krevelen diagrams, denoting unsaturated hydrocarbons, lignin and protein. Moreover, characteristics of these organo-iodine compounds, such as their relatively low O/C ratios (< 0.2 or < 0.4) and yet some degree of un-saturation close to that of lignin, have multiple important environmental implications concerning possibly less sterically-hindered aromatic ring system for iodine to get access to and a lower hydrophilicity of the molecules thus to retard their migration in the natural aquatic systems. Lastly, ∼ 69% of the identified organo-iodine species contains nitrogen, which is presumably present as -NH{sub 2} or -HNCOR groups and a ring-activating functionality to favor the electrophilic substitution. The ESI-FTICR-MS technique provides novel evidence to better understand the reactivity and scavenging properties of NOM towards radioiodine and possible influence of NOM on {sup 129}I migration. Highlights: ► IO{sub 3}{sup

  17. Optical planar waveguides in photo-thermal-refractive glasses fabricated by single- or double-energy carbon ion implantation

    Science.gov (United States)

    Wang, Yue; Shen, Xiao-Liang; Zheng, Rui-Lin; Guo, Hai-Tao; Lv, Peng; Liu, Chun-Xiao

    2018-01-01

    Ion implantation has demonstrated to be an efficient and reliable technique for the fabrication of optical waveguides in a diversity of transparent materials. Photo-thermal-refractive glass (PTR) is considered to be durable and stable holographic recording medium. Optical planar waveguide structures in the PTR glasses were formed, for the first time to our knowledge, by the C3+-ion implantation with single-energy (6.0 MeV) and double-energy (5.5+6.0 MeV), respectively. The process of the carbon ion implantation was simulated by the stopping and range of ions in matter code. The morphologies of the waveguides were recorded by a microscope operating in transmission mode. The guided beam distributions of the waveguides were measured by the end-face coupling technique. Comparing with the single-energy implantation, the double-energy implantation improves the light confinement for the dark-mode spectrum. The guiding properties suggest that the carbon-implanted PTR glass waveguides have potential for the manufacture of photonic devices.

  18. Junctionless Diode Enabled by Self-Bias Effect of Ion Gel in Single-Layer MoS2 Device.

    Science.gov (United States)

    Khan, Muhammad Atif; Rathi, Servin; Park, Jinwoo; Lim, Dongsuk; Lee, Yoontae; Yun, Sun Jin; Youn, Doo-Hyeb; Kim, Gil-Ho

    2017-08-16

    The self-biasing effects of ion gel from source and drain electrodes on electrical characteristics of single layer and few layer molybdenum disulfide (MoS 2 ) field-effect transistor (FET) have been studied. The self-biasing effect of ion gel is tested for two different configurations, covered and open, where ion gel is in contact with either one or both, source and drain electrodes, respectively. In open configuration, the linear output characteristics of the pristine device becomes nonlinear and on-off ratio drops by 3 orders of magnitude due to the increase in "off" current for both single and few layer MoS 2 FETs. However, the covered configuration results in a highly asymmetric output characteristics with a rectification of around 10 3 and an ideality factor of 1.9. This diode like behavior has been attributed to the reduction of Schottky barrier width by the electric field of self-biased ion gel, which enables an efficient injection of electrons by tunneling at metal-MoS 2 interface. Finally, finite element method based simulations are carried out and the simulated results matches well in principle with the experimental analysis. These self-biased diodes can perform a crucial role in the development of high-frequency optoelectronic and valleytronic devices.

  19. Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis

    Science.gov (United States)

    Sikora, Grzegorz; Wyłomańska, Agnieszka; Gajda, Janusz; Solé, Laura; Akin, Elizabeth J.; Tamkun, Michael M.; Krapf, Diego

    2017-12-01

    Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface. We specifically study the dynamics of the K+ channel Kv1.4 and the Na+ channel Nav1.6 on the surface of cultured hippocampal neurons at the single-molecule level. We find that both these molecules are expressed in two different forms with distinct kinetics with regards to surface interactions, emphasizing the complex proteomic landscape of the neuronal surface. Further, the tools presented in this work provide new methods for the analysis of membrane nanodomains, transient confinement, and identification of populations within single-particle trajectories.

  20. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    Science.gov (United States)

    Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

    2016-07-01

    The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  1. Investigations on heavy ion induced Single-Event Transients (SETs) in highly-scaled FinFETs

    International Nuclear Information System (INIS)

    Gaillardin, M.; Raine, M.; Paillet, P.; Adell, P.C.; Girard, S.; Duhamel, O.; Andrieu, F.; Barraud, S.; Faynot, O.

    2015-01-01

    We investigate Single-Event Transients (SET) in different designs of multiple-gate devices made of FinFETs with various geometries. Heavy ion experimental results are explained by using a thorough charge collection analysis of fast transients measured on dedicated test structures. Multi-level simulations are performed to get new insights into the charge collection mechanisms in multiple-gate devices. Implications for multiple-gate device design hardening are finally discussed.

  2. Tumor induction in mice after local irradiation with single doses of either carbon-ion beams or gamma rays.

    Science.gov (United States)

    Ando, Koichi; Koike, Sachiko; Ohmachi, Yasushi; Ando, Yutaka; Kobashi, Gen

    2014-12-01

    To determine the dose-dependent relative biological effectiveness (RBE) for tumor prevalence in mice receiving single localized doses to their right leg of either carbon ions (15, 45 or 75 keV/μm) or 137Cs gamma rays. A total of 1647 female C3H mice were irradiated to their hind legs with a localized dose of either reference gamma rays or 15, 45 or 75 keV/μm carbon-ion beams. Irradiated mice were evaluated for tumors twice a month during their three-year life span, and the dimensions of any tumors found were measured with a caliper. The tumor induction frequency was calculated by Kaplan-Meier analysis. The incidence of tumors from 50 Gy of 45 keV/μm carbon ions was marginally higher than those from 50 Gy of gamma rays. However, 60 Gy of 15 keV/μm carbon ions induced significantly fewer tumors than did gamma rays. RBE values of 0.87 + 0.12, 1.29 + 0.08 or 2.06 + 0.39 for lifetime tumorigenesis were calculated for 15, 45 or 75 keV/μm carbon-ion beams, respectively. Fibrosarcoma predominated, with no Linear Energy Transfer (LET)-dependent differences in the tumor histology. Experiments measuring the late effect of leg skin shrinkage suggested that the carcinogenic damage of 15 keV/μm carbon ions would be less than that of gamma rays. We conclude that patients receiving radiation doses to their normal tissues would face less risk of secondary tumor induction by carbon ions of intermediate LET values compared to equivalent doses of photons.

  3. Single daily dosing of antibiotics: importance of in vitro killing rate, serum half-life, and protein binding.

    Science.gov (United States)

    Potel, G; Chau, N P; Pangon, B; Fantin, B; Vallois, J M; Faurisson, F; Carbon, C

    1991-10-01

    The relative importance of pharmacokinetic and pharmacodynamic parameters for the feasibility of a single daily dose (SDD) of antibiotics remains to be established. Therefore, we studied the relationship between in vitro bacteriological parameters (MIC, MBC, and killing rate [KR], defined as the reduction in the inoculum within 3 h), pharmacokinetic parameters (t1/2 and protein binding [PB], and in vivo antibacterial effect of a single antibiotic dose in an experimental rabbit model of Escherichia coli endocarditis. Nine antibiotics were investigated: two aminoglycosides, two quinolones, and five beta-lactams. For each drug, the minimal effective dose (MED) (in milligrams per kilogram) was defined as the lowest dose able to achieve a significant difference (P less than 0.05) of CFU in the vegetations in comparison with controls 24 h after a single intravenous injection. Aminoglycosides and quinolones had the lowest MEDs, followed by beta-lactams. Univariate regression analysis showed that KR was the major determinant of MED. A stepwise regression analysis showed that t1/2 significantly improved the predictive value of KR, while PB, MIC, and MBC did not. The final equation was MED = 1,586-238 KR-297 t1/2 (r = 0.90, P = 0.01). We concluded that the pharmacodynamic parameters (especially the high KR) of aminoglycosides and quinolones explained their low MEDs and might allow SDD. In contrast, the low KR of beta-lactams emphasized the critical importance of a long t1/2, as for ceftriaxone, allowing the use of this beta-lactam alone in SDD.

  4. Determination and shaping of the ion-velocity distribution function in a single-ended Q machine

    DEFF Research Database (Denmark)

    Andersen, S.A.; Jensen, Vagn Orla; Michelsen, Poul

    1971-01-01

    An electrostatic energy analyzer with a resolution better than 0.03 eV was constructed. This analyzer was used to determine the ion-velocity distribution function at different densities and plate temperatures in a single-ended Q machine. In all regions good agreement with theoretical predictions...... based on simple, physical pictures is obtained. It is shown that within certain limits the velocity distribution function can be shaped; double-humped distribution functions have been obtained. The technique used here is suggested as an accurate method for determination of plasma densities within 10......% in single-ended Q machines...

  5. Application of Ann for Prediction of Co2+, Cd2+ and Zn2+ Ions Uptake by R. Squarrosus Biomass in Single and Binary Mixtures

    Directory of Open Access Journals (Sweden)

    Nemeček Peter

    2014-06-01

    Full Text Available Discharge of heavy metals into aquatic ecosystems has become a matter of concern over the last few decades. The search for new technologies involving the removal of toxic metals from wastewaters has directed the attention to biosorption, based on metal binding capacities of various biological materials. Degree of sorbent affinity for the sorbate determines its distribution between the solid and liquid phases and this behavior can be described by adsorption isotherm models (Freundlich and Langmuir isotherm models representing the classical approach. In this study, an artificial neural network (ANN was proposed to predict the sorption efficiency in single and binary component solutions of Cd2+, Zn2+ and Co2+ ions by biosorbent prepared from biomass of moss Rhytidiadelphus squarrosus. Calculated non-linear ANN models presented in this paper are advantageous for its capability of successful prediction, which can be problematic in the case of classical isotherm approach. Quality of prediction was proved by strong agreement between calculated and measured data, expressed by the coefficient of determination in both, single and binary metal systems (R2= 0.996 and R2= 0.987, respectively. Another important benefit of these models is necessity of significantly smaller amount of data (about 50% for the model calculation. Also, it is possible to calculate Qeq for all studied metals by one combined ANN model, which totally overcomes a classical isotherm approach

  6. A novel aptasensor based on single-molecule force spectroscopy for highly sensitive detection of mercury ions.

    Science.gov (United States)

    Li, Qing; Michaelis, Monika; Wei, Gang; Colombi Ciacchi, Lucio

    2015-08-07

    We have developed a novel aptasensor based on single-molecule force spectroscopy (SMFS) capable of detecting mercury ions (Hg(2+)) with sub-nM sensitivity. The single-strand (ss) DNA aptamer used in this work is rich in thymine (T) and readily forms T-Hg(2+)-T complexes in the presence of Hg(2+). The aptamer was conjugated to an atomic force microscope (AFM) probe, and the adhesion force between the probe and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). The presence of Hg(2+) ions above a concentration threshold corresponding to the affinity constant of the ions for the aptamer (about 5 × 10(9) M(-1)) could be easily detected by a change of the measured adhesion force. With our chosen aptamer, we could reach an Hg(2+) detection limit of 100 pM, which is well below the maximum allowable level of Hg(2+) in drinking water. In addition, this aptasensor presents a very high selectivity for Hg(2+) over other metal cations, such as K(+), Ca(2+), Zn(2+), Fe(2+), and Cd(2+). Furthermore, the effects of the ionic strength and loading rate on the Hg(2+) detection were evaluated. Its simplicity, reproducibility, high selectivity and sensitivity make our SMFS-based aptasensor advantageous with respect to other current Hg(2+) sensing methods. It is expected that our strategy can be exploited for monitoring the pollution of water environments and the safety of potentially contaminated food.

  7. A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding.

    Directory of Open Access Journals (Sweden)

    Mousheng Wu

    Full Text Available The HIV-1 Nef accessory protein is essential for viral pathogenicity and AIDS progression. Nef forms complexes with multiple host cell factors to facilitate viral replication and promote immune escape of HIV-infected cells. Previous X-ray crystal structures demonstrate that Nef forms homodimers, the orientation of which are influenced by host cell binding partners. In cell-based fluorescence complementation assays, Nef forms homodimers at the plasma membrane. However, recombinant Nef proteins often exist as monomers in solution, suggesting that membrane interaction may also trigger monomer to dimer transitions. In this study, we show that monomeric Nef core proteins can be induced to form dimers in the presence of low concentrations of the non-ionic surfactant, β-octyl glucoside (βOG. X-ray crystallography revealed that a single βOG molecule is present in the Nef dimer, with the 8-carbon acyl chain of the ligand binding to a hydrophobic pocket formed by the dimer interface. This Nef-βOG dimer interface involves helix αB, as observed in previous dimer structures, as well as a helix formed by N-terminal residues 54-66. Nef dimer formation is stabilized in solution by the addition of βOG, providing biochemical validation for the crystal structure. These observations together suggest that the interaction with host cell lipid mediators or other hydrophobic ligands may play a role in Nef dimerization, which has been previously linked to multiple Nef functions including host cell protein kinase activation, CD4 downregulation, and enhancement of HIV-1 replication.

  8. Correlative single photon emission computed tomography imaging of [123I]altropane binding in the rat model of Parkinson's

    International Nuclear Information System (INIS)

    Gleave, Jacqueline A.; Farncombe, Troy H.; Saab, Chantal; Doering, Laurie C.

    2011-01-01

    Introduction: This study used the dopamine transporter (DAT) probe, [ 123 I]-2β-carbomethoxy-3β-(4-fluorophenyl)-N-(3-iodo-E-allyl)nortropane ([ 123 I]altropane), to assess the DAT levels in the 6-hydroxydopamine rat model of Parkinson's disease. We sought to assess if the right to left [ 123 I]altropane striatal ratios correlated with dopamine content in the striatum and substantia nigra and with behavioural outcomes. Methods: [ 123 I]altropane images taken pre- and postlesion were acquired before and after the transplantation of neural stem/progenitor cells. The images obtained using [ 123 I]altropane and single photon emission computed tomography (SPECT) were compared with specific behavioural tests and the dopamine content assessed by high-performance liquid chromatography. Results: [ 123 I]altropane binding correlated with the content of dopamine in the striatum; however, [ 123 I]altropane binding did not correlate with the dopamine content in the substantia nigra. There was a significant correlation of altropane ratios with the cylinder test and the postural instability test, but not with amphetamine rotations. The low coefficient of determination (r 2 ) for these correlations indicated that [ 123 I]altropane SPECT was not a good predictor of behavioural outcomes. Conclusion: Our data reveal that [ 123 I]altropane predicts the integrity of the striatal dopamine nerve terminals, but does not predict the integrity of the nigrostriatal system. [ 123 I]altropane could be a useful marker to measure dopamine content in cell replacement therapies; however, it would not be able to evaluate outcomes for neuroprotective strategies.

  9. Lithium ions in the van der Waals gap of Bi2Se3 single crystals

    International Nuclear Information System (INIS)

    Bludska, J.; Jakubec, I.; Karamazov, S.; Horak, J.; Uher, C.

    2010-01-01

    Insertion/extraction of lithium ions into/from Bi 2 Se 3 crystals was investigated by means of cyclic voltammetry. The process of insertion is reflected in the appearance of two bands on voltammograms at ∼1.7 and ∼1.5 V, corresponding to the insertion of Li + ions into octahedral and tetrahedral sites of the van der Waals gap of these layered crystals. The process of extraction of Li + ions from the gap results in the appearance of four bands on the voltammograms. The bands 1 and 2 at ∼2.1 and ∼2.3 V correspond to the extraction of a part of Li + guest ions from the octahedral and tetrahedrals sites and this extraction has a character of a reversible intercalation/deintercalation process. A part of Li + ions is bound firmly in the crystal due to the formation of negatively charged clusters of the (LiBiSe 2 .Bi 3 Se 4 - ) type. A further extraction of Li + ions from the van der Waals gap is associated with the presence of bands 3 and 4 placed at ∼2.5 and ∼2.7 V on the voltammograms as their extraction needs higher voltage due to the influence of negative charges localized on these clusters. -- Graphical abstract: Insertion/extraction of lithium ions into/from Bi 2 Se 3 layered crystals was investigated by cyclic voltammetry. The extraction of Li + results in the appearance of four bands on the voltammograms. The first two bands have a character of a reversible process. A part of Li + ions is bound firmly in the crystal due to the formation of negatively charged clusters of the (LiBiSe 2 .Bi 3 Se 4 - ) type. Their extraction needs higher voltage due to the negative charge. Display Omitted

  10. Binding of nickel and zinc ions with activated carbon prepared from sugar cane fibre (Saccharum officinarum L.

    Directory of Open Access Journals (Sweden)

    E.U. Ikhuoria

    2007-04-01

    Full Text Available Activated carbon was prepared from sugar cane fibre by carbonizing at 500 oC for 30 minutes. This was followed by activation with ammonium chloride. The activated carbon was characterised in terms of pH, bulk density, ash content, surface area and surface charge. Equilibrium sorption of nickel and zinc ions by the activated carbon was studied using a range of metal ion concentrations. The sorption data was observed to have an adequate fit for the Langmuir isotherm equation. The level of metal ion uptake was found to be of the order: Ni2+ > Zn2+. The difference in the removal efficiency could be explained in terms of the hydration energy of the metal ions. The distribution coefficient for a range of concentration of the metal ions at the sorbent water interface is found to be higher than the concentration in the continuous phase.

  11. Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans-Expression and characterization.

    Directory of Open Access Journals (Sweden)

    Marcin Olszewski

    Full Text Available DNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the Taq DNA Stoffel domain and a single-stranded DNA binding-like protein of Nanoarchaeum equitans in order to significantly improve the properties of DNA polymerase. The DNA coding sequence of Taq Stoffel DNA polymerase and the nonspecific DNA-binding protein of Nanoarchaeum equitans (NeqSSB-like protein were fused. A novel recombinant gene was obtained which was cloned into the pET-30 Ek/LIC vector and introduced into E. coli for expression. The recombinant enzyme was purified and its enzymatic properties including DNA polymerase activity, PCR amplification rate, thermostability, processivity and resistance to inhibitors, were tested. The yield of the target protein reached approximately 18 mg/l after 24 h of the IPTG induction. The specific activity of the polymerase was 2200 U/mg. The recombinant NeqSSB-TaqS exhibited a much higher extension rate (1000 bp template in 20 s, processivity (19 nt, thermostability (half-life 35 min at 95°C and higher tolerance to PCR inhibitors (0.3-1.25% of whole blood, 0.84-13.5 μg of lactoferrin and 4.7-150 ng of heparin than Taq Stoffel DNA polymerase. Furthermore, our studies show that NeqSSB-TaqS DNA polymerase has a high level of flexibility in relation to Mg2+ ions (from 1 to 5 mM and KCl or (NH42SO4 salts (more than 60 mM and 40 mM, respectively. Using NeqSSB-TaqS DNA polymerase instead of the Taq DNA polymerase could be a better choice in many PCR applications.

  12. Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

    Science.gov (United States)

    Carvalho, Nathalia F; Pliego, Josefredo R

    2015-10-28

    Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

  13. The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2–His2 zinc finger motif

    Science.gov (United States)

    Dathan, Nina; Zaccaro, Laura; Esposito, Sabrina; Isernia, Carla; Omichinski, James G.; Riccio, Andrea; Pedone, Carlo; Di Blasio, Benedetto; Fattorusso, Roberto; Pedone, Paolo V.

    2002-01-01

    The Arabidopsis SUPERMAN (SUP) gene has been shown to be important in maintaining the boundary between stamens and carpels, and is presumed to act by regulating cell proliferation. In this work, we show that the SUP protein, which contains a single Cys2–His2 zinc finger domain including the QALGGH sequence, highly conserved in the plant zinc finger proteins, binds DNA. Using a series of deletion mutants, it was determined that the minimal domain required for specific DNA binding (residues 15–78) includes the single zinc finger and two basic regions located on either side of this motif. Furthermore, amino acid substitutions in the zinc finger or in the basic regions, including a mutation that knocks out the function of the SUP protein in vivo (glycine 63 to aspartate), have been found to abolish the activity of the SUP DNA-binding domain. These results strongly suggest that the SUP protein functions in vivo by acting as a DNA-binding protein, likely involved in transcriptional regulation. The association of both an N-terminal and a C-terminal basic region with a single Cys2–His2 zinc finger represents a novel DNA-binding motif suggesting that the mechanism of DNA recognition adopted by the SUP protein is different from that described so far in other zinc finger proteins. PMID:12433998

  14. ACE applied to the quantitative characterization of benzo-18-crown-6-ether binding with alkali metal ions in a methanol-water solvent system

    Czech Academy of Sciences Publication Activity Database

    Ehala, Sille; Makrlík, E.; Toman, Petr; Kašička, Václav

    2010-01-01

    Roč. 31, č. 4 (2010), s. 702-708 ISSN 0173-0835 R&D Projects: GA ČR(CZ) GA203/08/1428; GA ČR(CZ) GA203/09/0675; GA AV ČR 1ET400500402 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40500505 Keywords : affinity capillary electrophoresis * alkali metal ions * binding constant Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 3.569, year: 2010

  15. Alkyladenine DNA glycosylase (AAG) localizes to mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB).

    Science.gov (United States)

    van Loon, Barbara; Samson, Leona D

    2013-03-01

    Due to a harsh environment mitochondrial genomes accumulate high levels of DNA damage, in particular oxidation, hydrolytic deamination, and alkylation adducts. While repair of alkylated bases in nuclear DNA has been explored in detail, much less is known about the repair of DNA alkylation damage in mitochondria. Alkyladenine DNA glycosylase (AAG) recognizes and removes numerous alkylated bases, but to date AAG has only been detected in the nucleus, even though mammalian mitochondria are known to repair DNA lesions that are specific substrates of AAG. Here we use immunofluorescence to show that AAG localizes to mitochondria, and we find that native AAG is present in purified human mitochondrial extracts, as well as that exposure to alkylating agent promotes AAG accumulation in the mitochondria. We identify mitochondrial single-stranded binding protein (mtSSB) as a novel interacting partner of AAG; interaction between mtSSB and AAG is direct and increases upon methyl methanesulfonate (MMS) treatment. The consequence of this interaction is specific inhibition of AAG glycosylase activity in the context of a single-stranded DNA (ssDNA), but not a double-stranded DNA (dsDNA) substrate. By inhibiting AAG-initiated processing of damaged bases, mtSSB potentially prevents formation of DNA breaks in ssDNA, ensuring that base removal primarily occurs in dsDNA. In summary, our findings suggest the existence of AAG-initiated BER in mitochondria and further support a role for mtSSB in DNA repair. Copyright © 2012. Published by Elsevier B.V.

  16. Interaction of singly and multiply charged ions with a lithium-fluoride surface

    CERN Document Server

    Wirtz, L

    2001-01-01

    Charge transfer between slow ions and an ionic crystal surface still poses a considerable challenge to theory due to the intrinsic many-body character of the system. For the neutralization of multiply charged ions in front of metal surfaces, the Classical Over the Barrier (COB) model is a widely used tool. We present an extension of this model to ionic crystal surfaces where the localization of valence electrons at the anion sites and the lack of cylindrical symmetry of the ion-surface system impede a simple analytical estimate of electron transfer rates. We use a classical trajectory Monte Carlo approach to calculate electron transfer rates for different charge states of the projectile ion. With these rates we perform a Monte Carlo simulation of the neutralization of slow Ne10+ ions in vertical incidence on an LiF surface. Capture of one or several electrons may lead to a local positive charge up of the surface. The projectile dynamics depends on the balance between the repulsion due to this charge and the a...

  17. Dynamic fluorescence spectroscopy on single tryptophan mutants of EIImtl in detergent micelles : Effects of substrate binding and phosphorylation on the fluorescence and anisotropy decay

    NARCIS (Netherlands)

    Swaving Dijkstra, Dolf; Broos, J.; Visser, Antonie J.W.G.; van Hoek, A.; Robillard, George

    1997-01-01

    The effects of substrate and substrate analogue binding and phosphorylation on the conformational dynamics of the mannitol permease of Escherichia coli were investigated, using time-resolved fluorescence spectroscopy on mutants containing five single tryptophans situated in the membrane-embedded C

  18. Single and binary adsorption of heavy metal ions from aqueous solutions using sugarcane cellulose-based adsorbent.

    Science.gov (United States)

    Wang, Futao; Pan, Yuanfeng; Cai, Pingxiong; Guo, Tianxiang; Xiao, Huining

    2017-10-01

    A high efficient and eco-friendly sugarcane cellulose-based adsorbent was prepared in an attempt to remove Pb 2+ , Cu 2+ and Zn 2+ from aqueous solutions. The effects of initial concentration of heavy metal ions and temperature on the adsorption capacity of the bioadsorbent were investigated. The adsorption isotherms showed that the adsorption of Pb 2+ , Cu 2+ and Zn 2+ followed the Langmuir model and the maximum adsorptions were as high as 558.9, 446.2 and 363.3mg·g -1 , respectively, in single component system. The binary component system was better described with the competitive Langmuir isotherm model. The three dimensional sorption surface of binary component system demonstrated that the presence of Pb 2+ decreased the sorption of Cu 2+ , but the adsorption amount of other metal ions was not affected. The result from SEM-EDAX revealed that the adsorption of metal ions on bioadsorbent was mainly driven by coordination, ion exchange and electrostatic association. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Single-ion triblock copolymer electrolytes based on poly(ethylene oxide) and methacrylic sulfonamide blocks for lithium metal batteries

    Science.gov (United States)

    Porcarelli, Luca; Aboudzadeh, M. Ali; Rubatat, Laurent; Nair, Jijeesh R.; Shaplov, Alexander S.; Gerbaldi, Claudio; Mecerreyes, David

    2017-10-01

    Single-ion conducting polymer electrolytes represent the ideal solution to reduce concentration polarization in lithium metal batteries (LMBs). This paper reports on the synthesis and characterization of single-ion ABA triblock copolymer electrolytes comprising PEO and poly(lithium 1-[3-(methacryloyloxy)propylsulfonyl]-1-(trifluoromethylsulfonyl)imide) blocks, poly(LiMTFSI). Block copolymers are prepared by reversible addition-fragmentation chain transfer polymerization, showing low glass transition temperature (-55 to 7 °C) and degree of crystallinity (51-0%). Comparatively high values of ionic conductivity are obtained (up to ≈ 10-4 S cm-1 at 70 °C), combined with a lithium-ion transference number close to unity (tLi+ ≈ 0.91) and a 4 V electrochemical stability window. In addition to these promising features, solid polymer electrolytes are successfully tested in lithium metal cells at 70 °C providing long lifetime up to 300 cycles, and stable charge/discharge cycling at C/2 (≈100 mAh g-1).

  20. Analysis of trace inorganic anions in weak acid salts by single pump cycling-column-switching ion chromatography.

    Science.gov (United States)

    Huang, Zhongping; Ni, Chengzhu; Zhu, Zhuyi; Pan, Zaifa; Wang, Lili; Zhu, Yan

    2015-05-01

    The application of ion chromatography with the single pump cycling-column-switching technique was described for the analysis of trace inorganic anions in weak acid salts within a single run. Due to the hydrogen ions provided by an anion suppressor electrolyzing water, weak acid anions could be transformed into weak acids, existing as molecules, after passing through the suppressor. Therefore, an anion suppressor and ion-exclusion column were adopted to achieve on-line matrix elimination of weak acid anions with high concentration for the analysis of trace inorganic anions in weak acid salts. A series of standard solutions consisting of target anions of various concentrations from 0.005 to 10 mg/L were analyzed, with correlation coefficients r ≥ 0.9990. The limits of detection were in the range of 0.67 to 1.51 μg/L, based on the signal-to-noise ratio of 3 and a 25 μL injection volume. Relative standard deviations for retention time, peak area, and peak height were all less than 2.01%. A spiking study was performed with satisfactory recoveries between 90.3 and 104.4% for all anions. The chromatographic system was successfully applied to the analysis of trace inorganic anions in five weak acid salts. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Single-Event Effects in Power MOSFETs During Heavy Ion Irradiations Performed After Gamma-Ray Degradation

    Science.gov (United States)

    Busatto, G.; De Luca, V.; Iannuzzo, F.; Sanseverino, A.; Velardi, F.

    2013-10-01

    The robustness of commercial power metal-oxide semiconductor field-effect transistors to combined gamma-heavy ion irradiation has been investigated, evidence that the degradation of the gate oxide caused by the γ irradiation can severely corrupt the robustness to single-event effects and drastically modify the physical behavior of the device under test after the impact of a heavy ion. A decrease of the critical voltages at which destructive burnouts and gate ruptures for heavy ion impact appear, has been detected in the devices under test, which were previously irradiated with γ rays. In addition, the amount of critical voltage reduction is strictly related to the amount of the absorbed γ-ray dose. Furthermore, at the failure voltage, the behavior of the device is affected by the conduction of a current through the gate oxide. Moreover, the single-event gate rupture” of the device appears at lower voltages because of the reduction of the Fowler-Nordheim limit in the γ-irradiated devices.

  2. A Nanophase-Separated, Quasi-Solid-State Polymeric Single-Ion Conductor: Polysulfide Exclusion for Lithium–Sulfur Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jinhong; Song, Jongchan; Lee, Hongkyung; Noh, Hyungjun; Kim, Yun-Jung; Kwon, Sung Hyun; Lee, Seung Geol; Kim, Hee-Tak

    2017-04-19

    Formation of soluble polysulfide (PS), which is a key feature of lithium sulfur (Li–S) batteries, provides a fast redox kinetic based on a liquid–solid mechanism; however, it imposes the critical problem of PS shuttle. Here, we address the dilemma by exploiting a solvent-swollen polymeric single-ion conductor (SPSIC) as the electrolyte medium of the Li–S battery. The SPSIC consisting of a polymeric single-ion conductor and lithium salt-free organic solvents provides Li ion hopping by forming a nanoscale conducting channel and suppresses PS shuttle according to the Donnan exclusion principle when being employed for Li–S batteries. The organic solvents at the interface of the sulfur/carbon composite and SPSIC eliminate the poor interfacial contact and function as a soluble PS reservoir for maintaining the liquid–solid mechanism. Furthermore, the quasi-solid-state SPSIC allows the fabrication of a bipolar-type stack, which promises the realization of a high-voltage and energy-dense Li–S battery.

  3. Ion Density Analysis of Single-Stranded DNA in Liquid Crystal

    Science.gov (United States)

    Iwabata, Kazuki; Seki, Yasutaka; Toizumi, Ryota; Shimada, Yuki; Furue, Hirokazu; Sakaguchi, Kengo

    2013-09-01

    With the widespread use of liquid crystals (LCs) in liquid crystal displays, we have looked into the application of liquid crystals in biotechnology. The purpose of the study described here is to investigate the physical properties of DNA using LCs. Synthetic oligonucleotide molecules were dispersed in MLC6884, the sample injected into antiparallel cells, and the amount of mobile ions was measured. The LC cell doped with oligonucleotide molecules showed a sequence-dependent, specific correlation between oligonucleotide concentration and the amount of mobile ions in the LC cells. In the framework of the Stokes model and polyacrylamide gel electrophoresis (PAGE) analysis, we speculate that this result arises from the difference in ion mobility, which is caused by the shape of the oligonucleotide molecule in the LC.

  4. Functional modulation of cerebral gamma-aminobutyric acidA receptor/benzodiazepine receptor/chloride ion channel complex with ethyl beta-carboline-3-carboxylate: Presence of independent binding site for ethyl beta-carboline-3-carboxylate

    Energy Technology Data Exchange (ETDEWEB)

    Taguchi, J.; Kuriyama, K. (Kyoto Prefectural Univ. of Medicine (Japan))

    1990-05-01

    Effect of ethyl beta-carboline-3-carboxylate (beta-CCE) on the function of gamma-aminobutyric acid (GABA)A receptor/benzodiazepine receptor/chloride ion channel complex was studied. Beta-CCE noncompetitively and competitively inhibited (3H)flunitrazepam binding to benzodiazepine receptor, but not (3H)muscimol binding to GABAA receptor as well as t-(3H)butylbicycloorthobenzoate (( 3H) TBOB) binding to chloride ion channel, in particulate fraction of the mouse brain. Ro15-1788 also inhibited competitively (3H) flunitrazepam binding. On the other hand, the binding of beta-(3H)CCE was inhibited noncompetitively and competitively by clonazepam and competitively by Ro15-1788. In agreement with these results, benzodiazepines-stimulated (3H)muscimol binding was antagonized by beta-CCE and Ro15-1788. Gel column chromatography for the solubilized fraction from cerebral particulate fraction by 0.2% sodium deoxycholate (DOC-Na) in the presence of 1 M KCl indicated that beta-(3H)CCE binding site was eluted in the same fraction (molecular weight, 250,000) as the binding sites for (3H)flunitrazepam, (3H)muscimol and (3H)TBOB. GABA-stimulated 36Cl- influx into membrane vesicles prepared from the bovine cerebral cortex was stimulated and attenuated by flunitrazepam and beta-CCE, respectively. These effects of flunitrazepam and beta-CCE on the GABA-stimulated 36Cl- influx were antagonized by Ro15-1788. The present results suggest that the binding site for beta-CCE, which resides on GABAA receptor/benzodiazepine receptor/chloride ion channel complex, may be different from that for benzodiazepine. Possible roles of beta-CCE binding site in the allosteric inhibitions on benzodiazepine binding site as well as on the functional coupling between chloride ion channel and GABAA receptor are also suggested.

  5. Positron bound states on hydride ions in thermochemically reduced MgO single crystals

    International Nuclear Information System (INIS)

    Monge, M.A.; Pareja, R.; Gonzalez, R.; Chen, Y.

    1996-01-01

    Positron-lifetime and Doppler-broadening techniques were used to unambiguously identify positronium hydrides in thermochemically reduced MgO crystals at low temperatures. Positrons trapped at H - ions, forming PsH, yield a lifetime of (640±40) ps, independent of temperature. Complementary evidence for this identification was provided by Doppler-broadening experiments, in which positrons were trapped at H 2- sites at low temperatures. The H 2- ions were formed via H - +e - →H 2- by the capturing of an electron released from Fe + impurity under blue-light stimulation. copyright 1996 The American Physical Society

  6. Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI.

    Science.gov (United States)

    Robbins, Justin B; Murphy, Mary C; White, Bryan A; Mackie, Roderick I; Ha, Taekjip; Cann, Isaac K O

    2004-02-20

    Single-stranded DNA-binding proteins and their functional homologs, replication protein A, are essential components of cellular DNA replication, repair and recombination. We describe here the isolation and characterization of multiple replication protein A homologs, RPA1, RPA2, and RPA3, from the archaeon Methanosarcina acetivorans. RPA1 comprises four single-stranded DNA-binding domains, while RPA2 and RPA3 are each composed of two such domains and a zinc finger domain. Gel filtration analysis suggested that RPA1 exists as homotetramers and homodimers in solution, while RPA2 and RPA3 form only homodimers. Unlike the multiple RPA proteins found in other Archaea and eukaryotes, each of the M. acetivorans RPAs can act as a distinct single-stranded DNA-binding protein. Fluorescence resonance energy transfer and fluorescence polarization anisotropy studies revealed that the M. acetivorans RPAs bind to as few as 10 single-stranded DNA bases. However, more stable binding is achieved with single-stranded DNA of 18-23 bases, and for such substrates the estimated Kd was 3.82 +/- 0.28 nM, 173.6 +/- 105.17 nM, and 5.92 +/- 0.23 nM, for RPA1, RPA2, and RPA3, respectively. The architectures of the M. acetivorans RPAs are different from those of hitherto reported homologs. Thus, these proteins may represent novel forms of replication protein A. Most importantly, our results show that the three RPAs and their combinations highly stimulate the primer extension capacity of M. acetivorans DNA polymerase BI. Although bacterial SSB and eukaryotic RPA have been shown to stimulate DNA synthesis by their cognate DNA polymerases, our findings provide the first in vitro biochemical evidence for the conservation of this property in an archaeon.

  7. Sputtering of lunar regolith simulant by protons and singly and multicharged Ar ions at solar wind energies

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, F.W., E-mail: meyerfw@ornl.gov [Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Harris, P.R.; Taylor, C.N. [Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Meyer III, H.M. [MST Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Barghouty, A.F.; Adams, J.H. [NASA-Marshall Space Flight Center, Huntsville, AL 35812 (United States)

    2011-06-01

    We report preliminary results on sputtering of a lunar regolith simulant at room temperature by singly and multiply charged solar wind ions using quadrupole and time-of-flight (TOF) mass spectrometry approaches. Sputtering of the lunar regolith by solar-wind heavy ions may be an important particle source that contributes to the composition of the lunar exosphere, and is a possible mechanism for lunar surface ageing and compositional modification. The measurements were performed in order to assess the relative sputtering efficiency of protons, which are the dominant constituent of the solar wind, and less abundant heavier multicharged solar wind constituents, which have higher physical sputtering yields than same-velocity protons, and whose sputtering yields may be further enhanced due to potential sputtering. Two different target preparation approaches using JSC-1A AGGL lunar regolith simulant are described and compared using SEM and XPS surface analysis.

  8. Metallization of Single-Stranded Polyl by Zn2+ Ions in Neutral Solutions

    Czech Academy of Sciences Publication Activity Database

    Sorokin, V. A.; Valeev, V. A.; Usenko, E. L.; Andrushchenko, Valery

    2014-01-01

    Roč. 118, č. 43 (2014), s. 12360-12365 ISSN 1520-6106 Institutional support: RVO:61388963 Keywords : nucleic acid metallization * zinc ion * differential UV spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

  9. Spectroscopic properties of LaAlO3 single-crystal doped with Tb3+ ions

    Science.gov (United States)

    Sztolberg, D.; Brzostowski, B.; Dereń, P. J.

    2018-04-01

    LaAlO3 monocrystal doped with 0.5 wt% Tb3+ ions was grown by the Czochralski method. Absorption, emission and emission decay time were measured 300 K in the IR, visible and near UV range. The Tb3+ energy levels in LaAlO3 were assigned both from the absorption and emission spectra.

  10. Single-Ion Deconvolution of Mass Peak Overlaps for Atom Probe Microscopy.

    Science.gov (United States)

    London, Andrew J; Haley, Daniel; Moody, Michael P

    2017-04-01

    Due to the intrinsic evaporation properties of the material studied, insufficient mass-resolving power and lack of knowledge of the kinetic energy of incident ions, peaks in the atom probe mass-to-charge spectrum can overlap and result in incorrect composition measurements. Contributions to these peak overlaps can be deconvoluted globally, by simply examining adjacent peaks combined with knowledge of natural isotopic abundances. However, this strategy does not account for the fact that the relative contributions to this convoluted signal can often vary significantly in different regions of the analysis volume; e.g., across interfaces and within clusters. Some progress has been made with spatially localized deconvolution in cases where the discrete microstructural regions can be easily identified within the reconstruction, but this means no further point cloud analyses are possible. Hence, we present an ion-by-ion methodology where the identity of each ion, normally obscured by peak overlap, is resolved by examining the isotopic abundance of their immediate surroundings. The resulting peak-deconvoluted data are a point cloud and can be analyzed with any existing tools. We present two detailed case studies and discussion of the limitations of this new technique.

  11. Fluorescence-based high-throughput functional profiling of ligand-gated ion channels at the level of single cells.

    Directory of Open Access Journals (Sweden)

    Sahil Talwar

    Full Text Available Ion channels are involved in many physiological processes and are attractive targets for therapeutic intervention. Their functional properties vary according to their subunit composition, which in turn varies in a developmental and tissue-specific manner and as a consequence of pathophysiological events. Understanding this diversity requires functional analysis of ion channel properties in large numbers of individual cells. Functional characterisation of ligand-gated channels involves quantitating agonist and drug dose-response relationships using electrophysiological or fluorescence-based techniques. Electrophysiology is limited by low throughput and high-throughput fluorescence-based functional evaluation generally does not enable the characterization of the functional properties of each individual cell. Here we describe a fluorescence-based assay that characterizes functional channel properties at single cell resolution in high throughput mode. It is based on progressive receptor activation and iterative fluorescence imaging and delivers >100 dose-responses in a single well of a 384-well plate, using α1-3 homomeric and αβ heteromeric glycine receptor (GlyR chloride channels as a model system. We applied this assay with transiently transfected HEK293 cells co-expressing halide-sensitive yellow fluorescent protein and different GlyR subunit combinations. Glycine EC50 values of different GlyR isoforms were highly correlated with published electrophysiological data and confirm previously reported pharmacological profiles for the GlyR inhibitors, picrotoxin, strychnine and lindane. We show that inter and intra well variability is low and that clustering of functional phenotypes permits identification of drugs with subunit-specific pharmacological profiles. As this method dramatically improves the efficiency with which ion channel populations can be characterized in the context of cellular heterogeneity, it should facilitate systems

  12. Radiation-induced effects in MgO single crystal by 200 keV and 1 MeV Ni ion implantation

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Ryohei; Nakai, Yoshihiro; Hamaguchi, Dai [Kyoto Inst. of Tech. (Japan)] [and others

    1997-03-01

    MgO(100) single crystals were implanted with 1.0 MeV and 200 keV Ni ions between 10{sup 15} and 10{sup 17} ions/cm{sup 2} at room temperature. Before and after thermal annealing the radiation damage and the lattice location of implanted Ni ions were analyzed by using Rutherford backscattering spectrometry with channeling and optical absorption measurements. For 1.0 MeV Ni ions, the disorder of Mg atoms increased slowly with ion dose near surface region, while it increased sharply and saturated with ion dose from 2x10{sup 16} ions/cm{sup 2} near ion range. The radiation damage was recovered and implanted Ni ions diffused to the whole of crystal and occupied substitutional positions after 1400degC annealing. For 200 keV Ni ions, the disorder of Mg atoms increased with dose near ion range and had a maximum at about 5x10{sup 16} ions/cm{sup 2}. This tendency agrees with the behavior of color centers obtained from optical measurements. For thermal annealing the radiation damage did not change during 500degC annealing, but the aggregate centers appeared after 300degC annealing. (author)

  13. Conserved epitope on several human vitamin K-dependent proteins: location of the antigenic site and influence of metal ions on antibody binding

    International Nuclear Information System (INIS)

    Church, W.R.; Messier, T.; Howard, P.R.; Amiral, J.; Meyer, D.; Mann, K.G.

    1988-01-01

    A murine monoclonal antibody (designated H-11) produced by injecting mice with purified human protein C was found to bind several human vitamin K-dependent proteins. Using a solid-phase competitive radioimmunoassay with antibody immobilized onto microtiter plates, binding of 125 I-labeled protein C to the antibody was inhibited by increasing amounts of protein C, prothrombin, and Factors X and VII over a concentration range of 1 x 10 -8 to 1 x 10 -6 M. Chemical treatment of prothrombin with a variety of agents did not destroy the antigenic site recognized by the antibody as measured by immunoblotting of prothrombin or prothrombin derivative immobilized onto nitrocellulose. Immunoblotting of purified vitamin K-dependent polypeptides with the monoclonal antibody following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrophoretic transfer to nitrocellulose indicated that the antigenic site was found on the light chains of protein C and Factor X. The exact location of the antigenic determinant for antibody H-11 was established using synthetic peptides. Comparison of protein sequences of bovine and human vitamin K-dependent proteins suggests that the sequence Phe-Leu-Glu-Glu-Xaa-Arg/Lys is required for antibody binding. Increasing concentrations of Ca 2+ , Mg 2+ , or Mn 2+ partially inhibited binding of 125 I-protein C to the antibody in a solid-phase assay system with half-maximal binding observed at divalent metal ion concentrations of 2, 4, and 0.6 mM, respectively. The antigenic site thus recognized by monoclonal antibody H-11 is located at the amino-terminal region in the highly conserved γ-carboxyglutamic acid-containing domains of several, but not all, vitamin K-dependent proteins

  14. Novel short-chain analogues of somatostatin as ligands for Cu(II) ions. Role of the metal ion binding on the spatial structure of the ligand.

    Science.gov (United States)

    Marciniak, Aleksandra; Cebrat, Marek; Czyżnikowska, Żaneta; Brasuń, Justyna

    2012-12-01

    In this paper we present the studies on coordination abilities of two short-chain analogues of somatostatin with free N-terminal and protected amino group towards copper (II) ions. The octreotide is the most popular analogue of the somatostatin (peptide hormone) used in medicine. Somatostatin analogues are used in diagnosis and treatment of the neuroendocrine tumors. Both analyzed analogues are characterized by the presence of two His instead of Cys residues in characteristic fragment of native peptide. We characterize coordination abilities of the ligands using potentiometric and spectroscopic methods. His-analogues of somatostatin are effective ligands for copper (II) ions. Both peptides are able to form the complexes with the cyclic structure. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Generation of vacancy cluster-related defects during single MeV silicon ion implantation of silicon

    Energy Technology Data Exchange (ETDEWEB)

    Pastuović, Ž., E-mail: zkp@ansto.gov.au [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC NSW 2232 (Australia); Capan, I. [Ruđer Bošković Institute, Bijenička cesta 54, P.O. Box 180, 10002 Zagreb (Croatia); Siegele, R. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC NSW 2232 (Australia); Jačimović, R. [Jozef Stefan Institute, 1000 Ljubljana (Slovenia); Forneris, J. [Physics Department and NIS Excellence Centre, University of Torino, INFN – sez. Torino, CNISM – sez. Torino, via P. Giuria 1, 10125 Torino (Italy); Cohen, D.D. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC NSW 2232 (Australia); Vittone, E. [Physics Department and NIS Excellence Centre, University of Torino, INFN – sez. Torino, CNISM – sez. Torino, via P. Giuria 1, 10125 Torino (Italy)

    2014-08-01

    Deep Level Transient Spectroscopy (DLTS) has been used to study defects formed in bulk silicon after implantation of 8.3 MeV {sup 28}Si{sup 3+} ions at room temperature. For this study, Schottky diodes prepared from n-type Czohralski-grown silicon wafers have been implanted in the single ion regime up to fluence value of 1 × 10{sup 10} cm{sup −2} utilizing the scanning focused ion microbeam as implantation tool and the Ion Beam Induced Current (IBIC) technique for ion counting. Differential DLTS analysis of the vacancy-rich region in self-implanted silicon reveals a formation of the broad vacancy-related defect state(s) at E{sub c} −0.4 eV. Direct measurements of the electron capture kinetics associated with this trap at E{sub c} −0.4 eV, prior to any annealing do not show an exponential behaviour typical for the simple point-like defects. The logarithmic capture kinetics is in accordance with the theory of majority carrier capture at extended or cluster-related defects. We have detected formation of two deep electron traps at E{sub c} −0.56 eV and E{sub c} −0.61 eV in the interstitial-rich region of the self-implanted silicon, before any annealing. No DLTS signal originating from vacancy-oxygen trap at E{sub c} −0.17 eV, present in the sample irradiated with 0.8 MeV neutrons, has been recorded in the self-implanted sample.

  16. Comparison of single and mixed ion implantation effects on the changes of the surface hardness, light transmittance, and electrical conductivity of polymeric materials

    International Nuclear Information System (INIS)

    Park, J. W.; Lee, J. H.; Lee, J. S.; Kil, J. G.; Choi, B. H.; Han, Z. H.

    2001-01-01

    Single or mixed ions of N, He, C were implanted onto the transparent PET(Polyethylen Terephtalate) with the ion energies of less than 100 keV and the surface hardness, light transmittance and electrical conductivity were examined. As measured with nanoindentation, mixed ion implantations such as N + +He + or N + + C + exhibited more increase in the surface hardness than the single ion implantation. Especially, implantation of C+N ions increased the surface hardness by about three times as compared to the implantation of N ion alone, which means more than 10 times increase than the untreated PET. Surface electrical conductivity was increased along with the hardness increase. The conductivity increase was more proportional to the hardness when used the higher ion energy and ion dose, while it did not show any relationship at as low as 50 keV of ion energy. The light at the 550 nm wavelength (visual range) transmitted more than 85%, which is close to that of as-received PET, and at the wavelength below 300 nm(UV range) the rays were absorbed more than 95% as traveling through the sheet, implying that there are processing parameters which the ion implanted PET maintains the transparency and absorbs the UV rays

  17. Inhibition by divalent metal ions of human histidine triad nucleotide binding protein1 (hHint1), a regulator of opioid analgesia and neuropathic pain.

    Science.gov (United States)

    Shah, Rachit; Chou, Tsui-Fen; Maize, Kimberly M; Strom, Alexander; Finzel, Barry C; Wagner, Carston R

    2017-09-23

    Human histidine triad nucleotide binding protein 1 (hHint1) is a purine nucleoside phosphoramidase and adenylate hydrolase that has emerged as a potential therapeutic target for the management of pain. However, the molecular mechanism of Hint1 in the signaling pathway has remained less clear. The role of metal ions in regulating postsynaptic transmission is well known, and the active site of hHint1 contains multiple histidines. Here we have investigated the effect of divalent metal ions (Cd 2+ , Cu 2+ , Mg 2+ , Mn 2+ , Ni 2+ , and Zn 2+ ) on the structural integrity and catalytic activity of hHint1. With the exception of Mg 2+ , all the divalent ions inhibited hHint1, the rank of order was found to be Cu 2+ >Zn 2+ >Cd 2+ ≥Ni 2+ >Mn 2+ based on their IC 50 and k in /K I values. A crystal structure of hHint1 with bound Cu 2+ is described to explain the competitive reversible inactivation of hHint1 by divalent cations. All the metal ions exhibited time- and concentration- dependent inhibition, with the rate of inactivation highly dependent on alterations of the C-terminus. With the exception of Cu 2+ ; restoration of inhibition was observed for all the metal ions after treatment with EDTA. Our studies reveal a loss in secondary structure and aggregation of hHint1 upon incubation with 10-fold excess of copper. Thus, hHint1 appears to be structurally sensitive to irreversible inactivation by copper, which may be of neurotoxicological and pharmacological significance. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Demonstration of a reduction in muscarinic receptor binding in early Alzheimer's disease using iodine-123 dexetimide single-photon emission tomography

    International Nuclear Information System (INIS)

    Claus, J.J.; Dubois, E.A.; Booij, J.; Habraken, J.; Munck, J.C. van; Herk, M. van; Verbeeten, B. Jr.; Royen, E.A. van

    1997-01-01

    Decreased muscarinic receptor binding has been suggested in single-photon emission tomography (SPET) studies of Alzheimer's disease. However, it remains unclear whether these changes are present in mildly demented patients, and the role of cortical atrophy in receptor binding assessment has not been investigated. We studied muscarinic receptor binding normalized to neostriatum with SPET using [ 123 I[4-iododexetimide in five mildly affected patients with probable Alzheimer's disease and in five age-matched control subjects. Region of interest (ROI) analysis was performed in a consensus procedure blind to clinical diagnosis using matched magnetic resonance (MRI) images. Cortical atrophy was assessed by calculating percentages of cerebrospinal fluid in each ROI. An observer study with three observers was conducted to validate this method. Alzheimer patients showed statistically significantly less [ 123 I[4-iododexetimide binding in left temporal and right temporo-parietal cortex compared with controls, independent of age, sex and cortical atrophy. Mean intra-observer variability was 3.6% and inter-observer results showed consistent differences in [ 123 I[4-iododexetimide binding between observers. However, differences between patients and controls were comparable among observers and statistically significant in the same regions as in the consensus procedure. Using an MRI-SPET matching technique, we conclude that [ 123 I[4-iododexetimide binding is reduced in patients with mild probable Alzheimer's disease in areas of temporal and temporo-parietal cortex. (orig.). With 1 fig., 4 tabs

  19. Phase diagrams of the ternary alloy with a single-ion anisotropy in the mean-field approximation

    International Nuclear Information System (INIS)

    Dely, J.; Bobak, A.

    2006-01-01

    The phase diagram of the AB p C 1-p ternary alloy consisting of Ising spins S A =32, S B =2, and S C =52 is investigated by the use of a mean-field theory based on the Bogoliubov inequality for the Gibbs free energy. The effect of the single-ion anisotropy on the phase diagrams is discussed by changing values of the parameters in the model Hamiltonian and comparison is made with the recently reported finite-temperature phase diagrams for the ternary alloy having spin S B =1

  20. The influence of elastic subsystem on phase transitions in ferromagnets with competitive exchange and single-ion anisotropies

    International Nuclear Information System (INIS)

    Freedman, Yu.A.; Klevets, F.N.; Matunin, D.A.

    2006-01-01

    The influence of planar and bulk elastic interactions on the phase states of an ultrathin ferromagnetic film with anisotropic exchange interaction is investigated for different relationships among the material constants. It is shown that when the elastic interactions, with competing exchange and single-ion anisotropies, and the magnetic dipole interaction are taken into account, a cascade of phase transitions appears. Furthermore, taking the 'planar' elastic interaction into account leads to realization of an additional phase, with an easy axis in the film plane. This state is absent in the case of a bulk elastic subsystem

  1. Ion sensing method

    Science.gov (United States)

    Smith, Richard Harding; Martin, Glenn Brian

    2004-05-18

    The present invention allows the determination of trace levels of ionic substances in a sample solution (ions, metal ions, and other electrically charged molecules) by coupling a separation method, such as liquid chromatography, with ion selective electrodes (ISE) prepared so as to allow detection at activities below 10.sup.-6 M. The separation method distributes constituent molecules into fractions due to unique chemical and physical properties, such as charge, hydrophobicity, specific binding interactions, or movement in an electrical field. The separated fractions are detected by means of the ISE(s). These ISEs can be used singly or in an array. Accordingly, modifications in the ISEs are used to permit detection of low activities, specifically, below 10.sup.-6 M, by using low activities of the primary analyte (the molecular species which is specifically detected) in the inner filling solution of the ISE. Arrays constructed in various ways allow flow-through sensing for multiple ions.

  2. Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

    Science.gov (United States)

    Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Gadura, N.; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T. D.

    2009-08-01

    The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

  3. UPregulated single-stranded DNA-binding protein 1 induces cell chemoresistance to cisplatin in lung cancer cell lines.

    Science.gov (United States)

    Zhao, Xiang; He, Rong; Liu, Yu; Wu, Yongkai; Kang, Leitao

    2017-07-01

    Cisplatin and its analogues are widely used as anti-tumor drugs in lung cancer but many cisplatin-resistant lung cancer cases have been identified in recent years. Single-stranded DNA-binding protein 1 (SSDBP1) can effectively induce H69 cell resistance to cisplatin in our previous identification; thus, it is necessary to explore the mechanism underlying the effects of SSDBP1-induced resistance to cisplatin. First, SSDBP1-overexpressed or silent cell line was constructed and used to analyze the effects of SSDBP1 on chemoresistance of lung cancer cells to cisplatin. SSDBP1 expression was assayed by real-time PCR and Western blot. Next, the effects of SSDBP1 on cisplatin sensitivity, proliferation, and apoptosis of lung cancer cell lines were assayed by MTT and flow cytometry, respectively; ABC transporters, apoptosis-related genes, and cell cycle-related genes by real-time PCR, and DNA wound repair by comet assay. Low expression of SSDBP1 was observed in H69 cells, while increased expression in cisplatin-resistant H69 cells. Upregulated expression of SSDBP1 in H69AR cells was identified to promote proliferation and cisplatin resistance and inhibit apoptosis, while downregulation of SSDBP1 to inhibit cisplatin resistance and proliferation and promoted apoptosis. Moreover, SSDBP1 promoted the expression of P2gp, MRP1, Cyclin D1, and CDK4 and inhibited the expression of caspase 3 and caspase 9. Furthermore, SSDBP1 promoted the DNA wound repair. These results indicated that SSDBP1 may induce cell chemoresistance of cisplatin through promoting DNA repair, resistance-related gene expression, cell proliferation, and inhibiting apoptosis.

  4. Effects of Metal Ions on Conductivity and Structure of Single DNA Molecule in Different Environmental Conditions

    Directory of Open Access Journals (Sweden)

    Dong Ruixin

    2010-01-01

    Full Text Available Abstract We design a novel nano-gap electrode to measure the current of DNA molecule, by which the current–voltage characteristics of individual native DNA, Ag-DNA and Ni-DNA molecules are obtained, respectively. The results show that the voltage gap of Ag- and Ni-DNA is higher than that of native DNA, and the conductance is lower than native DNA in neutral environment. The structure transition from B- to Z-DNA is observed in the presence of high concentrations of nickel ions and Ag-DNA appears chaos state by STM image and U-V spectra characterization. But in alkaline environment, the conductance of Ni-DNA rises and the voltage gap decreases with the increasing of nickel ion concentration denotes that the conductive ability of Ni-DNA is higher than that of native DNA.

  5. Simple and cooperative electrostatic binding of amonium ions to phosphate-polyions: NMR, infrared and theoretical study

    Czech Academy of Sciences Publication Activity Database

    Kříž, Jaroslav; Dybal, Jiří

    2004-01-01

    Roč. 108, č. 26 (2004), s. 9306-9314 ISSN 1520-6106 R&D Projects: GA AV ČR KSK4050111 Institutional research plan: CEZ:AV0Z4050913 Keywords : cooperative interactions * electrostatic binding * hydrophobic interactions Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.834, year: 2004

  6. Formation of Mixed-Ligand Complexes of Pd2+ with Nucleoside 5'-Monophosphates and Some Metal-Ion-Binding Nucleoside Surrogates

    Directory of Open Access Journals (Sweden)

    Oleg Golubev

    2014-10-01

    Full Text Available Formation of mixed-ligand Pd2+ complexes between canonical nucleoside 5'-monophosphates and five metal-ion-binding nucleoside analogs has been studied by 1H-NMR spectroscopy to test the ability of these nucleoside surrogates to discriminate between unmodified nucleobases by Pd2+-mediated base pairing. The nucleoside analogs studied included 2,6-bis(3,5-dimethylpyrazol-1-yl-, 2,6-bis(1-methylhydrazinyl- and 6-(3,5-dimethylpyrazol-1-yl-substituted 9-(β-d-ribofuranosylpurines 1–3, and 2,4-bis(3,5-dimethylpyrazol-1-yl- and 2,4-bis(1-methylhydrazinyl-substituted 5-(β-d-ribofuranosyl-pyrimidines 4–5. Among these, the purine derivatives 1-3 bound Pd2+ much more tightly than the pyrimidine derivatives 4, 5 despite apparently similar structures of the potential coordination sites. Compounds 1 and 2 formed markedly stable mixed-ligand Pd2+ complexes with UMP and GMP, UMP binding favored by 1 and GMP by 2. With 3, formation of mixed-ligand complexes was retarded by binding of two molecules of 3 to Pd2+.

  7. Development of a single ion micro-irradiation facility for experimental radiobiology at cell level

    International Nuclear Information System (INIS)

    Barberet, Ph.

    2003-10-01

    A micro-irradiation device has been developed for radiobiology applications at the scale of the cell. This device is based on an upgrade of an existing micro-beam line that was already able to deliver a 1 to 3 MeV proton or alpha beam of low intensity and whose space resolution is lower than 1 micrometer in vacuum. The important part of this work has been the development of an irradiation stage designed to fit on the micro-probe and able to deliver ions in the air with an absolute accuracy of a few micrometers. A program has been set up to monitor the complete irradiation line in testing and in automatic irradiation operating phases. Simulation tools based on Monte-Carlo calculations have been validated through comparisons with experimental data particularly in the field of spatial resolution and of the number of ions delivered. The promising results show the possibility in a near future to use this tool to study the response of cells to very low irradiation doses down to the extreme limit of one ion per cell

  8. Spectroscopic capture and reactivity of a low-spin cobalt(IV)-oxo complex stabilized by binding redox-inactive metal ions.

    Science.gov (United States)

    Hong, Seungwoo; Pfaff, Florian Felix; Kwon, Eunji; Wang, Yong; Seo, Mi-Sook; Bill, Eckhard; Ray, Kallol; Nam, Wonwoo

    2014-09-22

    High-valent cobalt-oxo intermediates are proposed as reactive intermediates in a number of cobalt-complex-mediated oxidation reactions. Herein we report the spectroscopic capture of low-spin (S=1/2) Co(IV)-oxo species in the presence of redox-inactive metal ions, such as Sc(3+), Ce(3+), Y(3+), and Zn(2+), and the investigation of their reactivity in C-H bond activation and sulfoxidation reactions. Theoretical calculations predict that the binding of Lewis acidic metal ions to the cobalt-oxo core increases the electrophilicity of the oxygen atom, resulting in the redox tautomerism of a highly unstable [(TAML)Co(III)(O˙)](2-) species to a more stable [(TAML)Co(IV)(O)(M(n+))] core. The present report supports the proposed role of the redox-inactive metal ions in facilitating the formation of high-valent metal-oxo cores as a necessary step for oxygen evolution in chemistry and biology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Radiation damage induced in Al2O3 single crystal by 90 MeV Xe ions

    Science.gov (United States)

    Zirour, H.; Izerrouken, M.; Sari, A.

    2015-12-01

    Radiation damage induced in Al2O3 single crystal by 90 MeV Xe ions were investigated by optical absorption measurements, Raman spectroscopy and X-ray diffraction (XRD) techniques. The irradiations were performed at the GANIL accelerator in Caen, France for the fluence in the range from 1012 to 6 × 1013 cm-2 at room temperature under normal incidence. The F+ and F2+enters kinetic as a function of fluence deduced from the optical measurements explains that the single defects (F and F+) aggregate to F center clusters (F2 , F2+, F22+) during irradiation at high fluence (>1013 cm-2). Raman and XRD analysis reveal a partial disorder of 40% of Al2O3 in the studied fluence range in accordance with Kabir et al. (2008) study. The result suggests that this is due to the stress relaxation process which occurs at high fluence (>1013 cm-2).

  10. Hyperfine-Interaction-Driven Suppression of Quantum Tunneling at Zero Field in a Holmium(III) Single-Ion Magnet.

    Science.gov (United States)

    Chen, Yan-Cong; Liu, Jun-Liang; Wernsdorfer, Wolfgang; Liu, Dan; Chibotaru, Liviu F; Chen, Xiao-Ming; Tong, Ming-Liang

    2017-04-24

    An extremely rare non-Kramers holmium(III) single-ion magnet (SIM) is reported to be stabilized in the pentagonal-bipyramidal geometry by a phosphine oxide with a high energy barrier of 237(4) cm -1 . The suppression of the quantum tunneling of magnetization (QTM) at zero field and the hyperfine structures originating from field-induced QTMs can be observed even from the field-dependent alternating-current magnetic susceptibility in addition to single-crystal hysteresis loops. These dramatic dynamics were attributed to the combination of the favorable crystal-field environment and the hyperfine interactions arising from 165 Ho (I=7/2) with a natural abundance of 100 %. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Hyperfine-interaction-driven suppression of quantum tunneling at zero field in a holmium(III) single-ion magnet

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yan-Cong; Liu, Jun-Liang; Chen, Xiao-Ming; Tong, Ming-Liang [Key Lab. of Bioinorganic and Synthetic Chemistry of Ministry of Education, School of Chemistry, Sun Yat-Sen Univ., Guangzhou (China); Wernsdorfer, Wolfgang [Institut Neel, CNRS and Universite Joseph Fournier, Grenoble (France); Institute of Nanotechnology, Karlsruhe Institute of Technology (Germany); Physikalisches Institut, Karlsruhe Institute of Technology (Germany); Liu, Dan; Chibotaru, Liviu F. [Theory of Nanomaterials Group and INPAC-Institute of Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven (Belgium)

    2017-04-24

    An extremely rare non-Kramers holmium(III) single-ion magnet (SIM) is reported to be stabilized in the pentagonal-bipyramidal geometry by a phosphine oxide with a high energy barrier of 237(4) cm{sup -1}. The suppression of the quantum tunneling of magnetization (QTM) at zero field and the hyperfine structures originating from field-induced QTMs can be observed even from the field-dependent alternating-current magnetic susceptibility in addition to single-crystal hysteresis loops. These dramatic dynamics were attributed to the combination of the favorable crystal-field environment and the hyperfine interactions arising from {sup 165}Ho (I=7/2) with a natural abundance of 100 %. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Fabrication of single-crystal silicon nanotubes with sub-10 nm walls using cryogenic inductively coupled plasma reactive ion etching

    Science.gov (United States)

    Li, Zhiqin; Chen, Yiqin; Zhu, Xupeng; Zheng, Mengjie; Dong, Fengliang; Chen, Peipei; Xu, Lihua; Chu, Weiguo; Duan, Huigao

    2016-09-01

    Single-crystal silicon nanostructures have attracted much attention in recent years due in part to their unique optical properties. In this work, we demonstrate direct fabrication of single-crystal silicon nanotubes with sub-10 nm walls which show low reflectivity. The fabrication was based on a cryogenic inductively coupled plasma reactive ion etching process using high-resolution hydrogen silsesquioxane nanostructures as the hard mask. Two main etching parameters including substrate low-frequency power and SF6/O2 flow rate ratio were investigated to determine the etching mechanism in the process. With optimized etching parameters, high-aspect-ratio silicon nanotubes with smooth and vertical sub-10 nm walls were fabricated. Compared to commonly-used antireflection silicon nanopillars with the same feature size, the densely packed silicon nanotubes possessed a lower reflectivity, implying possible potential applications of silicon nanotubes in photovoltaics.

  13. Optical parameters and dispersion behavior of potassium magnesium chloride sulfate single crystals doped with Co+2 ions.

    Science.gov (United States)

    Abu El-Fadl, A; Abd-Elsalam, A M

    2018-05-05

    Single crystals of potassium magnesium chloride sulfate (KMCS) doped with cobalt ions were grown by slow cooling method. Powder XRD study confirmed the monoclinic structure of the grown crystals. The functional group vibrations were checked through FTIR spectroscopy measurements. In optical studies, the absorbance behavior of the crystals and their optical energy gap were established by Tauc plot. The refractive index, the extinction coefficient and other optical constants were calculated for the grown crystals. The normal dispersion of the refractive index was analyzed according to single oscillator Sellmeier's model. The Urbach's rule was applied to analyze the localized states density in the forbidden gap. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    Science.gov (United States)

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. Copyright © 2012 Elsevier

  15. Surgical cardiac denervation therapy for treatment of congenital ion channelopathies in pediatric patients: a contemporary, single institutional experience.

    Science.gov (United States)

    Costello, John P; Wilson, Jennifer K; Louis, Clauden; Peer, Syed M; Zurakowski, David; Nadler, Evan P; Qureshi, Faisal G; Jonas, Richard A; Greene, E Anne; Berul, Charles I; Moak, Jeffrey P; Nath, Dilip S

    2015-01-01

    Congenital ion channel disorders, including congenital long QT syndrome (LQTS), cause significant morbidity in pediatric patients. When medication therapy does not control symptoms or arrhythmias, more invasive treatment strategies may be necessary. This study examines our institution's clinical experience with surgical cardiac denervation therapy for management of these arrhythmogenic disorders in children. An institutional review board-approved retrospective review identified ten pediatric patients with congenital ion channelopathies who underwent surgical cardiac denervation therapy at a single institution between May 2011 and April 2014. Eight patients had a diagnosis of congenital LQTS, two patients were diagnosed with catecholaminergic polymorphic ventricular tachycardia (CPVT). All patients underwent sympathectomy and partial stellate ganglionectomy via video-assisted thoracoscopic surgery (VATS). Six of the ten patients had documented ventricular arrhythmias preoperatively, and 70% of the patients had preoperative syncope. The corrected QT interval decreased in 75% of patients with LQTS following sympathectomy. Postoperative arrhythmogenic symptoms were absent in 88% of congenital LQTS patients, but both patients with CPVT continued to have symptoms throughout the duration of follow-up. All patients were alive after a median follow-up period of 10 months. Surgical cardiac denervation therapy via VATS is a useful treatment strategy for congenital LQTS patients who fail medical management, and its potential benefit in the management of CPVT is unclear. A prospective comparison of the efficacy of surgical cardiac denervation therapy and implantable cardioverter-defibrillator use in congenital ion channelopathies is timely and crucial. © The Author(s) 2014.

  16. Enzymatically mediated bioprecipitation of heavy metals from industrial wastes and single ion solutions by mammalian alkaline phosphatase.

    Science.gov (United States)

    Chaudhuri, Gouri; Shah, Gaurav A; Dey, Pritam; S, Ganesh; Venu-Babu, P; Thilagaraj, W Richard

    2013-01-01

    The study was aimed at investigating the potential use of calf intestinal alkaline phosphatase (CIAP) enzyme in the removal of heavy metals (Cd(2+), Ni(2+), Co(2+) and Cr(3+/6+)) from single ion solutions as well as tannery and electroplating effluents. CIAP mediated bioremediation (white biotechnology) is a novel technique that is eco-friendly and cost effective unlike the conventional chemical technologies. Typical reactions containing the enzyme (CIAP) and p-nitrophenyl phosphate (pNPP) as substrate in Tris-HCl buffer (pH 8 and 11) and either single ion metal solutions (250 ppm and 1000 ppm) or effluents from tannery or electroplating industry were incubated at 37°C for 30 min, 60 min and 120 min. The inorganic phosphate (P(i)) generated due to catalytic breakdown of pNPP complexes free metal ions as metal-phosphate and the amount of metal precipitated was derived by estimating the reduction in the free metal ion present in the supernatant of reactions employing atomic absorption spectrophotometer (AAS). Better precipitation of metal was obtained at pH 11 than at pH 8 and between the two concentrations of different metals tested, an initial metal concentration of 250 ppm in the reaction gave more precipitation than with 1000 ppm. Experimental data showed that at pH 11, the percentage of removal of metal ions (for an initial concentration of 250 ppm) was in the following order: Cd(2+) (80.99%) > Ni(2+) (64.78%) > Cr(3+) > (46.15%) > Co(2+) (36.47%) > Cr(6+) (32.33%). The overall removal of Cr(3+) and Cr(6+) from tannery effluent was 32.77% and 37.39% respectively in 120 min at pH 11. Likewise, the overall removal of Cd(2+), Co(2+) and Ni(2+) from electroplating effluent was 50.42%, 13.93% and 38.64% respectively in 120 min at pH 11. The study demonstrates that bioprecipitation by CIAP may be a viable and environmental friendly method for clean-up of heavy metals from tannery and electroplating effluents.

  17. Mesodermal repression of single-minded in Drosophila embryo is mediated by a cluster of Snail-binding sites proximal to the early promoter

    Directory of Open Access Journals (Sweden)

    Kye Won Park1 & Joung-Woo Hong2,*

    2012-10-01

    Full Text Available single-minded (sim is a master regulatory gene that directs differentiationin the central nervous system during Drosophilaembryogenesis. Recent identification of the mesectoderm enhancer(MSE of sim has led to the hypothesis that two Snail(Sna-binding sites in the MSE may repress sim expression inthe presumptive mesoderm. We provide evidence here thatthree Sna-binding sites proximal to the sim promoter, but notthose of the MSE, are responsible for the mesodermal repressionof sim in vivo. Using transgenic embryos injectedwith lacZ transgenes, we showed that sim repression in themesoderm requires the three promoter-proximal Sna-bindingsites. These results suggest that Sna represses the mesectodermalexpression of sim by directly repressing the nearby promoter,and not by quenching adjacent transcriptional activatorsin the MSE. These data also showed how the MSE, lackingthe three proximal Sna-binding sites, reproduced the endogenouspattern of sim expression in transgenic embryos.

  18. Quantifying the binding strength of salicylaldoxime-uranyl complexes relative to competing salicylaldoxime-transition metal ion complexes in aqueous solution: a combined experimental and computational study.

    Science.gov (United States)

    Mehio, Nada; Ivanov, Alexander S; Williams, Neil J; Mayes, Richard T; Bryantsev, Vyacheslav S; Hancock, Robert D; Dai, Sheng

    2016-05-31

    The design of new ligands and investigation of UO2(2+) complexations are an essential aspect of reducing the cost of extracting uranium from seawater, improving the sorption efficiency for uranium and the selectivity for uranium over competing ions (such as the transition metal cations). The binding strengths of salicylaldoxime-UO2(2+) complexes were quantified for the first time and compared with the binding strengths of salicylic acid-UO2(2+) and representative amidoxime-UO2(2+) complexes. We found that the binding strengths of salicylaldoxime-UO2(2+) complexes are ∼2-4 log β2 units greater in magnitude than their corresponding salicylic acid-UO2(2+) and representative amidoxime-UO2(2+) complexes; moreover, the selectivity of salicylaldoxime towards the UO2(2+) cation over competing Cu(2+) and Fe(3+) cations is far greater than those reported for salicylic acid and glutarimidedioxime in the literature. The higher UO2(2+) selectivity can likely be attributed to the different coordination modes observed for salicylaldoxime-UO2(2+) and salicylaldoxime-transition metal complexes. Density functional theory calculations indicate that salicylaldoxime can coordinate with UO2(2+) as a dianion species formed by η(2) coordination of the aldoximate and monodentate binding of the phenolate group. In contrast, salicylaldoxime coordinates with transition metal cations as a monoanion species via a chelate formed between phenolate and the oxime N; the complexes are stabilized via hydrogen bonding interactions between the oxime OH group and phenolate. By coupling the experimentally determined thermodynamic constants and the results of theoretical computations, we are able to derive a number of ligand design principles to further improve the UO2(2+) cation affinity, and thus further increase the selectivity of salicylaldoxime derivatives.

  19. Deep reactive ion etching of fused silica using a single-coated soft mask layer for bio-analytical applications

    International Nuclear Information System (INIS)

    Ray, Tathagata; Zhu, Haixin; Meldrum, Deirdre R

    2010-01-01

    In this note, we present our results from process development and characterization of reactive ion etching (RIE) of fused silica using a single-coated soft masking layer (KMPR® 1025, Microchem Corporation, Newton, MA). The effects of a number of fluorine-radical-based gaseous chemistries, the gas flow rate, RF power and chamber pressure on the etch rate and etching selectivity of fused silica were studied using factorial experimental designs. RF power and pressure were found to be the most important factors in determining the etch rate. The highest fused silica etch rate obtained was about 933 Å min −1 by using SF 6 -based gas chemistry, and the highest etching selectivity between the fused silica and KMPR® 1025 was up to 1.2 using a combination of CF 4 , CHF 3 and Ar. Up to 30 µm deep microstructures have been successfully fabricated using the developed processes. The average area roughness (R a ) of the etched surface was measured and results showed it is comparable to the roughness obtained using a wet etching technique. Additionally, near-vertical sidewalls (with a taper angle up to 85°) have been obtained for the etched microstructures. The processes developed here can be applied to any application requiring fabrication of deep microstructures in fused silica with near-vertical sidewalls. To our knowledge, this is the first note on deep RIE of fused silica using a single-coated KMPR® 1025 masking layer and a non-ICP-based reactive ion etcher. (technical note)

  20. The structural and compositional analysis of single crystal surfaces using low energy ion scattering

    International Nuclear Information System (INIS)

    Armour, D.G.; Van der Berg, J.A.; Verheij, IL.K.

    1979-01-01

    The use of ion scattering for surface composition and structure analysis has been reviewed. The extreme surface specificity of this technique has been widely used to obtain quitative information in a straightforward way, but the/aolc/currence of charge exchange processes, thermal lattice vibrations and multiple scattering have precluded quantitative analysis of experimental data. Examples are quoted to illustrate the progress that has been made in understanding these fundamental processes and in applying this knowledge to the development of the analytical capabilities of the technique. (author)

  1. Giant plasmon excitation in single and double ionization of C60 by fast highly charged Si and O ions

    Science.gov (United States)

    Kelkar, A. H.; Kadhane, U.; Misra, D.; Tribedi, L. C.

    2007-09-01

    Se have investigated single and double ionization of C60 molecule in collisions with 2.33 MeV/u Siq+ (q=6-14) and 3.125 MeV/u Oq+ (q=5-8) projectiles. The projectile charge state dependence of the single and double ionization yields of C60 are then compared to those for an ion-atom collision system using Ne gas as a target. A large difference between the gas and the cluster target behaviour was partially explained in terms of a model based on collective excitation namely the giant dipole plasmon resonance (GDPR). The qualitative agreement between the data and GDPR model prediction for single and double ionization signifies the importance of single and double plasmon excitations in the ionization process. A large deviation of the GDPR model for triple and quadruple ionization from the experimental data imply the importance of the other low impact parameter processes such as evaporation, fragmentation and a possible solid-like dynamical screening.

  2. Giant plasmon excitation in single and double ionization of C60 by fast highly charged Si and O ions

    International Nuclear Information System (INIS)

    Kelkar, A H; Kadhane, U; Misra, D; Tribedi, L C

    2007-01-01

    Se have investigated single and double ionization of C 60 molecule in collisions with 2.33 MeV/u Si q+ (q=6-14) and 3.125 MeV/u O q+ (q=5-8) projectiles. The projectile charge state dependence of the single and double ionization yields of C 60 are then compared to those for an ion-atom collision system using Ne gas as a target. A large difference between the gas and the cluster target behaviour was partially explained in terms of a model based on collective excitation namely the giant dipole plasmon resonance (GDPR). The qualitative agreement between the data and GDPR model prediction for single and double ionization signifies the importance of single and double plasmon excitations in the ionization process. A large deviation of the GDPR model for triple and quadruple ionization from the experimental data imply the importance of the other low impact parameter processes such as evaporation, fragmentation and a possible solid-like dynamical screening

  3. Supramolecular Nanoparticles via Single-Chain Folding Driven by Ferrous Ions.

    Science.gov (United States)

    Wang, Fei; Pu, Hongting; Jin, Ming; Wan, Decheng

    2016-02-01

    Single-chain nanoparticles can be obtained via single-chain folding assisted by intramolecular crosslinking reversibly or irreversibly. Single-chain folding is also an efficient route to simulate biomacromolecules. In present study, poly(N-hydroxyethylacrylamide-co-4'-(propoxy urethane ethyl acrylate)-2,2':6',2''-terpyridine) (P(HEAm-co-EMA-Tpy)) is synthesized via reversible addition fragmentation chain transfer polymerization. Single-chain folding and intramolecular crosslinking of P(HEAm-co-EMA-Tpy) are achieved via metal coordination chemistry. The intramolecular interaction is characterized on ultraviolet/visible spectrophotometer (UV-vis spectroscopy), proton nuclear magnetic resonance ((1)H NMR), and differential scanning calorimetry (DSC). The supramolecular crosslinking mediated by Fe(2+) plays an important role in the intramolecular collapsing of the single-chain and the formation of the nanoparticles. The size and morphology of the nanoparticles can be controlled reversibly via metal coordination chemistry, which can be characterized by dynamic light scattering (DLS), transmission electron microscope (TEM), and atomic force microscope (AFM). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-07-28

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  5. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor

    Science.gov (United States)

    Vivas, Paula; Velmurugu, Yogambigai; Kuznetsov, Serguei V.; Rice, Phoebe A.; Ansari, Anjum

    2013-09-01

    Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SKbi ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SKuni protein-DNA contacts in the fully wrapped complex

  6. Mutational analysis of divalent metal ion binding in the active site of class II α-mannosidase from sulfolobus solfataricus

    DEFF Research Database (Denmark)

    Hansen, Dennis K.; Webb, Helen; Nielsen, Jonas Willum

    2015-01-01

    +). Some mutant enzyme forms displayed an altered preference for the metal ion compared to that of the wild type-enzyme. Furthermore, the H228Q, H533E, and H533Q enzymes were inhibited at increasing Zn2+ concentrations. The catalytic rate was reduced for all enzymes compared to that of the wild-type enzyme......Mutational analysis of Sulfolobus solfataricus class II α-mannosidase was focused on side chains that interact with the hydroxyls of the-1 mannosyl of the substrate (Asp-534) or form ligands to the active site divalent metal ion (His-228 and His-533) judged from crystal structures of homologous...... enzymes. D534A and D534N appeared to be completely inactive. When compared to the wild-type enzyme, the mutant enzymes in general showed only small changes in KM for the substrate, p-nitrophenyl-α-mannoside, but elevated activation constants, KA, for the divalent metal ion (Co2+, Zn2+, Mn2+, or Cd2...

  7. Heavy Ion Irradiation Fluence Dependence for Single-Event Upsets in a NAND Flash Memory

    Science.gov (United States)

    Chen, Dakai; Wilcox, Edward; Ladbury, Raymond L.; Kim, Hak; Phan, Anthony; Seidleck, Christina; Label, Kenneth

    2016-01-01

    We investigated the single-event effect (SEE) susceptibility of the Micron 16 nm NAND flash, and found that the single-event upset (SEU) cross section varied inversely with cumulative fluence. We attribute the effect to the variable upset sensitivities of the memory cells. Furthermore, the effect impacts only single cell upsets in general. The rate of multiple-bit upsets remained relatively constant with fluence. The current test standards and procedures assume that SEU follow a Poisson process and do not take into account the variability in the error rate with fluence. Therefore, traditional SEE testing techniques may underestimate the on-orbit event rate for a device with variable upset sensitivity.

  8. Effects of single-base substitutions within the acanthamoeba castellanii rRNA promoter on transcription and on binding of transcription initiation factor and RNA polymerase I

    Energy Technology Data Exchange (ETDEWEB)

    Kownin, P.; Bateman, E.; Paule, M.R.

    1988-02-01

    Single-point mutations were introduced into the promoter region of the Acanthamoeba castellanii rRNA gene by chemical mutagen treatment of a single-stranded clone in vitro, followed by reverse transcription and cloning of the altered fragment. The promoter mutants were tested for transcription initiation factor (TIF) binding by a template commitment assay plus DNase I footprinting and for transcription by an in vitro runoff assay. Point mutations within the previously identified TIF interaction region (between -20 and -47, motifs A and B) indicated that TIF interacts most strongly with a sequence centered at -29 and less tightly with sequences upstream and downstream. Some alterations of the base sequence closer to the transcription start site (and outside the TIF-protected site) also significantly decrease specific RNA synthesis in vitro. These were within the region which is protected from DNAse I digestion by polymerase I, but these mutations did not detectably affect the binding of polymerase to the promoter.

  9. The binding of multiple nuclear receptors to a single regulatory region is important for the proper expression of EDG84A in Drosophila melanogaster.

    Science.gov (United States)

    Akagi, Kazutaka; Kageyama, Yuji; Kayashima, Yasunari; Takakura, Yusuke; Hirose, Susumu; Ueda, Hitoshi

    2013-01-09

    Nuclear receptor transcription factor family members share target sequence similarity; however, little is known about how these factors exert their specific regulatory control. Here, we examine the mechanism regulating the expression of the Drosophila EDG84A gene, a target gene of the orphan nuclear receptor βFTZ-F1, as a model to study the cooperative behavior among nuclear receptors. We show that the three nuclear receptors βFTZ-F1, DHR3, and DHR39 bind to a common element in the EDG84A promoter. The expression level of the EDG84A promoter-lacZ reporter genes in DHR39-induced and mutant animals, respectively, suggests that DHR39 works as a repressor. The activity of a reporter gene carrying a mutation preventing DHR3 binding was reduced in ftz-f1 mutants and rescued by the induced expression of βFTZ-F1, suggesting that DHR3 and βFTZ-F1 activate the EDG84A gene in a redundant manner. A reporter gene carrying a mutation that abolishes DHR39 and FTZ-F1 binding was prematurely expressed, and the expression level of the reporter gene carrying a mutation preventing DHR3 binding was reduced. These findings suggest that the temporal expression of this gene is mainly controlled by βFTZ-F1 but that the binding of DHR3 is also important. Comparison of the binding site sequence among Drosophila species suggests that DHR3 binding ability was gained after the melanogaster subgroup evolved, and this ability may contribute to the robust expression of this gene. These results show the complicated regulatory mechanisms utilized by multiple nuclear receptors to properly regulate the expression of their target gene through a single target site. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Microstructural evolution of reduced-activation martensitic steel under single and sequential ion irradiations

    International Nuclear Information System (INIS)

    Luo, Fengfeng; Guo, Liping; Jin, Shuoxue; Li, Tiecheng; Zheng, Zhongcheng; Yang, Feng; Xiong, Xuesong; Suo, Jinping

    2013-01-01

    Microstructural evolution of super-clean reduced-activation martensitic steels irradiated with single-beam (Fe + ) and sequential-beam (Fe + plus He + ) at 350 °C and 550 °C was studied. Sequential-beam irradiation induced smaller size and larger number density of precipitates compared to single-beam irradiation at 350 °C. The largest size of cavities was observed after sequential-beam irradiation at 550 °C. The segregation of Cr and W and depletion of Fe in carbides were observed, and the maximum depletion of Fe and enrichment of Cr occurred under irradiation at 350 °C

  11. Single-walled carbon nanotubes as stabilizing agents in red phosphorus Li-ion battery anodes

    KAUST Repository

    Smajic, Jasmin

    2017-08-16

    Phosphorus boasts extremely high gravimetric and volumetric capacities but suffers from poor electrochemical stability with significant capacity loss immediately after the first cycle. We propose to circumvent this issue by mixing amorphous red phosphorus with single-walled carbon nanotubes. Employing a non-destructive sublimation–deposition method, we have synthesized composites where the synergetic effect between red phosphorus and single-walled carbon nanotubes allows for a considerable improvement in the electrochemical stability of battery anodes. In contrast to the average 40% loss of capacity after 50 cycles for other phosphorus–carbon composites in the literature, our material shows losses of just 22% under analogous cycling conditions.

  12. Coupled aggregation of mitochondrial single-strand DNA-binding protein tagged with Eos fluorescent protein visualizes synchronized activity of mitochondrial nucleoids

    Czech Academy of Sciences Publication Activity Database

    Olejár, Tomáš; Pajuelo-Reguera, David; Alán, Lukáš; Dlasková, Andrea; Ježek, Petr

    2015-01-01

    Roč. 12, č. 4 (2015), s. 5185-5190 ISSN 1791-2997 R&D Projects: GA ČR(CZ) GAP302/10/0346; GA MŠk(CZ) EE2.3.30.0025 Institutional support: RVO:67985823 Keywords : mitochondrial nucleoid * single- strand ed DNA -binding protein * photoconvertible fluorescent protein Eos Subject RIV: EA - Cell Biology Impact factor: 1.559, year: 2015

  13. Formation of oriented nitrides by N{sup +} ion implantation in iron single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Costa, A.R.G. [CFMC, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Silva, R.C. da [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Ferreira, L.P. [CFMC, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Dep. Física, Fac. Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra (Portugal); Carvalho, M.D. [CCMM/Dep. Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Silva, C. [CFMC, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Dep. Física, Fac. Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Franco, N. [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Godinho, M. [CFMC, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Dep. Física, Fac. Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); and others

    2014-01-15

    Iron single crystals were implanted with nitrogen at room temperature, with a fluence of 5×10{sup 17} cm{sup −2} and 50 keV energy, to produce iron nitride phases and characterize the influence of the crystal orientation. The stability and evolution of the nitride phases and diffusion of implanted nitrogen were studied as a function of successive annealing treatments at 250 °C in vacuum. The composition, structure and magnetic properties were characterized using RBS/channeling, X-Ray Diffraction, Magnetic Force Microscopy, Magneto-optical Kerr Effect and Conversion Electron Mössbauer Spectroscopy. In the as-implanted state the formation of Fe{sub 2}N phase was clearly identified in all single crystals. This phase is not stable at 250 °C and annealing at this temperature promotes the formation of ε-Fe{sub 3}N, or γ′-Fe{sub 4}N, depending on the orientation of the substrate. - Highlights: • Oriented magnetic iron nitrides were obtained by nitrogen implantation into iron single crystals. • The stable magnetic nitride phase at 250 °C depends on the orientation of the host single crystal, being γ'-Fe{sub 4}N or ε-Fe{sub 3}N. • The easy magnetization axis was found to lay in the (100) plane for cubic γ'-Fe{sub 4}N and out of (100) plane for hexagonal ε-Fe{sub 3}N.

  14. High-energy heavy ion testing of VLSI devices for single event ...

    Indian Academy of Sciences (India)

    Unknown

    Single event upset is defined by NASA as 'radiation- induced errors in microelectronic circuits caused when charged particles (usually from the radiation belts or from cosmic rays) lose energy by ionizing the medium through which they pass, leaving behind a wake of elec- tron-hole pairs'. SEU are transient soft errors and ...

  15. Formation of oriented nitrides by N+ ion implantation in iron single crystals

    International Nuclear Information System (INIS)

    Costa, A.R.G.; Silva, R.C. da; Ferreira, L.P.; Carvalho, M.D.; Silva, C.; Franco, N.; Godinho, M.

    2014-01-01

    Iron single crystals were implanted with nitrogen at room temperature, with a fluence of 5×10 17 cm −2 and 50 keV energy, to produce iron nitride phases and characterize the influence of the crystal orientation. The stability and evolution of the nitride phases and diffusion of implanted nitrogen were studied as a function of successive annealing treatments at 250 °C in vacuum. The composition, structure and magnetic properties were characterized using RBS/channeling, X-Ray Diffraction, Magnetic Force Microscopy, Magneto-optical Kerr Effect and Conversion Electron Mössbauer Spectroscopy. In the as-implanted state the formation of Fe 2 N phase was clearly identified in all single crystals. This phase is not stable at 250 °C and annealing at this temperature promotes the formation of ε-Fe 3 N, or γ′-Fe 4 N, depending on the orientation of the substrate. - Highlights: • Oriented magnetic iron nitrides were obtained by nitrogen implantation into iron single crystals. • The stable magnetic nitride phase at 250 °C depends on the orientation of the host single crystal, being γ'-Fe 4 N or ε-Fe 3 N. • The easy magnetization axis was found to lay in the (100) plane for cubic γ'-Fe 4 N and out of (100) plane for hexagonal ε-Fe 3 N

  16. No significant effects of single intravenous, single oral and subchronic oral administration of acetylcholinesterase inhibitors on striatal [123I]FP-CIT binding in rats

    NARCIS (Netherlands)

    Knol, R. J. J.; de Bruin, K.; van Eck-Smit, B. L. F.; Booij, J.

    2008-01-01

    PURPOSE: [(123)I]FP-CIT SPECT is a valuable diagnostic tool to discriminate Lewy body dementia from Alzheimer's dementia. To date, however, it is uncertain whether the frequently used acetylcholinesterase inhibitors (AChEIs) by demented patients, have an effect on [(123)I]FP-CIT binding to dopamine

  17. Electrical properties of InP:Fe single crystals implanted by phosphorus ions

    International Nuclear Information System (INIS)

    Radautsan, S.I.; Tiginyanu, I.M.; Pyshnaya, N.B.

    1988-01-01

    Investigations of phosphorus ion implantation in InP:Fe monocrystals and of the post-implantation annealing process upon the electrical properties of InP:Fe were carried out. The electrical parameters of the samples have been determined by Hall effect measurements. The curves of electron surface concentration n s and mobility μ s as functions of annealing temperature in the range of 200 to 600 0 C are shown and discussed. In order to estimate the depth of donor levels in annealed samples the temperature dependence of the surface Hall coefficient has been studied in the range 100 to 400 K. The thermal electron activation energy has been determined to be 0.09 eV

  18. Monte Carlo prediction of crater formation by single ion impact on solid surface

    International Nuclear Information System (INIS)

    Perez-Martin, A.M.C.; Dominguez-Vazquez, J.; Jimenez-Rodriguez, J.J.; Collins, R.; Gras-Marti, A.

    1994-01-01

    A method is presented for predicting the topography changes following the impact of one energetic ion on the plane surface of a monatomic amorphous solid. This is done in two stages. The first is a Monte Carlo calculation of the sputter yield and interior distribution relocated atoms, with no compensation for local departures from equilibrium density. In the second stage there is a systematic relaxation of the solid, in which the density returns to its previous constant value and a crater develops in the surface. Two alternative methods of carrying out stage two are compared. In the first the solid is subdivided into cells within which relaxation is carried out normal to the surface, as in previous one-dimensional studies. The second method treats the solid as a 3-dimensional incompressible medium. Both seem to reproduce quite well the main features found experimentally. (orig.)

  19. RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates

    Science.gov (United States)

    Polevoda, Bogdan; McDougall, William M.; Tun, Bradley N.; Cheung, Michael; Salter, Jason D.; Friedman, Alan E.; Smith, Harold C.

    2015-01-01

    APOBEC3G (A3G) DNA deaminase activity requires a holoenzyme complex whose assembly on nascent viral reverse transcripts initiates with A3G dimers binding to ssDNA followed by formation of higher-order A3G homo oligomers. Catalytic activity is inhibited when A3G binds to RNA. Our prior studies suggested that RNA inhibited A3G binding to ssDNA. In this report, near equilibrium binding and gel shift analyses showed that A3G assembly and disassembly on ssDNA was an ordered process involving A3G dimers and multimers thereof. Although, fluorescence anisotropy showed that A3G had similar nanomolar affinity for RNA and ssDNA, RNA stochastically dissociated A3G dimers and higher-order oligomers from ssDNA, suggesting a different modality for RNA binding. Mass spectrometry mapping of A3G peptides cross-linked to nucleic acid suggested ssDNA only bound to three peptides, amino acids (aa) 181–194 in the N-terminus and aa 314–320 and 345–374 in the C-terminus that were part of a continuous exposed surface. RNA bound to these peptides and uniquely associated with three additional peptides in the N- terminus, aa 15–29, 41–52 and 83–99, that formed a continuous surface area adjacent to the ssDNA binding surface. The data predict a mechanistic model of RNA inhibition of ssDNA binding to A3G in which competitive and allosteric interactions determine RNA-bound versus ssDNA-bound conformational states. PMID:26424853

  20. Affinity capillary electrophoresis and quantum mechanical calculations applied to the investigation of hexaarylbenzene-based receptor binding with lithium ion

    Czech Academy of Sciences Publication Activity Database

    Ehala, Sille; Toman, Petr; Rathore, R.; Makrlík, E.; Kašička, Václav

    2011-01-01

    Roč. 34, č. 18 (2011), s. 2433-2440 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/08/1428; GA ČR(CZ) GA203/09/0675; GA AV ČR 1ET400500402 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40500505 Keywords : affinity capillary electrophoresis * binding constant * hexaarylbenzene-based receptor Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.733, year: 2011

  1. Polcalcin divalent ion-binding behavior and thermal stability: comparison of Bet v 4, Bra n 1, and Bra n 2 to Phl p 7.

    Science.gov (United States)

    Henzl, Michael T; Davis, Meredith E; Tan, Anmin

    2010-03-16

    Polcalcins are pollen-specific proteins containing two EF-hands. Atypically, the C-terminal EF-hand binding loop in Phl p 7 (from timothy grass) harbors five, rather than four, anionic side chains, due to replacement of the consensus serine at -x by aspartate. This arrangement has been shown to heighten parvalbumin Ca(2+) affinity. To determine whether Phl p 7 likewise exhibits anomalous divalent ion affinity, we have also characterized Bra n 1 and Bra n 2 (both from rapeseed) and Bet v 4 (from birch tree). Relative to Phl p 7, they exhibit N-terminal extensions of one, five, and seven residues, respectively. Interestingly, the divalent ion affinity of Phl p 7 is unexceptional. For example, at -17.84 +/- 0.13 kcal mol(-1), the overall standard free energy for Ca(2+) binding falls within the range observed for the other three proteins (-17.30 +/- 0.10 to -18.15 +/- 0.10 kcal mol(-1)). In further contrast to parvalbumin, replacement of the -x aspartate, via the D55S mutation, actually increases the overall Ca(2+) affinity of Phl p 7, to -18.17 +/- 0.13 kcal mol(-1). Ca(2+)-free Phl p 7 exhibits uncharacteristic thermal stability. Whereas wild-type Phl p 7 and the D55S variant denature at 77.3 and 78.0 degrees C, respectively, the other three polcalcins unfold between 56.1 and 57.9 degrees C. This stability reflects a low denaturational heat capacity increment. Phl p 7 and Phl p 7 D55S exhibit DeltaC(p) values of 0.34 and 0.32 kcal mol(-1) K(-1), respectively. The corresponding values for the other three polcalcins range from 0.66 to 0.95 kcal mol(-1) K(-1).

  2. Monolayer detection of ion binding at a crown ether-functionalised supramolecular surface via an integrated optical Bragg grating.

    Science.gov (United States)

    Parker, Richard M; Wales, Dominic J; Gates, James C; Frey, Jeremy G; Smith, Peter G R; Grossel, Martin C

    2014-06-07

    There have been significant recent developments in the field of integrated optical Bragg grating sensors for use in the biological domain, where changes in the thickness of a surface layer upon specific binding of biological targets allows quantitative detection. However in the chemical domain less work has been reported. We present here an integrated optical Bragg grating sensor, capable of evanescently detecting small changes in refractive index down to 10(-6) RIU at infrared wavelengths, within a microfluidic system. The high spectral fidelity of the Bragg gratings combined with precise thermal compensation enables direct monitoring of the surface throughout the experiment. This allows the sensor to probe surface changes in situ and in real-time, from preparation through to chemical modification of the surface, so that the progress of dynamic surface-localized interactions can be followed. Here we describe confirmatory studies to validate this approach, including a comparison with the modelled optical system, before assessing the ability to detect binding of Group I cations at a crown ether-functionalised supramolecular surface. Unlike larger biological entities, for these small chemical species, simple additive changes in film-thickness no longer prevail.

  3. Microstructural evolution of reduced-activation martensitic steel under single and sequential ion irradiations

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Fengfeng [Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and School of Physics and Technology, Wuhan University, Wuhan 430072 (China); Guo, Liping, E-mail: guolp@whu.edu.cn [Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and School of Physics and Technology, Wuhan University, Wuhan 430072 (China); Jin, Shuoxue; Li, Tiecheng; Zheng, Zhongcheng [Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory and School of Physics and Technology, Wuhan University, Wuhan 430072 (China); Yang, Feng; Xiong, Xuesong; Suo, Jinping [State Key Laboratory of Mould Technology, Institute of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2013-07-15

    Microstructural evolution of super-clean reduced-activation martensitic steels irradiated with single-beam (Fe{sup +}) and sequential-beam (Fe{sup +} plus He{sup +}) at 350 °C and 550 °C was studied. Sequential-beam irradiation induced smaller size and larger number density of precipitates compared to single-beam irradiation at 350 °C. The largest size of cavities was observed after sequential-beam irradiation at 550 °C. The segregation of Cr and W and depletion of Fe in carbides were observed, and the maximum depletion of Fe and enrichment of Cr occurred under irradiation at 350 °C.

  4. Focused-ion-beam overlay-patterning of three-dimensional diamond structures for advanced single-photon properties

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Qianqing; Liu, Dongqi; Liu, Gangqin; Chang, Yanchun; Li, Wuxia, E-mail: liwuxia@aphy.iphy.ac.cn, E-mail: czgu@aphy.iphy.ac.cn [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Pan, Xinyu; Gu, Changzhi, E-mail: liwuxia@aphy.iphy.ac.cn, E-mail: czgu@aphy.iphy.ac.cn [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100190 (China)

    2014-07-28

    Sources of single photons are of fundamental importance in many applications as to provide quantum states for quantum communication and quantum information processing. Color centers in diamond are prominent candidates to generate and manipulate quantum states of light, even at room temperature. However, the efficiency of photon collection of the color centers in bulk diamond is greatly reduced by refraction at the diamond/air interface. To address this issue, diamond structuring has been investigated by various methods. Among them, focused-ion-beam (FIB) direct patterning has been recognized as the most favorable technique. But it has been noted that diamond tends to present significant challenges in FIB milling, e.g., the susceptibility of forming charging related artifacts and topographical features. In this work, periodically-positioned-rings and overlay patterning with stagger-superimposed-rings were proposed to alleviate some problems encountered in FIB milling of diamond, for improved surface morphology and shape control. Cross-scale network and uniform nanostructure arrays have been achieved in single crystalline diamond substrates. High quality diamond solid immersion lens and nanopillars were sculptured with a nitrogen-vacancy center buried at the desired position. Compared with the film counterpart, an enhancement of about ten folds in single photon collection efficiency was achieved with greatly improved signal to noise ratio. All these results indicate that FIB milling through over-lay patterning could be an effective approach to fabricate diamond structures, potentially for quantum information studies.

  5. Single-molecule Imaging Analysis of Binding, Processive Movement, and Dissociation of Cellobiohydrolase Trichoderma reesei Cel6A and Its Domains on Crystalline Cellulose*

    Science.gov (United States)

    Nakamura, Akihiko; Tasaki, Tomoyuki; Ishiwata, Daiki; Yamamoto, Mayuko; Okuni, Yasuko; Visootsat, Akasit; Maximilien, Morice; Noji, Hiroyuki; Uchiyama, Taku; Samejima, Masahiro; Igarashi, Kiyohiko; Iino, Ryota

    2016-01-01

    Trichoderma reesei Cel6A (TrCel6A) is a cellobiohydrolase that hydrolyzes crystalline cellulose into cellobiose. Here we directly observed the reaction cycle (binding, surface movement, and dissociation) of single-molecule intact TrCel6A, isolated catalytic domain (CD), cellulose-binding module (CBM), and CBM and linker (CBM-linker) on crystalline cellulose Iα. The CBM-linker showed a binding rate constant almost half that of intact TrCel6A, whereas those of the CD and CBM were only one-tenth of intact TrCel6A. These results indicate that the glycosylated linker region largely contributes to initial binding on crystalline cellulose. After binding, all samples showed slow and fast dissociations, likely caused by the two different bound states due to the heterogeneity of cellulose surface. The CBM showed much higher specificity to the high affinity site than to the low affinity site, whereas the CD did not, suggesting that the CBM leads the CD to the hydrophobic surface of crystalline cellulose. On the cellulose surface, intact molecules showed slow processive movements (8.8 ± 5.5 nm/s) and fast diffusional movements (30–40 nm/s), whereas the CBM-Linker, CD, and a catalytically inactive full-length mutant showed only fast diffusional movements. These results suggest that both direct binding and surface diffusion contribute to searching of the hydrolysable point of cellulose chains. The duration time constant for the processive movement was 7.7 s, and processivity was estimated as 68 ± 42. Our results reveal the role of each domain in the elementary steps of the reaction cycle and provide the first direct evidence of the processive movement of TrCel6A on crystalline cellulose. PMID:27609516

  6. Absence of single critical dose for the amorphization of quartz under ion irradiation

    Science.gov (United States)

    Zhang, S.; Pakarinen, O. H.; Backholm, M.; Djurabekova, F.; Nordlund, K.; Keinonen, J.; Wang, T. S.

    2018-01-01

    In this work, we first simulated the amorphization of crystalline quartz under 50 keV 23 Na ion irradiation with classical molecular dynamics (MD). We then used binary collision approximation algorithms to simulate the Rutherford backscattering spectrometry in channeling conditions (RBS-C) from these irradiated MD cells, and compared the RBS-C spectra with experiments. The simulated RBS-C results show an agreement with experiments in the evolution of amorphization as a function of dose, showing what appears to be (by this measure) full amorphization at about 2.2 eVṡatom-1 . We also applied other analysis methods, such as angular structure factor, Wigner–Seitz, coordination analysis and topological analysis, to analyze the structural evolution of the irradiated MD cells. The results show that the atomic-level structure of the sample keeps evolving after the RBS signal has saturated, until the dose of about 5 eVṡatom-1 . The continued evolution of the SiO2 structure makes the definition of what is, on the atomic level, an amorphized quartz ambiguous.

  7. Charge transport and glassy dynamics of poly(ethylene oxide)-based single-ion conductors under geometrical confinement

    Science.gov (United States)

    Runt, James; Iacob, Ciprian

    2015-03-01

    Segmental and local dynamics as well as charge transport are investigated in a series of poly(ethylene oxide)-based single-ion conductors (ionomers) with varying counterions (Li +, Na +) confined in uni-directional nanoporous silica membranes. The dynamics are explored over a wide frequency and temperature range by broadband dielectric relaxation spectroscopy. Slowing of segmental dynamics and a decrease in dc conductivity (strongly coupled with segmental relaxation) of the confined ionomers are associated with surface effects - resulting from interfacial hydrogen bonding between the host nanoporous silica membrane and the guest ionomers. These effects are significantly reduced or eliminated upon pore surface modification through silanization. The primary transport properties for the confined ionomers decrease by about one decade compared to the bulk ionomer. A model assuming reduced mobility of an adsorbed layer at the pore wall/ionomer interface is shown to provide a quantitative explanation for the decrease in effective transport quantities in non-silanized porous silica membranes. Additionally, the effect of confinement on ion aggregation in ionomers by using X-ray scattering will also be discussed. Supported by the National Science Foundation, Polymers Program.

  8. Calculations of Q values in single- and double-charge-transfer collisions of highly charged ions with atoms

    International Nuclear Information System (INIS)

    Chen, Z.; Lin, C.D.; Toshima, N.

    1994-01-01

    Close-coupling calculations are carried out for the Q values for electron capture processes in collisions of multiply charged ions with atoms over a broad range of energies. For single-capture processes the results for N 7+ +He and O 8+ +He collisions are in good agreement with the experimental data of Wu et al. [preceding paper, Phys. Rev. A 50, 502 (1994)]. To compare with the experimental Q values for the transfer ionization (TI) and the true double-capture (TDC) processes, an independent-electron model was used to calculate double-electron-capture cross sections. By combining with the calculated average fluorescence yields, the theoretical Q values for TI and TDC processes are also found to be in fair agreement with the experimental data. We also compared the Q values calculated by the close-coupling method and by the classical-trajectory Monte Carlo method

  9. Upconversion study of singly activator ions doped La2O3 nanoparticle synthesized via optimized solvothermal method

    Science.gov (United States)

    Tiwari, S. P.; Singh, S.; Kumar, A.; Kumar, K.

    2016-05-01

    In present work, an optimized solvothermal method has been chosen to synthesize the singly doped Er3+ activator ions with La2O3 host matrix. The sample is annealed at 500 °C in order to remove the moisture and other organic impurities. The sample is characterized by using XRD and FESEM to find out the phase and surface morphology. The observed particle size is found almost 80 nm with spherical agglomerated shape. Upconversion spectra are recorded at room temperature using 976 nm diode laser excitation sources and consequently the emission peaks in green and red region are observed. The color coordinate diagram shows the results that the present material may be applicable in different light emitting sources.

  10. Negative Ion MALDI Mass Spectrometry of Polyoxometalates (POMs): Mechanism of Singly Charged Anion Formation and Chemical Properties Evaluation

    Science.gov (United States)

    Boulicault, Jean E.; Alves, Sandra; Cole, Richard B.

    2016-08-01

    MALDI-MS has been developed for the negative ion mode analysis of polyoxometalates (POMs). Matrix optimization was performed using a variety of matrix compounds. A first group of matrixes offers MALDI mass spectra containing abundant intact singly charged anionic adduct ions, as well as abundant in-source fragmentations at elevated laser powers. A relative ranking of the ability to induce POM fragmentation is found to be: DAN > CHCA > CNA > DIT> HABA > DCTB > IAA. Matrixes of a second group provide poorer quality MALDI mass spectra without observable fragments. Sample preparation, including the testing of salt additives, was performed to optimize signals for a model POM, POMc12, the core structure of which bears four negative charges. The matrix 9-cyanoanthracene (CNA) provided the best signals corresponding to singly charged intact POMc12 anions. Decompositions of these intact anionic species were examined in detail, and it was concluded that hydrogen radical-induced mechanisms were not prevalent, but rather that the observed prompt fragments originate from transferred energy derived from initial electronic excitation of the CNA matrix. Moreover, in obtained MALDI mass spectra, clear evidence of electron transfer to analyte POM species was found: a manifestation of the POMs ability to readily capture electrons. The affinity of polyanionic POMc12 toward a variety of cations was evaluated and the following affinity ranking was established: Fe3+ > Al3+ > Li+ > Ga3+ > Co2+ > Cr3+ > Cu2+ > [Mn2+, Mg2+] > [Na+, K+]. Thus, from the available cationic species, specific adducts are preferentially formed, and evidence is given that these higher affinity POM complexes are formed in the gas phase during the early stages of plume expansion.

  11. Characterization of the Single Stranded DNA Binding Protein SsbB Encoded in the Gonoccocal Genetic Island

    NARCIS (Netherlands)

    Jain, Samta; Zweig, Maria; Peeters, Eveline; Siewering, Katja; Hackett, Kathleen T.; Dillard, Joseph P.; van der Does, Chris

    2012-01-01

    Background: Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in

  12. Absolute experimental cross sections for the electron impact single, double, triple, and quadruple ionization of Cs/sup +/ ions. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Feeney, R.K.; Hertling, D.R.

    1981-02-28

    The absolute cross sections for the single, double, triple and quadruple ionization of Cs/sup +/ ions by electron impact have been measured from below their respective thresholds to approximately 5000 eV. This determination has been accomplshed using a crossed beam facility in which monoenergetic beams of ions and electrons are caused to intersect at right angles in a well-defined collision volume. Multiply charged, product ions born as a result of the electron impact are deflected into their respective detectors by cascaded electrostatic analyzers. The multiply charged beam current component is measured by means of a vibrating reed electrometer operating in the rate-of-charge mode.

  13. Role of crystallographic anisotropy in the formation of surface layers of single NiTi crystals after ion-plasma alloying

    Energy Technology Data Exchange (ETDEWEB)

    Poletika, T. M., E-mail: poletm@ispms.tsc.ru; Girsova, S. L., E-mail: llm@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); Meisner, L. L., E-mail: girs@ispms.tsc.ru; Meisner, S. N., E-mail: msn@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); National Research Tomsk State University, Tomsk, 634050 (Russian Federation); Shulepov, I. A., E-mail: iashulepov@tpu.ru [National Research Tomsk Polytechnic University, Tomsk, 634050 (Russian Federation)

    2015-10-27

    The structure of the surface and near-surface layers of single crystals of NiTi, differently oriented relative to the direction of ion beam treatment was investigated. The role of the crystallographic orientation in formation of structure of surface layers after ion-plasma alloying was revealed. It was found that the orientation effects of selective sputtering and channeling determine the thickness of the oxide and amorphous layers, the depth of penetration of ions and impurities, the distribution of Ni with depth.

  14. Development of sugar chain-binding single-chain variable fragment antibody to adult T-cell leukemia cells using glyco-nanotechnology and phage display method.

    Science.gov (United States)

    Muchima, Kaname; Todaka, Taro; Shinchi, Hiroyuki; Sato, Ayaka; Tazoe, Arisa; Aramaki, Rikiya; Kakitsubata, Yuhei; Yokoyama, Risa; Arima, Naomichi; Baba, Masanori; Wakao, Masahiro; Ito, Yuji; Suda, Yasuo

    2018-04-01

    Adult T-cell leukemia (ATL) is an intractable blood cancer caused by the infection of human T-cell leukemia virus type-1, and effective medical treatment is required. It is known that the structure and expression levels of cell surface sugar chains vary depending on cell states such as inflammation and cancer. Thus, it is expected that the antibody specific for ATL cell surface sugar chain would be an effective diagnostic tool and a strong candidate for the development of an anti-ATL drug. Here, we developed a stable sugar chain-binding single-chain variable fragment antibody (scFv) that can bind to ATL cells using a fibre-type Sugar Chip and phage display method. The fiber-type Sugar Chips were prepared using O-glycans released from ATL cell lines. The scFv-displaying phages derived from human B cells (diversity: 1.04 × 108) were then screened using the fiber-type Sugar Chips, and an O-glycan-binding scFv was obtained. The flow cytometry analysis revealed that the scFv predominantly bound to ATL cell lines. The sugar chain-binding properties of the scFv was evaluated by array-type Sugar Chip immobilized with a library of synthetic glycosaminoglycan disaccharide structures. Highly sulphated disaccharide structures were found to have high affinity to scFv.

  15. Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics.

    Science.gov (United States)

    Blair, Rebecca H; Goodrich, James A; Kugel, Jennifer F

    2012-09-25

    TATA binding protein (TBP) is a key component of the eukaryotic RNA polymerase II transcription machinery that binds to TATA boxes located in the core promoter regions of many genes. Structural and biochemical studies have shown that when TBP binds DNA, it sharply bends the DNA. We used single-molecule fluorescence resonance energy transfer (smFRET) to study DNA bending by human TBP on consensus and mutant TATA boxes in the absence and presence of TFIIA. We found that the state of the bent DNA within populations of TBP-DNA complexes is homogeneous; partially bent intermediates were not observed. In contrast to the results of previous ensemble studies, TBP was found to bend a mutant TATA box to the same extent as the consensus TATA box. Moreover, in the presence of TFIIA, the extent of DNA bending was not significantly changed, although TFIIA did increase the fraction of DNA molecules bound by TBP. Analysis of the kinetics of DNA bending and unbending revealed that on the consensus TATA box two kinetically distinct populations of TBP-DNA complexes exist; however, the bent state of the DNA is the same in the two populations. Our smFRET studies reveal that human TBP bends DNA in a largely uniform manner under a variety of different conditions, which was unexpected given previous ensemble biochemical studies. Our new observations led to us to revise the model for the mechanism of DNA binding by TBP and for how DNA bending is affected by TATA sequence and TFIIA.

  16. Dielectronic recombination experiments with tungsten ions at the test storage ring and development of a single-particle detector at the cryogenic storage ring

    International Nuclear Information System (INIS)

    Spruck, Kaija

    2015-05-01

    This work is about electron-ion collision experiments at the ion storage rings of the Max Planck Institute for Nuclear Physics in Heidelberg. Absolute recombination rate coefficients of highly-charged tungsten ions featuring an open 4-f-shell structure have been measured at the heavy-ion storage ring TSR. The resulting plasma rate coefficients have been used to probe the significance of newly developed theoretical approaches. Plasma rate coefficients of highly-charged tungsten ions are in particular interesting for the development of plasma models for nuclear fusion reactors, since tungsten is a foreseeable impurity in the fusion plasma. In the relevant temperature range, the experimental results exceed the theoretical data used so far by up to a factor of 10, showing the need for more reliable theoretical calculations. Furthermore, based on the design of the detectors which have been used in the experiments at TSR, a movable single-particle detector for electron-ion recombination studies at the cryogenic storage ring CSR has been developed and installed within the scope of this work. The device has been designed specifically to meet the requirements of the CSR regarding low ion energies and cryogenic ambient temperature conditions. In a series of experiments, the detector was carefully characterised and successfully tested for its compatibility with these requirements. The detector was part of the infrastructure used for the room-temperature commissioning of CSR (2014) and is currently operated as a single-particle counter during the first cryogenic operation of CSR in 2015.

  17. Union Jack and checkerboard lattices with easy plane single ion anisotropy

    Science.gov (United States)

    Pires, A. S. T.

    2017-11-01

    The zero-temperature phase diagrams of the antiferromagnetic Union Jack and checkerboard lattices, with spin one and an easy-plane single anisotropy term, are studied using the SU(3) Schwinger boson formalism (also known as flavor wave theory). We find that the Union Jack lattice has a quantum phase transition (QPT) at J2/J1 = 0.707 between a Néel and a collinear phase, while the checkerboard lattice has a QPT at J2/J1 = 0.785, from the Néel to a magnetically disordered phase. The ground state phase diagrams of the two models are different, both from each other and from that of the square lattice antiferromagnet with all the next nearest neighbors. For the checkerboard lattice, we calculate the spin gap and the ground state energy in the disordered phase. This phase is a candidate for a spin liquid state.

  18. Chemical properties of astatine positive single-charged ion in aqueous solutions

    International Nuclear Information System (INIS)

    Milanov, M.; Doberents, V.; Khalkin, V.A.; Marinov, A.

    1983-01-01

    The mobility of the oxidized astatine in solutions H(Na)ClO 4 (μ=0.4 M) - 1x10 -4 M K 2 Cr 2 O 7 has been measured at 25 deg C in the interval 0.63 -4 cm 2 V -1 s -1 , pH 0.63 Usub(c)=2.67x10 -4 cm 2 V -1 s -1 . The effect agrees with the opinion that a single-charged cation of astatine formed in acidic solutions is a strong aquacomplex ((Hsub(2)O)sub(x)At)sup(+) (x=1-2) (protonized hypoastatine acid). Deprotonization constant of this cation is Ksub(dp)=0.032+-0.005. Specific properties of the astatine cation are given. They can be explained, probability, through the peculiarities of its structure

  19. Selection of single chain antibody fragments