Development of pulsation technique for single ion hit system

Energy Technology Data Exchange (ETDEWEB)

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

1996-12-01

When a high energy heavy ion enters into a substance, high density of ionization and excitement occurrs along its flying trace. Especially, when such an ion enters into a semiconductor cell, a bit inversion called single event is occurred or a phenomenon destroyed element itself on case of the worst is formed. The present semiconductor cell is made in a size of some micron square, as different from its accumulated degree. In order to analyze the single event phenomenon formed by entering ion into such fine region in detail, a technique possible enter heavy ion beam with space resolution under 1 micron to each sample is necessary. In order to develop this technique, a static type high speed beam switch for control of entering a beam into a sample and a single ion detector for detecting entrance of ion into the sample were installed to heavy ion microbeam forming apparatus. The single ion hit system in Takasaki Radiation Chemistry Research Establishment, JAERI succeeded in detection and control technique of the single ion and control of noise due to pulsization and finished development of basic technique of the single ion hit, since now. After today, it is planned to hit actually the single ion onto the sample and evaluate its accuracy. (G.K.)

Metastable decay and binding energies of van der Waals cluster ions

International Nuclear Information System (INIS)

Ernstberger, B.; Krause, H.; Neusser, H.J.

1991-01-01

In this work the appearance potentials for the metastable decay channel of a series of van der Waals dimer ions are presented. Ionization and metastable dissociation is achieved by resonance-enhanced two-photon absorption in a linear reflectron time-of-flight mass spectrometer. From the appearance potentials the binding energy of the neutral dimers is obtained and from the additionally measured ionization potentials binding energies of the dimer cations are achieved. The contribution of charge transfer resonance interaction to the binding in cluster ions is evaluated by investigation of several homo- and heterodimers of aromatic components and the heterodimer benzene/cyclohexane as an example for a dimer consisting of an aromatic and a nonaromatic component. (orig.)

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

Science.gov (United States)

Cao, Xiaoyong; Hu, Xiuzhen; 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.

Electron-ion correlation effects in ion-atom single ionization

Energy Technology Data Exchange (ETDEWEB)

Colavecchia, F.D.; Garibotti, C.R. [Centro Atomico Bariloche and Consejo Nacional de Investigaciones Cientificas y Tecnicas, 8400 San Carlos de Bariloche (Argentina); Gasaneo, G. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina)

2000-06-28

We study the effect of electron-ion correlation in single ionization processes of atoms by ion impact. We present a distorted wave model where the final state is represented by a correlated function solution of a non-separable three-body continuum Hamiltonian, that includes electron-ion correlation as coupling terms of the wave equation. A comparison of the electronic differential cross sections computed with this model with other theories and experimental data reveals that the influence of the electron-ion correlation is more significant for low energy emitted electrons. (author). Letter-to-the-editor.

An automated single ion hit at JAERI heavy ion microbeam to observe individual radiation damage

International Nuclear Information System (INIS)

Kamiya, Tomihiro; Sakai, Takuro; Naitoh, Yutaka; Hamano, Tsuyoshi; Hirao, Toshio

1999-01-01

Microbeam scanning and a single ion hit technique have been combined to establish an automated beam positioning and single ion hit system at the JAERI Takasaki heavy ion microbeam system. Single ion irradiation on preset points of a sample in various patterns can be performed automatically in a short period. The reliability of the system was demonstrated using CR-39 nuclear track detectors. Single ion hit patterns were achieved with a positioning accuracy of 2 μm or less. In measurement of single event transient current using this system, the reduction of the pulse height by accumulation of radiation damages was observed by single ion injection to the same local areas. This technique showed a possibility to get some quantitative information about the lateral displacement of an individual radiation effect in silicon PIN photodiodes. This paper will give details of the irradiation system and present results from several experiments

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.

Binding of ferric ions is essential for the biological activity of glycine-extended gastrin

International Nuclear Information System (INIS)

Baldwin, G.S.; Pannequin, J.; Hollande, F.; Shulkes, A.

2002-01-01

Full text: Non-amidated gastrins, such as glycine-extended gastrin17 (Ggly), are now known to be biologically active. Ggly stimulates cell proliferation and migration, and was recently shown to bind two ferric ions with high affinity. The objective of the present work was to define the structure of Ggly for the first time, and to investigate the role of ferric ions in biological activity. Methods: The structure of Ggly, and the identity of the ammo acids that act as ferric ion ligands, were determined by NMR and fluorescence spectroscopy. The effect on the gastric epithelial cell line IMGE-5 of Ggly fragments, and of Ggy mutants with some or all of the five consecutive glutamate residues replaced by alanine, was measured in terms of cell proliferation, cell migration and phosphorylation of focal adhesion kinase. Results: Ggly adopts a well-defined loop stabilised by hydrophobic interactions between Leu5, Tyrl2, Trp 14 and Phe17. Studies with Ggly fragments indicated that ferric ions bind via the pentaglutamate sequence, which is necessary but not sufficient for full activity Selective replacement of some or all of the glutamates results in a reduction in ferric ion binding, and complete loss of biological activity. Conclusion: Our results are consistent with the hypothesis that ferric ion binding is necessary for biological activity

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.

Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC.

Science.gov (United States)

Chen, Qiang; Kinde, Monica N; Arjunan, Palaniappa; Wells, Marta M; Cohen, Aina E; Xu, Yan; Tang, Pei

2015-09-08

Pentameric ligand-gated ion channels (pLGICs) are targets of general anesthetics, but molecular mechanisms underlying anesthetic action remain debatable. We found that ELIC, a pLGIC from Erwinia chrysanthemi, can be functionally inhibited by isoflurane and other anesthetics. Structures of ELIC co-crystallized with isoflurane in the absence or presence of an agonist revealed double isoflurane occupancies inside the pore near T237(6') and A244(13'). A pore-radius contraction near the extracellular entrance was observed upon isoflurane binding. Electrophysiology measurements with a single-point mutation at position 6' or 13' support the notion that binding at these sites renders isoflurane inhibition. Molecular dynamics simulations suggested that isoflurane binding was more stable in the resting than in a desensitized pore conformation. This study presents compelling evidence for a direct pore-binding mechanism of isoflurane inhibition, which has a general implication for inhibitory action of general anesthetics on pLGICs.

A reliable method for the counting and control of single ions for single-dopant controlled devices

International Nuclear Information System (INIS)

Shinada, T; Kurosawa, T; Nakayama, H; Zhu, Y; Hori, M; Ohdomari, I

2008-01-01

By 2016, transistor device size will be just 10 nm. However, a transistor that is doped at a typical concentration of 10 18 atoms cm -3 has only one dopant atom in the active channel region. Therefore, it can be predicted that conventional doping methods such as ion implantation and thermal diffusion will not be available ten years from now. We have been developing a single-ion implantation (SII) method that enables us to implant dopant ions one-by-one into semiconductors until the desired number is reached. Here we report a simple but reliable method to control the number of single-dopant atoms by detecting the change in drain current induced by single-ion implantation. The drain current decreases in a stepwise fashion as a result of the clusters of displaced Si atoms created by every single-ion incidence. This result indicates that the single-ion detection method we have developed is capable of detecting single-ion incidence with 100% efficiency. Our method potentially could pave the way to future single-atom devices, including a solid-state quantum computer

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

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

Science.gov (United States)

Jiang, Wen-Yan; Ran, Shi-Yong

2018-05-01

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag+-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO3 solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag+ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag+-DNA complex decreased with an increase in Ag+ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO3]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag+-DNA complex formation to a large extent.

Electron impact single detachment on the F- ions using the heavy ion storage ring CRYRING: cross-section determination

International Nuclear Information System (INIS)

Andersson, K.; Hanstorp, D.; Oesterdahl, F.; Danared, H.; Kaellberg, A.

2001-01-01

Electron Impact Single Detachment (EISD) of F - has been studied using the heavy ion storage ring CRYRING at the Manne Siegbahn Laboratory, Stockholm, Sweden. F - ions stored in the ring were merged with an electron beam in one of the ring sections. Neutral F atoms produced in the EISD process were detected in the zero-degree direction using a surface barrier detector. The threshold for the detachment process was found to be around 7.6 eV, thus more than twice the binding energy of F - . The cross-sections increased smoothly up to 55 eV where it reached a maximum of 1.9 x 10 -16 cm 2 . At higher energies a slow decrease of the cross-section was observed, which follows the energy dependence predicted by the Bethe-Born approximation. The experiment showed that CRYRING can be used favourably for studies of anions, and several experiments are forthcoming. (orig.)

Single-ion irradiation: physics, technology and applications

International Nuclear Information System (INIS)

Ohdomari, Iwao

2008-01-01

Among the various radiation effects which involve the study of radiation environments, responses of materials and devices to radiation, radiation testing and radiation hardening of devices and equipment, this review mainly considers the radiation effects induced by alpha particles and other ions used in semiconductor technology on Si crystals and Si devices. We first describe the single-ion microprobe that enables the study of the site dependence of radiation hardness in a semiconductor device. Next, we describe single-ion implantation as a tool for suppressing fluctuation in device function induced by the discrete number and random position of dopant atoms. Finally, we describe the common features associated with both 'probing' and 'modification' in terms of the nature and behaviour of defect clusters induced by single-ion irradiation. A special feature of the review is that the radiation effects discussed here are induced by 'single' particles, and not by particle beams. Although there is a great amount of accumulated data on radiation effects, they are discussed in the conventional terms of 'dose' or 'fluence,' whose unit is cm -2 . Therefore, this review provides complementary information on radiation effects. (topical review)

Crater formation by single ions, cluster ions and ion "showers"

CERN Document Server

Djurabekova, Flyura; Timko, Helga; Nordlund, Kai; Calatroni, Sergio; Taborelli, Mauro; Wuensch, Walter

2011-01-01

The various craters formed by giant objects, macroscopic collisions and nanoscale impacts exhibit an intriguing resemblance in shapes. At the same time, the arc plasma built up in the presence of sufficiently high electric fields at close look causes very similar damage on the surfaces. Although the plasma–wall interaction is far from a single heavy ion impact over dense metal surfaces or the one of a cluster ion, the craters seen on metal surfaces after a plasma discharge make it possible to link this event to the known mechanisms of the crater formations. During the plasma discharge in a high electric field the surface is subject to high fluxes (~1025 cm-2s-1) of ions with roughly equal energies typically of the order of a few keV. To simulate such a process it is possible to use a cloud of ions of the same energy. In the present work we follow the effect of such a flux of ions impinging the surface in the ‘‘shower’’ manner, to find the transition between the different mechanisms of crater formati...

Design and simulation of ion optics for ion sources for production of singly charged ions

Science.gov (United States)

Zelenak, A.; Bogomolov, S. L.

2004-05-01

During the last 2 years different types of the singly charged ion sources were developed for FLNR (JINR) new projects such as Dubna radioactive ion beams, (Phase I and Phase II), the production of the tritium ion beam and the MASHA mass separator. The ion optics simulations for 2.45 GHz electron cyclotron resonance source, rf source, and the plasma ion source were performed. In this article the design and simulation results of the optics of new ion sources are presented. The results of simulation are compared with measurements obtained during the experiments.

Design and simulation of ion optics for ion sources for production of singly charged ions

International Nuclear Information System (INIS)

Zelenak, A.; Bogomolov, S.L.

2004-01-01

During the last 2 years different types of the singly charged ion sources were developed for FLNR (JINR) new projects such as Dubna radioactive ion beams, (Phase I and Phase II), the production of the tritium ion beam and the MASHA mass separator. The ion optics simulations for 2.45 GHz electron cyclotron resonance source, rf source, and the plasma ion source were performed. In this article the design and simulation results of the optics of new ion sources are presented. The results of simulation are compared with measurements obtained during the experiments

Improvement of the Energy Stability of the Single Ion Microbeam

International Nuclear Information System (INIS)

Zhan Furu; Qi Xuehong; Xu Mingliang; Chen Lianyun; Yu Zengliang

2008-01-01

Energy instability strongly affects the state and the beam size of the single ion microbeam. A facility based on the Generating Voltmeter was developed to improve the energy stability of the CAS-LIBB (Chinese Academy of Sciences, key laboratory of ion beam bioengineering) single ion microbeam. This paper presents the analysis of the energy instability of the single ion microbeam. A simplified theoretical model is set up to calculate the relationship between the energy instability and the beam spot size. By using this technique, the energy instability is adjusted to about 1%. Stable run-time is over 6 hours. The radius of the single ion beam is reduced by 10% compared to the previous one.

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.)

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.

Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii

OpenAIRE

Stroud, A. L.

2012-01-01

Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. Haloferax volcanii encodes three RPAs – RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). ...

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels.

Science.gov (United States)

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L

2013-03-05

AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level

Science.gov (United States)

Koslover, Daniel J.; Fazal, Furqan M.; Mooney, Rachel A.; Landick, Robert; Block, Steven M.

2012-01-01

Rho termination factor is an essential hexameric helicase responsible for terminating 20–50% of all mRNA synthesis in E. coli. We used single- molecule force spectroscopy to investigate Rho-RNA binding interactions at the Rho- utilization (rut) site of the ? tR1 terminator. Our results are consistent with Rho complexes adopting two states, one that binds 57 ±2 nucleotides of RNA across all six of the Rho primary binding sites, and another that binds 85 ±2 nucleotides at the six primary sites plus a single secondary site situated at the center of the hexamer. The single-molecule data serve to establish that Rho translocates 5′-to-3′ towards RNA polymerase (RNAP) by a tethered-tracking mechanism, looping out the intervening RNA between the rut site and RNAP. These findings lead to a general model for Rho binding and translocation, and establish a novel experimental approach that should facilitate additional single- molecule studies of RNA-binding proteins. PMID:22885804

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.

Heavy ion and proton-induced single event multiple upset

International Nuclear Information System (INIS)

Reed, R.A.; Carts, M.A.; Marshall, P.W.

1997-01-01

Individual ionizing heavy ion events are shown to cause two or more adjacent memory cells to change logic states in a high density CMOS SRAM. A majority of the upsets produced by normally incident heavy ions are due to single-particle events that causes a single cell to upset. However, for grazing angles a majority of the upsets produced by heavy-ion irradiation are due to single-particle events that cause two or more cells to change logic states. Experimental evidence of a single proton-induced spallation reaction that causes two adjacent memory cells to change logic states is presented. Results from a dual volume Monte-Carlo simulation code for proton-induced single-event multiple upsets are within a factor of three of experimental data for protons at normal incidence and 70 degrees

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.

Selective binding of oligonucleotide on TiO2 surfaces modified by swift heavy ion beam lithography

International Nuclear Information System (INIS)

Vicente Pérez-Girón, J.; Hirtz, M.; McAtamney, C.; Bell, A.P.; Antonio Mas, J.; Jaafar, M.; Luis, O. de; Fuchs, H.

2014-01-01

We have used swift heavy-ion beam based lithography to create patterned bio-functional surfaces on rutile TiO 2 single crystals. The applied lithography method generates a permanent and well defined periodic structure of micrometre sized square holes having nanostructured TiO 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 2 substrates useful for potential biosensor applications

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.

Photoemission and electron-stimulated desorption studies of H on W(110): Single- versus two-binding-site models

International Nuclear Information System (INIS)

Weng, S.

1982-01-01

The chemisorption of H on W(110) at room temperature is studied with the use of angle-integrated photoemission and electron-stimulated desorption (ESD). The ESD cross sections of H + are found to be sol low that no significant H + signals with meaningful ion energy distributions are observed. The photoemission results show, however, two types of H adatoms, referred to as β 2 and β 1 states, for this chemisorptive system. Both states are found to appear simultaneously rather than sequentially as suggested by previous studies, and exhibit a simple 1-theta adsorption kinetics with different initial sticking coefficients. The β 2 state induces two binding energy levels at -2.0 and -6.0 eV, respectively, whereas the β 1 state induces a level at -3.8 eV. The work-function change (with a maximum value of -0.45 eV) is found to follow exactly with the intensity of the β 2 state. These results are found to be compatible with the two-binding-site model, inherently suggested by the reflection high-enery electron-diffraction data. However, the results can also be consistent with a single-binding-site model suggested by a recent angle-resolved photoemission and inelastic electron scattering study. A model based on the present results is proposed and critically compared with previous studies. Unresolved problems associated with both single- and two-binding-site models are also discussed

Adsorption of surfactant ions and binding of their counterions at an air/water interface.

Science.gov (United States)

Tagashira, Hiroaki; Takata, Youichi; Hyono, Atsushi; Ohshima, Hiroyuki

2009-01-01

An expression for the surface tension of an aqueous mixed solution of surfactants and electrolyte ions in the presence of the common ions was derived from the Helmholtz free energy of an air/water surface. By applying the equation to experimental data for the surface tension, the adsorption constant of surfactant ions onto the air/water interface, the binding constant of counterions on the surfactants, and the surface potential and surface charge density of the interface were estimated. The adsorption constant and binding constant were dependent on the species of surfactant ion and counterion, respectively. Taking account of the dependence of surface potential and surface charge density on the concentration of electrolyte, it was suggested that the addition of electrolyte to the aqueous surfactant solution brings about the decrease in the surface potential, the increase in the surface density of surfactant ions, and consequently, the decrease in the surface tension. Furthermore, it was found that the configurational entropy plays a predominant role for the surface tension, compared to the electrical work.

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

Calcium ion binding properties and the effect of phosphorylation on the intrinsically disordered Starmaker protein.

Science.gov (United States)

Wojtas, Magdalena; Hołubowicz, Rafał; Poznar, Monika; Maciejewska, Marta; Ożyhar, Andrzej; Dobryszycki, Piotr

2015-10-27

Starmaker (Stm) is an intrinsically disordered protein (IDP) involved in otolith biomineralization in Danio rerio. Stm controls calcium carbonate crystal formation in vivo and in vitro. Phosphorylation of Stm affects its biomineralization properties. This study examined the effects of calcium ions and phosphorylation on the structure of Stm. We have shown that CK2 kinase phosphorylates 25 or 26 residues in Stm. Furthermore, we have demonstrated that Stm's affinity for calcium binding is dependent on its phosphorylation state. Phosphorylated Stm (StmP) has an estimated 30 ± 1 calcium binding sites per protein molecule with a dissociation constant (KD) of 61 ± 4 μM, while the unphosphorylated protein has 28 ± 3 sites and a KD of 210 ± 22 μM. Calcium ion binding induces a compaction of the Stm molecule, causing a significant decrease in its hydrodynamic radius and the formation of a secondary structure. The screening effect of Na(+) ions on calcium binding was also observed. Analysis of the hydrodynamic properties of Stm and StmP showed that Stm and StmP molecules adopt the structure of native coil-like proteins.

AFM studies on heavy ion irradiated YBCO single crystals

International Nuclear Information System (INIS)

Lakhani, Archana; Marhas, M.K.; Saravanan, P.; Ganesan, V.; Srinivasan, R.; Kanjilal, D.; Mehta, G.K.; Elizabeth, Suja; Bhat, H.L.

2000-01-01

Atomic Force Microscopy (AFM) is extensively used to characterise the surface morphology of high energy ion irradiated single crystals of high temperature superconductor - YBCO. Our earlier systematic studies on thin films of YBCO under high energy and heavy ion irradiation shows clear evidence of ion induced sputtering or erosion, even though the effect is more on the grain boundaries. These earlier results were supported by electrical resistance measurements. In order to understand more clearly, the nature of surface modification at these high energies, AFM studies were carried out on single crystals of YBCO. Single crystals were chosen in order to see the effect on crystallites alone without interference from grain boundaries. 200 MeV gold ions were used for investigation using the facilities available at Nuclear Science Centre, New Delhi. The type of ion and the range of energies were chosen to meet the threshold for electronically mediated defect production. The results are in conformity with our earlier studies and will be described in detail in the context of electronic energy loss mediated sputtering or erosion. (author)

Single ion hit detection set-up for the Zagreb ion microprobe

Science.gov (United States)

Smith, R. W.; Karlušić, M.; Jakšić, M.

2012-04-01

Irradiation of materials by heavy ions accelerated in MV tandem accelerators may lead to the production of latent ion tracks in many insulators and semiconductors. If irradiation is performed in a high resolution microprobe facility, ion tracks can be ordered by submicrometer positioning precision. However, full control of the ion track positioning can only be achieved by a reliable ion hit detection system that should provide a trigger signal irrespectively of the type and thickness of the material being irradiated. The most useful process that can be utilised for this purpose is emission of secondary electrons from the sample surface that follows the ion impact. The status report of the set-up presented here is based on the use of a channel electron multiplier (CEM) detector mounted on an interchangable sample holder that is inserted into the chamber in a close geometry along with the sample to be irradiated. The set-up has been tested at the Zagreb ion microprobe for different ions and energies, as well as different geometrical arrangements. For energies of heavy ions below 1 MeV/amu, results show that efficient (100%) control of ion impact can be achieved only for ions heavier than silicon. The successful use of the set-up is demonstrated by production of ordered single ion tracks in a polycarbonate film and by monitoring fluence during ion microbeam patterning of Foturan glass.

Spectroscopic studies on Titanium ion binding to the apo lactoferrin

International Nuclear Information System (INIS)

Moshtaghie, A.A.; Ani, M.; Arabi, M.H.

2006-01-01

Titanium is a relatively abundant element that has found growing applications in medical science and recently some of Titanium compounds are introduced as anticancer drugs. In spite of very limited data which exist on the Titanium metabolism, some proteins might be involved in the mechanism of action of Titanium up to our knowledge, there is not any report in the literature concerning binding of Titanium to apo lactoferrin. Binding of apo lactoferrin with Ti(IV)-citrate was studied by spectroflourimeterey and spectrophotometery techniques under physiological conditions. The spectroflourimeteric studies revealed a significant fluorescence quenching, that indicated binding of apo lactoferrin with Ti(IV). The same reaction was monitored through spectrophotometry technique; this represents a characteristic UV difference band at 267 nm, which is different from lac-Fe (III). Titration studies how that lactoferrin specifically binds two moles Ti(IV) as complex with citrate per mol protein. Spectroflourimeterey and spectrophotometery techniques indicated that Ti(IV) ions cause a reduction (13%-14%) in binding of Fe(III) to lactoferrin. In overall, we may come to this conclusion that this element might be involved in the iron metabolism

Plastic flow produced by single ion impacts on metals

International Nuclear Information System (INIS)

Birtcher, R. C.

1998-01-01

Single ion impacts have been observed using in situ transmission electron microscopy and video recording with a time resolution of 33 milliseconds. Gold was irradiated at 50 K and room temperature. Single ion impacts produce holes, modify existing holes, and extrude material into the initial specimen hole and holes formed by other ion impacts. The same behavior is observed at both temperatures. At both temperatures, ion impacts result in craters and ejected material. Ion impacts produce more small craters than large ones for all ion masses, while heavier mass ions produce more and larger craters than lighter mass ions. This comparison is affected by the ion energy. As the energy of an ion is increased, the probability for deposition near the surface decreases and fewer craters are formed. For a given ion mass, crater production depends on the probability for displacement cascade production in the near surface region. Crater and holes are stable at room temperature, however, ion impacts near an existing crater may cause flow of material into the crater either reshaping or annihilating it. Holes and craters result from the explosive outflow of material from the molten zone of near-surface cascades. The outflow may take the form of molten material, a solid lid or an ejected particle. The surface is a major perturbation on displacement cascades resulting from ion impacts

Improved single ion cyclotron resonance mass spectroscopy

International Nuclear Information System (INIS)

Boyce, K.R.

1993-01-01

The author has improved the state of the art for precision mass spectroscopy of a mass doublet to below one part in 10 10 . By alternately loading single ions into a Penning trap, the author has determined the mass ratio M(CO + )/M(N + 2 ) = 0.999 598 887 74(11), an accuracy of 1 x 10 -10 . This is a factor of 4 improvement over previous measurements, and a factor of 10 better than the 1985 atomic mass table adjustment [WAA85a]. Much of the author's apparatus has been rebuilt, increasing the signal-to-noise ratio and improving the reliability of the machine. The typical time needed to make and cool a single ion has been reduced from about half an hour to under 5 minutes. This was done by a combination of faster ion-making and a much faster procedure for driving out ions of the wrong species. The improved S/N, in combination with a much better signal processing algorithm to extract the ion phase and frequency from the author's data, has substantially reduced the time required for the actual measurements. This is important now that the measurement time is a substantial fraction of the cycle time (the time to make a new ion and measure it). The improvements allow over 30 comparisons in one night, compared to 2 per night previously. This not only improves the statistics, but eliminates the possibility of large non-Gaussian errors due to sudden magnetic field shifts

Screened ion-ion interaction in mercury-chain compounds: Single chain

International Nuclear Information System (INIS)

Mohan, M.M.; Griffin, A.

1985-01-01

At room temperature, the mercury chains in Hg/sub 3-delta/AsF 6 exhibit phonons characteristic of a one-dimensional lattice. We calculate the screening of the Hg ion-ion interaction in a single chain by electrons moving in a cylindrical potential of finite radius, within the random-phase approximation. The resulting Bohm-Staver-type expression for the phonon velocity is (Z 2 mN/sub I//MN/sub e/)/sup 1/2/v/sub F/, where Z is the Hg ionic charge and N/sub I/ (N/sub e/) is the number of ions (electrons) per unit length. Use of the Tomonaga-Luttinger solution for the electronic response function (keeping only the small-momentum scattering processes) just renormalizes the Fermi velocity in this expression

Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting.

Science.gov (United States)

Swainsbury, David J K; Martin, Elizabeth C; Vasilev, Cvetelin; Parkes-Loach, Pamela S; Loach, Paul A; Neil Hunter, C

2017-11-01

The reaction centre-light harvesting 1 (RC-LH1) complex of Thermochromatium (Tch.) tepidum has a unique calcium-ion binding site that enhances thermal stability and red-shifts the absorption of LH1 from 880nm to 915nm in the presence of calcium-ions. The LH1 antenna of mesophilic species of phototrophic bacteria such as Rhodobacter (Rba.) sphaeroides does not possess such properties. We have engineered calcium-ion binding into the LH1 antenna of Rba. sphaeroides by progressively modifying the native LH1 polypeptides with sequences from Tch. tepidum. We show that acquisition of the C-terminal domains from LH1 α and β of Tch. tepidum is sufficient to activate calcium-ion binding and the extent of red-shifting increases with the proportion of Tch. tepidum sequence incorporated. However, full exchange of the LH1 polypeptides with those of Tch. tepidum results in misassembled core complexes. Isolated α and β polypeptides from our most successful mutant were reconstituted in vitro with BChl a to form an LH1-type complex, which was stabilised 3-fold by calcium-ions. Additionally, carotenoid specificity was changed from spheroidene found in Rba. sphaeroides to spirilloxanthin found in Tch. tepidum, with the latter enhancing in vitro formation of LH1. These data show that the C-terminal LH1 α/β domains of Tch. tepidum behave autonomously, and are able to transmit calcium-ion induced conformational changes to BChls bound to the rest of a foreign antenna complex. Thus, elements of foreign antenna complexes, such as calcium-ion binding and blue/red switching of absorption, can be ported into Rhodobacter sphaeroides using careful design processes. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

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.

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...... 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....

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.

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.

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.

Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain.

Science.gov (United States)

Sriram, M; Osipiuk, J; Freeman, B; Morimoto, R; Joachimiak, A

1997-03-15

The 70 kDa heat shock proteins (Hsp70) are a family of molecular chaperones, which promote protein folding and participate in many cellular functions. The Hsp70 chaperones are composed of two major domains. The N-terminal ATPase domain binds to and hydrolyzes ATP, whereas the C-terminal domain is required for polypeptide binding. Cooperation of both domains is needed for protein folding. The crystal structure of bovine Hsc70 ATPase domain (bATPase) has been determined and, more recently, the crystal structure of the peptide-binding domain of a related chaperone, DnaK, in complex with peptide substrate has been obtained. The molecular chaperone activity and conformational switch are functionally linked with ATP hydrolysis. A high-resolution structure of the ATPase domain is required to provide an understanding of the mechanism of ATP hydrolysis and how it affects communication between C- and N-terminal domains. The crystal structure of the human Hsp70 ATPase domain (hATPase) has been determined and refined at 1. 84 A, using synchrotron radiation at 120K. Two calcium sites were identified: the first calcium binds within the catalytic pocket, bridging ADP and inorganic phosphate, and the second calcium is tightly coordinated on the protein surface by Glu231, Asp232 and the carbonyl of His227. Overall, the structure of hATPase is similar to bATPase. Differences between them are found in the loops, the sites of amino acid substitution and the calcium-binding sites. Human Hsp70 chaperone is phosphorylated in vitro in the presence of divalent ions, calcium being the most effective. The structural similarity of hATPase and bATPase and the sequence similarity within the Hsp70 chaperone family suggest a universal mechanism of ATP hydrolysis among all Hsp70 molecular chaperones. Two calcium ions have been found in the hATPase structure. One corresponds to the magnesium site in bATPase and appears to be important for ATP hydrolysis and in vitro phosphorylation. Local changes

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.

Lanthanide and actinide ion phytoextraction: investigations of biosorption chemistry

International Nuclear Information System (INIS)

Rayson, Gary D.; Serna, Debbie D.; Moore, Jessica L.

2009-01-01

Investigations of the chemical interactions responsible for passive biosorption of a lanthanide (Eu (III)) and an actinide (U (VI)) metal ion is described. Spectroscopic methods for the elucidation of chemical functionalities on cultured anther cell walls from the plant Datura innoxia include metal ion luminescence measurements. These have revealed the presence of distinctly different binding environments involving one, two, and three carboxylate moieties for Eu (III) and UO 2 2+ binding and sulfonates (or sulfates) and phosphates for sequestration of Eu (III) on the uranyl ion, respectively. Additional investigations of the apparent affinities of these metals to this material have revealed the presence of both low and high affinity sites for the binding of Eu (III) with weak electrostatic attractions proposed for binding at high metal concentrations (i.e., low affinities) and surface coordination interactions responsible for higher affinities. Conversely, total uranyl ion binding revealed only a single distribution of interactions based on apparent affinities. (author)

Single-Ion Implantation for the Development of Si-Based MOSFET Devices with Quantum Functionalities

Directory of Open Access Journals (Sweden)

Jeffrey C. McCallum

2012-01-01

Full Text Available Interest in single-ion implantation is driven in part by research into development of solid-state devices that exhibit quantum behaviour in their electronic or optical characteristics. Here, we provide an overview of international research work on single ion implantation and single ion detection for development of electronic devices for quantum computing. The scope of international research into single ion implantation is presented in the context of our own research in the Centre for Quantum Computation and Communication Technology in Australia. Various single ion detection schemes are presented, and limitations on dopant placement accuracy due to ion straggling are discussed together with pathways for scale-up to multiple quantum devices on the one chip. Possible future directions for ion implantation in quantum computing and communications are also discussed.

Heavy ion microbeam system for study of single event effects

International Nuclear Information System (INIS)

Kamiya, Tomihiro; Utsunomiya, Nobuhiro; Minehara, Eiichi; Tanaka, Ryuichi; Ohmura, Miyoshi; Kohno, Kazuhiro; Iwamoto, Eiji.

1992-01-01

A high-energy heavy ion microbeam system has been developed and installed on a beam line of a 3 MV tandem electrostatic accelerator mainly for analysis of basic mechanism of single event upset (SEU) of semiconductor devices in spacecraft. The SEU is now the most serious problem for highly reliable spacecraft electronics system with long space mission. However, the mechanism has not been understood on the basis of microscopic process of SEU. The SEU phenomena depends not only upon hitting particles, but also upon the hit position on the microcircuit. To observe the transient charge pulse from a SEU, a single ion particle must hit exactly the desired position of the microcircuit. Such an experiment requires the microbeam spot size within 1 μm, the beam positioning accuracy within ±1 μm, and single ion hitting. The microbeam system has been designed to meet the above technical requirements. The system is equipped with two lens systems: one to control the target beam current in a wide range down to extremely low current without any change of the beam optics, and the other to focus heavy ion beams within a spot size of 1 μm. The final goal is to hit a microscopic target area with a single 15 MeV nickel ion. The beam spot size has been evaluated by Gaussian fitting of secondary electron profiles with microbeam scanning across the fine Cu mesh. The single ion detection has been also tested to generate a trigger signal for closing beam shutter to prevent further hits. This paper outlines the new microbeam system and describes methods to realize these techniques. (author)

pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-β peptide

International Nuclear Information System (INIS)

Ghalebani, Leila; Wahlström, Anna; Danielsson, Jens; Wärmländer, Sebastian K.T.S.; Gräslund, Astrid

2012-01-01

Highlights: ► Cu(II) and Zn(II) display pH-dependent binding to the Aβ(1–40) peptide. ► At pH 7.4 both metal ions display residue-specific binding to the Aβ peptide. ► At pH 5.5 the binding specificity is lost for Zn(II). ► Differential Cu(II) and Zn(II) binding may help explain metal-induced AD toxicity. -- Abstract: Metal ions like Cu(II) and Zn(II) are accumulated in Alzheimer’s disease amyloid plaques. The amyloid-β (Aβ) peptide involved in the disease interacts with these metal ions at neutral pH via ligands provided by the N-terminal histidines and the N-terminus. The present study uses high-resolution NMR spectroscopy to monitor the residue-specific interactions of Cu(II) and Zn(II) with 15 N- and 13 C, 15 N-labeled Aβ(1–40) peptides at varying pH levels. At pH 7.4 both ions bind to the specific ligands, competing with one another. At pH 5.5 Cu(II) retains its specific histidine ligands, while Zn(II) seems to lack residue-specific interactions. The low pH mimics acidosis which is linked to inflammatory processes in vivo. The results suggest that the cell toxic effects of redox active Cu(II) binding to Aβ may be reversed by the protective activity of non-redox active Zn(II) binding to the same major binding site under non-acidic conditions. Under acidic conditions, the protective effect of Zn(II) may be decreased or changed, since Zn(II) is less able to compete with Cu(II) for the specific binding site on the Aβ peptide under these conditions.

THE EFFECTS OF COPPER AND ZINC IONS DURING THEIR BINDING WITH HUMAN SERUM γ-GLOBULIN

Directory of Open Access Journals (Sweden)

S. B. Cheknev

2006-01-01

Full Text Available Abstract. Conformational changes of human serum γ-globulin were studied during and after its binding with copper and zinc ions, using molecular ultrafiltration and differential spectrophotometry. The contents of nonbound metals in the filtrate were evaluated, resp., with sodium diethyl thyocarbamate and o-phenanthroline. It has been shown that copper and zinc exhibited common biological properties during their interactions with protein, but the binding differed sufficiently under similar experimental conditions. E.g., it was confirmed that copper was more active at the external sites of γ-globulin molecule, whereas zinc demonstrated tropicity for the areas of protein intraglobular compartments. The metal-binding sites have been described that differ in their parameters of interactions with cations and their spatial location within globular domains. Approaches are suggested for dynamic analysis of saturation for these differently located sites by the metal ions. We discuss the issues of altered conformational state of the γ-globulin molecule during the binding of cations, as well as potential usage of these data in clinical immunology.

Calcium ion binding properties of Medicago truncatula calcium/calmodulin-dependent protein kinase.

Science.gov (United States)

Swainsbury, David J K; Zhou, Liang; Oldroyd, Giles E D; Bornemann, Stephen

2012-09-04

A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (~125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.

Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites.

Science.gov (United States)

Li, Shunyi; Yang, Wei; Maniccia, Anna W; Barrow, Doyle; Tjong, Harianto; Zhou, Huan-Xiang; Yang, Jenny J

2008-10-01

Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.

Binding energy and single-particle energies in the 16O Region

International Nuclear Information System (INIS)

Fiase, J.O.; Sharma, L.K.

2004-01-01

In this paper we present the binding energy of 16 O together with single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Nijmegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.Our calculated binding energy, E B = - 127.8 MeV with r c = 0.241 fm compares well with the experimental binding energy, E B = - 127.6 MeV

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.

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

Application of heavy-ion microbeam system at Kyoto University: Energy response for imaging plate by single ion irradiation

International Nuclear Information System (INIS)

Tosaki, M.; Nakamura, M.; Hirose, M.; Matsumoto, H.

2011-01-01

A heavy-ion microbeam system for cell irradiation has been developed using an accelerator at Kyoto University. We have successfully developed proton-, carbon-, fluorine- and silicon-beams in order to irradiate a micro-meter sized area with ion counting, especially single ion irradiation. In the heavy-ion microbeam system, an imaging plate (IP) was utilized for beam diagnostics on the irradiation. The IP is widely used for radiography studies in biology. However, there are a few studies on the low linear energy transfer (LET) by single ions, i.e., low-intensity exposure. Thus we have investigated the energy response for the IP, which can be utilized for microbeam diagnostics.

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.

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)

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....

Resonator QED experiments with single 40Ca+ ions

International Nuclear Information System (INIS)

Lange, B.

2006-01-01

Combining an optical resonator with an ion trap provides the possibility for QED experiments with single or few particles interacting with a single mode of the electro-magnetic field (Cavity-QED). In the present setup, fluctuations in the count rate on a time scale below 30 seconds were purely determined by the photon statistics due to finite emission and detection efficiency, whereas a marginal drift of the system was noticeable above 200 seconds. To find methods to increase the efficiency of the photon source, investigations were conducted and experimental improvements of the setup implemented in the frame of this thesis. Damping of the resonator field and coupling of ion and field were considered as the most important factors. To reduce the damping of the resonator field, a resonator with a smaller transmissivity of the output mirror was set up. The linear trap used in the experiment allows for the interaction of multiple ions with the resonator field, so that more than one photon may be emitted per pump pulse. This was investigated in this thesis with two ions coupled to the resonator. The cross correlation of the emitted photons was measured with the Hanbury Brown-Twiss method. (orig.)

Picomolar selective detection of mercuric ion (Hg{sup 2+}) using a functionalized single plasmonic gold nanoparticle

Energy Technology Data Exchange (ETDEWEB)

Song, Hyeon Don; Choi, Inhee; Yang, Young In; Hong, Surin; Lee, Suseung; Yi, Jongheop [School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 151-742 (Korea, Republic of); Kang, Taewook, E-mail: xinly601@snu.ac.kr, E-mail: iniini79@snu.ac.kr, E-mail: netmo00@snu.ac.kr, E-mail: pell2004@snu.ac.kr, E-mail: jazz1863@snu.ac.kr, E-mail: twkang@sogang.ac.kr, E-mail: jyi@snu.ac.kr [Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742 (Korea, Republic of)

2010-04-09

A highly sensitive method for the selective detection and quantification of mercuric ions (Hg{sup 2+}) using single plasmonic gold nanoparticle (GNP)-based dark-field microspectroscopy (DFMS) is demonstrated. The method is based on the scattering property of a single GNP that is functionalized with thiolated molecules, which is altered when analytes bind to the functionalized GNP. The spectral resolution of the system is 0.26 nm and a linear response to Hg{sup 2+} was found in the dynamic range of 100 pM-10 {mu}M. The method permits Hg{sup 2+} to be detected at the picomolar level, which is a remarkable reduction in the detection limit, considering the currently proscribed Environmental Protection Agency regulation level (10 nM, or 2 ppb) and the detection limits of other optical methods for detecting Hg{sup 2+} (recently approx. 1-10 nM). In addition, Hg{sup 2+} can be sensitively detected in the presence of Cd{sup 2+}, Pb{sup 2+}, Cu{sup 2+}, Zn{sup 2+} and Ni{sup 2+}, which do not interfere with the analysis. Based on the findings reported herein, it is likely that single-nanoparticle-based metal ion sensing can be extended to the development of other chemo- and biosensors for the direct detection of specific targets in an intracellular environment as well as in environmental monitoring.

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.

Revealing dynamically-organized receptor ion channel clusters in live cells by a correlated electric recording and super-resolution single-molecule imaging approach.

Science.gov (United States)

Yadav, Rajeev; Lu, H Peter

2018-03-28

The N-methyl-d-aspartate (NMDA) receptor ion-channel is activated by the binding of ligands, along with the application of action potential, important for synaptic transmission and memory functions. Despite substantial knowledge of the structure and function, the gating mechanism of the NMDA receptor ion channel for electric on-off signals is still a topic of debate. We investigate the NMDA receptor partition distribution and the associated channel's open-close electric signal trajectories using a combined approach of correlating single-molecule fluorescence photo-bleaching, single-molecule super-resolution imaging, and single-channel electric patch-clamp recording. Identifying the compositions of NMDA receptors, their spatial organization and distributions over live cell membranes, we observe that NMDA receptors are organized inhomogeneously: nearly half of the receptor proteins are individually dispersed; whereas others exist in heterogeneous clusters of around 50 nm in size as well as co-localized within the diffraction limited imaging area. We demonstrate that inhomogeneous interactions and partitions of the NMDA receptors can be a cause of the heterogeneous gating mechanism of NMDA receptors in living cells. Furthermore, comparing the imaging results with the ion-channel electric current recording, we propose that the clustered NMDA receptors may be responsible for the variation in the current amplitude observed in the on-off two-state ion-channel electric signal trajectories. Our findings shed new light on the fundamental structure-function mechanism of NMDA receptors and present a conceptual advancement of the ion-channel mechanism in living cells.

Determining time-weighted average concentrations of nitrate and ammonium in freshwaters using DGT with ion exchange membrane-based binding layers

DEFF Research Database (Denmark)

Huang, Jianyin; Bennett, William W.; Welsh, David T.

2016-01-01

Commercially-available AMI-7001 anion exchange and CMI-7000 cation exchange membranes were utilised as binding layers for DGT measurements of NO3-N and NH4-N in freshwaters. These ion exchange membranes are easier to prepare and handle than DGT binding layers consisting of hydrogels cast with ion...... exchange resins. The membranes showed good uptake and elution efficiencies for both NO3-N and NH4-N. The membrane-based DGTs are suitable for pH 3.5-8.5 and ionic strength ranges (0.0001-0.014 and 0.0003-0.012 mol L−1 as NaCl for the AMI-7001 and CMI-7000 membrane, respectively) typical of most natural...... freshwaters. The binding membranes had high intrinsic binding capacities for NO3-N and NH4-N of 911 ± 88 μg and 3512 ± 51 μg, respectively. Interferences from the major competing ions for membrane-based DGTs are similar to DGTs employing resin-based binding layers but with slightly different selectivity...

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.

Experimental investigations of single-electron detachment processes from H- ions colliding with MeV/u, highly charged ions

International Nuclear Information System (INIS)

Tawara, H.; Tonuma, T.; Kumagai, H.; Imai, T.; Uskov, D.B.; Presnyakov, L.P.

1999-01-01

Single electron detachment processes from negative hydrogen ions under collisions with MeV/u highly charged ions have been investigated using the so-called crossed-beams technique. The preliminary results of the single-electron detachment cross sections obtained is found to be in crude agreement with some empirical and theoretical estimations. (orig.)

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.

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.

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

KAUST Repository

Tu, Zhengyuan; Choudhury, Snehashis; Zachman, Michael J.; Wei, Shuya; Zhang, Kaihang; Kourkoutis, Lena F.; Archer, Lynden A.

2017-01-01

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

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.)

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.

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

Science.gov (United States)

Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

2015-10-31

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

Spectroscopy and nonclassical fluorescence properties of single trapped Ba+ ions

International Nuclear Information System (INIS)

Bolle, J.

1998-06-01

This thesis reports on the setup and application of an experimental apparatus for spectroscopic and quantum optical investigations of a single Barium ion in a Paul trap. The realization of the apparatus, which consists of the ion trap in ultra high vacuum, two laser systems, and a photon counting detection system, is described in detail, with particular consideration of the noise sources like stray light and laser frequency instabilities. The two lasers at 493 nm and 650 nm needed to continuously excite resonance fluorescence from the Barium ion have been realized using diode lasers only. The preparation of a single localized Barium ion is described, in particular its optical cooling with the laser light and the minimization of induced vibration in the trapping potential. The purely quantum mechanical property of antibunching is observed by measuring the intensity correlation function of resonance fluorescence from the trapped and cooled ion. Interference properties of the single ion resonance fluorescence are investigated with a Mach-Zehnder interferometer. From the measured high-contrast interference signal it is proven that each individual fluorescence photon interferes with itself. The fluorescence excitation spectrum, on varying one laser frequency, is also measured and exhibits dark resonances. These measurements are compared to calculations based on optical Bloch equations for the 8 atomic levels involved. Future experiments, in particular the detection of reduced quantum fluctuations (squeezing) in one quadrature component of the resonance fluorescence, are discussed. (author)

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.

Simple method for determining binding energies of fullerene and complex atomic negative ions

Science.gov (United States)

Felfli, Zineb; Msezane, Alfred

2017-04-01

A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

Probing Surface Electric Field Noise with a Single Ion

Science.gov (United States)

2013-07-30

potentials is housed inside a Faraday cage providing more than 40 dB of attenuation for electromagnetic fields in the range of frequencies between 200...and measuring the ion quantum state [16]. Thus, by measuring the effect of electric field noise on the motional quantum state of the ion, one can probe...understand these effects . In summary, we have probed the electric field noise near an aluminum-copper surface at room temperature using a single trapped ion

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.

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

Energy Technology Data Exchange (ETDEWEB)

Omichi, Masaaki [Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871 (Japan); Center for Collaborative Research, Anan National College of Technology, Anan, Tokushima 774-0017 (Japan); Choi, Wookjin; Sakamaki, Daisuke; Seki, Shu, E-mail: seki@chem.eng.osaka-u.ac.jp [Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871 (Japan); Tsukuda, Satoshi [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Sugimoto, Masaki [Japan Atomic Energy Agency, Takasaki Advanced Radiation Research Institute, Gunma, Gunma 370-1292 (Japan)

2014-11-15

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.

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)

Ion implantation of CdTe single crystals

International Nuclear Information System (INIS)

Wiecek, Tomasz; Popovich, Volodymir; Bester, Mariusz; Kuzma, Marian

2017-01-01

Ion implantation is a technique which is widely used in industry for unique modification of metal surface for medical applications. In semiconductor silicon technology ion implantation is also widely used for thin layer electronic or optoelectronic devices production. For other semiconductor materials this technique is still at an early stage. In this paper based on literature data we present the main features of the implantation of CdTe single crystals as well as some of the major problems which are likely to occur when dealing with them. The most unexpected feature is the high resistance of these crystals against the amorphization caused by ion implantation even at high doses (10"1"7 1/cm"2). The second property is the disposal of defects much deeper in the sample then it follows from the modeling calculations. The outline of principles of the ion implantation is included in the paper. The data based on RBS measurements and modeling results obtained by using SRIM software were taken into account.

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.

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.

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.

Engineering [Ln(DPA){sub 3}]{sup 3-} binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions

Energy Technology Data Exchange (ETDEWEB)

Jia Xinying; Yagi, Hiromasa; Su Xuncheng; Stanton-Cook, Mitchell; Huber, Thomas; Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)

2011-08-15

Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and independent of cysteine residues. It relies on preferential binding of the complex between three dipicolinic acid molecules (DPA) and a lanthanide ion (Ln{sup 3+}), [Ln(DPA){sub 3}]{sup 3-}, to a pair of positively charged amino acids whose charges are not compensated by negatively charged residues nearby. This situation rarely occurs in wild-type proteins, allowing the creation of specific binding sites simply by introduction of positively charged residues that are positioned far from glutamate or aspartate residues. The concept is demonstrated with the hnRNPLL RRM1 domain. In addition, we show that histidine- and arginine-tags present binding sites for [Ln(DPA){sub 3}]{sup 3-}.

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).

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

Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics.

Science.gov (United States)

Pandit, Sagar A; Bostick, David; Berkowitz, Max L

2003-11-01

Two mixed bilayers containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine at a ratio of 5:1 are simulated in NaCl electrolyte solutions of different concentration using the molecular dynamics technique. Direct NH.O and CH.O hydrogen bonding between lipids was observed to serve as the basis of interlipid complexation. It is deduced from our results and previous studies that dipalmitoylphosphatidylcholine alone is less likely to form interlipid complexes than in the presence of bound ions or other bilayer "impurities" such as dipalmitoylphosphatidylserine. The binding of counterions is observed and quantitated. Based upon the calculated ion binding constants, the Gouy-Chapman surface potential (theta) is calculated. In addition we calculated the electrostatic potential profile (Phi) by twice integrating the system charge distribution. A large discrepancy between and the value of Phi at the membrane surface is observed. However, at "larger" distance from the bilayer surface, a qualitative similarity in the z-profiles of Phi and psi(GC) is seen. The discrepancy between the two potential profiles near the bilayer surface is attributed to the discrete and nonbulk-like nature of water in the interfacial region and to the complex geometry of this region.

Sub-Poissonian statistics of quantum jumps in single molecule or atomic ion

International Nuclear Information System (INIS)

Osad'ko, I.S.; Gus'kov, D.N.

2007-01-01

A theory for statistics of quantum jumps in single molecule or ion driven by continues wave laser field is developed. These quantum jumps can relate to nonradiative singlet-triplet transitions in a molecule or to on → off jumps in a single ion with shelving processes. Distribution function w N (T) of quantum jumps in time interval T is found. Computer simulation of quantum jumps is realized. Statistical treatment of simulated jumps reveals sub-Poissonian statistics of quantum jumps. The theoretical distribution function w N (T) fits well the distribution of jumps found from simulated data. Experimental data on quantum jumps found in experiments with single Hg + ion are described by the function w N (T) well

Substrate binding to SGLT1 investigated by single molecule force spectroscopy

International Nuclear Information System (INIS)

Neundlinger, I. J.

2010-01-01

D-glucose serves as one of the most important fuels in various organism due to its fundamental role in ATP-, protein and lipid synthesis. Thus, sustaining glucose homeostasis is a crucial issue of life as disorders can cause severe malfunctions such as glucose-galactose-malabsorbtion (GGM). Sodium-glucose co-transporter, SGLTs, especially the high affinity transporter SGLT1, play a crucial role in accumulation of glucose in the cell as they facilitate transport of the sugar into the cytoplasma across the cell membrane by a Na+-electrochemical potential. Even recently, members of the SGLT transporter family have become a therapeutic target for the treatment of hyperglycemia in type 2 diabetes. Hence, it is of particular importance to gain insights on the dynamic behavior of SGLTs during substrate binding and transport across the cell membrane on the single molecular level. In the present study, the Atomic Force Microscope (AFM) was employed to investigate the dynamic properties of the sodium-glucose co-transporter SGLT1 upon substrate binding under nearly physiological conditions. Hereto, new glucose derivatives were synthesized in order to probe the recognition efficiency of these molecules to SGLT1 embedded in the plasma membrane of living cells. A well established coupling protocol was used to covalently link (i) amino-modified D-glucose owning a conserved pyranose ring, (ii) 1-thio-β-D-glucose having a sulphur atom at C1 of the pyranose ring and (iii) the competitive inhibitor phlorizin to the AFM tip via poly(ethylene)glycol (PEG)-tether using different functional end groups and varying lengths. Binding characteristics, e.g. binding probability, interaction forces, influence of substances (glucose, phlorizin, sodium) and of molecule-linker compounds were obtained by performing single molecular recognition force spectroscopy (SMRFS) measurements. Moreover, temperature controlled radioactive binding/transport assays and SMRFS experiments yielded insights into

U/Th dating by SHRIMP RG ion-microprobe mass spectrometry using single ion-exchange beads

Science.gov (United States)

Bischoff, J.L.; Wooden, J.; Murphy, F.; Williams, Ross W.

2005-01-01

We present a new analytical method for U-series isotopes using the SHRIMP RG (Sensitive High mass Resolution Ion MicroProbe) mass spectrometer that utilizes the preconcentration of the U-series isotopes from a sample onto a single ion-exchange bead. Ion-microprobe mass spectrometry is capable of producing Th ionization efficiencies in excess of 2%. Analytical precision is typically better than alpha spectroscopy, but not as good as thermal ionization mass spectroscopy (TIMS) and inductively coupled plasma multicollector mass spectrometry (ICP-MS). Like TIMS and ICP-MS the method allows analysis of small samples sizes, but also adds the advantage of rapidity of analysis. A major advantage of ion-microprobe analysis is that U and Th isotopes are analyzed in the same bead, simplifying the process of chemical separation. Analytical time on the instrument is ???60 min per sample, and a single instrument-loading can accommodate 15-20 samples to be analyzed in a 24-h day. An additional advantage is that the method allows multiple reanalyses of the same bead and that samples can be archived for reanalysis at a later time. Because the ion beam excavates a pit only a few ??m deep, the mount can later be repolished and reanalyzed numerous times. The method described of preconcentrating a low concentration sample onto a small conductive substrate to allow ion-microprobe mass spectrometry is potentially applicable to many other systems. Copyright ?? 2005 Elsevier Ltd.

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.

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

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)

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.

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.

Cavity QED with single trapped Ca+-ions

International Nuclear Information System (INIS)

Mundt, A.B.

2003-02-01

This thesis reports on the design and setup of a vacuum apparatus allowing the investigation of cavity QED effects with single trapped 40 Ca + ions. The weak coupling of ion and cavity in the 'bad cavity limit' may serve to inter--convert stationary and flying qubits. The ion is confined in a miniaturized Paul trap and cooled via the Doppler effect to the Lamb--Dicke regime. The extent of the atomic wave function is less than 30 nm. The ion is enclosed by a high finesse optical cavity. The technically--involved apparatus allows movement of the trap relative to the cavity and the trapped ion can be placed at any position in the standing wave. By means of a transfer lock the cavity can be resonantly stabilized with the S 1/2 ↔ D 5/2 quadrupole transition at 729 nm (suitable as a qubit) without light at that wavelength being present in the cavity. The coupling of the cavity field to the S 1/2 ↔ D 5/2 quadrupole transition is investigated with various techniques in order to determine the spatial dependence as well as the temporal dynamics. The orthogonal coupling of carrier and first--order sideband transitions at field nodes and antinodes is explored. The coherent interaction of the ion and the cavity field is confirmed by exciting Rabi oscillations with short resonant pulses injected into the cavity. Finally, first experimental steps towards the observation of cavity enhanced spontaneous emission have been taken. (author)

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

Science.gov (United States)

Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

2016-08-25

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of

Extending the applicability of an open-ring trap to perform experiments with a single laser-cooled ion

Energy Technology Data Exchange (ETDEWEB)

Cornejo, J. M.; Colombano, M.; Doménech, J.; Rodríguez, D., E-mail: danielrodriguez@ugr.es [Departamento de Física Atómica, Molecular y Nuclear, Universidad de Granada, 18071 Granada (Spain); Block, M. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt (Germany); Helmholtz-Institut Mainz, 55099 Mainz (Germany); Institut für Kernchemie, University of Mainz, 55099 Mainz (Germany); Delahaye, P. [Grand Accélérateur National d’Ions Lourds, 14000 Caen (France)

2015-10-15

A special ion trap was initially built up to perform β-ν correlation experiments with radioactive ions. The trap geometry is also well suited to perform experiments with laser-cooled ions, serving for the development of a new type of Penning trap, in the framework of the project TRAPSENSOR at the University of Granada. The goal of this project is to use a single {sup 40}Ca{sup +} ion as detector for single-ion mass spectrometry. Within this project and without any modification to the initial electrode configuration, it was possible to perform Doppler cooling on {sup 40}Ca{sup +} ions, starting from large clouds and reaching single ion sensitivity. This new feature of the trap might be important also for other experiments with ions produced at radioactive ion beam facilities. In this publication, the trap and the laser system will be described, together with their performance with respect to laser cooling applied to large ion clouds down to a single ion.

On the single-ion Magnetic Anisotropy of the Rare-Earth Metals

DEFF Research Database (Denmark)

Kolmakova, N.P.; Tishin, A.M.; Bohr, Jakob

1996-01-01

The temperature dependences of the single-ion magnetic anisotropy constants for Tb and Dy metals are calculated in terms of the multipole moments of the rare-earth ions utilizing the available crystal-field parameters. The results are compared with the existing experimental data....

Raman spectroscopy and single-photon source in an ion-cavity system

International Nuclear Information System (INIS)

Goncalves de Barros, H.

2010-01-01

The work presented in this thesis explores the interaction between a single trapped 40Ca+ ion and the electromagnetic field inside a high-finesse optical cavity. The coupling takes place via the use of a vacuum stimulated Raman transition, which transfers atomic population from the S1/2 to the D3/2 manifolds of the calcium ion producing a photon in the cavity. This photon is measured and properties of the system are evaluated. Spectroscopy measurements of the Raman transitions are performed and all possible transitions are identified for different polarizations of both drive laser and cavity fields. The system is also used to deterministically produce single photons. Simulation curves quantitatively match the experimental results within calibration error bars. The single-photon creation efficiency obtained in this work overcomes previous ion-cavity setups and is comparable to state-of-the-art systems composed of a neutral atom and a cavity operating in the strong coupling regime. (author)

Creation and recovery of a W(111) single atom gas field ion source

International Nuclear Information System (INIS)

Pitters, Jason L.; Urban, Radovan; Wolkow, Robert A.

2012-01-01

Tungsten single atom tips have been prepared from a single crystal W(111) oriented wire using the chemical assisted field evaporation and etching method. Etching to a single atom tip occurs through a symmetric structure and leads to a predictable last atom unlike etching with polycrystalline tips. The single atom tip formation procedure is shown in an atom by atom removal process. Rebuilds of single atom tips occur on the same crystalline axis as the original tip such that ion emission emanates along a fixed direction for all tip rebuilds. This preparation method could be utilized and developed to prepare single atom tips for ion source development.

Improved generation of single nitrogen-vacancy centers in diamond by ion implantation

Energy Technology Data Exchange (ETDEWEB)

Naydenov, Boris; Beck, Johannes; Steiner, Matthias; Balasubramanian, Gopalakrishnan; Jelezko, Fedor; Wrachtrup, Joerg [3. Institute of Physics, University of Stuttgart (Germany); Richter, Vladimir; Kalish, Rafi [Solid State Institute, Technion City, Haifa (Israel); Achard, Jocelyn [Laboratoire d' Ingenieurie des Materiaux et des Hautes Pressions, CNRS, Villetaneuse (France)

2010-07-01

Nitrogen-vacancy (NV) centers in diamond have recently attracted the attention of many research groups due to their possible application as quantum bits (qubits), ultra low magnetic field sensors and single photon sources. These color centers can be produced by nitrogen ion implantation, although the yield is usually below 5 % at low ion energies. Here we report an increase of the NV production efficiency by subsequently implanting carbon ions in the area of implanted nitrogen ions. This method improves the production yield by more than 50 %. We also show that very low nitrogen concentration (below 0.1 ppb) in diamond can be determined by converting the intrinsic nitrogen atoms to single NV centers and detecting the latter using a confocal microscope.

Single-molecule analysis reveals the kinetics and physiological relevance of MutL-ssDNA binding.

Directory of Open Access Journals (Sweden)

Jonghyun Park

2010-11-01

Full Text Available DNA binding by MutL homologs (MLH/PMS during mismatch repair (MMR has been considered based on biochemical and genetic studies. Bulk studies with MutL and its yeast homologs Mlh1-Pms1 have suggested an integral role for a single-stranded DNA (ssDNA binding activity during MMR. We have developed single-molecule Förster resonance energy transfer (smFRET and a single-molecule DNA flow-extension assays to examine MutL interaction with ssDNA in real time. The smFRET assay allowed us to observe MutL-ssDNA association and dissociation. We determined that MutL-ssDNA binding required ATP and was the greatest at ionic strength below 25 mM (K(D = 29 nM while it dramatically decreases above 100 mM (K(D>2 µM. Single-molecule DNA flow-extension analysis suggests that multiple MutL proteins may bind ssDNA at low ionic strength but this activity does not enhance stability at elevated ionic strengths. These studies are consistent with the conclusion that a stable MutL-ssDNA interaction is unlikely to occur at physiological salt eliminating a number of MMR models. However, the activity may infer some related dynamic DNA transaction process during MMR.

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

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.

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

1997-12-31

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.

Sputtering of Au induced by single Xe ion impacts

International Nuclear Information System (INIS)

Birtcher, R. C.; Donnelly, S. E.

1999-01-01

Sputtering of Au thin films has been determined for Xe ions with energies between 50 and 600 keV. In-situ transmission electron microscopy was used to observe sputtered Au during deposition on a carbon foil near the specimen. Total reflection and transmission sputtering yields for a 62 nm thick Au thin film were determined by ex-situ measurement of the total amount of Au on the carbon foils. In situ observations show that individual Xe ions eject Au nanoparticles as large as 7 nm in diameter with an average diameter of approximately 3 nm. Particle emission correlates with crater formation due to single ion impacts. Nanoparticle emission contributes significantly to the total sputtering yield for Xe ions in this energy range in either reflection or transmission geometry

Plastic Flow Induced by Single Ion Impacts on Gold

International Nuclear Information System (INIS)

Birtcher, R.C.; Donnelly, S.E.

1996-01-01

The formation of holes in thin gold foils as a result of single ion impacts by 200keV Xe ions has been followed using transmission electron microscopy. Video recording provided details of microstructure evolution with a time resolution of 1/30th sec. Hole formation involves the movement by plastic flow of massive amounts of material, on the order of tens of thousands of Au atoms per ion impact. Plastic flow, as a consequence of individual ion impacts, results in a continual filling of both holes and craters as well as a thickening of the gold foil. Changes in morphology during irradiation is attributed to a localized, thermal-spike induced melting, coupled with plastic flow of effected material under the influence of surface forces. copyright 1996 The American Physical Society

Long-Distance Single Photon Transmission from a Trapped Ion via Quantum Frequency Conversion

Science.gov (United States)

Walker, Thomas; Miyanishi, Koichiro; Ikuta, Rikizo; Takahashi, Hiroki; Vartabi Kashanian, Samir; Tsujimoto, Yoshiaki; Hayasaka, Kazuhiro; Yamamoto, Takashi; Imoto, Nobuyuki; Keller, Matthias

2018-05-01

Trapped atomic ions are ideal single photon emitters with long-lived internal states which can be entangled with emitted photons. Coupling the ion to an optical cavity enables the efficient emission of single photons into a single spatial mode and grants control over their temporal shape. These features are key for quantum information processing and quantum communication. However, the photons emitted by these systems are unsuitable for long-distance transmission due to their wavelengths. Here we report the transmission of single photons from a single 40Ca+ ion coupled to an optical cavity over a 10 km optical fiber via frequency conversion from 866 nm to the telecom C band at 1530 nm. We observe nonclassical photon statistics of the direct cavity emission, the converted photons, and the 10 km transmitted photons, as well as the preservation of the photons' temporal shape throughout. This telecommunication-ready system can be a key component for long-distance quantum communication as well as future cloud quantum computation.

Soil-modified carbon paste electrode: a useful tool in environmental assessment of heavy metal ion binding interactions.

Science.gov (United States)

Svegl, I G; Ogorevc, B

2000-08-01

Carbon paste electrodes (CPEs) modified with different soils in their native form were prepared to create a soil-like solid phase suitable for application in studies of heavy metal ion uptake and binding interactions. The preparation of CPEs modified with five different soils was examined and their heavy metal ion uptake behavior investigated using a model Cu(II) aqueous solution. Metal ions were accumulated under open circuit conditions and were determined after a medium exchange using differential pulse anodic stripping voltammetry, applying preelectrolysis at -0.7 V. The soil-modified CPE accumulation behavior, including the linearity of the current response versus Cu(II) concentration, the influence of the pH on the solution, and the uptake kinetics, was thoroughly investigated. The correlation between the soil-modified CPE uptake capability and the standard soil parameters, such as ion exchange capacity, soil pH, organic matter and clay content, were evaluated for all five examined soils. The influence of selected endogenous cations (K(I), Ca(II), Fe(III)) on the transfer of Cu(II) ions from a solution to the simulated soil solid phase was examined and is discussed. Preliminary examinations of the soil-modified CPE uptake behavior with some exogenous heavy metal ions of strong environmental interest (Pb(II), Hg(II), Cd(II) and Ag(I)) are also presented. This work demonstrates some attractive possibilities for the application of a soil-modified CPE in studying soil-heavy metal ion binding interactions, with a further potential use as a new environmental sensor appropriate for fist on-site testing of polluted soils.

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.

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.

High-energy heavy ion testing of VLSI devices for single event ...

Indian Academy of Sciences (India)

Unknown

per describes the high-energy heavy ion radiation testing of VLSI devices for single event upset (SEU) ... The experimental set up employed to produce low flux of heavy ions viz. silicon ... through which they pass, leaving behind a wake of elec- ... for use in Bus Management Unit (BMU) and bulk CMOS ... was scheduled.

Single-ion polymer electrolyte membranes enable lithium-ion batteries with a broad operating temperature range.

Science.gov (United States)

Cai, Weiwei; Zhang, Yunfeng; Li, Jing; Sun, Yubao; Cheng, Hansong

2014-04-01

Conductive processes involving lithium ions are analyzed in detail from a mechanistic perspective, and demonstrate that single ion polymeric electrolyte (SIPE) membranes can be used in lithium-ion batteries with a wide operating temperature range (25-80 °C) through systematic optimization of electrodes and electrode/electrolyte interfaces, in sharp contrast to other batteries equipped with SIPE membranes that display appreciable operability only at elevated temperatures (>60 °C). The performance is comparable to that of batteries using liquid electrolyte of inorganic salt, and the batteries exhibit excellent cycle life and rate performance. This significant widening of battery operation temperatures coupled with the inherent flexibility and robustness of the SIPE membranes makes it possible to develop thin and flexible Li-ion batteries for a broad range of applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Indian Academy of Sciences (India)

PRAKASH KUMAR

loss in protein−DNA binding affinity and specificity upon single point ..... we computed the root–mean–square–deviations (RMSDs) of each residue's ...... Petsko G and Ringe D 1984 Fluctuations in protein structure from. X-ray diffraction; Annu.

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...... as a new tool for future cavity quantum electrodynamics experiments in the Ion trap group at Aarhus University.......-wave. Besides providing a better understanding of the dynamics of an ion subjected to varying trapping conditions, this work establishes a basis for future studies of various quantum many-body physics models, for manipulations of the structure of large ion Coulomb crystals, and for optimization...... of the interaction between light and matter in connection with quantum information experiments. In addition to the deep, three-dimensional harmonic potential of the linear Paul trap which confines the ion in regions of several millimeters, one of the directions of the ion motion is constrained by the application...

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

Impact-parameter dependence of energy loss for 625-keV H+ ions in Si single crystals

International Nuclear Information System (INIS)

Dygo, A.; Boshart, M.A.; Seiberling, L.E.; Kabachnik, N.M.

1994-01-01

The energy distributions for 625-keV H + ions transmitted through thin Si single crystals are studied for detailed angular scans through the left-angle 110 right-angle and left-angle 100 right-angle axial as well as the {111} and {110} planar channels. Well-resolved structures in the distributions taken near the left-angle 110 right-angle axial direction are observed. The experimental energy-loss distributions are very well reproduced by a Monte Carlo simulation using the semiclassical approximation model for core electrons and the two-component free-electron-gas model for valence electrons. The best fit to the data is obtained if the model energy losses are scaled up for core electrons and down for valence electrons by several percent. The experimental distributions can also be reproduced by assuming the mean excitation energy for distant collisions of the ion with core electrons equal to 1.4 times the binding energy for a given shell. No significant differences between the distributions obtained using the solid-state and free-atom valence electron densities have been found. The evolution of the distributions for the left-angle 110 right-angle axial scan is discussed in terms of ion trajectories and the flux distribution. Also, the azimuthally averaged mean energy loss is studied as a function of tilt angle with respect to the left-angle 110 right-angle axis

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.

Ferrimagnetic Properties of Bond Dilution Mixed Blume-Capel Model with Random Single-Ion Anisotropy

International Nuclear Information System (INIS)

Liu Lei; Yan Shilei

2005-01-01

We study the ferrimagnetic properties of spin 1/2 and spin-1 systems by means of the effective field theory. The system is considered in the framework of bond dilution mixed Blume-Capel model (BCM) with random single-ion anisotropy. The investigation of phase diagrams and magnetization curves indicates the existence of induced magnetic ordering and single or multi-compensation points. Special emphasis is placed on the influence of bond dilution and random single-ion anisotropy on normal or induced magnetic ordering states and single or multi-compensation points. Normal magnetic ordering states take on new phase diagrams with increasing randomness (bond and anisotropy), while anisotropy induced magnetic ordering states are always occurrence no matter whether concentration of anisotropy is large or small. Existence and disappearance of compensation points rely strongly on bond dilution and random single-ion anisotropy. Some results have not been revealed in previous papers and predicted by Neel theory of ferrimagnetism.

Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

Directory of Open Access Journals (Sweden)

Ankur Bikash Pradhan

Full Text Available Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride with single and double stranded form of polyriboadenylic acid (hereafter poly-A using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A with high affinity while it does not interact at all with the double stranded (ds form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

Focused ion beam patterning to dielectrophoretically assemble single nanowire based devices

International Nuclear Information System (INIS)

La Ferrara, V; Massera, E; Francia, G Di; Alfano, B

2010-01-01

Direct-write processing is increasingly taking place in nanodevice fabrication. In this work, Focused Ion Beam (FIB), a powerful tool in maskless micromachining, is used for electrode patterning onto a silicon/silicon nitride substrate. Then a single palladium nanowire is assembled between electrodes by means of dielectrophoresis (DEP). The nanowire morphology depends on the electrode pattern when DEP conditions are fixed. FIB/DEP combination overcomes the problem of nanowire electrical contamination due to gallium ion bombardment and the as-grown nanowire retains its basic electrical properties. Single nanowire based devices have been fabricated with this novel approach and have been tested as hydrogen sensors, confirming the reliability of this technology.

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

International Nuclear Information System (INIS)

Zheng Liping; Zhu Zhiyuan; Li Yong; Zhu Dezhang; Xia Huihao

2008-01-01

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

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.

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

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...... on a Ni thin film on Cu(100) single-crystalline surfaces. X-ray magnetic circular dichroism (XMCD) measurements performed on Au(111) samples covered with molecular monolayers held at temperatures down to 4 K suggest that the easy axes of the strongly anisotropic molecules are randomly oriented...... pathways toward optical addressing of surface-deposited single-ion magnets....

Positive and negative ion mode comparison for the determination of DNA/peptide noncovalent binding sites through the formation of "three-body" noncovalent fragment ions.

Science.gov (United States)

Brahim, Bessem; Tabet, Jean-Claude; Alves, Sandra

2018-02-01

Gas-phase fragmentation of single strand DNA-peptide noncovalent complexes is investigated in positive and negative electrospray ionization modes.Collision-induced dissociation experiments, performed on the positively charged noncovalent complex precursor ions, have confirmed the trend previously observed in negative ion mode, i.e. a high stability of noncovalent complexes containing very basic peptidic residues (i.e. R > K) and acidic nucleotide units (i.e. Thy units), certainly incoming from the existence of salt bridge interactions. Independent of the ion polarity, stable noncovalent complex precursor ions were found to dissociate preferentially through covalent bond cleavages of the partners without disrupting noncovalent interactions. The resulting DNA fragment ions were found to be still noncovalently linked to the peptides. Additionally, the losses of an internal nucleic fragment producing "three-body" noncovalent fragment ions were also observed in both ion polarities, demonstrating the spectacular salt bridge interaction stability. The identical fragmentation patterns (regardless of the relative fragment ion abundances) observed in both polarities have shown a common location of salt bridge interaction certainly preserved from solution. Nonetheless, most abundant noncovalent fragment ions (and particularly three-body ones) are observed from positively charged noncovalent complexes. Therefore, we assume that, independent of the preexisting salt bridge interaction and zwitterion structures, multiple covalent bond cleavages from single-stranded DNA/peptide complexes rely on an excess of positive charges in both electrospray ionization ion polarities.

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

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.

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)

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

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.

Swift heavy ion irradiation of CaF2 - from grooves to hillocks in a single ion track

Science.gov (United States)

Gruber, Elisabeth; Salou, Pierre; Bergen, Lorenz; El Kharrazi, Mourad; Lattouf, Elie; Grygiel, Clara; Wang, Yuyu; Benyagoub, Abdenacer; Levavasseur, Delphine; Rangama, Jimmy; Lebius, Henning; Ban-d'Etat, Brigitte; Schleberger, Marika; Aumayr, Friedrich

2016-10-01

A novel form of ion-tracks, namely nanogrooves and hillocks, are observed on CaF2 after irradiation with xenon and lead ions of about 100 MeV kinetic energy. The irradiation is performed under grazing incidence (0.3°-3°) which forces the track to a region in close vicinity to the surface. Atomic force microscopy imaging of the impact sites with high spatial resolution reveals that the surface track consists in fact of three distinct parts: each swift heavy ion impacting on the CaF2 surface first opens a several 100 nm long groove bordered by a series of nanohillocks on both sides. The end of the groove is marked by a huge single hillock and the further penetration of the swift projectile into deeper layers of the target is accompanied by a single protrusion of several 100 nm in length slowly fading until the track vanishes. By comparing experimental data for various impact angles with results of a simulation, based on a three-dimensional version of the two-temperature-model (TTM), we are able to link the crater and hillock formation to sublimation and melting processes of CaF2 due to the local energy deposition by swift heavy ions.

Receptor binding of somatostatin-14 and somatostatin-28 in rat brain: differential modulation by nucleotides and ions.

Science.gov (United States)

Srikant, C B; Dahan, A; Craig, C

1990-02-04

The tissue-selective binding of the two principal bioactive forms of somatostatin, somatostatin-14 (SS-14) and somatostatin-28 (SS-28), their ability to modulate cAMP-dependent and -independent regulation of post-receptor events to different degrees and the documentation of specific labelling of SS receptor subtypes with SS-28 but not SS-14 in discrete regions of rat brain suggest the existence of distinct SS-14 and SS-28 binding sites. Receptor binding of SS-14 ligands has been shown to be modulated by nucleotides and ions, but the effect of these agents on SS-28 binding has not been studied. In the present study we investigated the effects of adenine and guanine nucleotides as well as monovalent and divalent cations on rat brain SS receptors quantitated with radioiodinated analogs of SS-14 ([125I-Tyr11]SS14, referred to in this paper as SS-14) and SS-28 ([Leu8, D-Trp22, 125I-Tyr25] SS-28, referred to as LTT* SS-28) in order to determine if distinct receptor sites for SS-14 and SS-28 could be distinguished on the basis of their modulation by nucleotides and ions. GTP as well as ATP exerted a dose-dependent inhibition (over a concentration range of 10(-7)-10(-3) M) of the binding of the two radioligands. The nucleotide inhibition of binding resulted in a decrease the Bmax of the SS receptors, the binding affinity remaining unaltered. GTP (10(-4) M) decreased the Bmax of LTT* SS-28 binding sites to a greater extent than ATP (145 +/- 10 and 228 +/- 16 respectively, compared to control value of 320 +/- 20 pmol mg-1). Under identical conditions GTP was less effective than ATP in reducing the number of T* SS-14 binding sites (Bmax = 227 +/- 8 and 182 +/- 15, respectively, compared to 340 +/- 15 pmol mg-1 in the absence of nucleotides). Monovalent cations inhibited the binding of both radioligands, Li+ and Na+ inhibited the binding of T* SS-14 to a greater extent than K+. The effect of divalent cations on the other hand was varied. At low concentration (2 mM) Mg2+, Ba2

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.

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

Science.gov (United States)

Collepardo-Guevara, Rosana; Schlick, Tamar

2012-01-01

Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of dynamic-linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression. PMID:22790986

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...

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.

Vasoactive intestinal peptide (VIP) binds to guinea pig peritoneal eosinophils: A single class of binding sites with low affinity and high capacity

International Nuclear Information System (INIS)

Sakakibara, H.; Shima, K.; Takamatsu, J.; Said, S.I.

1990-01-01

VIP binds to specific receptors on lymphocytes and mononuclear cells and exhibits antiinflammatory properties. Eosinophils (Eos) contribute to inflammatory reactions but the regulation of Eos function is incompletely understood. The authors examined the binding of monoradioiodinated VIP, [Tyr( 125 I) 10 ] VIP ( 125 I-VIP), to Eos in guinea pigs. The interaction of 125 i-VIP with Eos was rapid, reversible, saturable and linearly dependent on the number of cells. At equilibrium the binding was competitively inhibited by native peptide or by the related peptide helodermin. Scatchard analysis suggested the presence of a single class of VIP binding sites with a low affinity and a high capacity. In the presence of isobutyl-methylxanthine, VIP, PHI or helodermin did not stimulate cyclic AMP accumulation in intact Eos, while PGE 2 or 1-isoproterenol did. VIP also did not inhibit superoxide anion generation from Eos stimulated by phorbol myristate acetate. The authors conclude that: (1) VIP binds to low-affinity, specific sites on guinea pig peritoneal eosinophils; (2) this binding is not coupled to stimulation of adenylate cyclase; and (3) the possible function of these binding sites is at present unknown

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.

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

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 T_g 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 T_g we have managed for polyanions conducting Li⁺ is -60 °C. In contrast, polysiloxanes with PEO side chains and tetrabutylphosphonium cationic side groups have T_g ≈ -75 °C that barely increases with ion content, as anticipated by DFT. A survey of all polyanions in the literature suggests that T_g < -80 °C is needed to achieve the 10^-4 S/cm conductivity needed for battery separators.

Understanding the Effect of Carbonate Ion on Cisplatin Binding to DNA

Science.gov (United States)

Todd, Ryan C.; Lovejoy, Katherine S.; Lippard, Stephen J.

2008-01-01

The role of carbonate in the binding of cis-diamminedichloroplatinum(II) to DNA was investigated in order to understand the potential involvement of carbonato-cisplatin species in the mechanism of action of platinum anticancer agents. Cisplatin was allowed to react with both double- and single-stranded DNA in carbonate, phosphate, and HEPES buffers, and the products were analyzed by agarose gel electrophoresis and enzymatic digestion/mass spectrometry, respectively. The data from these experiments demonstrate (1) that carbonate, like other biological nucleophiles, forms relatively inert complexes with platinum that inactivate cisplatin, and (2) that the major cisplatin-DNA adduct formed is a bifunctional cross-link. These results are in accord with previous studies of cisplatin-DNA binding and reveal that the presence of carbonate has no consequence on the nature of the resulting adducts. PMID:17465550

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.

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

2016-01-15

Steady-state and time-resolved fluorescence quenching measurements supported by Isothermal Titration Calorimetry (ITC) were used to study the interactions of Cu(2+) 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 298.15K in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution with a pH of 6. The fluorescence of all peptides was quenched by Cu(2+) ions. The stoichiometry, conditional stability constants and thermodynamic parameters for the interactions of the Cu(2+) 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 Cu(2+) ions are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Coupled acoustic-gravity field for dynamic evaluation of ion exchange with a single resin bead.

Science.gov (United States)

Kanazaki, Takahiro; Hirawa, Shungo; Harada, Makoto; Okada, Tetsuo

2010-06-01

A coupled acoustic-gravity field is efficient for entrapping a particle at the position determined by its acoustic properties rather than its size. This field has been applied to the dynamic observation of ion-exchange reactions occurring in a single resin bead. The replacement of counterions in an ion-exchange resin induces changes in its acoustic properties, such as density and compressibility. Therefore, we can visually trace the advancement of an ion-exchange reaction as a time change in the levitation position of a resin bead entrapped in the field. Cation-exchange reactions occurring in resin beads with diameters of 40-120 microm are typically completed within 100-200 s. Ion-exchange equilibrium or kinetics is often evaluated with off-line chemical analyses, which require a batch amount of ion exchangers. Measurements with a single resin particle allow us to evaluate ion-exchange dynamics and kinetics of ions including those that are difficult to measure by usual off-line analyses. The diffusion properties of ions in resins have been successfully evaluated from the time change in the levitation positions of resin beads.

A study of single and binary ion plasma expansion into laboratory-generated plasma wakes

Science.gov (United States)

Wright, Kenneth Herbert, Jr.

1988-01-01

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.

Visualization of metallodrugs in single cells by secondary ion mass spectrometry imaging.

Science.gov (United States)

Wu, Kui; Jia, Feifei; Zheng, Wei; Luo, Qun; Zhao, Yao; Wang, Fuyi

2017-07-01

Secondary ion mass spectrometry, including nanoscale secondary ion mass spectrometry (NanoSIMS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), has emerged as a powerful tool for biological imaging, especially for single cell imaging. SIMS imaging can provide information on subcellular distribution of endogenous and exogenous chemicals, including metallodrugs, from membrane through to cytoplasm and nucleus without labeling, and with high spatial resolution and chemical specificity. In this mini-review, we summarize recent progress in the field of SIMS imaging, particularly in the characterization of the subcellular distribution of metallodrugs. We anticipate that the SIMS imaging method will be widely applied to visualize subcellular distributions of drugs and drug candidates in single cells, exerting significant influence on early drug evaluation and metabolism in medicinal and pharmaceutical chemistry. Recent progress of SIMS applications in characterizing the subcellular distributions of metallodrugs was summarized.

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.

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.

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

Quantitative autoradiographic distribution of L-[3H]glutamate-binding sites in rat central nervous system

International Nuclear Information System (INIS)

Greenamyre, J.T.; Young, A.B.; Penney, J.B.

1984-01-01

Quantitative autoradiography was used to determine the distribution of L-[3H]glutamate-binding sites in the rat central nervous system. Autoradiography was carried out in the presence of Cl- and Ca2+ ions. Scatchard plots and Hill coefficients of glutamate binding suggested that glutamate was interacting with a single population of sites having a K-D of about 300 nM and a capacity of 14.5 pmol/mg of protein. In displacement studies, ibotenate also appeared to bind to a single class of non-interacting sites with a KI of 28 microM. However, quisqualate displacement of [3H]glutamate binding revealed two well-resolved sites with KIS of 12 nM and 114 microM in striatum. These sites were unevenly distributed, representing different proportions of specific glutamate binding in different brain regions. The distribution of glutamate-binding sites correlated very well with the projection areas of putative glutamatergic pathways. This technique provides an extremely sensitive assay which can be used to gather detailed pharmacological and anatomical information about L-[3H]glutamate binding in the central nervous system

Characterization of the binding of multivalent ions to modified pluronic micelles by isothermal titration calorimetry and modified conductometry

NARCIS (Netherlands)

Nispen, van S.F.G.M.; Custers, J.P.A.; Broeke, van den L.J.P.; Keurentjes, J.T.F.

2010-01-01

CAE surfactants (carboxylic acid end-standing triblock copolymers of poly(ethylene oxide)–poly(propylene oxide)–poly(ethylene oxide)) are amphiphiles that are able to bind multivalent cations thermoreversibly; a property that can be used to develop new environmentally friendly separation and ion

Molecular determinants for the complex binding specificity of the PDZ domain in PICK1

DEFF Research Database (Denmark)

Madsen, Kenneth L; Beuming, Thijs; Niv, Masha Y

2005-01-01

PICK1 (protein interacting with C kinase 1) contains a single PDZ domain known to mediate interaction with the C termini of several receptors, transporters, ion channels, and kinases. In contrast to most PDZ domains, the PICK1 PDZ domain interacts with binding sequences classifiable as type I (te...

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...

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.

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)

Borophene as an anode material for Ca, Mg, Na or Li ion storage: A first-principle study

Science.gov (United States)

Mortazavi, Bohayra; Dianat, Arezoo; Rahaman, Obaidur; Cuniberti, Gianaurelio; Rabczuk, Timon

2016-10-01

Borophene, the boron atom analogue to graphene, being atomic thick have been just recently experimentally fabricated. In this work, we employ first-principles density functional theory calculations to investigate the interaction of Ca, Mg, Na or Li atoms with single-layer and free-standing borophene. We first identified the most stable binding sites and their corresponding binding energies as well and then we gradually increased the ions concentration. Our calculations predict strong binding energies of around 4.03 eV, 2.09 eV, 2.92 eV and 3.28 eV between the borophene substrate and Ca, Mg, Na or Li ions, respectively. We found that the binding energy generally decreases by increasing the ions content. Using the Bader charge analysis, we evaluate the charge transfer between the adatoms and the borophene sheet. Our investigation proposes the borophene as a 2D material with a remarkably high capacity of around 800 mA h/g, 1960 mA h/g, 1380 mA h/g and 1720 mA h/g for Ca, Mg, Na or Li ions storage, respectively. This study can be useful for the possible application of borophene for the rechargeable ion batteries.

Preparation and coherent manipulation of pure quantum states of a single molecular ion

Science.gov (United States)

Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

2017-05-01

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

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)

1994-12-31

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.

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.

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.

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.

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.

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.

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

Science.gov (United States)

Henry, Kevin A.; Sulea, Traian; van Faassen, Henk; Hussack, Greg; Purisima, Enrico O.; MacKenzie, C. Roger; Arbabi-Ghahroudi, Mehdi

2016-01-01

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. PMID:27631624

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 proteins have previously been found to be phosphorylated on tyrosine and arginine residues. While tyrosine phosphorylation was shown to enhance the DNA-binding properties of SsbA, arginine phosphorylation was not functionally characterized.Materials and methods: We used mass spectrometry analysis to detect...... phosphorylation of SsbA purified from B. subtilis cells. The detected phosphorylation site was assessed for its influence on DNA-binding in vitro, using electrophoretic mobility shift assays. The ability of B. subtilis serine/threonine kinases to phosphorylate SsbA was assessed using in vitro phosphorylation...

The molecular mechanism of multi-ion conduction in K{sup +} channels

Energy Technology Data Exchange (ETDEWEB)

Gwan, J.F.

2007-01-19

Steered molecular dynamics (SMD) simulation method is applied to a fully solvated membrane-channel model for studying the ion permeation process in potassium channels. The channel model is based on the crystallographic structure of a prokaryotic K{sup +} channel- the KcsA channel, which is a representative of most known eukaryotic K{sup +} channels. It has long been proposed that the ion transportation in a conventional K{sup +}-channel follows a multi-ion fashion: permeating ions line in a queue in the channel pore and move in a single file through the channel. The conventional view of multi-ion transportation is that the electrostatic repulsion between ions helps to overcome the attraction between ions and the channel pore. In this study, we proposed two SMD simulation schemes, referred to 'the single-ion SMD' simulations and 'the multi-ion SMD' simulations. Concerted movements of a K-W-K sequence in the selectivity filter were observed in the single-ion SMD simulations. The analysis of the concerted movement reveals the molecular mechanism of the multi-ion transportation. It shows that, rather than the long range electrostatic interaction, the short range polar interaction is a more dominant factor in the multi-ion transportation. The polar groups which play a role in the concerted transportation are the water molecules and the backbone carbonyl groups of the selectivity filter. The polar interaction is sensitive to the relative orientation of the polar groups. By changing the orientation of a polar group, the interaction may switch from attractive to repulsive or vice versa. By this means, the energy barrier between binding sites in the selectivity filter can be switched on and off, and therefore the K{sup +} may be able to move to the neighboring binding site without an external driving force. The concerted transportation in the selectivity filter requires a delicate cooperation between K{sup +}, waters, and the backbone carbonyl groups. To

Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc.

Science.gov (United States)

Cao, Kun; Li, Nan; Wang, Hongcui; Cao, Xin; He, Jiaojiao; Zhang, Bing; He, Qing-Yu; Zhang, Gong; Sun, Xuesong

2018-04-20

Zinc is an essential metal in bacteria. One important bacterial zinc transporter is AdcA, and most bacteria possess AdcA homologs that are single-domain small proteins due to better efficiency of protein biogenesis. However, a double-domain AdcA with two zinc-binding sites is significantly overrepresented in Streptococcus species, many of which are major human pathogens. Using molecular simulation and experimental validations of AdcA from Streptococcus pyogenes , we found here that the two AdcA domains sequentially stabilize the structure upon zinc binding, indicating an organization required for both increased zinc affinity and transfer speed. This structural organization appears to endow Streptococcus species with distinct advantages in zinc-depleted environments, which would not be achieved by each single AdcA domain alone. This enhanced zinc transport mechanism sheds light on the significance of the evolution of the AdcA domain fusion, provides new insights into double-domain transporter proteins with two binding sites for the same ion, and indicates a potential target of antimicrobial drugs against pathogenic Streptococcus species. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Application of silicene, germanene and stanene for Na or Li ion storage: A theoretical investigation

International Nuclear Information System (INIS)

Mortazavi, Bohayra; Dianat, Arezoo; Cuniberti, Gianaurelio; Rabczuk, Timon

2016-01-01

Silicene, germanene and stanene likely to graphene are atomic thick material with interesting properties. We employed first-principles density functional theory (DFT) calculations to investigate and compare the interaction of Na or Li ions on these films. We first identified the most stable binding sites and their corresponding binding energies for a single Na or Li adatom on the considered membranes. Then we gradually increased the ions concentration until the full saturation of the surfaces is achieved. Our Bader charge analysis confirmed complete charge transfer between Li or Na ions with the studied 2D sheets. We then utilized nudged elastic band method to analyze and compare the energy barriers for Li or Na ions diffusions along the surface and through the films thicknesses. Our investigation findings can be useful for the potential application of silicene, germanene and stanene for Na or Li ion batteries.

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.

Towards a precise measurement of atomic parity violation in a single Ra+ ion

International Nuclear Information System (INIS)

Nuñez Portela, M.; Berg, J. E. van den; Bekker, H.; Böll, O.; Dijck, E. A.; Giri, G. S.; Hoekstra, S.; Jungmann, K.; Mohanty, A.; Onderwater, C. J. G.; Santra, B.; Schlesser, S.; Timmermans, R. G. E.; Versolato, O. O.; Wansbeek, L. W.; Willmann, L.; Wilschut, H. W.

2013-01-01

A single trapped Ra  +  (Z = 88) ion provides a very promising route towards a most precise measurement of Atomic Parity Violation (APV), since APV effects grow faster than Z 3 . This experiment promises the best determination of the electroweak coupling constant at the lowest accessible energies. Such a measurement provides a sensitive test of the Standard Model in particle physics. At the present stage of the experiment, we focus on trapping and laser cooling stable Ba  +  ions as a precursor for radioactive Ra  +  . Online laser spectroscopy of the isotopes 209 − 214 Ra  +  in a linear Paul trap has provided information on transition wavelengths, fine and hyperfine structures and excited state lifetimes as test of atomic structure calculations. Additionaly, a single trapped Ra  +  ion could function as a very stable clock.

CDW-EIS model for single-electron capture in ion-atom collisions involving multielectronic targets

International Nuclear Information System (INIS)

Abufager, P N; MartInez, A E; Rivarola, R D; Fainstein, P D

2004-01-01

A generalization of the continuum distorted wave eikonal initial state (CDW-EIS) approximation, for the description of single-electron capture in ion-atom collisions involving multielectronic targets is presented. This approximation is developed within the framework of the independent electron model taking particular care of the representation of the bound and continuum target states. Total cross sections for single-electron capture from the K-shell of He, Ne and Ar noble gases by impact of bare ions are calculated. Present results are compared to previous CDW-EIS ones and to experimental data

GABA, depressants and chloride ions affect the rate of dissociation of 35S-t-butylbicyclophosphorothionate binding

International Nuclear Information System (INIS)

Maksay, G.; Ticku, M.K.

1985-01-01

The dissociation of 35 S-TBPS was studied from binding sites of rat cerebral cortex. Monophasic dissociation plots became polyphasic and accelerated in the presence of micromolar concentrations of GABA suggesting the involvement of low (or super-low) affinity GABA receptors. The presence of the depressants etazolate, R(-)MPPB and ethanol resulted in similarly accelerated dissociation patterns. In contrast, the convulsants S(+)MPPB and pentamethylenetetrazol did not significantly affect the dissociation of TBPS. Dissociation initiated by dilution was not affected either by an excess of picrotoxin or by varying the equilibrium occupancy of the TBPS sites. These findings rule out the possibility of a kinetic cooperativity for the binding of convulsants. The removal of chloride ions also enhanced the rate of TBPS dissociation. Kinetic heterogeneity of the TBPS binding sites can be interpreted with allosteric interactions mediated by various sites at the GABA receptor complex coupled to different states of the chloride ionophore. 15 references, 3 figures, 1 table

Research on generation mechanism of single event transient current generated in the semiconductor using ion accelerator

International Nuclear Information System (INIS)

Hirao, Toshio

2007-01-01

Single-event upset (SEU) is triggered when an amount of electric charges induced by energetic ion incidence exceeds a value known as a critical charge in a very short time period. Therefore, accurate evaluation of electric charge and understanding of basic mechanism of SEU are necessary for the improvement of SEU torrance of electronic devices. In this paper, the collected charges for the single event transient current induced on semiconductor by heavy ion microbeams, and application to use microbeam for single event studies are presented. (author)

Interaction of singly and multiply charged ions with a lithium-fluoride surface

International Nuclear Information System (INIS)

Wirtz, L.

2001-10-01

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 attraction due to the self-image potential. In a simulation that treats electronic and nuclear dynamics simultaneously, we show that the image attraction dominates over the repulsive force. Backscattering of very slow multiply charged projectiles high above the surface without touching it ('trampoline effect') does not take place. Instead, the projectile ion penetrates into the surface or is reflected due to close binary collision with surface ions. The case of a singly charged ion in front of an LiF surface is within the reach of ab-initio calculations. We use a multi-configuration self consistent field (MCSCF) and a multi-reference configuration interaction (MR-CI) method to calculate adiabatic potential energy curves for a system consisting of the projectile ion and an embedded cluster of surface ions. With increasing cluster size, the energy levels of the embedded cluster converge towards the band structure of the infinitely extended solid. Due to

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.

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.

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment

Science.gov (United States)

Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

2014-12-01

"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.

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.

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

Energy Technology Data Exchange (ETDEWEB)

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are

Covalent modifications of the amyloid beta peptide by hydroxynonenal: Effects on metal ion binding by monomers and insights into the fibril topology.

Science.gov (United States)

Grasso, G; Komatsu, H; Axelsen, P H

2017-09-01

Amyloid β peptides (Aβ) and metal ions are associated with oxidative stress in Alzheimer's disease (AD). Oxidative stress, acting on ω-6 polyunsaturated fatty acyl chains, produces diverse products, including 4-hydroxy-2-nonenal (HNE), which can covalently modify the Aβ that helped to produce it. To examine possible feedback mechanisms involving Aβ, metal ions and HNE production, the effects of HNE modification and fibril formation on metal ion binding was investigated. Results indicate that copper(II) generally inhibits the modification of His side chains in Aβ by HNE, but that once modified, copper(II) still binds to Aβ with high affinity. Fibril formation protects only one of the three His residues in Aβ from HNE modification, and this protection is consistent with proposed models of fibril structure. These results provide insight into a network of biochemical reactions that may be operating as a consequence of oxidative stress in AD, or as part of the pathogenic process. Copyright © 2016. Published by Elsevier Inc.

Ground-state phase diagram of an (S, S') = (1, 2) spin-alternating chain with competing single-ion anisotropies

International Nuclear Information System (INIS)

Tonegawa, T; Okamoto, K; Sakai, T; Kaburagi, M

2009-01-01

Employing various numerical methods, we determine the ground-state phase diagram of an (S, S') = (1, 2) spin-alternating chain with antiferromagnetic nearest-neighboring exchange interactions and uniaxial single-ion anisotropies. The resulting phase diagram consists of eight kinds of phases including two phases which accompany the spontaneous breaking of the translational symmetry and a ferrimagnetic phase in which the ground-state magnetization varies continuously with the uniaxial single-ion anisotropy constants for the S=1 and S =2 spins. The appearance of these three phases is attributed to the competition between the uniaxial single-ion anisotropies of both spins.

A conserved MCM single-stranded DNA binding element is essential for replication initiation.

Science.gov (United States)

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-04-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

High temperature electron beam ion source for the production of single charge ions of most elements of the Periodic Table

CERN Document Server

Panteleev, V N; Barzakh, A E; Fedorov, D V; Ivanov, V S; Moroz, F V; Orlov, S Y; Seliverstov, D M; Stroe, L; Tecchio, L B; Volkov, Y M

2003-01-01

A new type of a high temperature electron beam ion source (HTEBIS) with a working temperature up to 2500 deg. C was developed for production of single charge ions of practically all elements. Off-line tests and on-line experiments making use of the developed ion source coupled with uranium carbide targets of different density, have been carried out. The ionization efficiency measured for stable atoms of many elements varied in the interval of 1-6%. Using the HTEBIS, the yields and on-line production efficiency of neutron rich isotopes of Mn, Fe, Co, Cu, Rh, Pd, Ag, Cd, In, Sn and isotopes of heavy elements Pb, Bi, Po and some others have been determined. The revealed confinement effect of the ions produced in the narrow electron beam inside a hot ion source cavity has been discussed.

Effective tuning of the ratio of red to green emission of Ho"3"+ ions in single LiLuF_4 microparticle via codoping Ce"3"+ ions

International Nuclear Information System (INIS)

Gao, Wei; Dong, Jun; Liu, Jihong; Yan, Xuewen

2016-01-01

Yb"3"+/Ho"3"+ codoped LiLuF_4 microparticles have been successfully prepared via a facile hydrothermal method. The crystal phase and morphology of LiLuF_4 microparticles were inspected by x-ray diffraction and scanning electron microscope, respectively. The upconversion emission of single LiLuF_4: Yb"3"+/Ho"3"+ microparticle was carefully studied by a confocal microscopy setup under NIR 980 nm excitation. With the increase of Ce"3"+ ion concentrations of 12%, the ratio of red to green emission of the Ho"3"+ ions of single LiLuF_4 microparticle was boosted about 17-fold, and the output colors were tuned from green to red, which is due to the two efficient cross-relaxation between Ho"3"+ and Ce"3"+ ions enhances the red and suppresses the green in the emission processes. To investigate the optical properties of the single microparticle or nanoparticle through the confocal microscopy setup can effectively avoid the influence of surrounding particle or environment, and could provide more precise information for better exploring the emission mechanisms of rare earth ions. The tunable upconversion emission of Ho"3"+ in single LiLuF_4 microparticle in this work will have great potential applications in the micro optoelectronic devices and color display applications. - Highlights: • The optical properties of the single LiLuF4: Yb3+/Ho3+/Ce3+ microparticle were studied. • The output colors of single LiLuF4 microparticle were tuned from green to red. • The upconversion mechanisms between Ho3+ and Ce3+ ions were discussed based on emission spectrum.

Plasma immersion ion implantation: duplex layers from a single process

International Nuclear Information System (INIS)

Hutchings, R.; Collins, G.A.; Tendys, J.

1992-01-01

Plasma immersion ion implantation (PI 3 ) is an alternative non-line-of-sight technique for implanting ions directly from a plasma which surrounds the component to be treated. In contrast to plasma source ion implantation, the PI 3 system uses an inductively coupled r.f. plasma. It is shown that nitrogen can be retained during implantation at elevated temperatures, even for unalloyed steels. This allows controlled diffusion of nitrogen to greater depths, thereby improving the load bearing capacity of the implanted layer. Components can be heated directly, using the energy deposited by the incident ions during the pulsed implantation. The necessary temperature control can be accomplished simply by regulating the frequency and length of the high voltage pulses applied to the component. Chemical depth profiles and microstructural data obtained from H13 tool steel are used to show that PI 3 can, in a single process, effectively produce a duplex subsurface structure. This structure consists of an outer non-equilibrium layer typical of nitrogen implantation (containing in excess of 20 at.% nitrogen) backed by a substantial diffusion zone of much lower nitrogen content. The relationship between implantation temperature and the resultant subsurface microstructure is explored. (orig.)

Towards a precise measurement of atomic parity violation in a single Ra{sup +} ion

Energy Technology Data Exchange (ETDEWEB)

Nunez Portela, M., E-mail: nunez@kvi.nl; Berg, J. E. van den; Bekker, H.; Boell, O.; Dijck, E. A.; Giri, G. S.; Hoekstra, S.; Jungmann, K.; Mohanty, A.; Onderwater, C. J. G.; Santra, B.; Schlesser, S.; Timmermans, R. G. E.; Versolato, O. O.; Wansbeek, L. W.; Willmann, L.; Wilschut, H. W. [Kernfysisch Versneller Instituut (KVI) (Netherlands)

2013-03-15

A single trapped Ra{sup + } (Z = 88) ion provides a very promising route towards a most precise measurement of Atomic Parity Violation (APV), since APV effects grow faster than Z{sup 3}. This experiment promises the best determination of the electroweak coupling constant at the lowest accessible energies. Such a measurement provides a sensitive test of the Standard Model in particle physics. At the present stage of the experiment, we focus on trapping and laser cooling stable Ba{sup + } ions as a precursor for radioactive Ra{sup + }. Online laser spectroscopy of the isotopes {sup 209 - 214}Ra{sup + } in a linear Paul trap has provided information on transition wavelengths, fine and hyperfine structures and excited state lifetimes as test of atomic structure calculations. Additionaly, a single trapped Ra{sup + } ion could function as a very stable clock.

Precision laser spectroscopy of highly charged ions

International Nuclear Information System (INIS)

Kuehl, T.; Borneis, S.; Becker, S.; Dax, A.; Engel, T.; Grieser, R.; Huber, G.; Klaft, I.; Klepper, O.; Kohl, A.; Marx, D.; Meier, K.; Neumann, R.; Schmitt, F.; Seelig, P.; Voelker, L.

1996-01-01

Recently, intense beams of highly charged ions have become available at heavy ion cooler rings. The obstacle for producing these highly interesting candidates is the large binding energy of K-shell electrons in heavy systems in excess of 100 keV. One way to remove these electrons is to strip them off by passing the ion through material. In the cooler ring, the ions are cooled to a well defined velocity. At the SIS/ESR complex it is possible to produce, store, and cool highly charged ions up to bare uranium with intensities exceeding 10 8 atoms in the ring. This opens the door for precision laser spectroscopy of hydrogenlike-heavy ions, e.g. 209 Bi 82+ , and allows to examine the interaction of the single electron with the large fields of the heavy nucleus, exceeding any artificially produced electric and magnetic fields by orders of magnitude. In the electron cooler the interaction of electrons and highly charged ions otherwise only present in the hottest plasmas can be studied. (orig.)

Synthesizing single-phase β-FeSi2 via ion beam irradiations of Fe/Si bilayers

International Nuclear Information System (INIS)

Milosavljevic, M.; Dhar, S.; Schaaf, P.; Bibic, N.; Lieb, K.P.

2001-01-01

This paper presents results on the direct synthesis of the β-FeSi 2 phase by ion beam mixing of Fe/Si bilayers with Xe ions. The influence of the substrate temperature, ion fluence and energy on the growth of this phase was investigated using Rutherford backscattering (RBS), X-ray diffraction (XRD) and conversion electron Moessbauer spectroscopy (CEMS). Complete growth of single-phase β-FeSi 2 was achieved by 205 keV Xe ion irradiation to a fluence of 2x10 16 ions/cm 2 at 600 deg. C. We propose a two-step reaction mechanism involving thermal and ion beam energy deposition

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.

Metal binding proteins, recombinant host cells and methods

Science.gov (United States)

Summers, Anne O.; Caguiat, Jonathan J.

2004-06-15

The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

Tight binding electronic band structure calculation of achiral boron nitride single wall nanotubes

International Nuclear Information System (INIS)

Saxena, Prapti; Sanyal, Sankar P

2006-01-01

In this paper we report the Tight-Binding method, for the electronic structure calculations of achiral single wall Boron Nitride nanotubes. We have used the contribution of π electron only to define the electronic band structure for the solid. The Zone-folding method is used for the Brillouin Zone definition. Calculation of tight binding model parameters is done by fitting them to available experimental results of two-dimensional hexagonal monolayers of Boron Nitride. It has been found that all the boron nitride nanotubes (both zigzag and armchair) are constant gap semiconductors with a band gap of 5.27eV. All zigzag BNNTs are found to be direct gap semiconductors while all armchair nanotubes are indirect gap semiconductors. (author)

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.

Single trapped cold ions: a testing ground for quantum mechanics

International Nuclear Information System (INIS)

Maniscalco, S

2005-01-01

In this article I review some results obtained during my PhD work in the group of Professor Messina, at the University of Palermo. I discuss some proposals aimed at exploring fundamental issues of quantum theory, e.g. entanglement and quantum superpositions, in the context of single trapped ions. This physical context turns out to be extremely well suited both for studying fundamental features of quantum mechanics, such as the quantum-classical border, and for technological applications such as quantum logic gates and quantum registers. I focus on some procedures for engineering nonclassical states of the vibrational motion of the centre of mass of the ion. I consider both the case in which the ion interacts with classical laser beams and the case of interaction with a quantized mode of light. In particular, I discuss the generation of Schroedinger cat-like states, Bell states and Greenberger-Horn-Zeilinger states. The schemes for generating nonclassical states stem from two different quantum processes: the parity effect and the quantum state manipulation via quantum non-demolition measurement. Finally, I consider a microscopic theory of the interaction of a quantum harmonic oscillator (the centre of mass of the ion in the trapped ion context) with a bosonic thermal environment. Using an exact approach to the dynamics, I discuss a quantum theory of heating of trapped ions able to describe both the short time non-Markovian regime and the thermalization process. I conclude showing briefly how the trapped ion systems can be used as simulators of key models of open quantum systems such as the Caldeira-Leggett model. (phd tutorial)

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.

Influence of strong single-ion anisotropy on phase states of 3D and 2D frustrated magnets

International Nuclear Information System (INIS)

Fridman, Yu.A.; Kosmachev, O.A.; Matunin, D.A.; Gorelikov, G.A.; Klevets, Ph.N.

2010-01-01

We investigated the influence of strong single-ion anisotropy, exceeding exchange interaction, and frustrated exchange interaction on spin-wave excitation spectra and phase states using the Hubbard operators' technique, allowing the exact account of single-ion anisotropy. The results show that both the homogeneous phases (ferromagnetic and quadrupolar) and the spatially inhomogeneous phase (spiral structure) are possible in the 3D magnetic crystal. The region of existence of the spiral structure is considerably smaller than that in the analogues system, but with weak single-ion anisotropy. The situation is more complex in the 2D system; another spatially inhomogeneous state (the domain structure) can be realized in addition to the spiral magnetic structure. The phase diagrams for both the 3D and 2D systems were plotted.

Importance of length and sequence order on magnesium binding to surface-bound oligonucleotides studied by second harmonic generation and atomic force microscopy.

Science.gov (United States)

Holland, Joseph G; Geiger, Franz M

2012-06-07

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.

A semi-grand canonical Monte Carlo simulation model for ion binding to ionizable surfaces: proton binding of carboxylated latex particles as a case study.

Science.gov (United States)

Madurga, Sergio; Rey-Castro, Carlos; Pastor, Isabel; Vilaseca, Eudald; David, Calin; Garcés, Josep Lluís; Puy, Jaume; Mas, Francesc

2011-11-14

In this paper, we present a computer simulation study of the ion binding process at an ionizable surface using a semi-grand canonical Monte Carlo method that models the surface as a discrete distribution of charged and neutral functional groups in equilibrium with explicit ions modelled in the context of the primitive model. The parameters of the simulation model were tuned and checked by comparison with experimental titrations of carboxylated latex particles in the presence of different ionic strengths of monovalent ions. The titration of these particles was analysed by calculating the degree of dissociation of the latex functional groups vs. pH curves at different background salt concentrations. As the charge of the titrated surface changes during the simulation, a procedure to keep the electroneutrality of the system is required. Here, two approaches are used with the choice depending on the ion selected to maintain electroneutrality: counterion or coion procedures. We compare and discuss the difference between the procedures. The simulations also provided a microscopic description of the electrostatic double layer (EDL) structure as a function of pH and ionic strength. The results allow us to quantify the effect of the size of the background salt ions and of the surface functional groups on the degree of dissociation. The non-homogeneous structure of the EDL was revealed by plotting the counterion density profiles around charged and neutral surface functional groups. © 2011 American Institute of Physics

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.

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.

The GTP- and Phospholipid-Binding Protein TTD14 Regulates Trafficking of the TRPL Ion Channel in Drosophila Photoreceptor Cells

Science.gov (United States)

Cerny, Alexander C.; Altendorfer, André; Schopf, Krystina; Baltner, Karla; Maag, Nathalie; Sehn, Elisabeth; Wolfrum, Uwe; Huber, Armin

2015-01-01

Recycling of signaling proteins is a common phenomenon in diverse signaling pathways. In photoreceptors of Drosophila, light absorption by rhodopsin triggers a phospholipase Cβ-mediated opening of the ion channels transient receptor potential (TRP) and TRP-like (TRPL) and generates the visual response. The signaling proteins are located in a plasma membrane compartment called rhabdomere. The major rhodopsin (Rh1) and TRP are predominantly localized in the rhabdomere in light and darkness. In contrast, TRPL translocates between the rhabdomeral plasma membrane in the dark and a storage compartment in the cell body in the light, from where it can be recycled to the plasma membrane upon subsequent dark adaptation. Here, we identified the gene mutated in trpl translocation defective 14 (ttd14), which is required for both TRPL internalization from the rhabdomere in the light and recycling of TRPL back to the rhabdomere in the dark. TTD14 is highly conserved in invertebrates and binds GTP in vitro. The ttd14 mutation alters a conserved proline residue (P75L) in the GTP-binding domain and abolishes binding to GTP. This indicates that GTP binding is essential for TTD14 function. TTD14 is a cytosolic protein and binds to PtdIns(3)P, a lipid enriched in early endosome membranes, and to phosphatidic acid. In contrast to TRPL, rhabdomeral localization of the membrane proteins Rh1 and TRP is not affected in the ttd14 P75L mutant. The ttd14 P75L mutation results in Rh1-independent photoreceptor degeneration and larval lethality suggesting that other processes are also affected by the ttd14 P75L mutation. In conclusion, TTD14 is a novel regulator of TRPL trafficking, involved in internalization and subsequent sorting of TRPL into the recycling pathway that enables this ion channel to return to the plasma membrane. PMID:26509977

The GTP- and Phospholipid-Binding Protein TTD14 Regulates Trafficking of the TRPL Ion Channel in Drosophila Photoreceptor Cells.

Directory of Open Access Journals (Sweden)

Alexander C Cerny

2015-10-01

Full Text Available Recycling of signaling proteins is a common phenomenon in diverse signaling pathways. In photoreceptors of Drosophila, light absorption by rhodopsin triggers a phospholipase Cβ-mediated opening of the ion channels transient receptor potential (TRP and TRP-like (TRPL and generates the visual response. The signaling proteins are located in a plasma membrane compartment called rhabdomere. The major rhodopsin (Rh1 and TRP are predominantly localized in the rhabdomere in light and darkness. In contrast, TRPL translocates between the rhabdomeral plasma membrane in the dark and a storage compartment in the cell body in the light, from where it can be recycled to the plasma membrane upon subsequent dark adaptation. Here, we identified the gene mutated in trpl translocation defective 14 (ttd14, which is required for both TRPL internalization from the rhabdomere in the light and recycling of TRPL back to the rhabdomere in the dark. TTD14 is highly conserved in invertebrates and binds GTP in vitro. The ttd14 mutation alters a conserved proline residue (P75L in the GTP-binding domain and abolishes binding to GTP. This indicates that GTP binding is essential for TTD14 function. TTD14 is a cytosolic protein and binds to PtdIns(3P, a lipid enriched in early endosome membranes, and to phosphatidic acid. In contrast to TRPL, rhabdomeral localization of the membrane proteins Rh1 and TRP is not affected in the ttd14P75L mutant. The ttd14P75L mutation results in Rh1-independent photoreceptor degeneration and larval lethality suggesting that other processes are also affected by the ttd14P75L mutation. In conclusion, TTD14 is a novel regulator of TRPL trafficking, involved in internalization and subsequent sorting of TRPL into the recycling pathway that enables this ion channel to return to the plasma membrane.

Possibilities of paired comparison of receptor binding parameters obtained in a single experiment

International Nuclear Information System (INIS)

Mashilova, K.V.; Kiriakov, G.V.; Malin, K.M.; Rozhanets, V.V.

1987-01-01

The authors explore the use of comparing control and experimental groups on the basis of extrapolation parameters obtained from a single pair of experiments. One of the experiments study the parameters of specific binding of 3 H-D-ala-2-enkephelin-5-D-leucine in the striatum of different groups of rats. The analysis was done by the Cornish-Bowden method

Modifications of gallium phosphide single crystals using slow highly charged ions and swift heavy ions

Energy Technology Data Exchange (ETDEWEB)

El-Said, A.S., E-mail: elsaid@kfupm.edu.sa [Physics Department, King Fahd University of Petroleum and Minerals, Dhahran 31261 (Saudi Arabia); Wilhelm, R.A.; Heller, R.; Akhmadaliev, Sh.; Schumann, E. [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden (Germany); Sorokin, M. [National Research Centre ’Kurchatov Institute’, Kurchatov Square 1, 123182 Moscow (Russian Federation); Facsko, S. [Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden (Germany); Trautmann, C. [GSI Helmholtz Centre for Heavy Ion Research, 64291 Darmstadt (Germany); Technische Universität Darmstadt, 64289 Darmstadt (Germany)

2016-09-01

GaP single crystals were irradiated with slow highly charged ions (HCI) using 114 keV {sup 129}Xe{sup (33–40)+} and with various swift heavy ions (SHI) of 30 MeV I{sup 9+} and 374 MeV–2.2 GeV {sup 197}Au{sup 25+}. The irradiated surfaces were investigated by scanning force microscopy (SFM). The irradiations with SHI lead to nanohillocks protruding from the GaP surfaces, whereas no changes of the surface topography were observed after the irradiation with HCI. This result indicates that a potential energy above 38.5 keV is required for surface nanostructuring of GaP. In addition, strong coloration of the GaP crystals was observed after irradiation with SHI. The effect was stronger for higher energies. This was confirmed by measuring an increased extinction coefficient in the visible light region.

Response of rat spinal cord to single and fractionated doses of accelerated heavy ions

International Nuclear Information System (INIS)

Leith, J.L.; McDonald, M.; Powers-Risius, P.; Bliven, S.F.; Walton, R.E.; Woodruff, K.H.; Howard, J.

1980-01-01

The response of rat spinal cord to irradiation with accelerated heavy ions, in particular carbon and neon ions has been studied. Two different ionization regions in the modified Bragg curve for each ion have been studied for both single and fractionated exposures. We have defined the paralytic response as a function of dose and dose per fraction, and we have determined RBE and repair values. The response of rat spinal cord is both dose and LET dependent, which allows the derivation of RBE and repair values

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.

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.

Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

Science.gov (United States)

Vernal, Javier; Serpa, Viviane I; Tavares, Carolina; Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

2007-05-01

An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

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.

Adsorption and diffusion of lithium on layered silicon for Li-ion storage.

Science.gov (United States)

Tritsaris, Georgios A; Kaxiras, Efthimios; Meng, Sheng; Wang, Enge

2013-05-08

The energy density of Li-ion batteries depends critically on the specific charge capacity of the constituent electrodes. Silicene, the silicon analogue to graphene, being of atomic thickness could serve as high-capacity host of Li in Li-ion secondary batteries. In this work, we employ first-principles calculations to investigate the interaction of Li with Si in model electrodes of free-standing single-layer and double-layer silicene. More specifically, we identify strong binding sites for Li, calculate the energy barriers accompanying Li diffusion, and present our findings in the context of previous theoretical work related to Li-ion storage in other structural forms of silicon: the bulk and nanowires. The binding energy of Li is ~2.2 eV per Li atom and shows small variation with respect to Li content and silicene thickness (one or two layers) while the barriers for Li diffusion are relatively low, typically less than 0.6 eV. We use our theoretical findings to assess the suitability of two-dimensional silicon in the form of silicene layers for Li-ion storage.

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

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

Quantum phase transitions in spin-1 X X Z chains with rhombic single-ion anisotropy

Science.gov (United States)

Ren, Jie; Wang, Yimin; You, Wen-Long

2018-04-01

We explore numerically the inverse participation ratios in the ground state of one-dimensional spin-1 X X Z chains with the rhombic single-ion anisotropy. By employing the techniques of density-matrix renormalization group, effects of the rhombic single-ion anisotropy on various information theoretical measures are investigated, such as the fidelity susceptibility, the quantum coherence, and the entanglement entropy. Their relations with the quantum phase transitions are also analyzed. The phase transitions from the Y -Néel phase to the large-Ex or the Haldane phase can be well characterized by the fidelity susceptibility. The second-order derivative of the ground-state energy indicates all the transitions are of second order. We also find that the quantum coherence, the entanglement entropy, the Schmidt gap, and the inverse participation ratios can be used to detect the critical points of quantum phase transitions. Results drawn from these quantum information observables agree well with each other. Finally we provide a ground-state phase diagram as functions of the exchange anisotropy Δ and the rhombic single-ion anisotropy E .

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.

Ion implantation effects in single crystal Si investigated by Raman spectroscopy

International Nuclear Information System (INIS)

Harriman, T.A.; Lucca, D.A.; Lee, J.-K.; Klopfstein, M.J.; Herrmann, K.; Nastasi, M.

2009-01-01

A study of the effects of Ar ion implantation on the structural transformation of single crystal Si investigated by confocal Raman spectroscopy is presented. Implantation was performed at 77 K using 150 keV Ar ++ with fluences ranging from 2 x 10 13 to 1 x 10 15 ions/cm 2 . The Raman spectra showed a progression from crystalline to highly disordered structure with increasing fluence. The 520 cm -1 c-Si peak was seen to decrease in intensity, broaden and exhibit spectral shifts indicating an increase in lattice disorder and changes in the residual stress state. In addition, an amorphous Si band first appeared as a shoulder on the 520 cm -1 peak and then shifted to lower wavenumbers as a single broadband peak with a spectral center of 465 cm -1 . Additionally, the emergence of the a-Si TA phonon band and the decrease of the c-Si 2TA and 2TO phonon bands also indicated the same structural transition from crystalline to highly disordered. The Raman results were compared to those obtained by channeling RBS.

Manipulating Ion Migration for Highly Stable Light-Emitting Diodes with Single-Crystalline Organometal Halide Perovskite Microplatelets.

Science.gov (United States)

Chen, Mingming; Shan, Xin; Geske, Thomas; Li, Junqiang; Yu, Zhibin

2017-06-27

Ion migration has been commonly observed as a detrimental phenomenon in organometal halide perovskite semiconductors, causing the measurement hysteresis in solar cells and ultrashort operation lifetimes in light-emitting diodes. In this work, ion migration is utilized for the formation of a p-i-n junction at ambient temperature in single-crystalline organometal halide perovskites. The junction is subsequently stabilized by quenching the ionic movement at a low temperature. Such a strategy of manipulating the ion migration has led to efficient single-crystalline light-emitting diodes that emit 2.3 eV photons starting at 1.8 V and sustain a continuous operation for 54 h at ∼5000 cd m -2 without degradation of brightness. In addition, a whispering-gallery-mode cavity and exciton-exciton interaction in the perovskite microplatelets have both been observed that can be potentially useful for achieving electrically driven laser diodes based on single-crystalline organometal halide perovskite semiconductors.

Nanopore Device for Reversible Ion and Molecule Sensing or Migration

Science.gov (United States)

Pourmand, Nader (Inventor); Vilozny, Boaz (Inventor); Actis, Paolo (Inventor); Seger, R. Adam (Inventor); Singaram, Bakthan (Inventor)

2015-01-01

Disclosed are methods and devices for detection of ion migration and binding, utilizing a nanopipette adapted for use in an electrochemical sensing circuit. The nanopipette may be functionalized on its interior bore with metal chelators for binding and sensing metal ions or other specific binding molecules such as boronic acid for binding and sensing glucose. Such a functionalized nanopipette is comprised in an electrical sensor that detects when the nanopipette selectively and reversibly binds ions or small molecules. Also disclosed is a nanoreactor, comprising a nanopipette, for controlling precipitation in aqueous solutions by voltage-directed ion migration, wherein ions may be directed out of the interior bore by a repulsing charge in the bore.

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)

Ionoluminescence analysis of glass scintillators and application to single-ion-hit real-time detection

Energy Technology Data Exchange (ETDEWEB)

Yokoyama, Akihito, E-mail: yokoyama.akihito@jaea.go.jp [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); Takasaki Advanced Radiation Research Institute (TARRI), Japan Atomic Energy Agency (JAEA), 1233 Watanuki-machi, Takasaki, Gunma 370-1292 (Japan); Kada, Wataru [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); Satoh, Takahiro; Koka, Masashi [Takasaki Advanced Radiation Research Institute (TARRI), Japan Atomic Energy Agency (JAEA), 1233 Watanuki-machi, Takasaki, Gunma 370-1292 (Japan); Shimada, Keisuke; Yokoata, Yuya; Miura, Kenta; Hanaizumi, Osamu [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan)

2016-03-15

In this paper, we propose and test a real-time detection system for single-ion hits using mega-electronvolt (MeV)-heavy ions. The system was constructed using G2000 and G9 glass scintillators, as well as an electron-multiplying charge-coupled device (EMCCD) camera combined with an inverted microscope with a 10× objective lens. Commercially available G2000 and G9 glass scintillators, which have been reported to exhibit strong photoluminescence at 489, 543, 585, and 622 nm as a result of the Tb{sup 3+} f–f transition, were employed for highly accurate ionized particle detection. The EMCCD camera had a resolution of 512 × 512 pixels, each with a size of 16 μm × 16 μm, and a maximum linear gain of 8 × 10{sup 5} electrons. For 260-MeV Ne, 3 ion hits/s were detected by our system. The intensity of the ionoluminescence (IL) peak induced by the heavy ions was 140 times the noise intensity. In contrast, the luminous diameter at the full width at half maximum (FWHM) in both the horizontal and vertical directions was calculated to be approximately 4.5 μm. These results suggest that our detection system can accurately detect single-ion hits with a diameter of the order of 1 μm.

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.

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

Bacterial exopolysaccharides as a modern biotechnological tool for modification of fungal laccase properties and metal ion binding.

Science.gov (United States)

Osińska-Jaroszuk, Monika; Jaszek, Magdalena; Starosielec, Magdalena; Sulej, Justyna; Matuszewska, Anna; Janczarek, Monika; Bancerz, Renata; Wydrych, Jerzy; Wiater, Adrian; Jarosz-Wilkołazka, Anna

2018-03-26

Four bacterial EPSs extracted from Rhizobium leguminosarum bv. trifolii Rt24.2, Sinorhizobium meliloti Rm1021, Bradyrhizobium japonicum USDA110, and Bradyrhizobium elkanii USDA76 were determined towards their metal ion adsorption properties and possible modification of Cerrena unicolor laccase properties. The highest magnesium and iron ion-sorption capacity (~ 42 and ~ 14.5%, respectively) was observed for EPS isolated from B. japonicum USDA110. An evident influence of EPSs on the stability of laccase compared to the control values (without EPSs) was shown after 30-day incubation at 25 °C. The residual activity of laccases was obtained in the presence of Rh76EPS and Rh1021EPS, i.e., 49.5 and 41.5% of the initial catalytic activity, respectively. This result was confirmed by native PAGE electrophoresis. The EPS effect on laccase stability at different pH (from 3.8 to 7.0) was also estimated. The most significant changes at the optimum pH value (pH 5.8) was observed in samples of laccase stabilized by Rh76EPS and Rh1021EPS. Cyclic voltamperometry was used for analysis of electrochemical parameters of laccase stabilized by bacterial EPS and immobilized on single-walled carbon nanotubes (SWCNTs) with aryl residues. Laccases with Rh76EPS and Rh1021EPS had an evident shift of the value of the redox potential compared to the control without EPS addition. In conclusion, the results obtained in this work present a new potential use of bacterial EPSs as a metal-binding component and a modulator of laccase properties especially stability of enzyme activity, which can be a very effective tool in biotechnology and industrial applications.

Probing the binding of fluoxetine hydrochloride to human serum albumin by multispectroscopic techniques

Science.gov (United States)

Katrahalli, Umesha; Jaldappagari, Seetharamappa; Kalanur, Shankara S.

2010-01-01

The interaction between human serum albumin (HSA) and fluoxetine hydrochloride (FLX) have been studied by using different spectroscopic techniques viz., fluorescence, UV-vis absorption, circular dichroism and FTIR under simulated physiological conditions. Fluorescence results revealed the presence of static type of quenching mechanism in the binding of FLX to HSA. The values of binding constant, K of FLX-HSA were evaluated at 289, 300 and 310 K and were found to be 1.90 × 10 3, 1.68 × 10 3 and 1.45 × 10 3 M -1, respectively. The number of binding sites, n was noticed to be almost equal to unity thereby indicating the presence of a single class of binding site for FLX on HSA. Based on the thermodynamic parameters, Δ H0 and Δ S0 nature of binding forces operating between HSA and FLX were proposed. Spectral results revealed the conformational changes in protein upon interaction. Displacement studies indicated the site I as the main binding site for FLX on HSA. The effect of common ions on the binding of FLX to HSA was also investigated.

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein.

Science.gov (United States)

Bertaccini, Edward J; Lindahl, Erik; Sixma, Titia; Trudell, James R

2008-04-01

Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

Science.gov (United States)

Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

2011-01-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

[Modification of retinal photoreceptor membranes and Ca ion binding].

Science.gov (United States)

Korchagin, V P; Berman, A L; Shukoliukov, S A; Rychkova, M P; Etingof, R N

1978-10-01

Calcium binding by modified photoreceptor membranes of cattle retina has been studied. Ca2+-binding the membranes significantly changes after C-phospholipase treatment, displaying the initial growth (less than 65% of lipid phosphorus removed) with subsequent decrease (more than 65% of phosphorus removed). Liposomes of the photoreceptor membranes lipids were found to bind more calcium than do the native photoreceptor membranes. Proteolytic enzymes (papaine, pronase) splitting some rhodopsin fragments do not affect the ability of the membrane to bind Ca2+. The increase of light-induced Ca-binding is observed only after the outer segments preincubation under conditions providing for rhodopsin phosphorylation. This effect was observed also after the splitting of the rhodopsin fragment by papaine. It is concluded that calcium binding in the photoreceptor membranes is mainly due to the phosphate groups of phospholipids.

Single-Stranded Nucleic Acids Bind to the Tetramer Interface of SAMHD1 and Prevent Formation of the Catalytic Homotetramer.

Science.gov (United States)

Seamon, Kyle J; Bumpus, Namandjé N; Stivers, James T

2016-11-08

Sterile alpha motif and HD domain protein 1 (SAMHD1) is a unique enzyme that plays important roles in nucleic acid metabolism, viral restriction, and the pathogenesis of autoimmune diseases and cancer. Although much attention has been focused on its dNTP triphosphohydrolase activity in viral restriction and disease, SAMHD1 also binds to single-stranded RNA and DNA. Here we utilize a UV cross-linking method using 5-bromodeoxyuridine-substituted oligonucleotides coupled with high-resolution mass spectrometry to identify the binding site for single-stranded nucleic acids (ssNAs) on SAMHD1. Mapping cross-linked amino acids on the surface of existing crystal structures demonstrated that the ssNA binding site lies largely along the dimer-dimer interface, sterically blocking the formation of the homotetramer required for dNTPase activity. Surprisingly, the disordered C-terminus of SAMHD1 (residues 583-626) was also implicated in ssNA binding. An interaction between this region and ssNA was confirmed in binding studies using the purified SAMHD1 583-626 peptide. Despite a recent report that SAMHD1 possesses polyribonucleotide phosphorylase activity, we did not detect any such activity in the presence of inorganic phosphate, indicating that nucleic acid binding is unrelated to this proposed activity. These data suggest an antagonistic regulatory mechanism in which the mutually exclusive oligomeric state requirements for ssNA binding and dNTP hydrolase activity modulate these two functions of SAMHD1 within the cell.

Single and binary adsorption of Cd (Ⅱ) and Zn (Ⅱ) ions from aqueous solutions onto bottom ash

Energy Technology Data Exchange (ETDEWEB)

Sukpreabprom, Hatairat; Arqueropanyo, Orn-anong; Naksata, Wimol; Janhom, Sorapong [Chiang Mai University, Chiang Mai (Thailand); Sooksamiti, Ponlayuth [The Office of Primary Industries and Mines Region 3, Chiang Mai (Thailand)

2015-05-15

Bottom ash, a waste obtained from coal-burning power plant, was used as a low cost adsorbent for the removal of Cd (Ⅱ) and Zn (Ⅱ) ions from single and binary systems in batch experiments. The results of adsorption capacity showed that bottom ash could be considered as a potential adsorbent. The uptake of Zn (Ⅱ) ion was greater than that of Cd (Ⅱ) ion. For single adsorption, based on the correlation coefficient (R{sup 2}) values, both Langmuir and Freundlich isotherms suitably described the adsorption equilibrium data in the initial metal ion concentration range of 10-50 mg/L. The multicomponent isotherms, including the extended Langmuir and IAST-Freundlich isotherms, were used to predict the binary adsorption of Cd (Ⅱ) and Zn (Ⅱ) ions. Furthermore, the appropriate multicomponent isotherm was investigated by minimizing the average relative error (ARE) function. It should be confirmed that the extended Langmuir isotherm fitted the binary adsorption equilibrium data satisfactorily.

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

Free-energy relationships in ion channels activated by voltage and ligand

Science.gov (United States)

Chowdhury, Sandipan

2013-01-01

Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866

New stable multiply charged negative atomic ions in linearly polarized superintense laser fields

International Nuclear Information System (INIS)

Wei Qi; Kais, Sabre; Moiseyev, Nimrod

2006-01-01

Singly charged negative atomic ions exist in the gas phase and are of fundamental importance in atomic and molecular physics. However, theoretical calculations and experimental results clearly exclude the existence of any stable doubly-negatively-charged atomic ion in the gas phase, only one electron can be added to a free atom in the gas phase. In this report, using the high-frequency Floquet theory, we predict that in a linear superintense laser field one can stabilize multiply charged negative atomic ions in the gas phase. We present self-consistent field calculations for the linear superintense laser fields needed to bind extra one and two electrons to form He - , He 2- , and Li 2- , with detachment energies dependent on the laser intensity and maximal values of 1.2, 0.12, and 0.13 eV, respectively. The fields and frequencies needed for binding extra electrons are within experimental reach. This method of stabilization is general and can be used to predict stability of larger multiply charged negative atomic ions

Response of rat spinal cord to single and fractionated doses of accelerated heavy ions

International Nuclear Information System (INIS)

Leith, J.T.; McDonald, M.; Powers-Risius, P.; Bliven, S.F.; Howard, J.

1982-01-01

The thoraco-lumbar (T12-L1) region of the spinal cord of rats was exposed to either single or fractionated (four daily exposures) doses of X rays (230 kVp) or heavy ions. The heavy ions used were carbon and neon, and the relative biological effectiveness (RBE) of both the plateau ionization region and the midpeak region of 4-cm spread-out Bragg peaks of each heavy ion were investigated. For single doses of carbon and neon ions in the plateau ionization region, RBE values of 1.45 +/- 0.25 (propagated 95% confidence limits) and 1.46 +/- 0.33, respectively, were obtained. In the spread peak regions for carbon and neon ions, the RBE values were 1.48 +/- 0.18 and 1.86 +/- 0.42, respectively. These values were obtained using the dose needed to produce 50% paralysis in a group of irradiated rats as the isoeffect comparison dose (ED 50 dose). Similarly, in groups of rats receiving four daily exposures, the RBE values for carbon and neon ions in the plateau ionization region were 1.31 +/- 0.27 and 1.80 +/- 0.24, respectively. In the spread peak regions of ionization for carbon and neon ions, the RBE values were 1.95 +/- 0.19 and 2.18 +/- 0.23, respectively. Similar values for RBE were obtained using changes in the activity of enzymes in spinal cord tissue (cyclic nucleotide phosphohydrolase and γ-glutamyl transpeptidase). Also, it was estimated that, for X irradiation, the fractional amount of dose repaired (at the ED 50 dose) was 0.64 +/- 0.10 (95% confidence limits). For carbon and neon ions in the plateau ionization region, the values for the fractional amount of dose repaired were 0.70 +/- 0.27 and 0.48 +/- 0.20, and for carbon and neon ions in the spread peak region of ionization, the fractional repair values were 0.40 +/- 0.10 and 0.52 +/- 0.17. Spinal cord tissue therefore shows a high capacity for subeffective damage repair

Binding of copper and nickel to cavities in silicon formed by helium ion implantation

International Nuclear Information System (INIS)

Myers, S.M.; Follstaedt, D.M.; Bishop, D.M.

1993-01-01

Cavities formed in Si by He ion implantation and annealing are shown to be strong traps for Cu and Ni impurities. Experiments utilizing ion-beam analysis and transmission electron microscopy indicate that Cu is trapped at the internal surfaces of cavities up to ∼1 monolayer coverage with a binding energy of 2.2±0.2 eV relative to solution. This is greater than the heat of solution from the precipitated Cu 3 Si phase, determined to be 1.7 eV in agreement with earlier work. Copper at cavity-wall sites is reversibly replaced by H during heating in H 2 gas, indicating the relative stability of the two surface terminations. Initial results for Ni impurities indicate that trapping at cavities is again energetically preferred to silicide formation. The saturation coverage of Ni on the internal surfaces, however, is an order of magnitude smaller for Ni than Cu, consistent with published studies of external-surface adsorption. These results suggest that cavity trapping may getter metallic impurities in Si more effectively than methods based on silicide precipitation

Cross-sections of charge and electronic states change of particles at ion-ion and ion-molecule collisions

International Nuclear Information System (INIS)

Panov, M.N.; Afrosimov, V.V.; Basalaev, A.A.; Guschina, N.A.; Nikulin, V.K.

2006-01-01

The interactions of protons and alpha-particles with hydrocarbons are investigated. A quantum-mechanical computation of the electronic structure of all hydrocarbons from methane to butane and its fragment ions was performed in the Hartree-Fock RHF/UHF approximation using a GAMESS program (General Atomic Molecular Electron Structure System). The correlation energy was taken into account within the framework of MP2 perturbation theory. The structural parameters of the hydrocarbon molecules and their charged and neutral fragments were calculated in two cases: in the geometry of the parent molecule or of the relaxation states. The difference of the full energy of the same fragments in and out of brackets gives us the vibration excitation energies of the fragments at the moment of creation. Additional Mulliken effective charges (in electron charge units) of atoms in the fragments have been calculated. The calculations show that removing one electron from the ethane molecule without electronic excitation produced a single charged molecular ion in vibration state with binding energy of hydrogen atoms, some decimal eV. As results we obtain C 2 H 6 + and C 2 H 5 + . Additional fragmentation of hydrocarbon needs electronic excitation of produced single charged ions. Cross sections for electron capture and excitation processes in collisions between the hydrogen-like He + , B 4+ and O 7+ ions have been evaluated. The purpose of the theory within this project during the period under review was to get for the first time new data on Single-Electron Capture (SEC) and Excitation Processes (EP) in collisions of He + (1s) ions with hydrogen-like impurity ions B 4+ (1s) and O 7+ (1s) in the energy range for He + ions from 0.2 MeV to 3.0 MeV. The calculations were carried out by using the method of close-coupling equations with basis sets of eleven and ten quasimolecular two-electron states for reactions (1, 2) and (3, 4), respectively (entrance channel, seven charge transfer channels

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}.

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.

A fast online hit verification method for the single ion hit system at GSI

International Nuclear Information System (INIS)

Du, G.; Fischer, B.; Barberet, P.; Heiss, M.

2006-01-01

For a single ion hit facility built to irradiate specific targets inside biological cells, it is necessary to prove that the ions hit the selected targets reliably because the ion hits usually cannot be seen. That ability is traditionally tested either indirectly by aiming at pre-etched tracks in a nuclear track detector or directly by making the ion tracks inside cells visible using a stain coupled to special proteins produced in response to ion hits. However, both methods are time consuming and hits can be verified only after the experiment. This means that targeting errors in the experiment cannot be corrected during the experiment. Therefore, we have developed a fast online hit verification method that measures the targeting accuracy electronically with a spatial resolution of ±1 μm before cell irradiation takes place. (authors)

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.

Design and Fabrication of a Single Cusp Magnetic Field Type Hydrogen ion Source

Energy Technology Data Exchange (ETDEWEB)

Kim, Su Hun

1996-02-15

A single-cusp type hydrogen ion source has been designed and fabricated. In order to increase the efficiency of the plasma production, a single-cusp type magnet circuit and an electrostatic reflector were installed. The Poission Group Code was used to predict the distribution of magnetic field in the plasma chamber. In order to design the accel.-decel. extraction part for forming the ion beam with low emmitance and high current density, EGUN code was used. The results of calculation show that the configuration of plasma electrode strongly affects the beam quality and the deceleration electrode only functions the repression of the electron stream. When the plasma-accel potential is -20kV and an accel.-decel. potential is 1kV, the calculated extraction current, normalized emittance and perveance are 20.6mA, 1.28x 10{sup -7} m {center_dot} rad and 7.87 x 10{sup -9}A {center_dot} V{sup -3/2}, respectively. This study on the improvement of beam quality and the achievement of high ion beam current will contribute to the analysis of fusion plasma and the research on the surface physics.

Design and Fabrication of a Single Cusp Magnetic Field Type Hydrogen ion Source

International Nuclear Information System (INIS)

Kim, Su Hun

1996-02-01

A single-cusp type hydrogen ion source has been designed and fabricated. In order to increase the efficiency of the plasma production, a single-cusp type magnet circuit and an electrostatic reflector were installed. The Poission Group Code was used to predict the distribution of magnetic field in the plasma chamber. In order to design the accel.-decel. extraction part for forming the ion beam with low emmitance and high current density, EGUN code was used. The results of calculation show that the configuration of plasma electrode strongly affects the beam quality and the deceleration electrode only functions the repression of the electron stream. When the plasma-accel potential is -20kV and an accel.-decel. potential is 1kV, the calculated extraction current, normalized emittance and perveance are 20.6mA, 1.28x 10 -7 m · rad and 7.87 x 10 -9 A · V -3/2 , respectively. This study on the improvement of beam quality and the achievement of high ion beam current will contribute to the analysis of fusion plasma and the research on the surface physics

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.

Features of produced flows of multiply charged ions at interaction of laser radiation with single-component solids

International Nuclear Information System (INIS)

Bedilov, M.R.; Bedilov, R.M.; Beysembaeva, H.B.; Sabitov, M.S.; Kamalova, J.O.

2006-01-01

Full text: The results of study features of formation multiply charged ions spectra of single-component solids depending on a target element composition in an interval of laser radiation power density q = 10 7 / 10 12 W/cm 2 with using of the laser multiply charged mass spectrometer [1] are given in this work. As single-component targets are used Be, B, C, Al, Ti, Fe, Co, Ni, Cu, Ag, Ta, W, Pt, Au as tablets in diameter of 10 mm and thickness of 3-5 mm. Analysis of the obtained mass-charge and energy spectra of multiply charged ions depending on a target element composition has allowed us to find features of formation spectra and escape multiply charged ions of a single-component targets. These features consist in characteristic changes: a threshold produced of ions; formation of mass-charge and energy spectra of multiply charged ions; nonlinear dependence of maximal charge number (Z max ) of ions from power density (q) of the laser; etc. Experimentally it was found that, with target atomic weight increase, threshold power of ions occurrence, nonlinearity ionization target structure, and intensity of ions, and energy spectra of ions increase. Let's note that, in case of targets Be, B, C, Al by laser radiation it is completely ionized and multiply charged ions and nuclei Be 4+ , B 5+ , C 6+ , Al 13+ are formed. The major level of ionization is attained in case of targets from Ti (Ti 17+ ) and Co (Co 18+ ). It is peculiar that structure formation and escape of multiply charged ion flows with Z max and nuclei depending on target element composition corresponds to various maximal values q of the laser. Increase of the maximal charge number of ions (atoms) observed with increase q of the laser for all investigated targets has nonlinear dependence in various levels that is especially shown beginning from q≥ 10 11 W/cm 2 . It is found that depending on target element composition multiply charged ions have a wide energy range with a maximum of allocation. With increase

Scaling of ion implanted Si:P single electron devices

International Nuclear Information System (INIS)

Escott, C C; Hudson, F E; Chan, V C; Petersson, K D; Clark, R G; Dzurak, A S

2007-01-01

We present a modelling study on the scaling prospects for phosphorus in silicon (Si:P) single electron devices using readily available commercial and free-to-use software. The devices comprise phosphorus ion implanted, metallically doped (n + ) dots (size range 50-500 nm) with source and drain reservoirs. Modelling results are compared to measurements on fabricated devices and discussed in the context of scaling down to few-electron structures. Given current fabrication constraints, we find that devices with 70-75 donors per dot should be realizable. We comment on methods for further reducing this number

Scaling of ion implanted Si:P single electron devices

Energy Technology Data Exchange (ETDEWEB)

Escott, C C [Centre for Quantum Computer Technology, School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia); Hudson, F E [Centre for Quantum Computer Technology, School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia); Chan, V C [Centre for Quantum Computer Technology, School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia); Petersson, K D [Centre for Quantum Computer Technology, School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia); Clark, R G [Centre for Quantum Computer Technology, School of Physics, UNSW, Sydney, 2052 (Australia); Dzurak, A S [Centre for Quantum Computer Technology, School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia)

2007-06-13

We present a modelling study on the scaling prospects for phosphorus in silicon (Si:P) single electron devices using readily available commercial and free-to-use software. The devices comprise phosphorus ion implanted, metallically doped (n{sup +}) dots (size range 50-500 nm) with source and drain reservoirs. Modelling results are compared to measurements on fabricated devices and discussed in the context of scaling down to few-electron structures. Given current fabrication constraints, we find that devices with 70-75 donors per dot should be realizable. We comment on methods for further reducing this number.

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.

A structural classification of substrate-binding proteins

NARCIS (Netherlands)

Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz; Slotboom, Dirk-Jan; Poolman, Bert

2010-01-01

Substrate-binding proteins (SBP) are associated with a wide variety of protein complexes. The proteins are part of ATP-binding cassette transporters for substrate uptake, ion gradient driven transporters, DNA-binding proteins, as well as channels and receptors from both pro-and eukaryotes. A wealth

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

Thermal properties of the mixed spin-1 and spin-3/2 Ising ferrimagnetic system with two different random single-ion anisotropies

Science.gov (United States)

Pereira, J. R. V.; Tunes, T. M.; de Arruda, A. S.; Godoy, M.

2018-06-01

In this work, we have performed Monte Carlo simulations to study a mixed spin-1 and spin-3/2 Ising ferrimagnetic system on a square lattice with two different random single-ion anisotropies. This lattice is divided in two interpenetrating sublattices with spins SA = 1 in the sublattice A and SB = 3 / 2 in the sublattice B. The exchange interaction between the spins on the sublattices is antiferromagnetic (J single-ion anisotropies, DiA and DjB , on the sublattices A and B, respectively. We have determined the phase diagram of the model in the critical temperature Tc versus strength of the random single-ion anisotropy D plane and we shown that it exhibits only second-order phase transition lines. We also shown that this system displays compensation temperatures for some cases of the random single-ion distribution.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

Science.gov (United States)

Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

2011-12-01

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. © The Author(s) 2011. Published by Oxford University Press.

Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect

International Nuclear Information System (INIS)

Saio, Tomohide; Ogura, Kenji; Yokochi, Masashi; Kobashigawa, Yoshihiro; Inagaki, Fuyuhiko

2009-01-01

Paramagnetic lanthanide ions fixed in a protein frame induce several paramagnetic effects such as pseudo-contact shifts and residual dipolar couplings. These effects provide long-range distance and angular information for proteins and, therefore, are valuable in protein structural analysis. However, until recently this approach had been restricted to metal-binding proteins, but now it has become applicable to non-metalloproteins through the use of a lanthanide-binding tag. Here we report a lanthanide-binding peptide tag anchored via two points to the target proteins. Compared to conventional single-point attached tags, the two-point linked tag provides two to threefold stronger anisotropic effects. Though there is slight residual mobility of the lanthanide-binding tag, the present tag provides a higher anisotropic paramagnetic effect

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

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.

Broadband Dielectric Spectroscopy and Quasi-Elastic Neutron Scattering on Single-Ion Polymer Conductors

Science.gov (United States)

Soles, Christopher; Peng, Hua-Gen; Page, Kirt; Snyder, Chad; Pandy, Ashoutosh; Jeong, Youmi; Runt, James; NIST Collaboration; Pennsylvania Collaboration

2011-03-01

The application of solid polymer electrolytes in rechargeable batteries has not been fully realized after decades of research due to its low conductivity. Dramatic increases of the ion conductivity are needed and this progress requires the understanding of conduction mechanism. We address this topic in two fronts, namely, the effect of plasticizer additives and geometric confinement on the charge transfer mechanism. To this end, we combine broadband dielectric spectroscopy (BDS) to characterize the ion mobility and quasi-elastic neutron scattering (QENS) to quantify segmental motion on a single-ion model polymer electrolyte. Deuterated small molecules were used as plasticizers so that the segmental motion of the polymer electrolyte could be monitored by QENS to understand the mechanism behind the increased conductivity. Anodic aluminum oxide (AAO) membranes with well defined channel sizes are used as the matrix to study the transport of ions solvated in a 1D polymer electrolyte.

The interaction of uranyl ions with inorganic pyrophosphatase from baker's yeast

International Nuclear Information System (INIS)

Bienwald, B.; Heitmann, P.

1978-01-01

The interaction of uranyl ions with inorganic pyrophosphatase from baker's yeast was investigated by measurement of their effect on the protein fluorescence. Fluorescence titrations of the native enzyme with uranyl nitrate show that there is a specific binding of uranyl ions to the enzyme. It was deduced that each subunit of the enzyme binds one uranyl ion. The binding constant was estimated to be in the order of 10 7 M -1 . The enzyme which contains a small number of chemically modified carboxyl groups was not able to bind uranyl ions specifically. The modification of carboxyl groups was carried out by use of a water soluble carbodiimide and the nucleophilic reagent N-(2,4-dinitro-phenyl)-hexamethylenediamine. The substrate analogue calcium pyrophosphate displaced the uranyl ions from their binding sites at the enzyme From the results it is concluded that carboxyl groups of the active site are the ligands for the binding of uranyl ions. (author)

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.

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

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.

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.

Sorption of Hg(II and Pb(II Ions on Chitosan-Iron(III from Aqueous Solutions: Single and Binary Systems

Directory of Open Access Journals (Sweden)

Byron Lapo

2018-03-01

Full Text Available The present work describes the study of mercury Hg(II and lead Pb(II removal in single and binary component systems into easily prepared chitosan-iron(III bio-composite beads. Scanning electron microscopy and energy-dispersive X-ray (SEM-EDX analysis, Fourier transform infrared spectroscopy (FTIR, thermogravimetric analysis (TGA and point of zero charge (pHpzc analysis were carried out. The experimental set covered pH study, single and competitive equilibrium, kinetics, chloride and sulfate effects as well as sorption–desorption cycles. In single systems, the Langmuir nonlinear model fitted the experimental data better than the Freundlich and Sips equations. The sorbent material has more affinity to Hg(II rather than Pb(II ions, the maximum sorption capacities were 1.8 mmol·g−1 and 0.56 mmol·g−1 for Hg(II and Pb(II, respectively. The binary systems data were adjusted with competitive Langmuir isotherm model. The presence of sulfate ions in the multicomponent system [Hg(II-Pb(II] had a lesser impact on the sorption efficiency than did chloride ions, however, the presence of chloride ions improves the selectivity towards Hg(II ions. The bio-based material showed good recovery performance of metal ions along three sorption–desorption cycles.

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

Osmotic stress regulates the strength and kinetics of sugar binding to the maltoporin channel

International Nuclear Information System (INIS)

Gurnev, Philip A; Bezrukov, Sergey M; Harries, Daniel; Adrian Parsegian, V

2010-01-01

We study the effect of osmotic stress, exerted by salts, on carbohydrate binding to the sugar-specific bacterial channel maltoporin. When the channel is reconstituted into planar lipid bilayers, single events of its occlusion by sugar are seen as transient interruptions in the flow of small ions. We find that, for most salts, changes in the free energy of maltoporin-sugar binding vary linearly with solution osmotic pressure. Such a change in binding with solution osmolarity indicates that for each salt a constant number of salt-excluding water molecules is released upon sugar-maltoporin association at all salt concentrations. We find that larger numbers of water molecules are released upon binding of the cyclic carbohydrate β-cyclodextrin (CD) than upon binding of the corresponding linear homologue maltoheptaose (m7). Remarkably, the extent to which salts affect the binding constants and rates depends sensitively on the type of salt; dehydration in solutions of different anions corresponds to the Hofmeister series. In sodium sulfate solutions, CD and m7 respectively release about 120 and 35 salt-excluding water molecules; in sodium chloride solutions, 35 and 15 waters. No water release is observed with sodium bromide. Finally, by adding adamantane, known to form an inclusion complex with CD, we can infer that CD not only dehydrates but also undergoes a conformational change upon binding to the channel. As a practical outcome, our results also demonstrate how osmotic stress can improve single-molecule detection of different solutes using protein-based nanopores.

Infrared laser dissociation of single megadalton polymer ions in a gated electrostatic ion trap: the added value of statistical analysis of individual events.

Science.gov (United States)

Halim, Mohammad A; Clavier, Christian; Dagany, Xavier; Kerleroux, Michel; Dugourd, Philippe; Dunbar, Robert C; Antoine, Rodolphe

2018-05-07

In this study, we report the unimolecular dissociation mechanism of megadalton SO 3 -containing poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) polymer cations and anions with the aid of infrared multiphoton dissociation coupled to charge detection ion trap mass spectrometry. A gated electrostatic ion trap ("Benner trap") is used to store and detect single gaseous polymer ions generated by positive and negative polarity in an electrospray ionization source. The trapped ions are then fragmented due to the sequential absorption of multiple infrared photons produced from a continuous-wave CO 2 laser. Several fragmentation pathways having distinct signatures are observed. Highly charged parent ions characteristically adopt a distinctive "stair-case" pattern (assigned to the "fission" process) whereas low charge species take on a "funnel like" shape (assigned to the "evaporation" process). Also, the log-log plot of the dissociation rate constants as a function of laser intensity between PAMPS positive and negative ions is significantly different.

Propensity rules for orientation in singly-charged ion-atom collisions

International Nuclear Information System (INIS)

Nielsen, S.E.; Dubois, A.; Hansen, J.P.

1990-01-01

Orientation effects for electron capture and excitation in singly-charged ion-atom collisions are analysed using the atomic basis impact parameter method with full inclusion of electron translational factors. We find that the orientation preferences previously predicted for excitation in terms of propensity rules may still be observed when capture is present in ion-atom collisions. Furthermore, in spite of intricate behaviour of the direct capture couplings during the collision, we draw some parallel conclusions for the orientation of the capture states. We illustrate these perturbative predictions by close-coupling calculations for H + -Na(3s) collisions where clear propensity for orientation of the H(2p) capture state is demonstrated in impact parameter and velocity dependences. Finally we predict pronounced orientation effects for H(2s) and H(2p) capture in collisions of H + with initially oriented Na(3p) states. (author)

Single-molecule photobleaching reveals increased MET receptor dimerization upon ligand binding in intact cells

International Nuclear Information System (INIS)

Dietz, Marina S; Haße, Daniel; Ferraris, Davide M; Göhler, Antonia; Niemann, Hartmut H; Heilemann, Mike

2013-01-01

The human receptor tyrosine kinase MET and its ligand hepatocyte growth factor/scatter factor are essential during embryonic development and play an important role during cancer metastasis and tissue regeneration. In addition, it was found that MET is also relevant for infectious diseases and is the target of different bacteria, amongst them Listeria monocytogenes that induces bacterial uptake through the surface protein internalin B. Binding of ligand to the MET receptor is proposed to lead to receptor dimerization. However, it is also discussed whether preformed MET dimers exist on the cell membrane. To address these issues we used single-molecule fluorescence microscopy techniques. Our photobleaching experiments show that MET exists in dimers on the membrane of cells in the absence of ligand and that the proportion of MET dimers increases significantly upon ligand binding. Our results indicate that partially preformed MET dimers may play a role in ligand binding or MET signaling. The addition of the bacterial ligand internalin B leads to an increase of MET dimers which is in agreement with the model of ligand-induced dimerization of receptor tyrosine kinases.

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...

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...

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)

Effect of 120 MeV Ag{sup 9+} ion irradiation of YCOB single crystals

Energy Technology Data Exchange (ETDEWEB)

Arun Kumar, R., E-mail: rarunpsgtech@yahoo.com [Crystal Growth Centre, Anna University, Chennai 600 025 (India); Department of Basic Sciences - Physics Division, PSG College of Technology, Coimbatore 641 004 (India); Dhanasekaran, R. [Crystal Growth Centre, Anna University, Chennai 600 025 (India)

2012-09-15

Single crystals of yttrium calcium oxy borate (YCOB) grown from boron-tri-oxide flux were subjected to swift heavy ion irradiation using silver Ag{sup 9+} ions from the 15 UD Pelletron facility at Inter University Accelerator Center, New Delhi. The crystals were irradiated at 1 Multiplication-Sign 10{sup 13}, 5 Multiplication-Sign 10{sup 13} and 1 Multiplication-Sign 10{sup 14} ions/cm{sup 2} fluences at room temperature and with 5 Multiplication-Sign 10{sup 13} ions/cm{sup 2} 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.

Quantum Heisenberg antiferromagnetic chains with exchange and single-ion anisotropies

International Nuclear Information System (INIS)

Peters, D; Selke, W; McCulloch, I P

2010-01-01

Using density matrix renormalization group calculations, ground state properties of the spin-1 Heisenberg chain with exchange and quadratic single-ion anisotropies in an external field are studied, for special choices of the two kinds of anisotropies. In particular, the phase diagram includes antiferromagnetic, spin-liquid (or spin-flop), IS2, and supersolid (or biconical) phases. Especially, new features of the spin-liquid and supersolid phases are discussed. Properties of the quantum chains are compared to those of corresponding classical spin chains.

Effective tuning of the ratio of red to green emission of Ho{sup 3+} ions in single LiLuF{sub 4} microparticle via codoping Ce{sup 3+} ions

Energy Technology Data Exchange (ETDEWEB)

Gao, Wei, E-mail: gaowei@xupt.edu.cn; Dong, Jun; Liu, Jihong; Yan, Xuewen

2016-09-15

Yb{sup 3+}/Ho{sup 3+} codoped LiLuF{sub 4} microparticles have been successfully prepared via a facile hydrothermal method. The crystal phase and morphology of LiLuF{sub 4} microparticles were inspected by x-ray diffraction and scanning electron microscope, respectively. The upconversion emission of single LiLuF{sub 4}: Yb{sup 3+}/Ho{sup 3+} microparticle was carefully studied by a confocal microscopy setup under NIR 980 nm excitation. With the increase of Ce{sup 3+} ion concentrations of 12%, the ratio of red to green emission of the Ho{sup 3+} ions of single LiLuF{sub 4} microparticle was boosted about 17-fold, and the output colors were tuned from green to red, which is due to the two efficient cross-relaxation between Ho{sup 3+} and Ce{sup 3+} ions enhances the red and suppresses the green in the emission processes. To investigate the optical properties of the single microparticle or nanoparticle through the confocal microscopy setup can effectively avoid the influence of surrounding particle or environment, and could provide more precise information for better exploring the emission mechanisms of rare earth ions. The tunable upconversion emission of Ho{sup 3+} in single LiLuF{sub 4} microparticle in this work will have great potential applications in the micro optoelectronic devices and color display applications. - Highlights: • The optical properties of the single LiLuF4: Yb3+/Ho3+/Ce3+ microparticle were studied. • The output colors of single LiLuF4 microparticle were tuned from green to red. • The upconversion mechanisms between Ho3+ and Ce3+ ions were discussed based on emission spectrum.

Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells.

Science.gov (United States)

Gao, Yunfeng; Foo, Yong Hwee; Winardhi, Ricksen S; Tang, Qingnan; Yan, Jie; Kenney, Linda J

2017-11-21

Nucleoid-associated proteins (NAPs) facilitate chromosome organization in bacteria, but the precise mechanism remains elusive. H-NS is a NAP that also plays a major role in silencing pathogen genes. We used genetics, single-particle tracking in live cells, superresolution microscopy, atomic force microscopy, and molecular dynamics simulations to examine H-NS/DNA interactions in single cells. We discovered a role for the unstructured linker region connecting the N-terminal oligomerization and C-terminal DNA binding domains. In the present work we demonstrate that linker amino acids promote engagement with DNA. In the absence of linker contacts, H-NS binding is significantly reduced, although no change in chromosome compaction is observed. H-NS is not localized to two distinct foci; rather, it is scattered all around the nucleoid. The linker makes DNA contacts that are required for gene silencing, while chromosome compaction does not appear to be an important H-NS function.

Yeast enolase: mechanism of activation by metal ions.

Science.gov (United States)

Brewer, J M

1981-01-01

Yeast enolase as prepared by current procedures is inherently chemically homogeneous, though deamidation and partial denaturation can produce electrophoretically distinct forms. A true isozyme of the enzyme exists but does not survive the purification procedure. The chemical sequence for both has been established. The enzyme behaves in solution like a compact, nearly spherical molecule of moderate hydration. Strong intramolecular forces maintain the structure of the individual subunits. The enzyme as isolated is dimeric. If dissociated in the presence of magnesium ions and substrate, then the subunits are active, but if the dissociation occurs in the absence of metal ions, they are inactive until they have reassociated and undergone a first order "annealing" process. Magnesium (II) enhances association. The interaction between the subunits is hydrophobic in character. The enzyme can bind up to 2 mol of most metal ions in "conformational" sites which then allows up to 2 mol of substrate or some substrate analogue to bind. This is not sufficient for catalysis, but conformational metal ions do more than just allow substrate binding. A change in the environment of the metal ions occurs on substrate or substrate analogue binding. There is an absolute correlation between the occurrence of a structural change undergone by the 3-amino analogue of phosphoenolpyruvate and whether the metal ions produce any level of enzymatic activity. For catalysis, two more moles of metal ions, called "catalytic", must bind. There is evidence that the enzymatic reaction involves a carbanion mechanism. It is likely that two more moles of metal ion can bind which inhibit the reaction. The requirement for 2 mol of metal ion per subunit which contribute in different ways to catalysis is exhibited by a number of other enzymes.

Nanoneedle transistor-based sensors for the selective detection of intracellular calcium ions.

Science.gov (United States)

Son, Donghee; Park, Sung Young; Kim, Byeongju; Koh, Jun Tae; Kim, Tae Hyun; An, Sangmin; Jang, Doyoung; Kim, Gyu Tae; Jhe, Wonho; Hong, Seunghun

2011-05-24

We developed a nanoneedle transistor-based sensor (NTS) for the selective detection of calcium ions inside a living cell. In this work, a single-walled carbon nanotube-based field effect transistor (swCNT-FET) was first fabricated at the end of a glass nanopipette and functionalized with Fluo-4-AM probe dye. The selective binding of calcium ions onto the dye molecules altered the charge state of the dye molecules, resulting in the change of the source-drain current of the swCNT-FET as well as the fluorescence intensity from the dye. We demonstrated the electrical and fluorescence detection of the concentration change of intracellular calcium ions inside a HeLa cell using the NTS.

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....

Binding energy and mechanical stability of single- and multi-walled carbon nanotube serpentines

International Nuclear Information System (INIS)

Zhao, Junhua; Lu, Lixin; Rabczuk, Timon

2014-01-01

Recently, Geblinger et al. [Nat. Nanotechnol. 3, 195 (2008)] and Machado et al. [Phys. Rev. Lett. 110, 105502 (2013)] reported the experimental and molecular dynamics realization of S-like shaped single-walled carbon nanotubes (CNTs), the so-called CNT serpentines. We reported here results from continuum modeling of the binding energy γ between different single- and multi-walled CNT serpentines and substrates as well as the mechanical stability of the CNT serpentine formation. The critical length for the mechanical stability and adhesion of different CNT serpentines are determined in dependence of E i I i , d, and γ, where E i I i and d are the CNT bending stiffness and distance of the CNT translation period. Our continuum model is validated by comparing its solution to full-atom molecular dynamics calculations. The derived analytical solutions are of great importance for understanding the interaction mechanism between different single- and multi-walled CNT serpentines and substrates

Anion binding in the C3v-symmetric cavity of a protonated tripodal amine receptor: potentiometric and single crystal X-ray studies.

Science.gov (United States)

Bose, Purnandhu; Ravikumar, I; Ghosh, Pradyut

2011-11-07

Tris(2-aminoethyl)amine (tren) based pentafluorophenyl-substituted tripodal L, tris[[(2,3,4,5,6-pentafluorobenzyl)amino]ethyl]amine receptor is synthesized in good yield and characterized by single crystal X-ray diffraction analysis. Detailed structural aspects of binding of different anionic guests toward L in its triprotonated form are examined thoroughly. Crystallographic results show binding of fluoride in the C(3v)-symmetric cavity of [H(3)L](3+) where spherical anion fluoride is in tricoordinated geometry via (N-H)(+)···F interaction in the complex [H(3)L(F)]·[F](2)·2H(2)O, (3). In the case of complexes [H(3)L(OTs)]·[OTs](2), (4) and [H(3)L(OTs)]·[NO(3)]·[OTs], (5), tetrahedral p-toluenesulphonate ion is engulfed in the cavity of [H(3)L](3+) via (N-H)(+)···O interactions. Interestingly, complex [(H(3)L)(2)(SiF(6))]·[BF(4)](4)·CH(3)OH·H(2)O, (6) shows encapsulation of octahedral hexafluorosilicate in the dimeric capsular assembly of two [H(3)L](3+) units, via a number of (N-H)(+)···F interactions. The kinetic parameters of L upon binding with different anions are evaluated using a potentiometric study in solution state. The potentiometric titration experiments in a polar protic methanol/water (1:1 v/v) binary solvent system show high affinity of the receptor toward more basic fluoride and acetate anions, with a lesser affinity for other inorganic anions (e.g., chloride, bromide, nitrate, sulfate, dihydrogenphosphate, and p-toluenesulphonate). © 2011 American Chemical Society

Shot-noise-limited monitoring and phase locking of the motion of a single trapped ion.

Science.gov (United States)

Bushev, P; Hétet, G; Slodička, L; Rotter, D; Wilson, M A; Schmidt-Kaler, F; Eschner, J; Blatt, R

2013-03-29

We perform a high-resolution real-time readout of the motion of a single trapped and laser-cooled Ba+ ion. By using an interferometric setup, we demonstrate a shot-noise-limited measurement of thermal oscillations with a resolution of 4 times the standard quantum limit. We apply the real-time monitoring for phase control of the ion motion through a feedback loop, suppressing the photon recoil-induced phase diffusion. Because of the spectral narrowing in the phase-locked mode, the coherent ion oscillation is measured with a resolution of about 0.3 times the standard quantum limit.

Self-supporting film method of silicon single crystal by ion implantation and it`s application

Energy Technology Data Exchange (ETDEWEB)

Saito, Kazuo; Nakao, Setsuo; Niwa, Hiroaki; Miyagawa, Soji [National Industrial Research Inst. of Nagoya (Japan)

1996-12-01

A few {mu}m of thickness of self-supporting film of silicon single crystal was produced by the ion implantation and the selective etching. This materials are distinguished by a uniform film thickness, good controllability, crystallization and the mechanical strength. For applying it to device, the detailed process has to be established, because there are some improved problems such as pinhole and morphology on the surface. This materials are very useful to the basic experiment of the base for epitaxial growth under irradiation of ion beams and the ion beam analysis in the atmosphere. (S.Y.)

Zinc Binding by Lactic Acid Bacteria

Directory of Open Access Journals (Sweden)

Jasna Mrvčić

2009-01-01

Full Text Available Zinc is an essential trace element in all organisms. A common method for the prevention of zinc deficiency is pharmacological supplementation, especially in a highly available form of a metalloprotein complex. The potential of different microbes to bind essential and toxic heavy metals has recently been recognized. In this work, biosorption of zinc by lactic acid bacteria (LAB has been investigated. Specific LAB were assessed for their ability to bind zinc from a water solution. Significant amount of zinc ions was bound, and this binding was found to be LAB species-specific. Differences among the species in binding performance at a concentration range between 10–90 mg/L were evaluated with Langmuir model for biosorption. Binding of zinc was a fast process, strongly influenced by ionic strength, pH, biomass concentration, and temperature. The most effective metal-binding LAB species was Leuconostoc mesenteroides (27.10 mg of Zn2+ per gram of dry mass bound at pH=5 and 32 °C, during 24 h. FT-IR spectroscopy analysis and electron microscopy demonstrated that passive adsorption and active uptake of the zinc ions were involved.

The nature of single-ion activity coefficients calculated from potentiometric measurements on cells with liquid junctions

Energy Technology Data Exchange (ETDEWEB)

Zarubin, Dmitri P., E-mail: dmitri.zarubin@mtu-net.ru [Department of Physical and Collod Chemistry, Moscow State University of Technology and Management, 73 Zemlyanoi Val, Moscow 109803 (Russian Federation)

2011-08-15

Highlights: > Problem of ionic activity coefficients, determined by potentiometry, is reconsidered. > They are found to be functions of mean activity coefficients and transport numbers of ions. > The finding is verified by calculations and comparing the results with reported data. > Calculations are performed for systems with single electrolytes and binary mixtures. - Abstract: Potentiometric measurements on cells with liquid junctions are sometimes used for calculations of single-ion activity coefficients in electrolyte solutions, the incidence of this being increased recently. As surmised by Guggenheim in the 1930s, such coefficients (of ions i), {gamma}{sub i}, are actually complicated functions of mean ionic activity coefficients, {gamma}{sub {+-}}, and transport numbers of ions, t{sub i}. In the present paper specific functions {gamma}{sub i}({gamma}{sub {+-}}, t{sub i}) are derived for a number of cell types with an arbitrary mixture of strong electrolytes in a one-component solvent in the liquid-junction system. The cell types include cells with (i) identical electrodes, (ii) dissimilar electrodes reversible to the same ions, (iii) dissimilar electrodes reversible to ions of opposite charge signs, (iv) dissimilar electrodes reversible to different ions of the same charge sign, and (v) identical reference electrodes and an ion-selective membrane permeable to ions of only one type. Pairs of functions for oppositely charged ions are found to be consistent with the mean ionic activity coefficients as would be expected for pairs of the proper {gamma}{sub i} quantities by definition of {gamma}{sub {+-}}. The functions are tested numerically on some of the reported {gamma}{sub i} datasets that are the more tractable. A generally good agreement is found with data reported for cells with single electrolytes HCl and KCl in solutions, and with binary mixtures in the liquid-junction systems of KCl from the reference solutions and NaCl and HCl from the test solutions. It

The impact of base stacking on the conformations and electrostatics of single-stranded DNA.

Science.gov (United States)

Plumridge, Alex; Meisburger, Steve P; Andresen, Kurt; Pollack, Lois

2017-04-20

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Polarization bremsstrahlung of a hydrogen-like ion in a single crystal

International Nuclear Information System (INIS)

Astapenko, V. A.

2009-01-01

Polarization bremsstrahlung (PB) that arises when a fast hydrogen-like ion is scattered in a single crystal is investigated theoretically. Four types of the process are analyzed that are caused by virtual excitation of electrons of the target and of the incident particle (IP), as well as by a coherent and incoherent interaction between the IP and the single crystal. The spectral, angular, and velocity (of the IP) characteristics of PB are calculated with regard to the spectral function of a photodetector. Optimal observation conditions and regions in which different types of PB are dominant are determined, and the dependence of these regions on the charge of the IP nucleus and of the target atoms is revealed

Energy loss of carbon transmitted 1-MeV H2+ ions

International Nuclear Information System (INIS)

Fritz, M.; Kimura, K.; Susuki, Y.; Mannami, M.

1994-01-01

Energy losses of 1-MeV H 2 + ions passing through carbon foils of 2-8 μg/cm 2 thickness have been measured and show besides the linear increase with target thickness a 0.4 keV offset. The stopping power derived from the observed energy losses is 1.15 times as large as the sum of the stopping powers for two single H + of the same velocity. Calculations of the stopping powers for H 2 + ions and diprotons, using first Born approximation, indicate that the H 2 + ions lose the binding electron upon entrance into the foil, traverse the target as diprotons and recapture target electrons at the exit surface, a scenario also supported by the 0.4 keV offset at zero thickness. (author)

Fully differential cross sections for the single ionization of helium by fast ions: Classical model calculations

Science.gov (United States)

Sarkadi, L.

2018-04-01

Fully differential cross sections (FDCSs) have been calculated for the single ionization of helium by 1- and 3-MeV proton and 100-MeV/u C6 + ion impact using the classical trajectory Monte Carlo (CTMC) method in the nonrelativistic, three-body approximation. The calculations were made employing a Wigner-type model in which the quantum-mechanical position distribution of the electron is approximated by a weighted integral of the microcanonical distribution over a range of the binding energy of the electron. In the scattering plane, the model satisfactorily reproduces the observed shape of the binary peak. In the region of the peak the calculated FDCSs agree well with the results of continuum-distorted-wave calculations for all the investigated collisions. For 1-MeV proton impact the experimentally observed shift of the binary peak with respect to the first Born approximation is compared with the shifts obtained by different higher-order quantum-mechanical theories and the present CTMC method. The best result was achieved by CTMC, but still a large part of the shift remained unexplained. Furthermore, it was found that the classical theory failed to reproduce the shape of the recoil peak observed in the experiments, it predicts a much narrower peak. This indicates that the formation of the recoil peak is dominated by quantum-mechanical effects. For 100-MeV/u C6 + ion impact the present CTMC calculations confirmed the existence of the "double-peak" structure of the angular distribution of the electron in the plane perpendicular to the momentum transfer, in accordance with the observation, the prediction of an incoherent semiclassical model, and previous CTMC results. This finding together with wave-packet calculations suggests that the "C6 + puzzle" may be solved by considering the loss of the projectile coherence. Experiments to be conducted using ion beams of anisotropic coherence are proposed for a more differential investigation of the ionization dynamics.

Binding energy and dephasing of biexcitons in In0.18Ga0.82As/GaAs single quantum wells

DEFF Research Database (Denmark)

Borri, Paola; Langbein, Wolfgang Werner; Hvam, Jørn Märcher

1999-01-01

Biexciton binding energies and biexciton dephasing in In0.18Ga0.82As/GaAs single quantum wells have been measured by time-integrated and spectrally resolved four-wave mixing. The biexciton binding energy increases from 1.5 to 2.6 meV for well widths increasing from 1 to 4 nm. The ratio between...... exciton and biexciton binding energy changes from 0.23 to 0.3 with increasing inhomogeneous broadening, corresponding to increasing well width. From the temperature dependence of the exciton and biexciton four-wave mixing signal decay, we have deduced the acoustic-phonon scattering of the exciton...

EPR study of manganese(II) binding to 55'-ATP, hemoglobin, and hemocyanin

Energy Technology Data Exchange (ETDEWEB)

Chang, S.S. (Duquesne Univ., Pittsburgh); Li, N.C.; Pratt, D.W.

1975-01-01

Several divalent metal ions affect the oxygen affinity of hemoglobin and hemocyanin. It is important, therefore, to understand the nature of metal-ion binding to these proteins. By comparing the EPR spectra of Mn(II), 0.001 M, in the absence and presence of carboxyhemoglobin or Limulus oxyhemocyanin (pH 7.3, Trizma buffer), the number of Mn binding sites, n, and the binding constant, K, can be determined. For carboxyhemoglobin, HbCO, we find 0.5 Mn binding sites per heme, K = 450 M/sup -1/. Each hemoglobin tetramer therefore binds two manganous ions suggesting that Mn(II), like Cu(II), may bind preferentially to one of the two types of subunits in hemoglobin. For hemocyanin, HcO/sub 2/, we find n = 5.8, K = 1.55 x 10/sup 3/ M/sup -1/. Each oxyhemocyanine therefore binds approximately six manganous ions, and the binding constant is three times larger than that for HbCO. We have also carried out similar experiments on 5'-ATP, and on solutions of HbCO and ATP containing McCl/sub 2/ or ZnCl/sub 2/. Zn(II) effectively competes with Mn(II) in binding hemoglobin and ATP, whereas Mg(II) does not, in accord with expectations from data on oxygen affinity of hemoglobin. (auth)

Sequential water molecule binding enthalpies for aqueous nanodrops containing a mono-, di- or trivalent ion and between 20 and 500 water molecules† †Electronic supplementary information (ESI) available: Detailed description of the experimental and computational modeling methods. Isolation, BIRD and UVPD sequence for [Ru(NH3)6]3+·(H2O)169–171, nanoESI spectra for 2+ and 3+ ions. Detailed description of the isotope distribution simulation program. Comparison between experimental and simulated 1+, 2+ and 3+ ion isotope distributions. Wavelength dependence of the deduced sequential binding enthalpies. Comparison of experimental UVPD binding enthalpies to the liquid drop model at different temperatures. Complete list of binding enthalpies and average number of water molecules lost upon UVPD. See DOI: 10.1039/c6sc04957e Click here for additional data file.

Science.gov (United States)

Heiles, Sven; Cooper, Richard J.; DiTucci, Matthew J.

2017-01-01

Sequential water molecule binding enthalpies, ΔH 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, ΔH 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 ΔH 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 ΔH 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 ΔH 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 ΔH 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. PMID:28451364

Systems and Methods for Ejection of Ions from an Ion Trap

Science.gov (United States)

Cooks, Robert Graham (Inventor); Snyder, Dalton (Inventor)

2018-01-01

The invention generally relates to systems and methods for ejection of ions from an ion trap. In certain embodiments, systems and methods of the invention sum two different frequency signals into a single summed signal that is applied to an ion trap. In other embodiments, an amplitude of a single frequency signal is modulated as the single frequency signal is being applied to the ion trap. In other embodiments, a first alternating current (AC) signal is applied to an ion trap that varies as a function of time, while a constant radio frequency (RF) signal is applied to the ion trap.

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.

Expressing a bacterial mercuric ion binding protein in plant for phytoremediation of heavy metals.

Science.gov (United States)

Hsieh, Ju-Liang; Chen, Ching-Yi; Chiu, Meng-Hsuen; Chein, Mei-Fang; Chang, Jo-Shu; Endo, Ginro; Huang, Chieh-Chen

2009-01-30

A specific mercuric ion binding protein (MerP) originating from transposon TnMERI1 of Bacillus megaterium strain MB1 isolated from Minamata Bay displayed good adsorption capability for a variety of heavy metals. In this study, the Gram-positive MerP protein was expressed in transgenic Arabidopsis to create a model system for phytoremediation of heavy metals. Under control of an actin promoter, the transgenic Arabidpsis showed higher tolerance and accumulation capacity for mercury, cadium and lead when compared with the control plant. Results from confocal microscopy analysis also indicate that MerP was localized at the cell membrane and vesicles of plant cells. The developed transgenic plants possessing excellent metal-accumulative ability could have potential applications in decontamination of heavy metals.

Properties of Folate Binding Protein Purified from Cow’s Milk

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SUBANDRATE

2012-09-01

Full Text Available Folic acid played an important role in the metabolism of the body. To measure the serum folic acid levels could use the folate binding protein (FBP from cow’s milk with a technique analogous to ELISA. The aims of this study were to identify characteristics of FBP from cow’s milk and binding capacity of FBP to folic acid and to purify FBP from other whey protein passed through DEAE-cellulose chromatography column. Each of DEAE-cellulose peaks was passed in affinity chromatography column. FBP was released from affinity column with sodium acetate buffer pH 3.5. The purity of obtained FBP was demonstrated by a single spot in SDS-PAGE analysis and the estimated molecular weight of FBP was around 31 kDa. Our study indicated that 1 mol FBP bound 1 mol folic acid. Alkylation with iodoacetic acid decreased the binding capacity of FBP which suggested the presence of a–SH or imidazol group in its active site. The importance of disulfide bridge was proven by decreasing of folate binding capacity of FBP after -mercaptoethanol treatment. In contrary, the folate binding didn need Ca2+ ion, as indicated by EDTA test which gave the same result as control.

Stimulation of chymosin secretion by simultaneous expression with chymosin-binding llama single-domain antibody fragments in yeast

NARCIS (Netherlands)

Harmsen, M.M.; Smits, C.B.; Geus, de B.

2002-01-01

We studied the effect of coexpression of chymosin and chymosin-binding llama single-domain antibody fragments (VHHs) on the secretion of chymosin by Saccharomyces cerevisiae cells. A VHH expression library containing chymosin-specific VHHs was obtained by immunization of a llama and coexpressed with

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.

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

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)

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.

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

The molecular mechanism of ion-dependent gating in secondary transporters.

Directory of Open Access Journals (Sweden)

Chunfeng Zhao

2013-10-01

Full Text Available LeuT-like fold Na-dependent secondary active transporters form a large family of integral membrane proteins that transport various substrates against their concentration gradient across lipid membranes, using the free energy stored in the downhill concentration gradient of sodium ions. These transporters play an active role in synaptic transmission, the delivery of key nutrients, and the maintenance of osmotic pressure inside the cell. It is generally believed that binding of an ion and/or a substrate drives the conformational dynamics of the transporter. However, the exact mechanism for converting ion binding into useful work has yet to be established. Using a multi-dimensional path sampling (string-method followed by all-atom free energy simulations, we established the principal thermodynamic and kinetic components governing the ion-dependent conformational dynamics of a LeuT-like fold transporter, the sodium/benzyl-hydantoin symporter Mhp1, for an entire conformational cycle. We found that inward-facing and outward-facing states of Mhp1 display nearly the same free energies with an ion absent from the Na2 site conserved across the LeuT-like fold transporters. The barrier separating an apo-state from inward-facing or outward-facing states of the transporter is very low, suggesting stochastic gating in the absence of ion/substrate bound. In contrast, the binding of a Na2 ion shifts the free energy stabilizing the outward-facing state and promoting substrate binding. Our results indicate that ion binding to the Na2 site may also play a key role in the intracellular thin gate dynamics modulation by altering its interactions with the transmembrane helix 5 (TM5. The Potential of Mean Force (PMF computations for a substrate entrance displays two energy minima that correspond to the locations of the main binding site S1 and proposed allosteric S2 binding site. However, it was found that substrate's binds to the site S1 ∼5 kcal/mol more favorable

Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry.

Science.gov (United States)

Xiang, Yun; Abliz, Zeper; Takayama, Mitsuo

2004-05-01

The dissociation reactions of the adduct ions derived from the four self-complementary deoxydinucleotides, d(ApT), d(TpA), d(CpG), d(GpC), and alkali-metal ions were studied in detail by positive ion electrospray ionization multiple-stage mass spectrometry (ESI-MS(n)). For the [M + H](+) ions of the four deoxydinucleotides, elimination of 5'-terminus base or loss of both of 5'-terminus base and a deoxyribose were the major dissociation pathway. The ESI-MS(n) spectra showed that Li(+), Na(+), and Cs(+) bind to deoxydinucleotides mainly by substituting the H(+) of phosphate group, and these alkali-metal ions preferred to bind to pyrimidine bases rather than purine bases. For a given deoxydinucleotide, the dissociation pathway of [M + K](+) ions differed clearly from that of [M + Li](+), [M + Na](+), and [M + Cs](+) ions. Some interesting and characteristic cleavage reactions were observed in the product-ion spectra of [M + K](+) ions, including direct elimination of deoxyribose and HPO(3) from molecular ions. The fragmentation behavior of the [M + K](+) and [M + W](+) (W = Li, Na, Cs) adduct ions depend upon the sequence of bases, the interaction between alkali-metal ions and nucleobases, and the steric hindrance caused by bases.

Heisenberg magnetic chain with single-ion easy-plane anisotropy: Hubbard operators approach

International Nuclear Information System (INIS)

Spirin, D.V.; Fridman, Y.A.

2003-01-01

We investigate the gap in excitation spectrum of one-dimensional S=1 ferro- and antiferromagnets with easy-plane single-ion anisotropy. The self-consistent modification of Hubbard operators approach which enables to account single-site term exactly is used. For antiferromagnetic model we found Haldane phase that exists up to point D=4J (where D is anisotropy parameter, J is exchange coupling), while quadrupolar phase realizes at larger values of anisotropy. Our results specify those of Golinelli et al. (Phys. Rev. B. 45 (1992) 9798), where similar model was studied. Besides the method gives gap value closer to numerical estimations than usual spin-wave theories

Experimental study on heavy-ion single event effect on nanometer DDR SRAM

International Nuclear Information System (INIS)

Luo Yinhong; Zhang Fengqi; Guo Hongxia; Zhou Hui; Wang Yanping; Zhang Keying

2013-01-01

Single event effect experimental study on 90 nm and 65 nm DDR SRAM were carried out, single event upset (SEU) cross section was discussed as a function of several parameters such as feature size, test pattern, incidence angle, supply voltage. Key influence factors and effect rule were analyzed. Feasibility of the current test method was discussed. Results indicate that, SEU cross section reduces as technologies scale down; the influence of test pattern and power supply on SEU cross section is small; tilt angle increases SEU cross section due to multiple upset increasement. The applicability of cosine tilt test method is correlative to ion species and linear energy transfer (LET) values. (authors)

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

DEFF Research Database (Denmark)

Mijakovic, Ivan; Petranovic, Dina; Macek, B

2006-01-01

for phosphotyrosine-containing proteins in Streptomyces griseus by immunoaffinity chromatography identified bacterial SSBs as a novel target of bacterial tyrosine kinases. Since genes encoding protein-tyrosine kinases (PTKs) have not been recognized in streptomycetes, and SSBs from Streptomyces coelicolor (Sc......SSB) and Bacillus subtilis (BsSSB) share 38.7% identity, we used a B.subtilis protein-tyrosine kinase YwqD to phosphorylate two cognate SSBs (BsSSB and YwpH) in vitro. We demonstrate that in vivo phosphorylation of B.subtilis SSB occurs on tyrosine residue 82, and this reaction is affected antagonistically...... 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...

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.)

Viral interference with DNA repair by targeting of the single-stranded DNA binding protein RPA.

Science.gov (United States)

Banerjee, Pubali; DeJesus, Rowena; Gjoerup, Ole; Schaffhausen, Brian S

2013-10-01

Correct repair of damaged DNA is critical for genomic integrity. Deficiencies in DNA repair are linked with human cancer. Here we report a novel mechanism by which a virus manipulates DNA damage responses. Infection with murine polyomavirus sensitizes cells to DNA damage by UV and etoposide. Polyomavirus large T antigen (LT) alone is sufficient to sensitize cells 100 fold to UV and other kinds of DNA damage. This results in activated stress responses and apoptosis. Genetic analysis shows that LT sensitizes via the binding of its origin-binding domain (OBD) to the single-stranded DNA binding protein replication protein A (RPA). Overexpression of RPA protects cells expressing OBD from damage, and knockdown of RPA mimics the LT phenotype. LT prevents recruitment of RPA to nuclear foci after DNA damage. This leads to failure to recruit repair proteins such as Rad51 or Rad9, explaining why LT prevents repair of double strand DNA breaks by homologous recombination. A targeted intervention directed at RPA based on this viral mechanism could be useful in circumventing the resistance of cancer cells to therapy.

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.

Multi-shell model of ion-induced nucleic acid condensation

Energy Technology Data Exchange (ETDEWEB)

Tolokh, Igor S. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Drozdetski, Aleksander V. [Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States); Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853-3501 (United States); Baker, Nathan A. [Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912 (United States); Onufriev, Alexey V. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States)

2016-04-21

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion

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

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.

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+.

Investigation of radial dose effect on single event upset cross-section due to heavy ions using GEANT4

International Nuclear Information System (INIS)

Boorboor, S.; Feghhi, S.A.H.; Jafari, H.

2015-01-01

The heavy ions are the main cause to produce single event upset (SEU) damage on electronic devices since they are high LET radiations. The dimension of electronic components in new technology, arise a challenge in radiation effect estimations. Accurate investigations require fully considering the ion track in energy deposition as a radial dose distribution. In this work, the distribution of delta rays as well as LET have been calculated to determine ionization structure around ion track by a Monte Carlo code, GEANT4. The radial dose of several heavy ions with different energy in silicon was investigated and compared with the works by other authors in this field. The results showed that heavy ions with identical LET can have different SEU cross-section in silicon transistors. As a demonstrative example, according to our results, the error probability for 4.8 GeV iron was 8 times greater than that for 15 MeV carbon ions, in transistors with new process technology which have small dimension and low critical charges. Our results show that considering radial dose distribution considerably improves the accuracy of the SEU cross-section estimation in electronic devices especially for new technologies. - Highlights: • The single event upset is produced by heavy ions interaction on electronic devices. • The radial dose of several heavy ions in silicon was calculated by GEANT4. • Heavy ions with identical LET had different SEU cross-section in silicon transistors. • Low dimension and critical charge devices were more sensitive to radial dose effect

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

Characterization of microdose damage caused by single heavy ion observed in trench type power MOSFETs

International Nuclear Information System (INIS)

Ikeda, Naomi; Kuboyama, Satoshi; Maru, Akifumi; Tamura, Takashi; Hirao, Toshio; Abe, Hiroshi

2010-01-01

It was demonstrated that anomalously large degradation observed in power MOSFETs was caused by a single heavy ion. It was identified as a microdose effect and successfully characterized by several parameters extracted from experimental data. (author)

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.

Electrostatic coupling of ion pumps.

Science.gov (United States)

Nieto-Frausto, J; Lüger, P; Apell, H J

1992-01-01

In this paper the electrostatic interactions between membrane-embedded ion-pumps and their consequences for the kinetics of pump-mediated transport processes have been examined. We show that the time course of an intrinsically monomolecular transport reaction can become distinctly nonexponential, if the reaction is associated with charge translocation and takes place in an aggregate of pump molecules. First we consider the electrostatic coupling of a single dimer of ion-pumps embedded in the membrane. Then we apply the treatment to the kinetic analysis of light-driven proton transport by bacteriorhodopsin which forms two-dimensional hexagonal lattices. Finally, for the case of nonordered molecules, we also consider a model in which the pumps are randomly distributed over the nodes of a lattice. Here the average distance is equal to that deduced experimentally and the elemental size of the lattice is the effective diameter of one single pump. This latter model is applied to an aggregate of membrane-embedded Na, K- and Ca-pumps. In all these cases the electrostatic potential considered is the exact solution calculated from the method of electrical images for a plane membrane of finite thickness immersed in an infinite aqueous solution environment. The distributions of charges (ions or charged binding sites) are considered homogeneous or discrete in the membrane and/or in the external solution. In the case of discrete distributions we compare the results from a mean field approximation and a stochastic simulation.

Space and phase resolved ion energy and angular distributions in single- and dual-frequency capacitively coupled plasmas

Energy Technology Data Exchange (ETDEWEB)

Zhang, Yiting; Kushner, Mark J. [Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Ave., Ann Arbor, Michigan 48109-2122 (United States); Moore, Nathaniel; Pribyl, Patrick; Gekelman, Walter [Department of Physics, University of California, Los Angeles, California 90095 (United States)

2013-11-15

The control of ion energy and angular distributions (IEADs) is critically important for anisotropic etching or deposition in microelectronic fabrication processes. With single frequency capacitively coupled plasmas (CCPs), the narrowing in angle and spread in energy of ions as they cross the sheath are definable functions of frequency, sheath width, and mean free path. With increases in wafer size, single frequency CCPs are finding difficulty in meeting the requirement of simultaneously controlling plasma densities, ion fluxes, and ion energies. Dual-frequency CCPs are being investigated to provide this flexible control. The high frequency (HF) is intended to control the plasma density and ion fluxes, while the ion energies are intended to be controlled by the low frequency (LF). However, recent research has shown that the LF can also influence the magnitude of ion fluxes and that IEADs are determined by both frequencies. Hence, separate control of fluxes and IEADs is complex. In this paper, results from a two-dimensional computational investigation of Ar/O{sub 2} plasma properties in an industrial reactor are discussed. The IEADs are tracked as a function of height above the substrate and phase within the rf cycles from the bulk plasma to the presheath and through the sheath with the goal of providing insights to this complexity. Comparison is made to laser-induced fluorescence experiments. The authors found that the ratios of HF/LF voltage and driving frequency are critical parameters in determining the shape of the IEADs, both during the transit of the ion through the sheath and when ions are incident onto the substrate. To the degree that contributions from the HF can modify plasma density, sheath potential, and sheath thickness, this may provide additional control for the IEADs.

The effect of incidence angle on ion bombardment induced surface topography development on single crystal copper

International Nuclear Information System (INIS)

Carter, G.; Nobes, M.J.; Lewis, G.W.; Whitton, J.L.

1982-01-01

The fluence dependence of development of microscopic surface features, particularly etch pits, during 9 keV Ar + ion bombardment of (11,3,1) oriented Cu single crystals has been studied employing quasi-dynamic irradiation and observation techniques in a scanning electron microscope-accelerator system. 9 keV ions are observed not to produce crystallographic pyramids under all irradiation conditions for this surface, a very different result from our earlier studies with higher energy ions. The bombardment does elaborate etch pits however, the habits and growth kinetics of which depend upon both polar and azimuthal angles of ion incidence to the surface. The results are explained in terms of differential erosion of crystal planes modified by the presence of pre-existing and irradiation induces extended defects. (orig.)

Zinc ions bind to and inhibit activated protein C

DEFF Research Database (Denmark)

Zhu, Tianqing; Ubhayasekera, Wimal; Nickolaus, Noëlle

2010-01-01

fold enhanced, presumably due to the Ca2+-induced conformational change affecting the conformation of the Zn2+-binding site. The inhibition mechanism was non-competitive both in the absence and presence of Ca2+. Comparisons of sequences and structures suggested several possible sites for zinc binding...

Single-color, in situ photolithography marking of individual CdTe/ZnTe quantum dots containing a single Mn{sup 2+} ion

Energy Technology Data Exchange (ETDEWEB)

Sawicki, K.; Malinowski, F. K.; Gałkowski, K.; Jakubczyk, T.; Kossacki, P.; Pacuski, W.; Suffczyński, J., E-mail: Jan.Suffczynski@fuw.edu.pl [Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 St., PL-02-093 Warsaw (Poland)

2015-01-05

A simple, single-color method for permanent marking of the position of individual self-assembled semiconductor Quantum Dots (QDs) at cryogenic temperatures is reported. The method combines in situ photolithography with standard micro-photoluminescence spectroscopy. Its utility is proven by a systematic magnetooptical study of a single CdTe/ZnTe QD containing a Mn{sup 2+} ion, where a magnetic field of up to 10 T in two orthogonal, Faraday and Voigt, configurations is applied to the same QD. The presented approach can be applied to a wide range of solid state nanoemitters.

Hemispherand-Strapped Calix[4]pyrrole: An Ion-pair Receptor for the Recognition and Extraction of Lithium Nitrite.

Science.gov (United States)

He, Qing; Zhang, Zhan; Brewster, James T; Lynch, Vincent M; Kim, Sung Kuk; Sessler, Jonathan L

2016-08-10

The hemispherand-strapped calix[4]pyrrole (1) acts as an ion pair receptor that exhibits selectivity for lithium salts. In organic media (CD2Cl2 and CD3OD, v/v, 9:1), receptor 1 binds LiCl with high preference relative to NaCl, KCl, and RbCl. DFT calculations provided support for the observed selectivity. Single crystal structures of five different lithium ion-pair complexes of 1 were obtained. In the case of LiCl, a single bridging water molecule between the lithium cation and chloride anion was observed, while tight contact ion pairs were observed in the case of the LiBr, LiI, LiNO3, and LiNO2 salts. Receptor 1 proved effective as an extractant for LiNO2 under both model solid-liquid and liquid-liquid extraction conditions.

Experimental study of single-electron loss by Ar+ ions in rare-gas atoms

Science.gov (United States)

Reyes, P. G.; Castillo, F.; Martínez, H.

2001-04-01

Absolute differential and total cross sections for single-electron loss were measured for Ar+ ions on rare-gas atoms in the laboratory energy range of 1.5 to 5.0 keV. The electron loss cross sections for all the targets studied are found to be in the order of magnitude between 10-19 and 10-22 cm2, and show a monotonically increasing behaviour as a function of the incident energy. The behaviour of the total single-electron loss cross sections with the atomic target number, Zt, shows different dependences as the collision energy increases. In all cases the present results display experimental evidence of saturation in the single-electron loss cross section as the atomic number of the target increases.

Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle.

Science.gov (United States)

Skinner, Gary M; Baumann, Christoph G; Quinn, Diana M; Molloy, Justin E; Hoggett, James G

2004-01-30

A single-molecule transcription assay has been developed that allows, for the first time, the direct observation of promoter binding, initiation, and elongation by a single RNA polymerase (RNAP) molecule in real-time. To promote DNA binding and transcription initiation, a DNA molecule tethered between two optically trapped beads was held near a third immobile surface bead sparsely coated with RNAP. By driving the optical trap holding the upstream bead with a triangular oscillation while measuring the position of both trapped beads, we observed the onset of promoter binding, promoter escape (productive initiation), and processive elongation by individual RNAP molecules. After DNA template release, transcription re-initiation on the same DNA template is possible; thus, multiple enzymatic turnovers by an individual RNAP molecule can be observed. Using bacteriophage T7 RNAP, a commonly used RNAP paradigm, we observed the association and dissociation (k(off)= 2.9 s(-1)) of T7 RNAP and promoter DNA, the transition to the elongation mode (k(for) = 0.36 s(-1)), and the processive synthesis (k(pol) = 43 nt s(-1)) and release of a gene-length RNA transcript ( approximately 1200 nt). The transition from initiation to elongation is much longer than the mean lifetime of the binary T7 RNAP-promoter DNA complex (k(off) > k(for)), identifying a rate-limiting step between promoter DNA binding and promoter escape.

Stimulation of eryptosis by aluminium ions

International Nuclear Information System (INIS)

Niemoeller, Olivier M.; Kiedaisch, Valentin; Dreischer, Peter; Wieder, Thomas; Lang, Florian

2006-01-01

Aluminium salts are utilized to impede intestinal phosphate absorption in chronic renal failure. Toxic side effects include anemia, which could result from impaired formation or accelerated clearance of circulating erythrocytes. Erythrocytes may be cleared secondary to suicidal erythrocyte death or eryptosis, which is characterized by cell shrinkage and exposure of phosphatidylserine (PS) at the erythrocyte surface. As macrophages are equipped with PS receptors, they bind, engulf and degrade PS-exposing cells. The present experiments have been performed to explore whether Al 3+ ions trigger eryptosis. The PS exposure was estimated from annexin binding and cell volume from forward scatter in FACS analysis. Exposure to Al 3+ ions (≥ 10 μM Al 3+ for 24 h) indeed significantly increased annexin binding, an effect paralleled by decrease of forward scatter at higher concentrations (≥ 30 μM Al 3+ ). According to Fluo3 fluorescence Al 3+ ions (≥ 30 μM for 3 h) increased cytosolic Ca 2+ activity. Al 3+ ions (≥ 10 μM for 24 h) further decreased cytosolic ATP concentrations. Energy depletion by removal of glucose similarly triggered annexin binding, an effect not further enhanced by Al 3+ ions. The eryptosis was paralleled by release of hemoglobin, pointing to loss of cell membrane integrity. In conclusion, Al 3+ ions decrease cytosolic ATP leading to activation of Ca 2+ -permeable cation channels, Ca 2+ entry, stimulation of cell membrane scrambling and cell shrinkage. Moreover, Al 3+ ions lead to loss of cellular hemoglobin, a feature of hemolysis. Both effects are expected to decrease the life span of circulating erythrocytes and presumably contribute to the development of anemia during Al 3+ intoxication

Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel

International Nuclear Information System (INIS)

Wang, Hailong; Cheng, Xiaolin

2011-01-01

The proton-gated ion channel from Gloeobacter violaceus (GLIC) is a prokaryotic homolog of the eukaryotic nicotinic acetylcholine receptor (nAChR) that responds to the binding of neurotransmitter acetylcholine and mediates fast signal transmission. Recent emergence of a high resolution crystal structure of GLIC captured in a potentially open state allowed detailed, atomic-level insight into ion conduction and selectivity mechanisms in these channels. Herein, we have examined the barriers to ion conduction and origins of ion selectivity in the GLIC channel by the construction of potential of mean force (PMF) profiles for sodium and chloride ions inside the transmembrane region. Our calculations reveal that the GLIC channel is open for a sodium ion to transport, but presents a ∼10 kcal/mol free energy barrier for a chloride ion, which arises primarily from the unfavorable interactions with a ring of negatively charged glutamate residues (E-2) at the intracellular end and a ring of hydrophobic residues (I9) in the middle of the transmembrane domain. Our collective findings further suggest that the charge selection mechanism can, to a large extent, be attributed to the narrow intracellular end and a ring of glutamate residues in this position their strong negative electrostatics and ability to bind cations. By contrast, E19 at the extracellular entrance only plays a minor role in ion selectivity of GLIC. In addition to electrostatics, both ion hydration and protein dynamics are found to be crucial for ion conduction as well, which explains why a chloride ion experiences a much greater barrier than a sodium ion in the hydrophobic region of the pore.

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.

Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

Science.gov (United States)

Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

2008-11-21

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.

Single-crystalline LiFePO4 nanosheets for high-rate Li-ion batteries.

Science.gov (United States)

Zhao, Yu; Peng, Lele; Liu, Borui; Yu, Guihua

2014-05-14

The lithiation/delithiation in LiFePO4 is highly anisotropic with lithium-ion diffusion being mainly confined to channels along the b-axis. Controlling the orientation of LiFePO4 crystals therefore plays an important role for efficient mass transport within this material. We report here the preparation of single crystalline LiFePO4 nanosheets with a large percentage of highly oriented {010} facets, which provide the highest pore density for lithium-ion insertion/extraction. The LiFePO4 nanosheets show a high specific capacity at low charge/discharge rates and retain significant capacities at high C-rates, which may benefit the development of lithium batteries with both favorable energy and power density.

Binding of ATP by pertussis toxin and isolated toxin subunits

International Nuclear Information System (INIS)

Hausman, S.Z.; Manclark, C.R.; Burns, D.L.

1990-01-01

The binding of ATP to pertussis toxin and its components, the A subunit and B oligomer, was investigated. Whereas, radiolabeled ATP bound to the B oligomer and pertussis toxin, no binding to the A subunit was observed. The binding of [ 3 H]ATP to pertussis toxin and the B oligomer was inhibited by nucleotides. The relative effectiveness of the nucleotides was shown to be ATP > GTP > CTP > TTP for pertussis toxin and ATP > GTP > TTP > CTP for the B oligomer. Phosphate ions inhibited the binding of [ 3 H]ATP to pertussis toxin in a competitive manner; however, the presence of phosphate ions was essential for binding of ATP to the B oligomer. The toxin substrate, NAD, did not affect the binding of [ 3 H]ATP to pertussis toxin, although the glycoprotein fetuin significantly decreased binding. These results suggest that the binding site for ATP is located on the B oligomer and is distinct from the enzymatically active site but may be located near the eukaryotic receptor binding site

Binding of ATP by pertussis toxin and isolated toxin subunits

Energy Technology Data Exchange (ETDEWEB)

Hausman, S.Z.; Manclark, C.R.; Burns, D.L. (Center for Biologics Evaluation and Research, Bethesda, MD (USA))

1990-07-03

The binding of ATP to pertussis toxin and its components, the A subunit and B oligomer, was investigated. Whereas, radiolabeled ATP bound to the B oligomer and pertussis toxin, no binding to the A subunit was observed. The binding of ({sup 3}H)ATP to pertussis toxin and the B oligomer was inhibited by nucleotides. The relative effectiveness of the nucleotides was shown to be ATP > GTP > CTP > TTP for pertussis toxin and ATP > GTP > TTP > CTP for the B oligomer. Phosphate ions inhibited the binding of ({sup 3}H)ATP to pertussis toxin in a competitive manner; however, the presence of phosphate ions was essential for binding of ATP to the B oligomer. The toxin substrate, NAD, did not affect the binding of ({sup 3}H)ATP to pertussis toxin, although the glycoprotein fetuin significantly decreased binding. These results suggest that the binding site for ATP is located on the B oligomer and is distinct from the enzymatically active site but may be located near the eukaryotic receptor binding site.

Quantitative imaging of magnesium distribution at single-cell resolution in brain tumors and infiltrating tumor cells with secondary ion mass spectrometry (SIMS)

Science.gov (United States)

Chandra, Subhash; Parker, Dylan J.; Barth, Rolf F.; Pannullo, Susan C.

2016-01-01

Glioblastoma multiforme (GBM) is one of the deadliest forms of human brain tumors. The infiltrative pattern of growth of these tumors includes the spread of individual and/or clusters of tumor cells at some distance from the main tumor mass in parts of the brain protected by an intact blood-brain-barrier. Pathophysiological studies of GBM could be greatly enhanced by analytical techniques capable of in situ single-cell resolution measurements of infiltrating tumor cells. Magnesium homeostasis is an area of active investigation in high grade gliomas. In the present study, we have used the F98 rat glioma as a model of human GBM and an elemental/isotopic imaging technique of secondary ion mass spectrometry (SIMS), a CAMECA IMS-3f ion microscope, for studying Mg distributions with single-cell resolution in freeze-dried brain tissue cryosections. Quantitative observations were made on tumor cells in the main tumor mass, contiguous brain tissue, and infiltrating tumor cells in adjacent normal brain. The brain tissue contained a significantly lower total Mg concentration of 4.70 ± 0.93 mmol/Kg wet weight (mean ± SD) in comparison to 11.64 ± 1.96 mmol/Kg wet weight in tumor cells of the main tumor mass and 10.72 ± 1.76 mmol/Kg wet weight in infiltrating tumor cells (p<0.05). The nucleus of individual tumor cells contained elevated levels of bound Mg. These observations demonstrate enhanced Mg-influx and increased binding of Mg in tumor cells and provide strong support for further investigation of GBMs for altered Mg homeostasis and activation of Mg-transporting channels as possible therapeutic targets. PMID:26703785

Binding SnO2 nanocrystals in nitrogen-doped graphene sheets as anode materials for lithium-ion batteries.

Science.gov (United States)

Zhou, Xiaosi; Wan, Li-Jun; Guo, Yu-Guo

2013-04-18

Hybrid anode materials for Li-ion batteries are fabricated by binding SnO2 nanocrystals (NCs) in nitrogen-doped reduced graphene oxide (N-RGO) sheets by means of an in situ hydrazine monohydrate vapor reduction method. The SnO2NCs in the obtained SnO2NC@N-RGO hybrid material exhibit exceptionally high specific capacity and high rate capability. Bonds formed between graphene and SnO2 nanocrystals limit the aggregation of in situ formed Sn nanoparticles, leading to a stable hybrid anode material with long cycle life. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrical characterization of single cells using polysilicon wire ion sensor in an isolation window.

Science.gov (United States)

Wu, You-Lin; Hsu, Po-Yen; Hsu, Chung-Ping; Wang, Chih-Cheng; Lee, Li-Wen; Lin, Jing-Jenn

2011-10-01

A polysilicon wire (PSW) sensor can detect the H(+) ion density (pH value) of the medium coated on its surface, and different cells produce different extracellular acidification and hence different H(+) ion densities. Based on this, we used a PSW sensor in combination with a mold-cast polydimethylsiloxane (PDMS) isolation window to detect the adhesion, apoptosis and extracellular acidification of single normal cells and single cancer cells. Single living human normal cells WI38, MRC5, and BEAS-2B as well as non-small-cell lung cancer (NSCLC) cells A549, H1299, and CH27 were cultivated separately inside the isolation window. The current flowing through the PSW channel was measured. From the PSW channel current change as a function of time, we determined the cell adhesion time by observing the time required for the current change to saturate, since a stable extracellular ion density was established after the cells were completely adhered to the PSW surface. The apoptosis of cells can also be determined when the channel current change drops to zero. We found that all the NSCLC cells had a higher channel current change and hence a lower pH value than the normal cells anytime after they were seeded. The corresponding average pH values were 5.86 for A549, 6.00 for H1299, 6.20 for CH27, 6.90 for BEAS-2B, 6.96for MRC5, and 7.02 for WI38, respectively, after the cells were completely adhered to the PSW surface. Our results show that NSCLC cells have a stronger cell-substrate adhesion and a higher extracellular acidification rate than normal cells.

Quantum phase transitions driven by rhombic-type single-ion anisotropy in the S =1 Haldane chain

Science.gov (United States)

Tzeng, Yu-Chin; Onishi, Hiroaki; Okubo, Tsuyoshi; Kao, Ying-Jer

2017-08-01

The spin-1 Haldane chain is an example of the symmetry-protected-topological (SPT) phase in one dimension. Experimental realization of the spin chain materials usually involves both the uniaxial-type, D (Sz)2 , and the rhombic-type, E [(Sx)2-(Sy)2] , single-ion anisotropies. Here, we provide a precise ground-state phase diagram for a spin-1 Haldane chain with these single-ion anisotropies. Using quantum numbers, we find that the Z2 symmetry breaking phase can be characterized by double degeneracy in the entanglement spectrum. Topological quantum phase transitions take place on particular paths in the phase diagram, from the Haldane phase to the large-Ex, large-Ey, or large-D phases. The topological critical points are determined by the level spectroscopy method with a newly developed parity technique in the density matrix renormalization group [Phys. Rev. B 86, 024403 (2012), 10.1103/PhysRevB.86.024403], and the Haldane-large-D critical point is obtained with an unprecedented precision, (D/J ) c=0.9684713 (1 ) . Close to this critical point, a small rhombic single-ion anisotropy |E |/J ≪1 can destroy the Haldane phase and bring the system into a y -Néel phase. We propose that the compound [Ni (HF2) (3-Clpy ) 4] BF4 is a candidate system to search for the y -Néel phase.

Crystal-field analysis of U3+ ions in K2LaX5 (X=Cl, Br or I) single crystals

Science.gov (United States)

Karbowiak, M.; Edelstein, N.; Gajek, Z.; Drożdżyński, J.

1998-11-01

An analysis of low temperature absorption spectra of U3+ ions doped in K2LaX5 (X=Cl, Br or I) single crystals is reported. The energy levels of the U3+ ion in the single crystals were assigned and fitted to a semiempirical Hamiltonian representing the combined atomic and crystal-field interactions at the Cs symmetry site. An analysis of the nephelauxetic effect and crystal-field splittings in the series of compounds is also reported.

Carrageenans as a new source of drugs with metal binding properties.

Science.gov (United States)

Khotimchenko, Yuri S; Khozhaenko, Elena V; Khotimchenko, Maxim Y; Kolenchenko, Elena A; Kovalev, Valeri V

2010-04-01

Carrageenans are abundant and safe non-starch polysaccharides exerting their biological effects in living organisms. Apart from their known pro-inflammation properties and some pharmacological activity, carrageenans can also strongly bind and hold metal ions. This property can be used for creation of the new drugs for elimination of metals from the body or targeted delivery of these metal ions for healing purposes. Metal binding activity of different carrageenans in aqueous solutions containing Y(3+) or Pb(2+) ions was studied in a batch sorption system. The metal uptake by carrageenans is not affected by the change of the pH within the range from 2.0 to 6.0. The rates and binding capacities of carrageenans regarding metal ions were evaluated. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants, and the sorption isothermal data could be explained well by the Langmuir equation. The results obtained through the study suggest that kappa-, iota-, and lambda-carrageenans are favorable sorbents. The largest amount of Y(3+) and Pb(2+) ions are bound by iota-carrageenan. Therefore, it can be concluded that this type of polysaccharide is the more appropriate substance for elaboration of the drugs with high selective metal binding properties.

Carrageenans as a New Source of Drugs with Metal Binding Properties

Directory of Open Access Journals (Sweden)

Yuri S. Khotimchenko

2010-04-01

Full Text Available Carrageenans are abundant and safe non-starch polysaccharides exerting their biological effects in living organisms. Apart from their known pro-inflammation properties and some pharmacological activity, carrageenans can also strongly bind and hold metal ions. This property can be used for creation of the new drugs for elimination of metals from the body or targeted delivery of these metal ions for healing purposes. Metal binding activity of different carrageenans in aqueous solutions containing Y3+ or Pb2+ ions was studied in a batch sorption system. The metal uptake by carrageenans is not affected by the change of the pH within the range from 2.0 to 6.0. The rates and binding capacities of carrageenans regarding metal ions were evaluated. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants, and the sorption isothermal data could be explained well by the Langmuir equation. The results obtained through the study suggest that κ-, ι-, and λ-carrageenans are favorable sorbents. The largest amount of Y3+ and Pb2+ ions are bound by i-carrageenan. Therefore, it can be concluded that this type of polysaccharide is the more appropriate substance for elaboration of the drugs with high selective metal binding properties.

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

Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations.

Science.gov (United States)

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

2016-09-01

Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process. Copyright © 2016 Elsevier B.V. All rights reserved.

Binding kinetics of magnetic nanoparticles on latex beads and yeast cells studied by magnetorelaxometry

International Nuclear Information System (INIS)

Eberbeck, Dietmar; Bergemann, Christian; Hartwig, Stefan; Steinhoff, Uwe; Trahms, Lutz

2005-01-01

The ion exchange mediated binding of magnetic nanoparticles (MNP) to modified latex spheres and yeast cells was quantified using magnetorelaxometry. By fitting subsequently recorded relaxation curves, the kinetics of the binding reactions was extracted. The signal of MNP with weak ion exchanger groups bound to latex and yeast cells scales linearly with the concentration of latex beads or yeast cells whereas that of MNP with strong ion exchanger groups is proportional to the square root of concentration. The binding of the latter leads to a much stronger aggregation of yeast cells than the former MNP

Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR

Energy Technology Data Exchange (ETDEWEB)

D' Aquino,J.; Tetenbaum-Novatt, J.; White, A.; Berkovitch, F.; Ringe, D.

2005-01-01

The diphtheria toxin repressor (DtxR) is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear. Calorimetric techniques have demonstrated that although binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 x 10{sup -7}, binding site 2 (primary) is a low-affinity binding site with a binding constant of 6.3 x 10{sup -4}. These two binding sites act in an independent fashion, and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A, C102D), reported here, and the previously reported DtxR(H79A) have allowed us to propose a mechanism of metal activation for DtxR.

EPR and optical absorption studies of paramagnetic molecular ion (VO2+) in Lithium Sodium Acid Phthalate single crystal

Science.gov (United States)

Subbulakshmi, N.; Kumar, M. Saravana; Sheela, K. Juliet; Krishnan, S. Radha; Shanmugam, V. M.; Subramanian, P.

2017-12-01

Electron Paramagnetic Resonance (EPR) spectroscopic studies of VO2+ ions as paramagnetic impurity in Lithium Sodium Acid Phthalate (LiNaP) single crystal have been done at room temperature on X-Band microwave frequency. The lattice parameter values are obtained for the chosen system from Single crystal X-ray diffraction study. Among the number of hyperfine lines in the EPR spectra only two sets are reported from EPR data. The principal values of g and A tensors are evaluated for the two different VO2+ sites I and II. They possess the crystalline field around the VO2+ as orthorhombic. Site II VO2+ ion is identified as substitutional in place of Na1 location and the other site I is identified as interstitial location. For both sites in LiNaP, VO2+ are identified in octahedral coordination with tetragonal distortion as seen from the spin Hamiltonian parameter values. The ground state of vanadyl ion in the LiNaP single crystal is dxy. Using optical absorption data the octahedral and tetragonal parameters are calculated. By correlating EPR and optical data, the molecular orbital bonding parameters have been discussed for both sites.

Quantum sensing of the phase-space-displacement parameters using a single trapped ion

Science.gov (United States)

Ivanov, Peter A.; Vitanov, Nikolay V.

2018-03-01

We introduce a quantum sensing protocol for detecting the parameters characterizing the phase-space displacement by using a single trapped ion as a quantum probe. We show that, thanks to the laser-induced coupling between the ion's internal states and the motion mode, the estimation of the two conjugated parameters describing the displacement can be efficiently performed by a set of measurements of the atomic state populations. Furthermore, we introduce a three-parameter protocol capable of detecting the magnitude, the transverse direction, and the phase of the displacement. We characterize the uncertainty of the two- and three-parameter problems in terms of the Fisher information and show that state projective measurement saturates the fundamental quantum Cramér-Rao bound.

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.

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.

Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.

Science.gov (United States)

Buczek, Pawel; Horvath, Martin P

2006-06-23

The Oxytricha nova telemere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (DeltaH), entropy (DeltaS), and dissociation constant (K(D-DNA)) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T(2)G(4)), d(T(4)G(4)), d(G(3)T(4)G(4)), and d(G(4)T(4)G(4)) each formed monovalent protein complexes. In the case of d(T(4)G(4)T(4)G(4)), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity "A site" has a dissociation constant, K(D-DNA(A)) = 13(+/-4) nM, while the low-affinity "B site" is characterized by K(D-DNA(B)) = 5600(+/-600) nM at 25 degrees C. Nucleotide substitution variants verified that the A site corresponds principally with the 3'-terminal portion of d(T(4)G(4)T(4)G(4)). The relative contributions of entropy (DeltaS) and enthalpy (DeltaH) for binding reactions were DNA length-dependent as was heat capacity (DeltaCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA-protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology.

Prolonged in vivo residence times of llama single-domain antibody fragments in pigs by binding to porcine immunoglobulins

NARCIS (Netherlands)

Harmsen, M.M.; Solt, van C.B.; Fijten, H.P.D.; Setten, van M.C.

2005-01-01

The therapeutic parenteral application of llama single-domain antibody fragments (VHHs) is hampered by their small size, resulting in a fast elimination from the body. Here we describe a method to increase the serum half-life of VHHs in pigs by fusion to another VHH binding to porcine immunoglobulin

Calculating tracer currents through narrow ion channels: Beyond the independent particle model.

Science.gov (United States)

Coalson, Rob D; Jasnow, David

2018-06-01

Discrete state models of single-file ion permeation through a narrow ion channel pore are employed to analyze the ratio of forward to backward tracer current. Conditions under which the well-known Ussing formula for this ratio hold are explored in systems where ions do not move independently through the channel. Building detailed balance into the rate constants for the model in such a way that under equilibrium conditions (equal rate of forward vs. backward permeation events) the Nernst Equation is satisfied, it is found that in a model where only one ion can occupy the channel at a time, the Ussing formula is always obeyed for any number of binding sites, reservoir concentrations of the ions and electric potential difference across the membrane which the ion channel spans, independent of the internal details of the permeation pathway. However, numerical analysis demonstrates that when multiple ions can occupy the channel at once, the nonequilibrium forward/backward tracer flux ratio deviates from the prediction of the Ussing model. Assuming an appropriate effective potential experienced by ions in the channel, we provide explicit formulae for the rate constants in these models. © 2018 IOP Publishing Ltd.

Ionization and single electron capture in collision of highly charged Ar16+ ions with helium

International Nuclear Information System (INIS)

Wang Fei; Gou Bingcong

2008-01-01

This paper uses the two-centre atomic orbital close-coupling method to study the ionization and the single electron capture in collision of highly charged Ar 16+ ions with He atoms in the velocity range of 1.2–1.9 a.u. The relative importance of single ionization (SI) to single capture (SC) is explored. The comparison between the calculation and experimental data shows that the SI/SC cross section ratios from this work are in good agreement with experimental data. The total single electron ionization cross sections and the total single electron capture cross sections are also given for this collision. The investigation of the partial electron capture cross section shows a general tendency of capture to larger n and l with increasing velocity from 1.2 to 1.9 a.u

Influence of copper single crystal structures on the reflection of low energy hydrogen and helium ions

International Nuclear Information System (INIS)

Feijen, H.H.W.

1975-01-01

A theoretical basis for the 'wedge-focussing' phenomenon is outlined. Investigations have been made to check up to what extent proton reflection can be simulated by using H 2 + or H 3 + as incident ions and analysing the reflected protons. The results of an experimental study of the influence of surface semi-channels on the reflection of low energy ( + , H 2 + and He + ions from copper single crystals with attention to the wedge-focussing effect are presented (G.T.H.)

Characterization of [125I]omega-conotoxin binding to brain N calcium channels and (-)[3H] desmethoxyverapamil binding to novel calcium channels in osteoblast-like osteosarcoma cells

International Nuclear Information System (INIS)

Wagner, J.A.

1987-01-01

This dissertation provides molecular evidence for a diversity of Ca 2+ channels in neuronal and non-neuronal tissues. First, I demonstrated specific, reversible, saturable binding sites for omega [ 125 I]conotoxin GVIA (omega[ 125 I]CTX) in rat brain and rabbit sympathetic ganglion. Omega [ 125 I]CTX binding has a unique pharmacology, ion selectivity, and anatomical distribution in rat brain. Omega [ 125 I]CTX binding was solubilized, retaining an appropriate pharmacology and ion selectivity. Omega[ 125 I]CTX binding may be associated with a Ca 2+ channel because the K/sub D/ of omega [ 125 I]CTX is similar to the IC 50 of inhibition of depolarization-induced 45 Ca 2+ flux into rat brain synaptosomes. Specific (-)[ 3 H]desmethoxyverapamil ((-)[ 3 H]DMV) binding sites were demonstrated on osteoblast-like osteosarcoma cell membranes

Synthesis and Characterization of Network Single Ion Conductors(NSIC) Based On Comb-Branched Polyepoxide Ethers and Lithium Bis(allylmalonato)borate

International Nuclear Information System (INIS)

Sun, Xiao-Guang; Kerr, John B.

2004-01-01

Network single ion conductors (NSICs) based on comb-branch polyepoxide ethers and lithium bis(allylmalonato) borate have been synthesized and thoroughly characterized by means of ionic conductivity measurements, electrochemical impedance and by dynamic mechanical analysis (DMA). The materials have been tested as battery electrolytes by cycling in symmetrical Li/Li half cells and in Li/V 6 O 13 full cells in which the NSIC was used as both binder and electrolyte in the cathode electrode and as the electrolyte separator membrane,. The substitution of the trimethylene oxide (TMO) unit into the side chains in place of ethylene oxide (EO) units increased the polymerion mobility (lower glass transition temperature). However, the ionic conductivity was nearly one and half orders of magnitude lower than the corresponding pure EO based single ion conductor at the same salt concentration. This effect may be ascribed to the lower dielectric constant of the TMO side chains that result in a lower concentration of free conducting lithium cations. For a highly cross-linked system (EO/Li=20), only 47 wt% plasticizing solvent (ethylene carbonate (EC)/ethyl methyl carbonate (EMC), 1/1 by wt) could be taken up and the ionic conductivity was only increased by one order of magnitude over the dry polyelectrolyte while for a less densely crosslinked system (EO/Li=80), up to 75 wt% plasticizer could be taken up and the ionic conductivity was increased by nearly two orders of magnitude. A Li/Li symmetric cell that was cycled at 85 C at a current density of 25(micro)Acm -2 showed no concentration polarization or diffusional relaxation, consistent with a lithium ion transference number of one. However, both the bulk and interfacial impedances increased after 20 cycles, apparently due to continued cross-linking reactions within the membrane and on the surface of the lithium electrodes. A Li/V 6 O 13 full cell constructed using a single ion conductor gel (propylene carbonate (PC)/EMC, 1/1 in

Structural and binding studies of a C-type galactose-binding lectin from Bothrops jararacussu snake venom.

Science.gov (United States)

Sartim, Marco A; Pinheiro, Matheus P; de Pádua, Ricardo A P; Sampaio, Suely V; Nonato, M Cristina

2017-02-01

BJcuL is a snake venom galactoside-binding lectin (SVgalL) isolated from Bothrops jararacussu and is involved in a wide variety of biological activities including triggering of pro-inflammatory response, disruption of microbial biofilm structure and induction of apoptosis. In the present work, we determined the crystallographic structure of BJcuL, the first holo structure of a SVgalL, and introduced the fluorescence-based thermal stability assay (Thermofluor) as a tool for screening and characterization of the binding mechanism of SVgalL ligands. BJcuL structure revealed the existence of a porous and flexible decameric arrangement composed of disulfide-linked dimers related by a five-fold symmetry. Each monomer contains the canonical carbohydrate recognition domain, a calcium ion required for BJcuL lectinic activity and a sodium ion required for protein stabilization. BJcuL thermostability was found to be induced by calcium ion and galactoside sugars which exhibit hyperbolic saturation profiles dependent on ligand concentration. Serendipitously, the gentamicin group of aminoglycoside antibiotics (gAGAs) was also identified as BJcuL ligands. On contrast, gAGAs exhibited a sigmoidal saturation profile compatible with a cooperative mechanism of binding. Thermofluor, hemagglutination inhibition assay and molecular docking strategies were used to identify a distinct binding site in BJcuL localized at the dimeric interface near the fully conserved intermolecular Cys86-Cys86 disulfide bond. The hybrid approach used in the present work provided novel insights into structural behavior and functional diversification of SVgaLs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Luminescence properties of Tm3+ ions single-doped YF3 materials in an unconventional excitation region.

Science.gov (United States)

Chen, Yuan; Liu, Qing; Lin, Han; Yan, Xiaohong

2018-05-01

According to the spectral distribution of solar radiation at the earth's surface, under the excitation region of 1150 to 1350 nm, the up-conversion luminescence of Tm 3+ ions was investigated. The emission bands were matched well with the spectral response region of silicon solar cells, achieved by Tm 3+ ions single-doped yttrium fluoride (YF 3 ) phosphor, which was different from the conventional Tm 3+ /Yb 3+ ion couple co-doped materials. Additionally, the similar emission bands of Tm 3+ ions were achieved under excitation in the ultraviolet region. It is expected that via up-conversion and down-conversion routes, Tm 3+ -sensitized materials could convert photons to the desired wavelengths in order to reduce the energy loss of silicon solar cells, thereby enhancing the photovoltaic efficiency. Copyright © 2018 John Wiley & Sons, Ltd.

Thermodynamics of binding interactions between extracellular polymeric substances and heavy metals by isothermal titration microcalorimetry.

Science.gov (United States)

Yan, Peng; Xia, Jia-Shuai; Chen, You-Peng; Liu, Zhi-Ping; Guo, Jin-Song; Shen, Yu; Zhang, Cheng-Cheng; Wang, Jing

2017-05-01

Extracellular polymeric substances (EPS) play a crucial role in heavy metal bio-adsorption using activated sludge, but the interaction mechanism between heavy metals and EPS remains unclear. Isothermal titration calorimetry was employed to illuminate the mechanism in this study. The results indicate that binding between heavy metals and EPS is spontaneous and driven mainly by enthalpy change. Extracellular proteins in EPS are major participants in the binding process. Environmental conditions have significant impact on the adsorption performance. Divalent and trivalent cations severely impeded the binding of heavy metal ions to EPS. Electrostatic interaction mainly attributed to competition between divalent cations and heavy metal ions; trivalent cations directly competed with heavy metal ions for EPS binding sites. Trivalent cations were more competitive than divalent cations for heavy metal ion binding because they formed complexing bonds. This study facilitates a better understanding about the interaction between heavy metals and EPS in wastewater treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermodynamics of Pb(ii) and Zn(ii) binding to MT-3, a neurologically important metallothionein.

Science.gov (United States)

Carpenter, M C; Shami Shah, A; DeSilva, S; Gleaton, A; Su, A; Goundie, B; Croteau, M L; Stevenson, M J; Wilcox, D E; Austin, R N

2016-06-01

Isothermal titration calorimetry (ITC) was used to quantify the thermodynamics of Pb(2+) and Zn(2+) binding to metallothionein-3 (MT-3). Pb(2+) binds to zinc-replete Zn7MT-3 displacing each zinc ion with a similar change in free energy (ΔG) and enthalpy (ΔH). EDTA chelation measurements of Zn7MT-3 and Pb7MT-3 reveal that both metal ions are extracted in a tri-phasic process, indicating that they bind to the protein in three populations with different binding thermodynamics. Metal binding is entropically favoured, with an enthalpic penalty that reflects the enthalpic cost of cysteine deprotonation accompanying thiolate ligation of the metal ions. These data indicate that Pb(2+) binding to both apo MT-3 and Zn7MT-3 is thermodynamically favourable, and implicate MT-3 in neuronal lead biochemistry.

Energy loss and charge exchange processes of high energy heavy ions channeled in crystals

International Nuclear Information System (INIS)

Poizat, J.C.; Andriamonje, S.; Anne, R.; Faria, N.V.d.C.; Chevallier, M.; Cohen, C.; Dural, J.; Farizon-Mazuy, B.; Gaillard, M.J.; Genre, R.; Hage-Ali, M.; Kirsch, R.; L'hoir, A.; Mory, J.; Moulin, J.; Quere, Y.; Remillieux, J.; Schmaus, D.; Toulemonde, M.

1990-01-01

The interaction of moving ions with single crystals is very sensitive to the orientation of the incident beam with respect to the crystalline directions of the target. Our experiments show that high energy heavy ion channeling deeply modifies their slowing down and charge exchange processes. This is due to the fact that channeled ions interact only with outershell target electrons, which means that the electron density they experience is very low and that the binding energy, and then the momentum distribution of these electrons, are quite different from the corresponding average values associated to random incidence. The two experimental studies presented here show the reduction of the energy loss rate for fast channeled heavy ions and illustrate the two aspects of channeling effects on charge exchange, the reduction of electron loss on one hand, and of electron capture on the other hand

Suitability of magnetic single- and multi-core nanoparticles to detect protein binding with dynamic magnetic measurement techniques

International Nuclear Information System (INIS)

Remmer, Hilke; Dieckhoff, Jan; Schilling, Meinhard; Ludwig, Frank

2015-01-01

We investigated the binding of biotinylated proteins to various streptavidin functionalized magnetic nanoparticles with different dynamic magnetic measurement techniques to examine their potential for homogeneous bioassays. As particle systems, single-core nanoparticles with a nominal core diameter of 30 nm as well as multi-core nanoparticles with hydrodynamic sizes varying between nominally 60 nm and 100 nm were chosen. As experimental techniques, fluxgate magnetorelaxometry (MRX), complex ac susceptibility (ACS) and measurements of the phase lag between rotating field and sample magnetization are applied. MRX measurements are only suited for the detection of small analytes if the multivalency of functionalized nanoparticles and analytes causes cross-linking, thus forming larger aggregates. ACS measurements showed for all nanoparticle systems a shift of the imaginary part's maximum towards small frequencies. In rotating field measurements only the single-core nanoparticle systems with dominating Brownian mechanism exhibit an increase of the phase lag upon binding in the investigated frequency range. The coexistence of Brownian and Néel relaxation processes can cause a more complex phase lag change behavior, as demonstrated for multi-core nanoparticle systems. - Highlights: • Cealization of homogeneous magnetic bioassays using different magnetic techniques. • Comparison of single- and multi-core nanoparticle systems. • ac Susceptibility favorable for detection of small analytes. • Magnetorelaxometry favorable for detection of large analytes or cross-linking assays

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.

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.

Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free energies

Science.gov (United States)

Pollard, Travis P.; Beck, Thomas L.

2018-06-01

Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of -0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane.

Engineering of microorganisms towards recovery of rare metal ions

Energy Technology Data Exchange (ETDEWEB)

Kuroda, Kouichi; Ueda, Mitsuyoshi [Kyoto Univ. (Japan). Div. of Applied Life Sciences

2010-06-15

The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/ peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved. (orig.)

Human chorionic ganodotropin binding sites in the human endometrium

International Nuclear Information System (INIS)

Bhattacharya, S.; Banerjee, J.; Sen, S.; Manna, P.R.

1993-01-01

The existence of high-affinity and low-capacity specific binding sites for luteinizing hormone/human chorionic gonadotropin (hCG) has been reported in porcine, rabbit and rat uteri. The authors have identified the hCG binding sites in the human endometrium collected from 35-42-year-old ovulatory and anovulatory women. The binding characteristics of hCG to endometrial tissue preparations from ovulatory and anovulatory women showed saturability with high affinity and low capacity. Scatchard plot analysis showed the dissociation constant of specific binding sites in the ovulatory women to be 3.5x10 -10 mol/l and in anovulatory women to be 3.1x10 -10 mol/l. The maximum binding capacity varied considerably between ovulatory and anovulatory endometrium. Among the divalent metal ions tested Zn 2+ effected a remarkable increase in [ 125 I]hCG binding to the endometrium, whereas Mn 2+ showed a marginal increase and other metal ions did not have any effect. Data obtained with human endometrium indicate an influence of the functional state of the ovary on [ 125 I]hCG binding to endometrium. 14 refs., 3 figs

Specific ion effects on membrane potential and the permselectivity of ion exchange membranes.

Science.gov (United States)

Geise, Geoffrey M; Cassady, Harrison J; Paul, Donald R; Logan, Bruce E; Hickner, Michael A

2014-10-21

Membrane potential and permselectivity are critical parameters for a variety of electrochemically-driven separation and energy technologies. An electric potential is developed when a membrane separates electrolyte solutions of different concentrations, and a permselective membrane allows specific species to be transported while restricting the passage of other species. Ion exchange membranes are commonly used in applications that require advanced ionic electrolytes and span technologies such as alkaline batteries to ammonium bicarbonate reverse electrodialysis, but membranes are often only characterized in sodium chloride solutions. Our goal in this work was to better understand membrane behaviour in aqueous ammonium bicarbonate, which is of interest for closed-loop energy generation processes. Here we characterized the permselectivity of four commercial ion exchange membranes in aqueous solutions of sodium chloride, ammonium chloride, sodium bicarbonate, and ammonium bicarbonate. This stepwise approach, using four different ions in aqueous solution, was used to better understand how these specific ions affect ion transport in ion exchange membranes. Characterization of cation and anion exchange membrane permselectivity, using these ions, is discussed from the perspective of the difference in the physical chemistry of the hydrated ions, along with an accompanying re-derivation and examination of the basic equations that describe membrane potential. In general, permselectivity was highest in sodium chloride and lowest in ammonium bicarbonate solutions, and the nature of both the counter- and co-ions appeared to influence measured permselectivity. The counter-ion type influences the binding affinity between counter-ions and polymer fixed charge groups, and higher binding affinity between fixed charge sites and counter-ions within the membrane decreases the effective membrane charge density. As a result permselectivity decreases. The charge density and polarizability

Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli

International Nuclear Information System (INIS)

Phillips, C.; Schreiter, E.; Stultz, C.; Drennan, C.

2010-01-01

Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel (Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148). While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface (Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681), the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 (angstrom) resolution and have obtained nickel anomalous data (1.4845 (angstrom)) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.

Reconstruction of calmodulin single-molecule FRET states, dye interactions, and CaMKII peptide binding by MultiNest and classic maximum entropy

Science.gov (United States)

DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.

2013-08-01

We analyzed single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.

Science.gov (United States)

Devore, Matthew S; Gull, Stephen F; Johnson, Carey K

2013-08-30

We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca 2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

Mechanical characterization of magnesium aluminate MgO·nAl2O3 spinel single crystals irradiated with Cu- ions

International Nuclear Information System (INIS)

Ohmura, Takahito; Lee, Chi-Gyu; Kishimoto, Naoki

2003-01-01

Ion-irradiation response of spinel single crystals was investigated using a nanoindentation technique. Specimens of stoichiometric (n=1) and non-stoichiometric (n=2.4) single crystals of MgO n(Al 2 O 3 ) spinel were irradiated with 60 keV Cu - ion at room temperature. Dose rate ranged from 1 to 100 μA/cm 2 , and a total dose was kept constant at 3x10 16 ions/cm 2 . Both plastic hardness and elastic modulus of all the irradiated specimens were softened. Radiation-induced swelling simultaneously occurred. Rutherford back scattering spectroscopy detected disordering of spinel crystalline structure. Accordingly, the radiation-induced softening and swelling are ascribed to accumulation of point defects associated with the disordering. In comparison between the stoichiometric and the non-stoichiometric specimens, the radiation-induced softening is suppressed in the non-stoichiometric composition. (author)

Experimental determination of electron shock excitation cross sections for a singly charged gadolinium ion

International Nuclear Information System (INIS)

Smirnov, Yu.M.

1995-01-01

The trends observed in the processes of excitation with simultaneous ionization have received little study. This is particularly so for rare-earth elements having electron shells of complex structure and optical spectra very rich in lines. Among the basic factors responsible for such a situation, we should mention two: the difficulty presented by theoretical analysis of the processes discussed and the absence of factual information about the excitation cross sections with simultaneous ionization for the majority of rare-earth elements. The aim of the present work is to investigate the excitation of a singly charged gadolinium ion in the collisions of monokinetic electrons with gadolinium atoms. Up to the present time, only the excitation cross sections of a gadolinium atom have been measured, where investigation of the electron shock excitation of gadolinium atoms in their free state is associated with overcoming large experimental difficulties. About 160 crosss sections for the excitation of a singly charged gadolinium ion were measured and for a third of the cross sections; the energy dependences were recorded for the change in energy of the elecrons from the excitation threshold up to 200 eV. Included are tables of the wavelength, transistion, internal quantum number, the energy of the lowere and upper levels, and the values of cross sections for the charged gadolinium ion. Diagrams of the transistion energy states of Gd (II) and spectroscopy are presented and explained

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).

Recoil ion spectroscopy with heavy ions

International Nuclear Information System (INIS)

Beyer, H.F.; Mann, R.

1984-01-01

This chapter examines the production of very high charge state ions in single ion-atom collisions. Topics considered include some aspects of highly ionized atoms, experimental approaches, the production of highly charged target ions (monoatomic targets, recoil energy distribution, molecular fragmentation, outer-shell rearrangement, lifetime measurements, a comparison of projectile-, target-, and plasma-ion stripping), and secondary collision experiments (selective electron capture, potential applications). The heavy-ion beams for the described experiments were provided by accelerators such as tandem Van de Graaff facility and the UNILAC

Ion Feedback Suppression Using Inclined MCP Holes in a Single-MCP+Micromegas+Pads Detector

International Nuclear Information System (INIS)

Va'vra, J.; Sumiyoshi, T.

2005-01-01

We show that the ion backflow to photocathode can be completely suppressed if one uses inclined MCP holes in a presence of magnetic field. The inclined hole angles are chosen to be aligned with the Lorentz electron angle allowing the electron transmission and amplification, while positive ions, traveling along a different angle, are caught on the MCP hole walls. The detector under investigation is a new gaseous detector structure based on a tandem of two parts, a single MCP (Microchannel) plate, a Micromegas with pad readout. We are aiming to develop a gaseous photon detector with the Bialkali photocathode, however, one could use some ideas in the paper for other types of detectors

Ion feedback suppression using inclined MCP holes in a 'single-MCP+micromegas+pads' detector

International Nuclear Information System (INIS)

Va'vra, J.; Sumiyoshi, T.

2005-01-01

We show that the ion backflow to photocathode can be completely suppressed if one uses inclined MCP holes in the presence of a magnetic field. The inclined hole angles are chosen to be aligned with the Lorentz electron angle allowing the electron transmission and amplification, while positive ions, traveling along a different angle, are caught on the MCP hole walls. The detector under investigation is a new gaseous detector structure based on a tandem of two parts, a single MCP (microchannel plate), a micromegas with pad readout. We are aiming to develop a gaseous photon detector with the Bialkali photocathode, however, one could use some ideas in the paper for other types of detectors

Raman spectroscopic investigations of swift heavy ion irradiation effects in single-walled carbon nanotubes

International Nuclear Information System (INIS)

Olejniczak, A.; Skuratov, V.A.; Lukaszewicz, J.P.

2013-01-01

In this study, we report the results on swift heavy ion irradiation effects in single-walled carbon nanotubes (SWNTs). Buckypapers, prepared of CVD grown, SWNTs were irradiated at room temperature with 167 MeV Xe ions to fluences in the range of 6×10 11 - 6.5×10 13 cm -2 and investigated using Raman spectroscopy. We observed a rich set of features in the intermediate frequency mode region. Some of them, being defect-induced, resembled fairly well the phonon density of states (DOS) of nanocrystalline glassy carbon. Analysis of the RBM modes has shown that the broader metallic tubes are characterized by higher radiation stability than thinner semiconducting ones. (authors)

Xe ion beam induced rippled structures on differently oriented single-crystalline Si surfaces

Energy Technology Data Exchange (ETDEWEB)

Hanisch, Antje; Grenzer, Joerg; Facsko, Stefan [Forschungszentrum Dresden-Rossendorf, Institut fuer Ionenstrahlphysik und Materialforschung, PO Box 510119, 01314 Dresden (Germany); Biermanns, Andreas; Pietsch, Ullrich, E-mail: A.Hanisch@fzd.d [Universitaet Siegen, Festkoerperphysik, 57068 Siegen (Germany)

2010-03-24

We report on Xe{sup +} induced ripple formation at medium energy on single-crystalline silicon surfaces of different orientations using substrates with an intentional miscut from the [0 0 1] direction and a [1 1 1] oriented wafer. The ion beam incidence angle with respect to the surface normal was kept fixed at 65{sup 0} and the ion beam projection was parallel or perpendicular to the [1 1 0] direction. By a combination of atomic force microscopy, x-ray diffraction and high-resolution transmission electron microscopy we found that the features of the surface and subsurface rippled structures such as ripple wavelength and amplitude and the degree of order do not depend on the surface orientation as assumed in recent models of pattern formation for semiconductor surfaces. (fast track communication)

Full characterization of laser-accelerated ion beams using Faraday cup, silicon carbide, and single-crystal diamond detectors

Science.gov (United States)

Margarone, D.; Krása, J.; Giuffrida, L.; Picciotto, A.; Torrisi, L.; Nowak, T.; Musumeci, P.; Velyhan, A.; Prokůpek, J.; Láska, L.; Mocek, T.; Ullschmied, J.; Rus, B.

2011-05-01

Multi-MeV beams of light ions have been produced using the 300 picosecond, kJ-class iodine laser, operating at the Prague Asterix Laser System facility in Prague. Real-time ion diagnostics have been performed by the use of various time-of-flight (TOF) detectors: ion collectors (ICs) with and without absorber thin films, new prototypes of single-crystal diamond and silicon carbide detectors, and an electrostatic ion mass spectrometer (IEA). In order to suppress the long photopeak induced by soft X-rays and to avoid the overlap with the signal from ultrafast particles, the ICs have been shielded with Al foil filters. The application of large-bandgap semiconductor detectors (>3 eV) ensured cutting of the plasma-emitted visible and soft-UV radiation and enhancing the sensitivity to the very fast proton/ion beams. Employing the IEA spectrometer, various ion species and charge states in the expanding laser-plasma have been determined. Processing of the experimental data based on the TOF technique, including estimation of the plasma fast proton maximum and peak energy, ion beam currents and total charge, total number of fast protons, as well as deconvolution processes, ion stopping power, and ion/photon transmission calculations for the different metallic filters used, are reported.

Electrospray Ionization Mass Spectrometry: From Cluster Ions to Toxic metal Ions in Biology

Energy Technology Data Exchange (ETDEWEB)

Lentz, Nicholas B. [Iowa State Univ., Ames, IA (United States)

2007-01-01

This dissertation focused on using electrospray ionization mass spectrometry to study cluster ions and toxic metal ions in biology. In Chapter 2, it was shown that primary, secondary and quarternary amines exhibit different clustering characteristics under identical instrument conditions. Carbon chain length also played a role in cluster ion formation. In Chapters 3 and 4, the effects of solvent types/ratios and various instrumental parameters on cluster ion formation were examined. It was found that instrument interface design also plays a critical role in the cluster ion distribution seen in the mass spectrum. In Chapter 5, ESI-MS was used to investigate toxic metal binding to the [Gln¹¹]-amyloid β-protein fragment (1-16). Pb and Cd bound stronger than Zn, even in the presence of excess Zn. Hg bound weaker than Zn. There are endless options for future work on cluster ions. Any molecule that is poorly ionized in positive ion mode can potentially show an increase in ionization efficiency if an appropriate anion is used to produce a net negative charge. It is possible that drug protein or drug/DNA complexes can also be stabilized by adding counter-ions. This would preserve the solution characteristics of the complex in the gas phase. Once in the gas phase, CID could determine the drug binding location on the biomolecule. There are many research projects regarding toxic metals in biology that have yet to be investigated or even discovered. This is an area of research with an almost endless future because of the changing dynamics of biological systems. What is deemed safe today may show toxic effects in the future. Evolutionary changes in protein structures may render them more susceptible to toxic metal binding. As the understanding of toxicity evolves, so does the demand for new toxic metal research. New instrumentation designs and software make it possible to perform research that could not be done in the past. What was undetectable yesterday will

Single capture and transfer ionization in collisions of Clq+ projectile ions incident on helium

International Nuclear Information System (INIS)

Wong, K.L.; Ben-Itzhak, I.; Cocke, C.L.; Giese, J.P.; Richard, P.

1995-01-01

The Kansas State University linac has been used to measure the ratio of the cross sections for the processes of transfer ionization (TI) and single capture (SC) for 2 MeV/amu Cl q+ where q=7, 9, 13, 14, and 15 projectile ions incident on a helium target. The ratio was determined using a helium gas jet target by measuring coincidences between projectile-ion and recoil-ion final charge states. The σ TI /σ SC for Cl q+ were compared to measurements of bare F 9+ and hydrogenlike F 8+ and O 7+ taken at the same velocity. The ratios deviate from a q 2 scaling which is predicted in the perturbative regime. This deviation is attributed to screening by the projectile electrons for low q=7 and 9, and to the collision being non-perturbative for high q. A possible saturation effect in the ratio was observed for q similar 14. (orig.)

Complete momentum balance for single ionization of helium by fast ion impact: I. Experiment

Energy Technology Data Exchange (ETDEWEB)

Moshammer, R.; Kollmus, H.; Unverzagt, M.; Schmidt-Boecking, H. [Frankfurt Univ. (Germany). Inst. fuer Kernphysik; Ullrich, J.; Schmitt, W. [Gesellschaft fuer Schwerionenforschung mbH, Darmstadt (Germany); Wood, C.J.; Olson, R.E. [Missouri Univ., Rolla, MO (United States). Dept. of Physics

1997-02-01

The collision dynamics of He single ionization by 3.6 MeV/u Se{sup 28+} impact was explored using the GSI-reaction microscope, a high resolution integrated multi electron - recoil-ion momentum spectrometer. The complete three particle final state momentum distribution (9 cartesian components p{sub i}) was imaged with a resolution of {Delta}p{sub i} {approx} {+-}0.1 a.u. by measuring the three momentum components of the emitted electron and the recoiling target-ion in coincidence. The projectile energy loss has been determined on a level of {Delta}E{sub p}/E{sub p} {approx} 10{sup -7} and projectile scattering angles as small as {Delta}{theta} {approx} 10{sup -7}rad became accessible. The experimental data which are compared with results of classical trajectory Monte-Carlo (CTMC) calculations reveal an unprecedented insight into the details of the electron emission and the collision dynamics for ionization of helium by fast heavy-ion impact. (orig.)

Complete momentum balance for single ionization of helium by fast ion impact: I. Experiment

International Nuclear Information System (INIS)

Moshammer, R.; Kollmus, H.; Unverzagt, M.; Schmidt-Boecking, H.; Wood, C.J.; Olson, R.E.

1997-02-01

The collision dynamics of He single ionization by 3.6 MeV/u Se 28+ impact was explored using the GSI-reaction microscope, a high resolution integrated multi electron - recoil-ion momentum spectrometer. The complete three particle final state momentum distribution (9 cartesian components p i ) was imaged with a resolution of Δp i ∼ ±0.1 a.u. by measuring the three momentum components of the emitted electron and the recoiling target-ion in coincidence. The projectile energy loss has been determined on a level of ΔE p /E p ∼ 10 -7 and projectile scattering angles as small as Δθ ∼ 10 -7 rad became accessible. The experimental data which are compared with results of classical trajectory Monte-Carlo (CTMC) calculations reveal an unprecedented insight into the details of the electron emission and the collision dynamics for ionization of helium by fast heavy-ion impact. (orig.)

Medium-energy heavy-ion single-event-burnout imaging of power MOSFETs

Energy Technology Data Exchange (ETDEWEB)

Musseau, O.; Torres, A.; Campbell, A.B.; Knudson, A.R.; Buchner, S.; Fischer, B.; Schloegl, M.; Briand, P.

1999-12-01

The authors present the first experimental determination of the SEB sensitive area in a power MOSFET irradiated with a high-LET heavy-ion microbeam. They used a spectroscopy technique to perform coincident measurements of the charge collected in both source and drain junctions together, with a non-destructive technique (current limitation). The resulting charge collection images are related to the physical structure of the individual cells. These experimental data reveal the complex 3-dimensional behavior of a real structure, which can not easily be simulated using available tools. As the drain voltage is increased, the onset of burnout is reached, characterized by a sudden change in the charge collection image. Hot spots are observed where the collected charge reaches its maximum value. Those spots, due to burnout triggering events, correspond to areas where the silicon is degraded through thermal effects along a single ion track. This direct observation of SEB sensitive areas as applications for, either device hardening, by modifying doping profiles or layout of the cells, or for code calibration and device simulation.

Evolution of Metal(Loid) Binding Sites in Transcriptional Regulators

Energy Technology Data Exchange (ETDEWEB)

Ordonez, E.; Thiyagarajan, S.; Cook, J.D.; Stemmler, T.L.; Gil, J.A.; Mateos, L.M.; Rosen, B.P.

2009-05-22

Expression of the genes for resistance to heavy metals and metalloids is transcriptionally regulated by the toxic ions themselves. Members of the ArsR/SmtB family of small metalloregulatory proteins respond to transition metals, heavy metals, and metalloids, including As(III), Sb(III), Cd(II), Pb(II), Zn(II), Co(II), and Ni(II). These homodimeric repressors bind to DNA in the absence of inducing metal(loid) ion and dissociate from the DNA when inducer is bound. The regulatory sites are often three- or four-coordinate metal binding sites composed of cysteine thiolates. Surprisingly, in two different As(III)-responsive regulators, the metalloid binding sites were in different locations in the repressor, and the Cd(II) binding sites were in two different locations in two Cd(II)-responsive regulators. We hypothesize that ArsR/SmtB repressors have a common backbone structure, that of a winged helix DNA-binding protein, but have considerable plasticity in the location of inducer binding sites. Here we show that an As(III)-responsive member of the family, CgArsR1 from Corynebacterium glutamicum, binds As(III) to a cysteine triad composed of Cys{sup 15}, Cys{sup 16}, and Cys{sup 55}. This binding site is clearly unrelated to the binding sites of other characterized ArsR/SmtB family members. This is consistent with our hypothesis that metal(loid) binding sites in DNA binding proteins evolve convergently in response to persistent environmental pressures.

Electron impact ionization of B-like ion N2+. Resonance enhancement of the single-channel cross section

International Nuclear Information System (INIS)

Li Guohe; Qian Xingzhong; Pan Soufu

1998-01-01

The electron impact ionization cross sections of B-like ion N 2+ are calculated in the Coulomb-Born no exchange approximation by using R-matrix method, and the single differential cross section is given. The calculated results exhibit the Rydberg series of resonances. The resonance enhancement of the single-channel cross section is significantly greater than direct ionization cross section. It is agreement with that of Chidichimo

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.

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

International Nuclear Information System (INIS)

Borràs, S.; Kaufmann, A.; Companyó, R.

2013-01-01

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