Science.gov

Sample records for ion track structure

  1. Low energy electrons and swift ion track structure in PADC

    SciTech Connect

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  2. Low energy electrons and swift ion track structure in PADC

    NASA Astrophysics Data System (ADS)

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-10-01

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d'Ions Lourds Dans l'Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Finally, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  3. Low energy electrons and swift ion track structure in PADC

    DOE PAGES

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; ...

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particularmore » incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.« less

  4. Ion track doping

    NASA Astrophysics Data System (ADS)

    Fink, D.; Chadderton, L. T.; Cruz, S. A.; Fahrner, W. R.; Hnatowicz, V.; Te Kaat, E. H.; Melnikov, A. A.; Varichenko, V. S.; Zaitsev, A. M.

    1994-10-01

    Longitudinal dopant distribution along ion tracks in soft (polymers [1?5]) and hard (diamond [6,7]) condensed carbonaceous matter have been studied by neutron depth profiling and cathodoluminesence. Both in-diffusion from the aqueous phase and energetic ion implantation were used in primary track doping. In-situ self-decoration of tracks and post-implantation with a secondary ion species were used in the specific case of ion implantation. Radial dopant distributions were also studied by means of a modified tomographic procedure. Decorative doping of ion bombarded solids is useful in probing track structure, and especially in pointing the way to potential development of nanometric-sized electronic devices.

  5. Track Structure in DNA Irradiated with Heavy Ions

    SciTech Connect

    Bowman, Michael K.; Becker, David; Sevilla, Michael D.; Zimbrick, John D.

    2005-04-01

    The spatial properties of trapped radicals produced in heavy ion-irradiated solid DNA at 77 K have been probed using pulsed Electron Paramagnetic Double Resonance (PELDOR or DEER) techniques. Salmon testes DNA hydrated to twelve water molecules per nucleotide was irradiated with 40Ar ions of energy 100 MeV/nucleon and LET ranging from 300 to 400 keV/?. Irradiated samples were maintained at cryogenic temperature at all times. PELDOR measurements were made using a refocused echo detection sequence that allows dipolar interaction between trapped radicals to be observed. The EPR spectrum is attributed to electron loss/gain DNA base radicals and neutral carbon-centered radicals that likely arise from sugar damage. We find a radical concentration of 13.5*1018 cm-3 in the tracks and a track radius of 6.79 nm. The cross section of these tracks is 144 nm2 yielding a lineal radical density of 2.6 radicals/nm. Based upon the yields previously determined for particles having calculated LET values of 300-400 keV/mm and our measured lineal density, we obtain an LET of 270 keV/mm, which is in good agreement with the calculated range of values. These measurements of radical density and spatial extent provide the first direct experimental determination of track characteristics in irradiated DNA.

  6. Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

    NASA Astrophysics Data System (ADS)

    Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

    2015-09-01

    The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  7. Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Wilson, John W.; Shavers, Mark R.; Katz, Robert

    1997-01-01

    In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, B. Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in V79 cells, and good agreement is found. Calculations show the high probability for mutation by relativistic ions due to the radial extension of ions track from delta rays. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) can be used to specify radiation quality for heavy ion bombardment.

  8. Monte-Carlo Simulations of Heavy Ions Track Structures and Applications

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francia A.

    2013-01-01

    In space, astronauts are exposed to protons, high ]energy heavy (HZE) ions that have a high charge (Z) and energy (E), and secondary radiation, including neutrons and recoil nuclei produced by nuclear reactions in spacecraft walls or in tissue. The astronauts can only be partly shielded from these particles. Therefore, on travelling to Mars, it is estimated that every cell nucleus in an astronaut fs body would be hit by a proton or secondary electron (e.g., electrons of the target atoms ionized by the HZE ion) every few days and by an HZE ion about once a month. The risks related to these heavy ions are not well known and of concern for long duration space exploration missions. Medical ion therapy is another situation where human beings can be irradiated by heavy ions, usually to treat cancer. Heavy ions have a peculiar track structure characterized by high levels of energy ]deposition clustering, especially in near the track ends in the so ]called eBragg peak f region. In radiotherapy, these features of heavy ions can provide an improved dose conformation with respect to photons, also considering that the relative biological effectiveness (RBE) of therapeutic ions in the plateau region before the peak is sufficiently low. Therefore, several proton and carbon ion therapy facilities are under construction at this moment

  9. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    PubMed Central

    Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; Pakarinen, Olli; Chisholm, Matthew F.; Zhang, Yanwen; Weber, William J.

    2015-01-01

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. In view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties. PMID:26555848

  10. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7.

    PubMed

    Aidhy, Dilpuneet S; Sachan, Ritesh; Zarkadoula, Eva; Pakarinen, Olli; Chisholm, Matthew F; Zhang, Yanwen; Weber, William J

    2015-11-10

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. In view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.

  11. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    DOE PAGES

    Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; ...

    2015-11-10

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallizationmore » during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. Lastly, in view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.« less

  12. Heavy ion track-structure calculations for radial dose in arbitrary materials

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Katz, Robert; Wilson, John W.; Dubey, Rajendra R.

    1995-01-01

    The delta-ray theory of track structure is compared with experimental data for the radial dose from heavy ion irradiation. The effects of electron transmission and the angular dependence of secondary electron ejection are included in the calculations. Several empirical formulas for electron range and energy are compared in a wide variety of materials in order to extend the application of the track-structure theory. The model of Rudd for the secondary electron-spectrum in proton collisions, which is based on a modified classical kinematics binary encounter model at high energies and a molecular promotion model at low energies, is employed. For heavier projectiles, the secondary electron spectrum is found by scaling the effective charge. Radial dose calculations for carbon, water, silicon, and gold are discussed. The theoretical data agreed well with the experimental data.

  13. Radical Formation and Chemical Track Structure in Ion-Beam Irradiated DNA

    NASA Astrophysics Data System (ADS)

    Becker, David; Adhikary, Amitava; Khanduri, Deepti; Sevilla, Michael D.

    2009-12-01

    Ion-beam irradiation of hydrated DNA at 77 K results in formation of at least three base radicals and a variety of radicals on the sugar phosphate backbone that can be observed using Electron Spin Resonance (ESR) spectroscopy. From dose-response curves for these radicals, we have formulated a radiation-chemical model of the track structure for ion-beam irradiated DNA. The model for chemical behavior posits that the base radicals trapped at 77 K are formed almost entirely in the track penumbra. The lower yields observed in ion-beam irradiated samples results from the fact that only a portion of the energy deposited by the ion beam ends up in this γ-like region. The remainder of the energy is deposited in the core in which the proximity of ion-radical formation results in the fast recombination of oppositely charged radicals, so few survive in the core at 77 K. However, a second group of radicals, neutral sugar radicals, are not as susceptible to recombination as are ion radicals, and can survive after formation in the core; these are presumed to form predominantly in the core. They include the sugar radicals, C1'ṡC3'ṡC5'ṡ, formed from oxidative processes, and C3'ṡdephos and phosphorous radicals which are formed after immediate strand breaks. The later species are thought to result from reductive cleavage by low energy electrons (LEE.) The high energy density in the core results in excited state processes that produce additional sugar radicals. The spatial characteristics of the radicals, deduced from PELDOR experiments, indicates that multiply damaged cluster sites (MDS) are formed in the core; these would be biologically significant, if formed in cells.

  14. Effects of track structure and cell inactivation on the calculation of heavy ion mutation rates in mammalian cells

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Wilson, J. W.; Shavers, M. R.; Katz, R.

    1996-01-01

    It has long been suggested that inactivation severely effects the probability of mutation by heavy ions in mammalian cells. Heavy ions have observed cross sections of inactivation that approach and sometimes exceed the geometric size of the cell nucleus in mammalian cells. In the track structure model of Katz the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated using the dose-response of the system to gamma-rays and the radial dose of the ions and may be equal to unity at small impact parameters for some ions. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections from heavy ions in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT mutations in Chinese hamster cells and good agreement is found. The resulting calculations qualitatively show that mutation cross sections for heavy ions display minima at velocities where inactivation cross sections display maxima. Also, calculations show the high probability of mutation by relativistic heavy ions due to the radial extension of ions track from delta-rays in agreement with the microlesion concept. The effects of inactivation on mutations rates make it very unlikely that a single parameter such as LET or Z*2/beta(2) can be used to specify radiation quality for heavy ion bombardment.

  15. Track structure based modelling of light ion radiation effects on nuclear and mitochondrial DNA

    NASA Astrophysics Data System (ADS)

    Schmitt, Elke; Ottolenghi, Andrea; Dingfelder, Michael; Friedland, Werner; Kundrat, Pavel; Baiocco, Giorgio

    2016-07-01

    Space radiation risk assessment is of great importance for manned spaceflights in order to estimate risks and to develop counter-measures to reduce them. Biophysical simulations with PARTRAC can help greatly to improve the understanding of initial biological response to ionizing radiation. Results from modelling radiation quality dependent DNA damage and repair mechanisms up to chromosomal aberrations (e.g. dicentrics) can be used to predict radiation effects depending on the kind of mixed radiation field exposure. Especially dicentric yields can serve as a biomarker for an increased risk due to radiation and hence as an indicator for the effectiveness of the used shielding. PARTRAC [1] is a multi-scale biophysical research MC code for track structure based initial DNA damage and damage response modelling. It integrates physics, radiochemistry, detailed nuclear DNA structure and molecular biology of DNA repair by NHEJ-pathway to assess radiation effects on cellular level [2]. Ongoing experiments with quasi-homogeneously distributed compared to sub-micrometre focused bunches of protons, lithium and carbon ions allow a separation of effects due to DNA damage complexity on nanometre scale from damage clustering on (sub-) micrometre scale [3, 4]. These data provide an unprecedented benchmark for the DNA damage response model in PARTRAC and help understand the mechanisms leading to cell killing and chromosomal aberrations (e.g. dicentrics) induction. A large part of space radiation is due to a mixed ion field of high energy protons and few heavier ions that can be only partly absorbed by the shielding. Radiation damage induced by low-energy ions significantly contributes to the high relative biological efficiency (RBE) of ion beams around Bragg peak regions. For slow light ions the physical cross section data basis in PARTRAC has been extended to investigate radiation quality effects in the Bragg peak region [5]. The resulting range and LET values agree with ICRU data

  16. Coating and functionalization of high density ion track structures by atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Mättö, Laura; Szilágyi, Imre M.; Laitinen, Mikko; Ritala, Mikko; Leskelä, Markku; Sajavaara, Timo

    2016-10-01

    In this study flexible TiO2 coated porous Kapton membranes are presented having electron multiplication properties. 800 nm crossing pores were fabricated into 50 μm thick Kapton membranes using ion track technology and chemical etching. Consecutively, 50 nm TiO2 films were deposited into the pores of the Kapton membranes by atomic layer deposition using Ti(iOPr)4 and water as precursors at 250 °C. The TiO2 films and coated membranes were studied by scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray reflectometry (XRR). Au metal electrode fabrication onto both sides of the coated foils was achieved by electron beam evaporation. The electron multipliers were obtained by joining two coated membranes separated by a conductive spacer. The results show that electron multiplication can be achieved using ALD-coated flexible ion track polymer foils.

  17. Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping

    PubMed Central

    Friedland, W.; Schmitt, E.; Kundrát, P.; Dingfelder, M.; Baiocco, G.; Barbieri, S.; Ottolenghi, A.

    2017-01-01

    Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25–256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs. The simulations show that protons and helium ions induce more DNA damage than heavier ions do at the same LET. With increasing LET, less DNA strand breaks are formed per unit dose, but due to their clustering the yields of double-strand breaks (DSB) increase, up to saturation around 300 keV/μm. Also individual DSB tend to cluster; DSB clusters peak around 500 keV/μm, while DSB multiplicities per cluster steadily increase with LET. Remarkably similar to patterns known from cell survival studies, LET-dependencies with pronounced maxima around 100–200 keV/μm occur on nanometre scale for sites that contain one or more DSB, and on micrometre scale for megabasepair-sized DNA fragments. PMID:28345622

  18. Gamma and ion-beam irradiation of DNA: Free radical mechanisms, electron effects, and radiation chemical track structure

    NASA Astrophysics Data System (ADS)

    Sevilla, Michael D.; Becker, David; Kumar, Anil; Adhikary, Amitava

    2016-11-01

    The focus of our laboratory's investigation is to study the direct-type DNA damage mechanisms resulting from γ-ray and ion-beam radiation-induced free radical processes in DNA which lead to molecular damage important to cellular survival. This work compares the results of low LET (γ-) and high LET (ion-beam) radiation to develop a chemical track structure model for ion-beam radiation damage to DNA. Recent studies on protonation states of cytosine cation radicals in the N1-substituted cytosine derivatives in their ground state and 5-methylcytosine cation radicals in ground as well as in excited state are described. Our results exhibit a radical signature of excitations in 5-methylcytosine cation radical. Moreover, our recent theoretical studies elucidate the role of electron-induced reactions (low energy electrons (LEE), presolvated electrons (epre-), and aqueous (or, solvated) electrons (eaq-)). Finally DFT calculations of the ionization potentials of various sugar radicals show the relative reactivity of these species.

  19. Track structure in biological models.

    PubMed

    Curtis, S B

    1986-01-01

    High-energy heavy ions in the galactic cosmic radiation (HZE particles) may pose a special risk during long term manned space flights outside the sheltering confines of the earth's geomagnetic field. These particles are highly ionizing, and they and their nuclear secondaries can penetrate many centimeters of body tissue. The three dimensional patterns of ionizations they create as they lose energy are referred to as their track structure. Several models of biological action on mammalian cells attempt to treat track structure or related quantities in their formulation. The methods by which they do this are reviewed. The proximity function is introduced in connection with the theory of Dual Radiation Action (DRA). The ion-gamma kill (IGK) model introduces the radial energy-density distribution, which is a smooth function characterizing both the magnitude and extension of a charged particle track. The lethal, potentially lethal (LPL) model introduces lambda, the mean distance between relevant ion clusters or biochemical species along the track. Since very localized energy depositions (within approximately 10 nm) are emphasized, the proximity function as defined in the DRA model is not of utility in characterizing track structure in the LPL formulation.

  20. SU-E-T-334: Track Structure Simulations of Charged Particles at Low and Intermediate Energies: Cross Sections Needs for Light and Heavy Ions

    SciTech Connect

    Dingfelder, M

    2014-06-01

    Purpose/Methods: Monte Carlo (MC) track structure simulations follow the primary as well as all produced secondary particles in an event-by-event manner, from starting or ejection energy down to total stopping. They provide useful information on physics and chemistry of the biological response to radiation. They depend on reliable interaction cross sections and transport models of the considered radiation quality with biologically relevant materials. Most transport models focus on sufficiently fast and bare (i.e., fully ionized) ions and cross sections calculated within the (relativistic) first Born or Bethe approximations. These theories consider the projectile as a point particle and rely on proton cross sections and simple charge-scaling methods; they neglect the atomic nature of the ion and break down at low and intermediate ion energies. Heavier ions are used in particle therapy and slow to intermediate and low energies in the biologically interesting Bragg peak. Lighter and slower fragment ions, including alpha particles, protons, and neutrons are also produced in nuclear and break up reactions of charged particles. Secondary neutrons also produce recoil protons and ions, mainly in the intermediate energy range. Results/Conclusion: This work reviews existing models for track structure simulations and cross section calculations for light and heavy ions focusing on the low and intermediate energy range. It also presents new and updated aspects on cross section calculations and simulation techniques for ions and discusses the need for new models, calculations, and experimental data.

  1. 3D visualisation of the stochastic patterns of the radial dose in nano-volumes by a Monte Carlo simulation of HZE ion track structure.

    PubMed

    Plante, Ianik; Ponomarev, Artem; Cucinotta, Francis A

    2011-02-01

    The description of energy deposition by high charge and energy (HZE) nuclei is of importance for space radiation risk assessment and due to their use in hadrontherapy. Such ions deposit a large fraction of their energy within the so-called core of the track and a smaller proportion in the penumbra (or track periphery). We study the stochastic patterns of the radial dependence of energy deposition using Monte Carlo track structure codes RITRACKS and RETRACKS, that were used to simulate HZE tracks and calculate energy deposition in voxels of 40 nm. The simulation of a (56)Fe(26+) ion of 1 GeV u(-1) revealed zones of high-energy deposition which maybe found as far as a few millimetres away from the track core in some simulations. The calculation also showed that ∼43 % of the energy was deposited in the penumbra. These 3D stochastic simulations combined with a visualisation interface are a powerful tool for biophysicists which may be used to study radiation-induced biological effects such as double strand breaks and oxidative damage and the subsequent cellular and tissue damage processing and signalling.

  2. Track Structure Model for Radial Distributions of Electron Spectra and Event Spectra from High-Energy Ions

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Katz, R.; Wilson, J. W.

    1998-01-01

    An analytic method is described for evaluating the average radial electron spectrum and the radial and total frequency-event spectrum for high-energy ions. For high-energy ions, indirect events make important contributions to frequency-event spectra. The method used for evaluating indirect events is to fold the radial electron spectrum with measured frequency-event spectrum for photons or electrons. The contribution from direct events is treated using a spatially restricted linear energy transfer (LET). We find that high-energy heavy ions have a significantly reduced frequency-averaged final energy (yF) compared to LET, while relativistic protons have a significantly increased yF and dose-averaged lineal energy (yD) for typical site sizes used in tissue equivalent proportional counters. Such differences represent important factors in evaluating event spectra with laboratory beams, in space- flight, or in atmospheric radiation studies and in validation of radiation transport codes. The inadequacy of LET as descriptor because of deviations in values of physical quantities, such as track width, secondary electron spectrum, and yD for ions of identical LET is also discussed.

  3. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    SciTech Connect

    Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; Pakarinen, Olli; Chisholm, Matthew F.; Zhang, Yanwen; Weber, William J.

    2015-11-10

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. Lastly, in view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.

  4. Track-Structure Simulations for Charged Particles

    PubMed Central

    Dingfelder, Michael

    2013-01-01

    Monte-Carlo track-structure simulations provide a detailed and accurate picture of radiation transport of charged particles through condensed matter of biological interest. Liquid water serves as surrogate for soft tissue and is used in most Monte-Carlo track-structure codes. Basic theories of radiation transport and track-structure simulations are discussed and differences to condensed history codes highlighted. Interaction cross sections for electrons, protons, alpha particles, light and heavy ions are required input data for track-structure simulations. Different calculation methods, including the plane-wave Born approximation, the dielectric theory, and semi-empirical approaches are presented using liquid water as a target. Low-energy electron transport and light ion transport are discussed as areas of special interest. PMID:23032889

  5. Online Simulation of Radiation Track Structure Project

    NASA Technical Reports Server (NTRS)

    Plante, Ianik

    2015-01-01

    Space radiation comprises protons, helium and high charged and energy (HZE) particles. High-energy particles are a concern for human space flight, because they are no known options for shielding astronauts from them. When these ions interact with matter, they damage molecules and create radiolytic species. The pattern of energy deposition and positions of the radiolytic species, called radiation track structure, is highly dependent on the charge and energy of the ion. The radiolytic species damage biological molecules, which may lead to several long-term health effects such as cancer. Because of the importance of heavy ions, the radiation community is very interested in the interaction of HZE particles with DNA, notably with regards to the track structure. A desktop program named RITRACKS was developed to simulate radiation track structure. The goal of this project is to create a web interface to allow registered internal users to use RITRACKS remotely.

  6. Nanodosimetric track structure in homogeneous extended beams.

    PubMed

    Conte, V; Moro, D; Colautti, P; Grosswendt, B

    2015-09-01

    Physical aspects of particle track structure are important in determining the induction of clustered damage in relevant subcellular structures like the DNA and higher-order genomic structures. The direct measurement of track-structure properties of ionising radiation is feasible today by counting the number of ionisations produced inside a small gas volume. In particular, the so-called track-nanodosimeter, installed at the TANDEM-ALPI accelerator complex of LNL, measures ionisation cluster-size distributions in a simulated subcellular structure of dimensions 20 nm, corresponding approximately to the diameter of the chromatin fibre. The target volume is irradiated by pencil beams of primary particles passing at specified impact parameter. To directly relate these measured track-structure data to radiobiological measurements performed in broad homogeneous particle beams, these data can be integrated over the impact parameter. This procedure was successfully applied to 240 MeV carbon ions and compared with Monte Carlo simulations for extended fields.

  7. Funnel-type etched ion tracks in polymers

    NASA Astrophysics Data System (ADS)

    Fink, D.; Vacík, J.; Hnatowicz, V.; Muñoz, G. H.; Alfonta, L.; Klinkovich, I.

    2010-05-01

    It is shown that conical track etching is a much more complicated process than generally assumed. The choice of the corresponding parameters (i.e. the ratios of concentrations and diffusion coefficients of both etchant (e.g. NaOH) and stopping solutions (e.g. HCl) and the etching temperature) determines the ratio of polymer dissolution to etchant penetration. The latter value controls the counterplay of diffusion, etching, ionic conductivity, field emission and capacitive effects, which is decisive for both the final track shapes and their electronic properties. The stages of track evolution during etching under different conditions are outlined in detail. Both transparent conical nanopores and "funnel-type" tracks can be obtained, the latter consisting of a shorter cone and a residual latent track. Depending on the internal structure of that latent track segment, such funnel-type tracks either allow smooth transmission of the rectified currents or they emit unipolar current spikes. Not only the study of electronic properties of single ion tracks, but also of a multitude of tracks makes sense. Depending on the applied parameters, the individual track properties may either just add up, or new effects may be found that emerge from the interaction of the tracks among each other. This is preferentially the case for spike-emitting tracks, where effects such as phase-locked spike synchronization can be found as described by neural network theory.

  8. RITRACKS: A Software for Simulation of Stochastic Radiation Track Structure, Micro and Nanodosimetry, Radiation Chemistry and DNA Damage for Heavy Ions

    NASA Technical Reports Server (NTRS)

    Plante, I; Wu, H

    2014-01-01

    The code RITRACKS (Relativistic Ion Tracks) has been developed over the last few years at the NASA Johnson Space Center to simulate the effects of ionizing radiations at the microscopic scale, to understand the effects of space radiation at the biological level. The fundamental part of this code is the stochastic simulation of radiation track structure of heavy ions, an important component of space radiations. The code can calculate many relevant quantities such as the radial dose, voxel dose, and may also be used to calculate the dose in spherical and cylindrical targets of various sizes. Recently, we have incorporated DNA structure and damage simulations at the molecular scale in RITRACKS. The direct effect of radiations is simulated by introducing a slight modification of the existing particle transport algorithms, using the Binary-Encounter-Bethe model of ionization cross sections for each molecular orbitals of DNA. The simulation of radiation chemistry is done by a step-by-step diffusion-reaction program based on the Green's functions of the diffusion equation]. This approach is also used to simulate the indirect effect of ionizing radiation on DNA. The software can be installed independently on PC and tablets using the Windows operating system and does not require any coding from the user. It includes a Graphic User Interface (GUI) and a 3D OpenGL visualization interface. The calculations are executed simultaneously (in parallel) on multiple CPUs. The main features of the software will be presented.

  9. Characterisation of a track structure imaging detector.

    PubMed

    Casiraghi, M; Bashkirov, V A; Hurley, R F; Schulte, R W

    2015-09-01

    The spatial distribution of radiation-induced ionisations in sub-cellular structures plays an important role in the initial formation of radiation damage to biological tissues. Using the nanodosimetry approach, physical characteristics of the track structure can be measured and correlated to DNA damage. In this work, a novel nanodosimeter is presented, which detects positive ions produced by radiation interacting with a gas-sensitive volume in order to obtain a high resolution image of the radiation track structure. The characterisation of the detector prototype was performed and different configurations of the device were tested by varying the detector cathode material and the working gas. Preliminary results show that the ionisation cluster size distribution can be obtained with this approach. Further work is planned to improve the detector efficiency in order to register the complete three-dimensional track structure of ionising radiation.

  10. Industrial applications of ion track technology

    NASA Astrophysics Data System (ADS)

    Hanot, H.; Ferain, E.

    2009-03-01

    It4ip sa is a spin out from the Université Catholique de Louvain (Belgium) dedicated to the development and production of unique templates and membranes based on the combination of ion track technology of polymers. It supplies customers with hi-tech products, state-of-the-art research and product development services with template capability to make high value added membranes. Notably based on results coming from several collaborative R&D projects supported by European and Regional funding, recent improvements of ion track technology open new doors for fast growing applications in niche markets. This paper reviews some of these Hi-Tec applications in different fields such as in healthcare (oncology, drug control release combined to implant and artificial organs etc.), energy (fuel cells and batteries etc.), water de-contamination and electronics (OLED etc.).

  11. Field Emitter Arrays and Displays Produced by Ion Tracking Lithography

    SciTech Connect

    Felter, T E; Musket, R G; Bernhardt, A F

    2004-12-28

    When ions of sufficient electronic energy loss traverse a dielectric film or foil, they alter the chemical bonding along their nominally straight path within the material. A suitable etchant can quickly dissolve these so-called latent tracks leaving holes of small diameter ({approx}10nm) but long length - several microns. Continuing the etching process gradually increases the diameter reproducibly and uniformly. The trackable medium can be applied as a uniform film onto large substrates. The small, monodisperse holes produced by this track etching can be used in conjunction with additional thin film processing to create functional structures attached to the substrate. For example, Lawrence Livermore National Laboratory and Candescent Technologies Corporation (CTC) co-developed a process to make arrays of gated field emitters ({approx}100nm diameter electron guns) for CTC's ThinCRT{trademark} displays, which have been fabricated to diagonal dimensions > 13. Additional technological applications of ion tracking lithography will be briefly covered.

  12. Atomistic simulation of track formation by energetic ions in zircon

    SciTech Connect

    Moreira, Pedro A.F.P.; Devanathan, Ram; Weber, William J

    2010-01-01

    We have performed classical molecular dynamics simulations of fission track formation in zircon. We simulated the passage of a swift heavy ion through crystalline zircon using cylindrical thermal spikes with energy deposition (dE/dx) of 2.5-12.8 keV nm{sup -1} and a radius of 3 nm. At a low dE/dx of 2.55 keV nm{sup -1}, the structural damage recovered almost completely and a damage track was not produced. At higher values of dE/dx, tracks were observed and the radius of the track increased with increasing dE/dx. Our structural analysis shows amorphization in the core of the track and phase separation into Si-rich regions near the center of the track and Zr-rich regions near the periphery. These simulations establish a threshold dE/dx for fission track formation in zircon that is relevant to thermochronology and nuclear waste immobilization.

  13. New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

    SciTech Connect

    Sachan, Ritesh; Zhang, Yanwen; Ou, Xin; Trautmann, Christina; Chisholm, Matthew F.; Weber, William J.

    2016-12-13

    Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd2Ti2O7 and Gd2TiZrO7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performed on the ion tracks. Finally, a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.

  14. New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

    DOE PAGES

    Sachan, Ritesh; Zhang, Yanwen; Ou, Xin; ...

    2016-12-13

    Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd2Ti2O7 and Gd2TiZrO7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performed on the ion tracks. Finally,more » a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.« less

  15. Effect of track structure and radioprotectors on the induction of oncogenic transformation in murine fibroblasts by heavy ions

    NASA Technical Reports Server (NTRS)

    Miller, R. C.; Martin, S. G.; Hanson, W. R.; Marino, S. A.; Hall, E. J.; Wachholz, B. W. (Principal Investigator)

    1998-01-01

    The oncogenic potential of high-energy 56Fe particles (1 GeV/nucleon) accelerated with the Alternating Gradient Synchrotron at the Brookhaven National Laboratory was examined utilizing the mouse C3H 10T1/2 cell model. The dose-averaged LET for high-energy 56Fe is estimated to be 143 keV/micrometer with the exposure conditions used in this study. For 56Fe ions, the maximum relative biological effectiveness (RBEmax) values for cell survival and oncogenic transformation were 7.71 and 16.5 respectively. Compared to 150 keV/micrometer 4He nuclei, high-energy 56Fe nuclei were significantly less effective in cell killing and oncogenic induction. The prostaglandin E1 analog misoprostol, an effective oncoprotector of C3H 10T1/2 cells exposed to X rays, was evaluated for its potential as a radioprotector of oncogenic transformation with high-energy 56Fe. Exposure of cells to misoprostol did not alter 56Fe cytotoxicity or the rate of 56Fe-induced oncogenic transformation.

  16. Effect of track structure and radioprotectors on the induction of oncogenic transformation in murine fibroblasts by heavy ions

    NASA Astrophysics Data System (ADS)

    Miller, R. C.; Martin, S. G.; Hanson, W. R.; Marino, S. A.; Hall, E. J.

    1998-11-01

    The oncogenic potential of high-energy 56Fe particles (1 GeV/nucleon) accelerated with the Alternating Gradient Synchrotron at the Brookhaven National Laboratory was examined utilizing the mouse C3H 10T12 cell model. The dose-averaged LET for high-energy 56Fe is estimated to be 143 keV/μm with the exposure conditions used in this study. For 56Fe ions, the maximum relative biological effectiveness (RBEmax) values for cell survival and oncogenic transformation were 7.71 and 16.5 respectively. Compared to 150 keV/μm 4He nuclei, high-energy 56Fe nuclei were significantly less effective in cell killing and oncogenic induction. The prostaglandin E1 analog misoprostol, an effective oncoprotector of C3H 10T12 cells exposed to X rays, was evaluated for its potential as a radioprotector of oncogenic transformation with high-energy 56Fe. Exposure of cells to misoprostol did not alter 56Fe cytotoxicity or the rate of 56Fe-induced oncogenic transformation.

  17. Insights on dramatic radial fluctuations in track formation by energetic ions

    SciTech Connect

    Sachan, Ritesh; Lang, Maik; Trautmann, Christina; Zhang, Yanwen; Chisholm, Matthew F.; Weber, William J.; Zarkadoula, Eva

    2016-06-02

    We discuss the insights on the unexpected dramatic radial variations in the ion tracks formed by energetic ion (2.3 GeV 208Pb) irradiation at a constant electronic energy-loss (~42 keV/nm) in pyrochlore structured Gd2TiZrO7. Though previous studies have shown track formation and average track diameter measurements, this work brings further clarity on why quantitative analysis of ion track formation in Gd2TixZr(1-x)O7 systems can be more complicated than the currently accepted behavior for ion tracks. The ion track profile is usually considered to be diametrically uniform at constant values of the electronic energy-loss. This study shows the diameter variations to be as large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to (i) the stochastic nature of inelastic energy loss along the track and (ii) the random substitution of Ti atoms by Zr atoms on the B-site in the pyrochlore lattice. Furthermore, the partial substitution of Ti by Zr increases the favorability of the defect-fluorite structure formation over amorphous phase stochastically, by introducing localized inhomogeneity in atomic structure, density and strain.

  18. Insights on dramatic radial fluctuations in track formation by energetic ions

    DOE PAGES

    Sachan, Ritesh; Lang, Maik; Trautmann, Christina; ...

    2016-06-02

    We discuss the insights on the unexpected dramatic radial variations in the ion tracks formed by energetic ion (2.3 GeV 208Pb) irradiation at a constant electronic energy-loss (~42 keV/nm) in pyrochlore structured Gd2TiZrO7. Though previous studies have shown track formation and average track diameter measurements, this work brings further clarity on why quantitative analysis of ion track formation in Gd2TixZr(1-x)O7 systems can be more complicated than the currently accepted behavior for ion tracks. The ion track profile is usually considered to be diametrically uniform at constant values of the electronic energy-loss. This study shows the diameter variations to be asmore » large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to (i) the stochastic nature of inelastic energy loss along the track and (ii) the random substitution of Ti atoms by Zr atoms on the B-site in the pyrochlore lattice. Furthermore, the partial substitution of Ti by Zr increases the favorability of the defect-fluorite structure formation over amorphous phase stochastically, by introducing localized inhomogeneity in atomic structure, density and strain.« less

  19. Composition dependent thermal annealing behaviour of ion tracks in apatite

    NASA Astrophysics Data System (ADS)

    Nadzri, A.; Schauries, D.; Mota-Santiago, P.; Muradoglu, S.; Trautmann, C.; Gleadow, A. J. W.; Hawley, A.; Kluth, P.

    2016-07-01

    Natural apatite samples with different F/Cl content from a variety of geological locations (Durango, Mexico; Mud Tank, Australia; and Snarum, Norway) were irradiated with swift heavy ions to simulate fission tracks. The annealing kinetics of the resulting ion tracks was investigated using synchrotron-based small-angle X-ray scattering (SAXS) combined with ex situ annealing. The activation energies for track recrystallization were extracted and consistent with previous studies using track-etching, tracks in the chlorine-rich Snarum apatite are more resistant to annealing than in the other compositions.

  20. Secondary ionisations in a wall-less ion-counting nanodosimeter: quantitative analysis and the effect on the comparison of measured and simulated track structure parameters in nanometric volumes

    NASA Astrophysics Data System (ADS)

    Hilgers, Gerhard; Bug, Marion U.; Gargioni, Elisabetta; Rabus, Hans

    2015-10-01

    The object of investigation in nanodosimetry is the physical characteristics of the microscopic structure of ionising particle tracks, i.e. the sequence of the interaction types and interaction sites of a primary particle and all its secondaries, which reflects the stochastic nature of the radiation interaction. In view of the upcoming radiation therapy with protons and carbon ions, the ionisation structure of the ion track is of particular interest. Owing to limitations in current detector technology, the only way to determine the ionisation cluster size distribution in a DNA segment is to simulate the particle track structure in condensed matter. This is done using dedicated computer programs based on Monte Carlo procedures simulating the interaction of the primary ions with the target. Hence, there is a need to benchmark these computer codes using suitable experimental data. Ionisation cluster size distributions produced in the nanodosimeter's sensitive volume by monoenergetic protons and alpha particles (with energies between 0.1 MeV and 20 MeV) were measured at the PTB ion accelerator facilities. C3H8 and N2 were alternately used as the working gas. The measured data were compared with the simulation results obtained with the PTB Monte-Carlo code PTra [B. Grosswendt, Radiat. Environ. Biophys. 41, 103 (2002); M.U. Bug, E. Gargioni, H. Nettelbeck, W.Y. Baek, G. Hilgers, A.B. Rosenfeld, H. Rabus, Phys. Rev. E 88, 043308 (2013)]. Measured and simulated characteristics of the particle track structure are generally in good agreement for protons over the entire energy range investigated. For alpha particles with energies higher than the Bragg peak energy, a good agreement can also be seen, whereas for energies lower than the Bragg peak energy differences of as much as 25% occur. Significant deviations are only observed for large ionisation cluster sizes. These deviations can be explained by a background consisting of secondary ions. These ions are produced in the

  1. Formation of swift heavy ion tracks on a rutile TiO2 (001) surface.

    PubMed

    Karlušić, Marko; Bernstorff, Sigrid; Siketić, Zdravko; Šantić, Branko; Bogdanović-Radović, Ivančica; Jakšić, Milko; Schleberger, Marika; Buljan, Maja

    2016-10-01

    Nanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions. Samples irradiated with different ion fluences were investigated using atomic force microscopy and grazing-incidence small-angle X-ray scattering. With these two complementary approaches, a detailed description of the swift heavy ion impact sites, i.e. the ion tracks on the surface, can be obtained even for the case of multiple ion track overlap. In addition to the structural investigation of surface ion tracks, the change in stoichiometry of the rutile TiO2 (001) surface during swift heavy ion irradiation was monitored using in situ time-of-flight elastic recoil detection analysis, and a preferential loss of oxygen was found.

  2. Formation of swift heavy ion tracks on a rutile TiO2 (001) surface1

    PubMed Central

    Karlušić, Marko; Bernstorff, Sigrid; Siketić, Zdravko; Šantić, Branko; Bogdanović-Radović, Ivančica; Jakšić, Milko; Schleberger, Marika; Buljan, Maja

    2016-01-01

    Nanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions. Samples irradiated with different ion fluences were investigated using atomic force microscopy and grazing-incidence small-angle X-ray scattering. With these two complementary approaches, a detailed description of the swift heavy ion impact sites, i.e. the ion tracks on the surface, can be obtained even for the case of multiple ion track overlap. In addition to the structural investigation of surface ion tracks, the change in stoichiometry of the rutile TiO2 (001) surface during swift heavy ion irradiation was monitored using in situ time-of-flight elastic recoil detection analysis, and a preferential loss of oxygen was found. PMID:27738417

  3. Track creation after swift heavy ion irradiation of insulators

    NASA Astrophysics Data System (ADS)

    Medvedev, N.; Osmani, O.; Rethfeld, B.; Schleberger, M.

    2010-10-01

    The dynamics of structural modifications of insulators irradiated with swift heavy ions were investigated theoretically applying a combination of Monte-Carlo method (MC), used to describe SHI penetration and following excitation and relaxation of the electronic subsystem, with Two Temperature Model (TTM) describing the heating of the lattice. This MC-TTM combination demonstrates that secondary ionizations play a very important role for the track formation process. They lead to an additional term in the heat diffusion equation related to energy stored in the hole subsystem. This storage of energy causes a significant delay of heating and prolongs the timescales up to tens of picoseconds.

  4. Monte-Carlo Simulation of Heavy Ion Track Structure Calculation of Local Dose and 3D Time Evolution of Radiolytic Species

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2010-01-01

    Heavy ions have gained considerable importance in radiotherapy due to their advantageous dose distribution profile and high Relative Biological Effectiveness (RBE). Heavy ions are difficult to produce on Earth, but they are present in space and it is impossible at this moment to completely shield astronauts from them. The risk of these radiations is poorly understood, which is a concern for a 3-years Mars mission. The effects of radiation are mainly due to DNA damage such as DNA double-strand breaks (DSBs), although non-targeted effects are also very important. DNA can be damaged by the direct interaction of radiation and by reactions with chemical species produced by the radiolysis of water. The energy deposition is of crucial importance to understand biological effects of radiation. Therefore, much effort has been done recently to improve models of radiation tracks.

  5. Track structure model of cell damage in space flight

    NASA Technical Reports Server (NTRS)

    Katz, Robert; Cucinotta, Francis A.; Wilson, John W.; Shinn, Judy L.; Ngo, Duc M.

    1992-01-01

    The phenomenological track-structure model of cell damage is discussed. A description of the application of the track-structure model with the NASA Langley transport code for laboratory and space radiation is given. Comparisons to experimental results for cell survival during exposure to monoenergetic, heavy-ion beams are made. The model is also applied to predict cell damage rates and relative biological effectiveness for deep-space exposures.

  6. Effect Of Auger Recombination In An Ion Track

    NASA Technical Reports Server (NTRS)

    Edmonds, Larry D.

    1993-01-01

    Report presents theoretical calculations of contribution of Auger recombination to depletion of charge carriers from ionization track left by passage of energetic heavy ion through silicon-based electronic device.

  7. A 3D feature point tracking method for ion radiation

    NASA Astrophysics Data System (ADS)

    Kouwenberg, Jasper J. M.; Ulrich, Leonie; Jäkel, Oliver; Greilich, Steffen

    2016-06-01

    A robust and computationally efficient algorithm for automated tracking of high densities of particles travelling in (semi-) straight lines is presented. It extends the implementation of (Sbalzarini and Koumoutsakos 2005) and is intended for use in the analysis of single ion track detectors. By including information of existing tracks in the exclusion criteria and a recursive cost minimization function, the algorithm is robust to variations on the measured particle tracks. A trajectory relinking algorithm was included to resolve the crossing of tracks in high particle density images. Validation of the algorithm was performed using fluorescent nuclear track detectors (FNTD) irradiated with high- and low (heavy) ion fluences and showed less than 1% faulty trajectories in the latter.

  8. Insights on dramatic radial fluctuations in track formation by energetic ions

    PubMed Central

    Sachan, Ritesh; Zarkadoula, Eva; Lang, Maik; Trautmann, Christina; Zhang, Yanwen; Chisholm, Matthew F.; Weber, William J.

    2016-01-01

    We report on unexpected dramatic radial variations in ion tracks formed by irradiation with energetic ions (2.3 GeV 208Pb) at a constant electronic energy-loss (~42 keV/nm) in pyrochlore-structured Gd2TiZrO7. Though previous studies have shown track formation and average track diameter measurements in the Gd2TixZr(1−x)O7 system, the present work clearly reveals the importance of the recrystallization process in ion track formation in this system, which leads to more morphological complexities in tracks than currently accepted behavior. The ion track profile is usually considered to be diametrically uniform for a constant value of electronic energy-loss. This study reveals the diameter variations to be as large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to the partial substitution of Ti atoms by Zr atoms, which have a large difference in ionic radii, on the B-site in pyrochlore lattice. This random distribution of Ti and Zr atoms leads to a local competition between amorphous phase formation (favored by Ti atoms) and defect-fluorite phase formation (favored by Zr atoms) during the recrystallization process and finally introduces large radial variations in track morphology. PMID:27250764

  9. Insights on dramatic radial fluctuations in track formation by energetic ions

    NASA Astrophysics Data System (ADS)

    Sachan, Ritesh; Zarkadoula, Eva; Lang, Maik; Trautmann, Christina; Zhang, Yanwen; Chisholm, Matthew F.; Weber, William J.

    2016-06-01

    We report on unexpected dramatic radial variations in ion tracks formed by irradiation with energetic ions (2.3 GeV 208Pb) at a constant electronic energy-loss (~42 keV/nm) in pyrochlore-structured Gd2TiZrO7. Though previous studies have shown track formation and average track diameter measurements in the Gd2TixZr(1‑x)O7 system, the present work clearly reveals the importance of the recrystallization process in ion track formation in this system, which leads to more morphological complexities in tracks than currently accepted behavior. The ion track profile is usually considered to be diametrically uniform for a constant value of electronic energy-loss. This study reveals the diameter variations to be as large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to the partial substitution of Ti atoms by Zr atoms, which have a large difference in ionic radii, on the B-site in pyrochlore lattice. This random distribution of Ti and Zr atoms leads to a local competition between amorphous phase formation (favored by Ti atoms) and defect-fluorite phase formation (favored by Zr atoms) during the recrystallization process and finally introduces large radial variations in track morphology.

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

    SciTech Connect

    Omichi, Masaaki; Choi, Wookjin; Sakamaki, Daisuke; Seki, Shu; Tsukuda, Satoshi; Sugimoto, Masaki

    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.

  11. Advances in Understanding of Swift Heavy-Ion Tracks in Complex Ceramics

    SciTech Connect

    Lang, Maik; Devanathan, Ram; Toulemonde, Marcel; Trautmann, Christina

    2015-02-01

    Tracks produced by swift heavy ions in ceramics are of interest for fundamental science as well as for applications covering different fields such as nanotechnology or fission-track dating of minerals. In the case of pyrochlores with general formula A2B2O7, the track structure and radiation sensitivity shows a clear dependence on the composition. Ion irradiated Gd2Zr2O7, e.g., retains its crystallinity while amorphous tracks are produced in Gd2Ti2O7. Tracks in Ti-containing compositions have a complex morphology consisting of an amorphous core surrounded by a shell of a disordered, defect-fluorite phase. The size of the amorphous core decreases with decreasing energy loss and with increasing Zr content, while the shell thickness seems to be similar over a wide range of energy loss values. The large data set and the complex track structure has made pyrochlore an interesting model system for a general theoretical description of track formation including thermal spike calculations (providing the spatial and temporal evolution of temperature around the ion trajectory) and molecular dynamics (MD) simulations (describing the response of the atomic system).Recent MD advances consider the sudden temperature increase by inserting data from the thermal spike. The combination allows the reproduction of the core-shell track characteristic and sheds light on the early stages of track formation including recrystallization of the molten material produced by the thermal spike.

  12. Structure tracking aided design and synthesis of Li3V2(PO4)3 nanocrystals as high-power cathodes for lithium ion batteries

    DOE PAGES

    Wang, Liping; Bai, Jianming; Gao, Peng; ...

    2015-07-30

    In this study, preparing new electrode materials with synthetic control of phases and electrochemical properties is desirable for battery applications but hardly achievable without knowing how the synthesis reaction proceeds. Herein, we report on structure tracking-aided design and synthesis of single-crystalline Li3V2(PO4)3 (LVP) nanoparticles with extremely high rate capability. A comprehensive investigation was made to the local structural orderings of the involved phases and their evolution toward forming LVP phase using in situ/ex situ synchrotron X-ray and electron-beam diffraction, spectroscopy, and imaging techniques. The results shed light on the thermodynamics and kinetics of synthesis reactions and enabled the design ofmore » a cost-efficient synthesis protocol to make nanocrystalline LVP, wherein solvothermal treatment is a crucial step leading to an amorphous intermediate with local structural ordering resembling that of LVP, which, upon calcination at moderate temperatures, rapidly transforms into the desired LVP phase. The obtained LVP particles are about 50 nm, coated with a thin layer of amorphous carbon and featured with excellent cycling stability and rate capability – 95% capacity retention after 200 cycles and 66% theoretical capacity even at a current rate of 10 C. The structure tracking based method we developed in this work offers a new way of designing battery electrodes with synthetic control of material phases and properties.« less

  13. Structured output tracking guided by keypoint matching

    NASA Astrophysics Data System (ADS)

    Fang, Zhiwen; Cao, Zhiguo; Xiao, Yang

    2016-10-01

    Current keypoint-based trackers are widely used in object tracking system because of their robust capability against scale, rotation and so on. However, when these methods are applied in tracking 3D target in a forward-looking image sequences, the tracked point usually shifts away from the correct position as time increases. In this paper, to overcome the tracked point drifting, structured output tracking is used to track the target point with its surrounding information based on Haar-like features. First, around the tracked point in the last frame, a local patch is cropped to extract Haar-like features. Second, using a structured output SVM framework, a prediction function is learned in a larger radius to directly estimate the patch transformation between frames. Finally, during tracking the prediction function is applied to search the best location in a new frame. In order to achieve the robust tracking in real time, keypoint matching is adopted to coarsely locate the searched field in the whole image before using the structured output tracking. Experimentally, we show that our algorithm is able to outperform state-of-the-art keypoint-based trackers.

  14. Track-structure investigations: A supplement to microdosimetry

    NASA Astrophysics Data System (ADS)

    Conte, V.; Grosswendt, B.; Colautti, P.; Moro, D.; De Nardo, L.

    2013-07-01

    We conceived and developed an experimental apparatus able to measure the track structure (the spatial distribution of the points of ionizing collisions) of light ions, allowing the investigation of the track-core and penumbra regions separately. The device is based on single-electron counting technique, and simulates a target volume V of about 20 nm in diameter that can be moved with respect to a narrow primary particle beam, allowing the measurement of the ionization-cluster-size distribution as a function of the impact parameter. The experimental set up is mounted at the Tandem-Alpi LNL particle accelerator complex. The goal of the experiment is to investigate the formation of ionization-cluster-size distributions caused in a nanometre-sized volume by different light ions of medical interest (protons, lithium ions and carbon ions), when penetrating through or passing by the target volume at a specified distance.

  15. Engineering cell-fluorescent ion track hybrid detectors

    PubMed Central

    2013-01-01

    Background The lack of sensitive biocompatible particle track detectors has so far limited parallel detection of physical energy deposition and biological response. Fluorescent nuclear track detectors (FNTDs) based on Al2O3:C,Mg single crystals combined with confocal laser scanning microscopy (CLSM) provide 3D information on ion tracks with a resolution limited by light diffraction. Here we report the development of next generation cell-fluorescent ion track hybrid detectors (Cell-Fit-HD). Methods The biocompatibility of FNTDs was tested using six different cell lines, i.e. human non-small cell lung carcinoma (A549), glioblastoma (U87), androgen independent prostate cancer (PC3), epidermoid cancer (A431) and murine (VmDk) glioma SMA-560. To evaluate cell adherence, viability and conformal coverage of the crystals different seeding densities and alternative coating with extracellular matrix (fibronectin) was tested. Carbon irradiation was performed in Bragg peak (initial 270.55 MeV u−1). A series of cell compartment specific fluorescence stains including nuclear (HOECHST), membrane (Glut-1), cytoplasm (Calcein AM, CM-DiI) were tested on Cell-Fit-HDs and a single CLSM was employed to co-detect the physical (crystal) as well as the biological (cell layer) information. Results The FNTD provides a biocompatible surface. Among the cells tested, A549 cells formed the most uniform, viable, tightly packed epithelial like monolayer. The ion track information was not compromised in Cell-Fit-HD as compared to the FNTD alone. Neither cell coating and culturing, nor additional staining procedures affected the properties of the FNTD surface to detect ion tracks. Standard immunofluorescence and live staining procedures could be employed to co-register cell biology and ion track information. Conclusions The Cell-Fit-Hybrid Detector system is a promising platform for a multitude of studies linking biological response to energy deposition at high level of optical microscopy

  16. Dynamic kirigami structures for integrated solar tracking.

    PubMed

    Lamoureux, Aaron; Lee, Kyusang; Shlian, Matthew; Forrest, Stephen R; Shtein, Max

    2015-09-08

    Optical tracking is often combined with conventional flat panel solar cells to maximize electrical power generation over the course of a day. However, conventional trackers are complex and often require costly and cumbersome structural components to support system weight. Here we use kirigami (the art of paper cutting) to realize novel solar cells where tracking is integral to the structure at the substrate level. Specifically, an elegant cut pattern is made in thin-film gallium arsenide solar cells, which are then stretched to produce an array of tilted surface elements which can be controlled to within ±1°. We analyze the combined optical and mechanical properties of the tracking system, and demonstrate a mechanically robust system with optical tracking efficiencies matching conventional trackers. This design suggests a pathway towards enabling new applications for solar tracking, as well as inspiring a broader range of optoelectronic and mechanical devices.

  17. Dynamic kirigami structures for integrated solar tracking

    PubMed Central

    Lamoureux, Aaron; Lee, Kyusang; Shlian, Matthew; Forrest, Stephen R.; Shtein, Max

    2015-01-01

    Optical tracking is often combined with conventional flat panel solar cells to maximize electrical power generation over the course of a day. However, conventional trackers are complex and often require costly and cumbersome structural components to support system weight. Here we use kirigami (the art of paper cutting) to realize novel solar cells where tracking is integral to the structure at the substrate level. Specifically, an elegant cut pattern is made in thin-film gallium arsenide solar cells, which are then stretched to produce an array of tilted surface elements which can be controlled to within ±1°. We analyze the combined optical and mechanical properties of the tracking system, and demonstrate a mechanically robust system with optical tracking efficiencies matching conventional trackers. This design suggests a pathway towards enabling new applications for solar tracking, as well as inspiring a broader range of optoelectronic and mechanical devices. PMID:26348820

  18. Dynamic kirigami structures for integrated solar tracking

    NASA Astrophysics Data System (ADS)

    Lamoureux, Aaron; Lee, Kyusang; Shlian, Matthew; Forrest, Stephen R.; Shtein, Max

    2015-09-01

    Optical tracking is often combined with conventional flat panel solar cells to maximize electrical power generation over the course of a day. However, conventional trackers are complex and often require costly and cumbersome structural components to support system weight. Here we use kirigami (the art of paper cutting) to realize novel solar cells where tracking is integral to the structure at the substrate level. Specifically, an elegant cut pattern is made in thin-film gallium arsenide solar cells, which are then stretched to produce an array of tilted surface elements which can be controlled to within +/-1°. We analyze the combined optical and mechanical properties of the tracking system, and demonstrate a mechanically robust system with optical tracking efficiencies matching conventional trackers. This design suggests a pathway towards enabling new applications for solar tracking, as well as inspiring a broader range of optoelectronic and mechanical devices.

  19. Cellular track model for study of heavy ion beams

    NASA Technical Reports Server (NTRS)

    Shinn, Judy L.; Katz, Robert; Cucinotta, Francis A.; Wilson, John W.; Ngo, Duc M.

    1993-01-01

    Track theory is combined with a realistic model of a heavy ion beam to study the effects of nuclear fragmentation on cell survival and biological effectiveness. The effects of secondary reaction products are studied as a function of depth in a water column. Good agreement is found with experimental results for the survival of human T-l cells exposed to monoenergetic carbon, neon, and argon beams under aerobic and hypoxia conditions. The present calculation, which includes the effect of target fragmentation, is a significant improvement over an earlier calculation because of the use of a vastly improved beam model with no change in the track theory or cellular response parameters.

  20. Predictive modeling of synergistic effects in nanoscale ion track formation

    DOE PAGES

    Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou; ...

    2015-08-05

    Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

  1. Monte Carlo track structure for radiation biology and space applications

    NASA Technical Reports Server (NTRS)

    Nikjoo, H.; Uehara, S.; Khvostunov, I. G.; Cucinotta, F. A.; Wilson, W. E.; Goodhead, D. T.

    2001-01-01

    Over the past two decades event by event Monte Carlo track structure codes have increasingly been used for biophysical modelling and radiotherapy. Advent of these codes has helped to shed light on many aspects of microdosimetry and mechanism of damage by ionising radiation in the cell. These codes have continuously been modified to include new improved cross sections and computational techniques. This paper provides a summary of input data for ionizations, excitations and elastic scattering cross sections for event by event Monte Carlo track structure simulations for electrons and ions in the form of parametric equations, which makes it easy to reproduce the data. Stopping power and radial distribution of dose are presented for ions and compared with experimental data. A model is described for simulation of full slowing down of proton tracks in water in the range 1 keV to 1 MeV. Modelling and calculations are presented for the response of a TEPC proportional counter irradiated with 5 MeV alpha-particles. Distributions are presented for the wall and wall-less counters. Data shows contribution of indirect effects to the lineal energy distribution for the wall counters responses even at such a low ion energy.

  2. Cosmic heavy ion tracks in mesoscopic biological test objects

    NASA Technical Reports Server (NTRS)

    Facius, R.

    1994-01-01

    Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on 'HZE particle effects in manned spaced flight', it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to 'large' fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too ('The BIOSTACK as an approach to high LET radiation research'), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions' trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series. Since biological investigations and physical measurements of particle tracks had to be performed in laboratories widely separated, the preferred fixed contact between biological test objects and the particle detectors

  3. Predictive modeling of synergistic effects in nanoscale ion track formation

    SciTech Connect

    Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou; Zhang, Yanwen; Weber, William J.

    2015-08-05

    Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

  4. Secondary particle tracks generated by ion beam irradiation

    NASA Astrophysics Data System (ADS)

    García, Gustavo

    2015-05-01

    The Low Energy Particle Track Simulation (LEPTS) procedure is a powerful complementary tool to include the effect of low energy electrons and positrons in medical applications of radiation. In particular, for ion-beam cancer treatments provides a detailed description of the role of the secondary electrons abundantly generated around the Bragg peak as well as the possibility of using transmuted positron emitters (C11, O15) as a complement for ion-beam dosimetry. In this study we present interaction probability data derived from IAM-SCAR corrective factors for liquid environments. Using these data, single electron and positron tracks in liquid water and pyrimidine have been simulated providing information about energy deposition as well as the number and type of interactions taking place in any selected ``nanovolume'' of the irradiated area. In collaboration with Francisco Blanco, Universidad Complutense de Madrid; Antonio Mu noz, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Diogo Almeida, Filipe Ferreira da Silva, Paulo Lim ao-Vieira, Universidade Nova de Lisboa. Supported by the Spanish and Portuguese governments.

  5. Top marine predators track Lagrangian coherent structures

    PubMed Central

    Tew Kai, Emilie; Rossi, Vincent; Sudre, Joel; Weimerskirch, Henri; Lopez, Cristobal; Hernandez-Garcia, Emilio; Marsac, Francis; Garçon, Veronique

    2009-01-01

    Meso- and submesoscales (fronts, eddies, filaments) in surface ocean flow have a crucial influence on marine ecosystems. Their dynamics partly control the foraging behavior and the displacement of marine top predators (tuna, birds, turtles, and cetaceans). In this work we focus on the role of submesoscale structures in the Mozambique Channel in the distribution of a marine predator, the Great Frigatebird. Using a newly developed dynamic concept, the finite-size Lyapunov exponent (FSLE), we identified Lagrangian coherent structures (LCSs) present in the surface flow in the channel over a 2-month observation period (August and September 2003). By comparing seabird satellite positions with LCS locations, we demonstrate that frigatebirds track precisely these structures in the Mozambique Channel, providing the first evidence that a top predator is able to track these FSLE ridges to locate food patches. After comparing bird positions during long and short trips and different parts of these trips, we propose several hypotheses to understand how frigatebirds can follow these LCSs. The birds might use visual and/or olfactory cues and/or atmospheric current changes over the structures to move along these biologic corridors. The birds being often associated with tuna schools around foraging areas, a thorough comprehension of their foraging behavior and movement during the breeding season is crucial not only to seabird ecology but also to an appropriate ecosystemic approach to fisheries in the channel. PMID:19416811

  6. Top marine predators track Lagrangian coherent structures.

    PubMed

    Tew Kai, Emilie; Rossi, Vincent; Sudre, Joel; Weimerskirch, Henri; Lopez, Cristobal; Hernandez-Garcia, Emilio; Marsac, Francis; Garçon, Veronique

    2009-05-19

    Meso- and submesoscales (fronts, eddies, filaments) in surface ocean flow have a crucial influence on marine ecosystems. Their dynamics partly control the foraging behavior and the displacement of marine top predators (tuna, birds, turtles, and cetaceans). In this work we focus on the role of submesoscale structures in the Mozambique Channel in the distribution of a marine predator, the Great Frigatebird. Using a newly developed dynamic concept, the finite-size Lyapunov exponent (FSLE), we identified Lagrangian coherent structures (LCSs) present in the surface flow in the channel over a 2-month observation period (August and September 2003). By comparing seabird satellite positions with LCS locations, we demonstrate that frigatebirds track precisely these structures in the Mozambique Channel, providing the first evidence that a top predator is able to track these FSLE ridges to locate food patches. After comparing bird positions during long and short trips and different parts of these trips, we propose several hypotheses to understand how frigatebirds can follow these LCSs. The birds might use visual and/or olfactory cues and/or atmospheric current changes over the structures to move along these biologic corridors. The birds being often associated with tuna schools around foraging areas, a thorough comprehension of their foraging behavior and movement during the breeding season is crucial not only to seabird ecology but also to an appropriate ecosystemic approach to fisheries in the channel.

  7. WE-D-BRF-01: FEATURED PRESENTATION - Investigating Particle Track Structures Using Fluorescent Nuclear Track Detectors and Monte Carlo Simulations

    SciTech Connect

    Dowdell, S; Paganetti, H; Schuemann, J; Greilich, S; Zimmerman, F; Evans, C

    2014-06-15

    Purpose: To report on the efforts funded by the AAPM seed funding grant to develop the basis for fluorescent nuclear track detector (FNTD) based radiobiological experiments in combination with dedicated Monte Carlo simulations (MCS) on the nanometer scale. Methods: Two confocal microscopes were utilized in this study. Two FNTD samples were used to find the optimal microscope settings, one FNTD irradiated with 11.1 MeV/u Gold ions and one irradiated with 428.77 MeV/u Carbon ions. The first sample provided a brightly luminescent central track while the latter is used to test the capabilities to observe secondary electrons. MCS were performed using TOPAS beta9 version, layered on top of Geant4.9.6p02. Two sets of simulations were performed, one with the Geant4-DNA physics list and approximating the FNTDs by water, a second set using the Penelope physics list in a water-approximated FNTD and a aluminum-oxide FNTD. Results: Within the first half of the funding period, we have successfully established readout capabilities of FNTDs at our institute. Due to technical limitations, our microscope setup is significantly different from the approach implemented at the DKFZ, Germany. However, we can clearly reconstruct Carbon tracks in 3D with electron track resolution of 200 nm. A second microscope with superior readout capabilities will be tested in the second half of the funding period, we expect an improvement in signal to background ratio with the same the resolution.We have successfully simulated tracks in FNTDs. The more accurate Geant4-DNA track simulations can be used to reconstruct the track energy from the size and brightness of the observed tracks. Conclusion: We have achieved the goals set in the seed funding proposal: the setup of FNTD readout and simulation capabilities. We will work on improving the readout resolution to validate our MCS track structures down to the nanometer scales.

  8. Monitoring structure movement with laser tracking technology

    NASA Astrophysics Data System (ADS)

    Barazzetti, Luigi; Giussani, Alberto; Roncoroni, Fabio; Previtali, Mattia

    2013-04-01

    This paper presents the use of laser tracking technology for structure monitoring. In this field the use of this precise instrument is innovative and therefore new investigations are needed for civil structures, especially for applications carried out during unstable environmental conditions. On the other hand, as laser trackers are today very used in industrial applications aimed at collecting data at high speed with precisions superior to +/-0.05 mm, they seem quite promising for those civil engineering applications where numerous geodetic tools, often coupled with mechanical and electrical instruments, are usually used to inspect structure movements. This work illustrates three real civil engineering monitoring applications where laser tracking technology was used to detect object movements. The first one is a laboratory testing for the inspection of a beam (bending moment and shear). The second experiment is the stability inspection of a bridge. The last experiment is one of the first attempts where laser trackers tried to substitute traditional high precision geometric leveling for monitoring an important historical building: the Cathedral of Milan. The achieved results, pro and contra along with some practical issues are described.

  9. Determination of ion track radii in amorphous matrices via formation of nano-clusters by ion-beam irradiation

    SciTech Connect

    Buljan, M.; Karlusic, M.; Bogdanovic-Radovic, I.; Jaksic, M.; Radic, N.; Salamon, K.; Bernstorff, S.

    2012-09-03

    We report on a method for the determination of ion track radii, formed in amorphous materials by ion-beam irradiation. The method is based on the addition to an amorphous matrix of a small amount of foreign atoms, which easily diffuse and form clusters when the temperature is sufficiently increased. The irradiation causes clustering of these atoms, and the final separations of the formed clusters are dependent on the parameters of the ion-beam. Comparison of the separations between the clusters that are formed by ions with different properties in the same type of material enables the determination of ion-track radii.

  10. Determination of ion track radii in amorphous matrices via formation of nano-clusters by ion-beam irradiation

    NASA Astrophysics Data System (ADS)

    Buljan, M.; Karlušić, M.; Bogdanović-Radović, I.; Jakšić, M.; Salamon, K.; Bernstorff, S.; Radić, N.

    2012-09-01

    We report on a method for the determination of ion track radii, formed in amorphous materials by ion-beam irradiation. The method is based on the addition to an amorphous matrix of a small amount of foreign atoms, which easily diffuse and form clusters when the temperature is sufficiently increased. The irradiation causes clustering of these atoms, and the final separations of the formed clusters are dependent on the parameters of the ion-beam. Comparison of the separations between the clusters that are formed by ions with different properties in the same type of material enables the determination of ion-track radii.

  11. Lateral charge transport from heavy-ion tracks in integrated circuit chips

    NASA Technical Reports Server (NTRS)

    Zoutendyk, J. A.; Schwartz, H. R.; Nevill, L. R.

    1988-01-01

    A 256K DRAM has been used to study the lateral transport of charge (electron-hole pairs) induced by direct ionization from heavy-ion tracks in an IC. The qualitative charge transport has been simulated using a two-dimensional numerical code in cylindrical coordinates. The experimental bit-map data clearly show the manifestation of lateral charge transport in the creation of adjacent multiple-bit errors from a single heavy-ion track. The heavy-ion data further demonstrate the occurrence of multiple-bit errors from single ion tracks with sufficient stopping power. The qualitative numerical simulation results suggest that electric-field-funnel-aided (drift) collection accounts for single error generated by an ion passing through a charge-collecting junction, while multiple errors from a single ion track are due to lateral diffusion of ion-generated charge.

  12. Status and Perspectives of Ion Track Electronics for Advanced Biosensing

    NASA Astrophysics Data System (ADS)

    Fink, D.; Muñoz, H. Gerardo; Alfonta, L.; Mandabi, Y.; Dias, J. F.; de Souza, C. T.; Bacakova, L. E.; Vacík, J.; Hnatowicz, V.; Kiv, A. E.; Fuks, D.; Papaleo, R. M.

    New multifunctional ion irradiation-based three-dimensional electronic structures are developed for biotechnological applications, specifically for sensing of biomaterials, bacteria and mammalian cells. This is accomplished by combined micrometric surface and nanometric bulk microstructuring of insulators (specifically of polymer foils and SiO2/Si hybride structures) by adequate ion beams. Our main goal is the production of a cheap small universal generic working platform with multifunctional properties for biomedical analysis. Surface engineering of this platform enables cell bonding and its bulk engineering enables the extraction of cell secrets, for the sake of intercepting and analyzing the biomolecules used in cell communication. The exact knowledge of the spectrum of these cell-secreted signalling molecules should enable one to identify unambiguously the cell type. This knowledge will help developing strategies for preventive quorum sensing of bacteria, with the aim of fighting bacterial infections in an ecologically secure way.

  13. Ion-ion dynamic structure factor of warm dense mixtures

    SciTech Connect

    Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; Saumon, D.

    2015-06-25

    In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ion dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.

  14. Impact of Track Structure Effects on Shielding and Dosimetry

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Cucinotta, F. A.; Schimmerling, W.; Kim, M. Y.

    1999-01-01

    Galactic cosmic rays (GCR) consisting of nuclei of all the known elements with kinetic energies extending from tens to millions of MeV pose a significant health hazard to future deep space operations. Even half of the radiation exposures expected in ISS will result from GCR components. The biological actions of these radiations are known to depend on the details of the energy deposition (not just linear energy transfer, LET, but the lateral dispersion of energy deposition about the particle track). Energy deposits in tissues are dominated by the transfer of tens to hundreds of eV to the tissue's atomic electrons. In the case of low LET radiations, the collisions are separated by large dimensions compared to the size of important biomolecular structures. If such events are also separated in time, then the radiation adds little to the background of radicals occurring from ordinary metabolic processes and causes little or no biological injury. Hence, dose rate is a strong determinant of the action of low LET exposures. The GCR exposures are dominated by ions of high charge and energy (HZE) characterized by many collisions with atomic electrons over biomolecular dimensions, resulting in high radical- density events associated with a few isolated ion paths through the cell and minimal dose rate dependence at ordinary exposure levels. The HZE energy deposit declines quickly laterally and merges with the background radical density in the track periphery for which the exact lateral distribution of the energy deposit is the determinant of the biological injury. Although little data exists on human exposures from HZE radiations, limited studies in mice and mammalian cell cultures allow evaluation of the effects of track structure on shield attenuation properties and evaluation of implications for dosimetry. The most complete mammalian cell HZE exposure data sets have been modeled including the C3H10T1/2 survival and transformation data of Yang et al., the V79 survival and

  15. Ion-ion dynamic structure factor of warm dense mixtures

    DOE PAGES

    Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

    2015-06-25

    In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

  16. Doping of 20 MeV fullerene ion tracks in polyimide

    NASA Astrophysics Data System (ADS)

    Fink, D.; Vacik, J.; Klett, R.; Chadderton, L. T.; Hnatowicz, V.

    1996-12-01

    Thin polymide foils were irradiated with 20 MeV C 60+ ions and subsequently doped with aqueous LiCl solution. The depth distributions of the dopant uptake were then recorded with the neutron depth profiling technique. In contrast to the doping of tracks of single-atomic ions or of small cluster ions, the dopant distribution extends far beyond the single-atomic ion range, indicating that some new secondary effects show up here. These may be attributed to the enhancement of cluster ion ranges in comparison to single-atomic ones [1,2], and additionally to the formation of micro- or nanocracks. The shapes of the dopant distributions are rather independent from the ion fluence, which indicates that the observed overrange effects are a peculiarity of individual fullerene ion tracks, and not just a high fluence effect for overlapping tracks. The total amount of dopant uptake increases with fluence. It scales with the total deposited energy density in a similar way as does the dopant uptake in tracks of single-atomic ions or of small cluster ions. First results with 30 MeV C 60+ ions reconfirm these findings.

  17. Heavy ion tracks in polycarbonate. Comparison with a heavy ion irradiated model compound (diphenyl carbonate)

    NASA Astrophysics Data System (ADS)

    Ferain, E.; Legras, R.

    1993-09-01

    The chemical modifications induced by energetic heavy ion irradiation of polycarbonate (PC) film are determined by GPC, HPLC, ESR, TGA, IR and UV spectrophotometry. The main results of the irradiation are creation of radicals, chain scission, cross-linking and appearance of new chemical groups in the main polymer chain. As far as the creation of new groups is concerned, they are determined by means of a model compound of PC: the diphenyl carbonate (DPC). The following compounds are identified after energetic heavy ion irradiation of DPC: salicylic acid, phenol, 4,4'-biphenol, 2,4'-biphenol, 2,2'-biphenol, 4-phenoxyphenol, 2-phenoxyphenol, phenyl ether, phenyl benzoate, phenyl salicylate, 2-phenylphenol and 2-phenoxyphenyl benzoate. A similarity between the heavy ion irradiation and a heat treatment has also been established with DPC. On the basis of these results, we try to give an explanation of the preferential attack along the tracks of the irradiated film. Also, an explanation of the well-known beneficial effect of an UV exposition of the irradiated film on the selectivity of this preferential chemical attack is suggested.

  18. Characterization of multiple-bit errors from single-ion tracks in integrated circuits

    NASA Technical Reports Server (NTRS)

    Zoutendyk, J. A.; Edmonds, L. D.; Smith, L. S.

    1989-01-01

    The spread of charge induced by an ion track in an integrated circuit and its subsequent collection at sensitive nodal junctions can cause multiple-bit errors. The authors have experimentally and analytically investigated this phenomenon using a 256-kb dynamic random-access memory (DRAM). The effects of different charge-transport mechanisms are illustrated, and two classes of ion-track multiple-bit error clusters are identified. It is demonstrated that ion tracks that hit a junction can affect the lateral spread of charge, depending on the nature of the pull-up load on the junction being hit. Ion tracks that do not hit a junction allow the nearly uninhibited lateral spread of charge.

  19. On the threshold for ion track formation in CaF2

    NASA Astrophysics Data System (ADS)

    Karlušić, M.; Ghica, C.; Negrea, R. F.; Siketić, Z.; Jakšić, M.; Schleberger, M.; Fazinić, S.

    2017-02-01

    There is an ongoing debate regarding the mechanism of swift heavy ion (SHI) track formation in CaF2. The objective of this study is to shed light on this important topic using a range of complementary experimental techniques. Evidence of the threshold for ion track formation being below 3 keV nm‑1 is provided by both transmission electron microscopy (TEM) and Rutherford backscattering spectroscopy in the channelling mode, which has direct consequences for the validity of models describing the response of CaF2 to SHI irradiation. Furthermore, information about the elemental composition within the ion tracks is obtained using scanning TEM, electron energy loss spectroscopy, and with respect to the stoichiometry of the materials surface by in situ time of flight elastic recoil detection analysis. Advances in the analyses of the experimental data presented here pave the way for a better understanding of the ion track formation.

  20. Irradiation of nuclear track emulsions with thermal neutrons, heavy ions, and muons

    SciTech Connect

    Artemenkov, D. A. Bradnova, V.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.; Kattabekov, R. R.; Mamatkulov, K. Z.; Rusakova, V. V.

    2015-07-15

    Exposures of test samples of nuclear track emulsion were analyzed. Angular and energy correlations of products originating from the thermal-neutron-induced reaction n{sub th} +{sup 10} B → {sup 7} Li + (γ)+ α were studied in nuclear track emulsions enriched in boron. Nuclear track emulsions were also irradiated with {sup 86}Kr{sup +17} and {sup 124}Xe{sup +26} ions of energy about 1.2 MeV per nucleon. Measurements of ranges of heavy ions in nuclear track emulsionsmade it possible to determine their energies on the basis of the SRIM model. The formation of high-multiplicity nuclear stars was observed upon irradiating nuclear track emulsions with ultrarelativistic muons. Kinematical features studied in this exposure of nuclear track emulsions for events of the muon-induced splitting of carbon nuclei to three alpha particles are indicative of the nucleardiffraction interaction mechanism.

  1. Ion tracks developed in polyimide resist on Si wafers as template for nanowires

    NASA Astrophysics Data System (ADS)

    Skupinski, Marek; Toulemonde, Marcel; Lindeberg, Mikael; Hjort, Klas

    2005-11-01

    Ion track technology makes it possible to produce low-cost templates for nanowires. In this study we have studied ion tracks in a polyimide resist on silicon. Spin coated, 1.5 μm thick polyimide resist on 4 in. Si wafers was irradiated by 129Xe27+ ions at low fluence. The irradiated resist was etched in sodium hypochlorite (NaClO) solution, and Ni nanowires were electroplated in the pores. Using scanning electron microscopy observations the ion track etch properties were obtained. The linear track etch rate of 0.6-1.0 μm/min was calculated from the conical aspect ratio of the nanowire, and from the pore diameter at the surface at different etch times the bulk etch rate in the halo at a distance longer than 5 nm from the ion axis was found to be 0.3 nm/min, while at a long distance from the ion axis the track etching velocity of the virgin material was 0.01 nm/min. Taking into account the big difference in the track etch velocity between the latent track and the material outside, a latent track diameter of 11 nm could be estimated. Such a diameter value is in good agreement with a prediction obtained from an inelastic thermal spike model. Furthermore, fabrication of 1.5 μm long magnetoresistive nanowires electroplated in ion tracks in the IC compatible polyimide resist may be a way to develop low-cost CMOS integrated magnetoresistive sensors.

  2. Tracking of Ions Produced at Near Barrier Energies in Nuclear Reactions

    SciTech Connect

    Shapira, Dan

    2010-01-01

    Examples of detectors, presently in use, for tracking products from nuclear reactions induced by radioactive ion beams are described. A new tracking detector is being designed to study the binary products from reactions induced by heavy neutron-rich radioactive ion beams on heavy neutron-rich target nuclei. The motivation for such studies and the features designed to accomplish this goal will be presented.

  3. Structure tracking aided design and synthesis of Li3V2(PO4)3 nanocrystals as high-power cathodes for lithium ion batteries

    SciTech Connect

    Wang, Liping; Bai, Jianming; Gao, Peng; Wang, Xiaoya; Looney, J. Patrick; Wang, Feng

    2015-07-30

    In this study, preparing new electrode materials with synthetic control of phases and electrochemical properties is desirable for battery applications but hardly achievable without knowing how the synthesis reaction proceeds. Herein, we report on structure tracking-aided design and synthesis of single-crystalline Li3V2(PO4)3 (LVP) nanoparticles with extremely high rate capability. A comprehensive investigation was made to the local structural orderings of the involved phases and their evolution toward forming LVP phase using in situ/ex situ synchrotron X-ray and electron-beam diffraction, spectroscopy, and imaging techniques. The results shed light on the thermodynamics and kinetics of synthesis reactions and enabled the design of a cost-efficient synthesis protocol to make nanocrystalline LVP, wherein solvothermal treatment is a crucial step leading to an amorphous intermediate with local structural ordering resembling that of LVP, which, upon calcination at moderate temperatures, rapidly transforms into the desired LVP phase. The obtained LVP particles are about 50 nm, coated with a thin layer of amorphous carbon and featured with excellent cycling stability and rate capability – 95% capacity retention after 200 cycles and 66% theoretical capacity even at a current rate of 10 C. The structure tracking based method we developed in this work offers a new way of designing battery electrodes with synthetic control of material phases and properties.

  4. Kinetics of Electrons from Plasma Discharge in a Latent Track Region Induced by Swift Heavy ION Irradiation

    NASA Astrophysics Data System (ADS)

    Minárik, Stanislav

    2015-08-01

    While passing swift heavy ion through a material structure, it produces a region of radiation affected material which is known as a "latent track". Scattering motions of electrons interacting with a swift heavy ion are dominant in the latent track region. These phenomena include the electron impurity and phonon scattering processes modified by the interaction with the ion projectile as well as the Coulomb scattering between two electrons. In this paper, we provide detailed derivation of a 3D Boltzmann scattering equation for the description of the relative scattering motion of such electrons. Phase-space distribution function for this non-equilibrioum system of scattering electrons can be found by the solution of mentioned equation.

  5. Distributions of deposited energy and ionization clusters around ion tracks studied with Geant4 toolkit.

    PubMed

    Burigo, Lucas; Pshenichnov, Igor; Mishustin, Igor; Hilgers, Gerhard; Bleicher, Marcus

    2016-05-21

    The Geant4-based Monte Carlo model for Heavy-Ion Therapy (MCHIT) was extended to study the patterns of energy deposition at sub-micrometer distance from individual ion tracks. Dose distributions for low-energy (1)H, (4)He, (12)C and (16)O ions measured in several experiments are well described by the model in a broad range of radial distances, from 0.5 to 3000 nm. Despite the fact that such distributions are characterized by long tails, a dominant fraction of deposited energy (∼80%) is confined within a radius of about 10 nm. The probability distributions of clustered ionization events in nanoscale volumes of water traversed by (1)H, (2)H, (4)He, (6)Li, (7)Li, and (12)C ions are also calculated. A good agreement of calculated ionization cluster-size distributions with the corresponding experimental data suggests that the extended MCHIT can be used to characterize stochastic processes of energy deposition to sensitive cellular structures.

  6. Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

    NASA Technical Reports Server (NTRS)

    Edmonds, Larry D.

    1991-01-01

    The theoretical analysis presented indicates that Auger recombination can reduce charge collection from very dense ion tracks in silicon devices. It is of marginal importance for tracks produced by 270-MeV krypton, and therefore it is of major importance for ions exhibiting a significantly larger loss. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a nonzero limiting value as t approaches infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

  7. Effect of Track Potentials on the Movement of Secondary Electrons due to Irradiation of Heavy Ions

    NASA Astrophysics Data System (ADS)

    Moribayashi, Kengo

    2017-02-01

    This paper quantitatively discusses the effect of positive nuclear track potentials on the motion of secondary electrons due to heavy-ion irradiation using a simulation model. This model reproduces the tendency of measurement of the number of secondary electrons. Using this model, physical phenomena can be treated closer to reality than those using the conventional models. Here, the track potential is defined as the potential formed from the electric field near the track of a heavy ion. This effect is expected to be given as functions of not only the mean paths (τ) between incident ion impact ionization events but also the average initial secondary electron energies. The results shown in this paper indicate that the effect of the track potential is mainly determined by τ.

  8. Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

    NASA Technical Reports Server (NTRS)

    Edmonds, Larry D.

    1991-01-01

    A recombination mechanism that significantly reduces charge collection from very dense ion tracks in silicon devices was postulated by Zoutendyk et al. The theoretical analysis presented here concludes that Auger recombination is such a mechanism and is of marginal importance for higher density tracks produced by 270-MeV krypton, but of major importance for higher density tracks. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a non-zero limiting value as t yields infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

  9. SAXS study on the morphology of etched and un-etched ion tracks in apatite

    NASA Astrophysics Data System (ADS)

    Nadzri, A.; Schauries, D.; Afra, B.; Rodriguez, M. D.; Mota-Santiago, P.; Muradoglu, S.; Hawley, A.; Kluth, P.

    2015-04-01

    Natural apatite samples were irradiated with 185 MeV Au and 2.3 GeV Bi ions to simulate fission tracks. The resulting track morphology was investigated using synchrotron small angle x-ray scattering (SAXS) measurements before and after chemical etching. We present preliminary results from the SAXS measurement showing the etching process is highly anisotropic yielding faceted etch pits with a 6-fold symmetry. The measurements are a first step in gaining new insights into the correlation between etched and unetched fission tracks and the use of SAXS as a tool for studying etched tracks.

  10. Production and distribution of aberrations in resting or cycling human lymphocytes following Fe-ion or Cr-ion irradiation: Emphasis on single track effects

    NASA Astrophysics Data System (ADS)

    Deperas-Standylo, Joanna; Lee, Ryonfa; Nasonova, Elena; Ritter, Sylvia; Gudowska-Nowak, Ewa

    2012-09-01

    In the present study we examined the cytogenetic effects of 177 MeV/u Fe-ions (LET = 335 keV/μm) and 4.1 MeV/u Cr-ions (LET = 3160 keV/μm) in human lymphocytes under exposure conditions that result on average in one particle hit per cell nucleus. In non-cycling (G0-phase) lymphocytes the induction and the repair of excess fragments was measured by means of the premature chromosome condensation (PCC) technique and the distribution of breaks among cells was analysed. The PCC-data were further compared with those reported recently for stimulated lymphocytes at the first post-irradiation mitosis. Our experiments show that a single nuclear traversal by a Fe-ion produced more initial chromatin breakage than one Cr-ion, but after 24 h of repair the number of excess fragments/cell was similar for both ion species. All distributions of aberrations were overdispersed. For low energy Cr-ions, where the track radius is smaller than the radius of the cell nucleus, the data could be well described by a Neyman type A distribution. In contrast, the data obtained for high energy Fe-ions were fitted with a convoluted Poisson-Neyman distribution to account for the fact that the dose is deposited not only in the cell actually traversed but also in neighbouring cells. By applying metaphase analysis a different picture emerged with respect to the aberration yield, i.e. more aberrations were detected in cells exposed to Fe-ions than in those irradiated with Cr-ions. Yet, as observed for non-cycling lymphocytes all aberration distributions generated for metaphase cells were overdispersed. The obtained results are discussed with respect to differences in particle track structure. Additionally, the impact of confounding factors such as apoptosis that affect the number of aberrations expressed in a cell population is addressed.

  11. Track lengths of energetic 132Xe ions in CR-39 detectors

    NASA Astrophysics Data System (ADS)

    Ghosh, S.; Raju, J.; Dwivedi, K. K.

    1994-06-01

    Studies of particle tracks in solids have wide ranging applications in many diverse fields of science and technology. Most of these studies require a precise knowledge of heavy ion track lengths or ranges in various knowledge of heavy ion track lengths or ranges in various commonly used solid dielectrics. We have measured the maximum etchable track lengths of 132Xe at 12 different energies ranging from 5.8 MeV/u to 17.0 MeV/u in CR-39 (Homalite). The ion beam with an initial energy of 17.0 MeV/u was degraded by aluminium foils of different thickness. The detectors were irradiated at an angle of 45° to the beam direction and were etched for a period of 2?6 hrs in 6N NaOH at 55°C to reveal the tracks. The track lengths were measured using an optical microscope and the maximum etchable track lengths were determined. The standard deviations have been evaluated and the experimental results are compared with theoretical values obtained from computer codes ?RANGE? and ?TRIM? and the program of Henke and Benton.

  12. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    PubMed Central

    2015-01-01

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radiofrequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radiofrequency (RF) “rung” electrodes, bordered by DC “guard” electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be “soft” in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply static or transient electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling high quality ion mobility separations. PMID:25152178

  13. Swift heavy ion irradiation of InP: Thermal spike modeling of track formation

    SciTech Connect

    Kamarou, A.; Wesch, W.; Wendler, E.; Undisz, A.; Rettenmayr, M.

    2006-05-01

    Irradiation of single-crystalline InP with swift heavy ions (SHI's) causes the formation of ion tracks for certain irradiation temperatures if the electronic energy deposition exceeds a threshold value. With increasing SHI fluence, more and more ion tracks are formed, until a continuous amorphous layer is produced due to the multiple overlapping of the tracks at high ion fluences. Single-crystalline InP samples were irradiated either at liquid nitrogen temperature (LNT) or at room temperature (RT) with Kr, Xe, or Au ions with specific energies ranging from ca. 0.3 to 3.0 MeV/u. Afterwards, the samples were investigated by means of Rutherford backscattering spectrometry and transmission electron microscopy in the plan-view and cross-section geometry. We show that the experimental data obtained can be qualitatively and quantitatively described on the basis of the inelastic thermal spike (TS) model, which was originally used only for metallic targets. The presented extension of the TS model on semiconductors covers mainly the very first stage of the energy transfer from SHI's (so-called 'ionization spikes'). Our results show that the extended TS model offers a self-consistent way to explain the influence of various irradiation conditions (ion mass, ion energy, irradiation temperature, etc.) on the ion track formation and damage accumulation in InP and, therefore, can make a contribution to a better understanding of the underlying mechanisms. Further, our results prejudice the amenity of a single value of the threshold electronic energy loss as a fundamental quantity that is commonly used for the description of track formation in solids irradiated with different ion species. There is no universal RT threshold for track formation in InP, but it is noticeably higher for lighter ions (12.0 and 14.8 keV/nm for RT irradiations with Au and Xe, respectively). Our experimental and simulation results support the idea that the formation of visible tracks requires a predamaging

  14. Swift heavy ion irradiation of InP: Thermal spike modeling of track formation

    NASA Astrophysics Data System (ADS)

    Kamarou, A.; Wesch, W.; Wendler, E.; Undisz, A.; Rettenmayr, M.

    2006-05-01

    Irradiation of single-crystalline InP with swift heavy ions (SHI’s) causes the formation of ion tracks for certain irradiation temperatures if the electronic energy deposition exceeds a threshold value. With increasing SHI fluence, more and more ion tracks are formed, until a continuous amorphous layer is produced due to the multiple overlapping of the tracks at high ion fluences. Single-crystalline InP samples were irradiated either at liquid nitrogen temperature (LNT) or at room temperature (RT) with Kr, Xe, or Au ions with specific energies ranging from ca. 0.3to3.0MeV/u . Afterwards, the samples were investigated by means of Rutherford backscattering spectrometry and transmission electron microscopy in the plan-view and cross-section geometry. We show that the experimental data obtained can be qualitatively and quantitatively described on the basis of the inelastic thermal spike (TS) model, which was originally used only for metallic targets. The presented extension of the TS model on semiconductors covers mainly the very first stage of the energy transfer from SHI’s (so-called “ionization spikes”). Our results show that the extended TS model offers a self-consistent way to explain the influence of various irradiation conditions (ion mass, ion energy, irradiation temperature, etc.) on the ion track formation and damage accumulation in InP and, therefore, can make a contribution to a better understanding of the underlying mechanisms. Further, our results prejudice the amenity of a single value of the threshold electronic energy loss as a fundamental quantity that is commonly used for the description of track formation in solids irradiated with different ion species. There is no universal RT threshold for track formation in InP, but it is noticeably higher for lighter ions (12.0 and 14.8keV/nm for RT irradiations with Au and Xe, respectively). Our experimental and simulation results support the idea that the formation of visible tracks requires a

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

    PubMed

    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

    2016-10-12

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. More Ions for Radiotherapy: About Treatment Planning and Track Simulations

    NASA Astrophysics Data System (ADS)

    Krämer, M.

    2017-03-01

    In the recent years, irradiation with swift light ions - from protons up to oxygen -has become an established method in tumour radiotherapy.A prerequisite for successful treatment is the sufficient knowledge of physical and radiobiological processes down to the microscopic or even nanoscopic scale. This report summarizes recent developments. In particular the application of ions other than protons and carbon will be addressed, as well as modelling approaches on the nanoscale.

  18. Fluence-based dosimetry of proton and heavier ion beams using single track detectors

    NASA Astrophysics Data System (ADS)

    Klimpki, G.; Mescher, H.; Akselrod, M. S.; Jäkel, O.; Greilich, S.

    2016-02-01

    Due to their superior spatial resolution, small and biocompatible fluorescent nuclear track detectors (FNTDs) open up the possibility of characterizing swift heavy charged particle fields on a single track level. Permanently stored spectroscopic information such as energy deposition and particle field composition is of particular importance in heavy ion radiotherapy, since radiation quality is one of the decisive predictors for clinical outcome. Findings presented within this paper aim towards single track reconstruction and fluence-based dosimetry of proton and heavier ion fields. Three-dimensional information on individual ion trajectories through the detector volume is obtained using fully automated image processing software. Angular distributions of multidirectional fields can be measured accurately within  ±2° uncertainty. This translates into less than 5% overall fluence deviation from the chosen irradiation reference. The combination of single ion tracking with an improved energy loss calibration curve based on 90 FNTD irradiations with protons as well as helium, carbon and oxygen ions enables spectroscopic analysis of a detector irradiated in Bragg peak proximity of a 270 MeV u-1 carbon ion field. Fluence-based dosimetry results agree with treatment planning software reference.

  19. Fluorescent tracking of nickel ions in human cultured cells

    SciTech Connect

    Ke Qingdong; Davidson, Todd; Kluz, Thomas; Oller, Adriana; Costa, Max . E-mail: costam01@nyu.edu

    2007-02-15

    The carcinogenic activity of various nickel (Ni) compounds is likely dependent upon their ability to enter cells and elevate intracellular levels of Ni ions. Water-insoluble Ni compounds such as NiS and Ni{sub 3}S{sub 2} were shown in vitro to enter cells by phagocytosis and potently induce tumors in experimental animals at the site of exposure. These water-insoluble nickel compounds are generally considered to be more potent carcinogens than the water-soluble forms. However, recent in vitro studies have shown similar effects for insoluble and soluble Ni compounds. Using a dye that fluoresces when intracellular Ni ion binds to it, we showed that both soluble and insoluble Ni compounds were able to elevate the levels of Ni ions in the cytoplasmic and nuclear compartments. However, when the source of Ni ions was removed from the culture dish, the intracellular Ni ions derived from soluble Ni compound were lost from the cells at a significantly faster rate than those derived from the insoluble Ni compound. Within 10 h after NiCl{sub 2} removal from the culture medium, Ni ions disappeared from the nucleus and were not detected in the cells by 16 h, while insoluble Ni{sub 3}S{sub 2} yielded Ni ions that persisted in the nucleus after 16 h and were detected in the cytoplasm even after 24 h following Ni removal. These effects are discussed in terms of whole body exposure to water-soluble and -insoluble Ni compounds and consistency with animal carcinogenicity studies.

  20. Growth of potassium iodide single-crystals using ion track membranes as templates

    NASA Astrophysics Data System (ADS)

    Dobrev, D.; Vetter, J.; Neumann, R.

    1998-12-01

    A principle possibility is demonstrated to apply the ion track membranes as a template for the crystallization of inorganic salts. As an example, potassium iodide has been grown in a matrix of etched ion tracks produced in polycarbonate foils. Arrays of stable free-standing cylindrical microcolumns are observed after dissolution of the organic matrix. They represent single crystals oriented with their <1 0 0> or <1 1 0> crystallographic directions along the cylinder axes. Possible ways to govern their predominant orientations are briefly discussed.

  1. Ion beams in radiotherapy - from tracks to treatment planning

    NASA Astrophysics Data System (ADS)

    Krämer, M.; Scifoni, E.; Wälzlein, C.; Durante, M.

    2012-07-01

    Several dozen clinical sites around the world apply beams of fast light ions for radiotherapeutical purposes. Thus there is a vested interest in the various physical and radiobiological processes governing the interaction of ion beams with matter, specifically living systems. We discuss the various modelling steps which lead from basic interactions to the application in actual patient treatment planning. The nano- and microscopic scale is covered by sample calculations with our TRAX code. On the macroscopic scale we feature the TRiP98 treatment planning system, which was clinically used in GSI's radiotherapy pilot project.

  2. Cosmic heavy ion tracks in mesoscopic biological test objects

    SciTech Connect

    Facius, R.

    1994-12-31

    Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on `HZE particle effects in manned spaced flight`, it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to `large` fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too (`The BIOSTACK as an approach to high LET radiation research`), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions` trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series.

  3. Track Structure and the Biological Effectiveness of Accelerated Particles for the Induction of Chromosome Damage

    NASA Technical Reports Server (NTRS)

    George, K.; Hada, M.; Chappell, L.; Cucinotta, F. A.

    2011-01-01

    Track structure models predict that at a fixed value of LET, particles with lower charge number, Z will have a higher biological effectiveness compared to particles with a higher Z. In this report we investigated how track structure effects induction of chromosomal aberration in human cells. Human lymphocytes were irradiated in vitro with various energies of accelerated iron, silicon, neon, or titanium ions and chromosome damage was assessed in using three color FISH chromosome painting in chemically induced PCC samples collected a first cell division post irradiation. The LET values for these ions ranged from 30 to195 keV/micron. Of the particles studied, Neon ions have the highest biological effectiveness for induction of total chromosome damage, which is consistent with track structure model predictions. For complex-type exchanges 64 MeV/ u Neon and 450 MeV/u Iron were equally effective and induced the most complex damage. In addition we present data on chromosomes exchanges induced by six different energies of protons (5 MeV/u to 2.5 GeV/u). The linear dose response term was similar for all energies of protons suggesting that the effect of the higher LET at low proton energies is balanced by the production of nuclear secondaries from the high energy protons.

  4. SAXS investigations of the morphology of swift heavy ion tracks in α-quartz.

    PubMed

    Afra, B; Rodriguez, M D; Trautmann, C; Pakarinen, O H; Djurabekova, F; Nordlund, K; Bierschenk, T; Giulian, R; Ridgway, M C; Rizza, G; Kirby, N; Toulemonde, M; Kluth, P

    2013-01-30

    The morphology of swift heavy ion tracks in crystalline α-quartz was investigated using small angle x-ray scattering (SAXS), molecular dynamics (MD) simulations and transmission electron microscopy. Tracks were generated by irradiation with heavy ions with energies between 27 MeV and 2.2 GeV. The analysis of the SAXS data indicates a density change of the tracks of ~2 ± 1% compared to the surrounding quartz matrix for all irradiation conditions. The track radii only show a weak dependence on the electronic energy loss at values above 17 keV nm(-1), in contrast to values previously reported from Rutherford backscattering spectrometry measurements and expectations from the inelastic thermal spike model. The MD simulations are in good agreement at low energy losses, yet predict larger radii than SAXS at high ion energies. The observed discrepancies are discussed with respect to the formation of a defective halo around an amorphous track core, the existence of high stresses and/or the possible presence of a boiling phase in quartz predicted by the inelastic thermal spike model.

  5. Latent tracks and associated strain in Al2O3 irradiated with swift heavy ions

    NASA Astrophysics Data System (ADS)

    O'Connell, J. H.; Rymzhanov, R. A.; Skuratov, V. A.; Volkov, A. E.; Kirilkin, N. S.

    2016-05-01

    The morphology of latent ion tracks induced by high energy heavy ions in Al2O3 was investigated using a combination of high resolution transmission electron microscopy (HRTEM), exit wave reconstruction, geometric phase analysis and numerical simulations. Single crystal α-Al2O3 crystals were irradiated with 167 MeV Xe ions along the c-axis to fluences between 1 × 1010 and 1 × 1013 cm-2. Planar TEM lamella were prepared by focused ion beam (FIB) and geometrical phase analysis was performed on the phase image of the reconstructed complex electron wave at the specimen exit surface in order to estimate the latent strain around individual track cores. In addition to the experimental data, the material excitation in a SHI track was numerically simulated by combining Monte-Carlo code, describing the excitation of the electronic subsystem, with classical molecular dynamics of the lattice atoms. Experimental and simulation data both showed that the relaxation of the excess lattice energy results in the formation of a cylinder-like disordered region of about 4 nm in diameter consisting of an underdense core surrounded by an overdense shell. Modeling of the passage of a second ion in the vicinity of this disordered region revealed that this damaged area can be restored to a near damage free state. The estimation of a maximal effective distance of recrystallization between the ion trajectories yields values of about 6-6.5 nm which are of the same order of magnitude as those estimated from the saturation density of latent ion tracks detected by TEM.

  6. Impact of time and space evolution of ion tracks in nonvolatile memory cells approaching nanoscale

    SciTech Connect

    Cellere, G.; Paccagnella, A.; Harboe-Sorensen, R.; Visconti, A.; Bonanomi, M.

    2010-12-15

    Swift heavy ions impacting on matter lose energy through the creation of dense tracks of charges. The study of the space and time evolution of energy exchange allows understanding the single event effects behavior in advanced microelectronic devices. In particular, the shrinking of minimum feature size of most advanced memory devices makes them very interesting test vehicles to study these effects since the device and the track dimensions are comparable; hence, measured effects are directly correlated with the time and space evolution of the energy release. In this work we are studying the time and space evolution of ion tracks by using advanced non volatile memories and Monte Carlo simulations. Experimental results are very well explained by the theoretical calculations.

  7. Non-invasive monitoring of therapeutic carbon ion beams in a homogeneous phantom by tracking of secondary ions.

    PubMed

    Gwosch, K; Hartmann, B; Jakubek, J; Granja, C; Soukup, P; Jäkel, O; Martišíková, M

    2013-06-07

    Radiotherapy with narrow scanned carbon ion beams enables a highly accurate treatment of tumours while sparing the surrounding healthy tissue. Changes in the patient's geometry can alter the actual ion range in tissue and result in unfavourable changes in the dose distribution. Consequently, it is desired to verify the actual beam delivery within the patient. Real-time and non-invasive measurement methods are preferable. Currently, the only technically feasible method to monitor the delivered dose distribution within the patient is based on tissue activation measurements by means of positron emission tomography (PET). An alternative monitoring method based on tracking of prompt secondary ions leaving a patient irradiated with carbon ion beams has been previously suggested. It is expected to help in overcoming the limitations of the PET-based technique like physiological washout of the beam induced activity, low signal and to allow for real-time measurements. In this paper, measurements of secondary charged particle tracks around a head-sized homogeneous PMMA phantom irradiated with pencil-like carbon ion beams are presented. The investigated energies and beam widths are within the therapeutically used range. The aim of the study is to deduce properties of the primary beam from the distribution of the secondary charged particles. Experiments were performed at the Heidelberg Ion Beam Therapy Center, Germany. The directions of secondary charged particles emerging from the PMMA phantom were measured using an arrangement of two parallel pixelated silicon detectors (Timepix). The distribution of the registered particle tracks was analysed to deduce its dependence on clinically important beam parameters: beam range, width and position. Distinct dependencies of the secondary particle tracks on the properties of the primary carbon ion beam were observed. In the particular experimental set-up used, beam range differences of 1.3 mm were detectable. In addition, variations in

  8. Monte-Carlo Simulation of Radiation Track Structure and Calculation of Dose Deposition in Nanovolumes

    NASA Technical Reports Server (NTRS)

    Plante, I.; Cucinotta, F. A.

    2010-01-01

    INTRODUCTION: The radiation track structure is of crucial importance to understand radiation damage to molecules and subsequent biological effects. Of a particular importance in radiobiology is the induction of double-strand breaks (DSBs) by ionizing radiation, which are caused by clusters of lesions in DNA, and oxidative damage to cellular constituents leading to aberrant signaling cascades. DSB can be visualized within cell nuclei with gamma-H2AX experiments. MATERIAL AND METHODS: In DSB induction models, the DSB probability is usually calculated by the local dose obtained from a radial dose profile of HZE tracks. In this work, the local dose imparted by HZE ions is calculated directly from the 3D Monte-Carlo simulation code RITRACKS. A cubic volume of 5 micron edge (Figure 1) is irradiated by a (Fe26+)-56 ion of 1 GeV/amu (LET approx.150 keV/micron) and by a fluence of 450 H+ ions, 300 MeV/amu (LET approx. 0.3 keV/micron). In both cases, the dose deposited in the volume is approx.1 Gy. The dose is then calculated into each 3D pixels (voxels) of 20 nm edge and visualized in 3D. RESULTS AND DISCUSSION: The dose is deposited uniformly in the volume by the H+ ions. The voxels which receive a high dose (orange) corresponds to electron track ends. The dose is deposited differently by the 56Fe26+ ion. Very high dose (red) is deposited in voxels with direct ion traversal. Voxels with electron track ends (orange) are also found distributed around the path of the track. In both cases, the appearance of the dose distribution looks very similar to DSBs seen in gammaH2AX experiments, particularly when the visualization threshold is applied. CONCLUSION: The refinement of the dose calculation to the nanometer scale has revealed important differences in the energy deposition between high- and low-LET ions. Voxels of very high dose are only found in the path of high-LET ions. Interestingly, experiments have shown that DSB induced by high-LET radiation are more difficult to

  9. Tracking Non-rigid Structures in Computer Simulations

    SciTech Connect

    Gezahegne, A; Kamath, C

    2008-01-10

    A key challenge in tracking moving objects is the correspondence problem, that is, the correct propagation of object labels from one time step to another. This is especially true when the objects are non-rigid structures, changing shape, and merging and splitting over time. In this work, we describe a general approach to tracking thousands of non-rigid structures in an image sequence. We show how we can minimize memory requirements and generate accurate results while working with only two frames of the sequence at a time. We demonstrate our results using data from computer simulations of a fluimix problem.

  10. Relative Displacement Method for Track-Structure Interaction

    PubMed Central

    Ramos, Óscar Ramón; Pantaleón, Marcos J.

    2014-01-01

    The track-structure interaction effects are usually analysed with conventional FEM programs, where it is difficult to implement the complex track-structure connection behaviour, which is nonlinear, elastic-plastic and depends on the vertical load. The authors developed an alternative analysis method, which they call the relative displacement method. It is based on the calculation of deformation states in single DOF element models that satisfy the boundary conditions. For its solution, an iterative optimisation algorithm is used. This method can be implemented in any programming language or analysis software. A comparison with ABAQUS calculations shows a very good result correlation and compliance with the standard's specifications. PMID:24634610

  11. Structural measures to track the evolution of SNOMED CT hierarchies.

    PubMed

    Wei, Duo; Helen Gu, Huanying; Perl, Yehoshua; Halper, Michael; Ochs, Christopher; Elhanan, Gai; Chen, Yan

    2015-10-01

    The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is an extensive reference terminology with an attendant amount of complexity. It has been updated continuously and revisions have been released semi-annually to meet users' needs and to reflect the results of quality assurance (QA) activities. Two measures based on structural features are proposed to track the effects of both natural terminology growth and QA activities based on aspects of the complexity of SNOMED CT. These two measures, called the structural density measure and accumulated structural measure, are derived based on two abstraction networks, the area taxonomy and the partial-area taxonomy. The measures derive from attribute relationship distributions and various concept groupings that are associated with the abstraction networks. They are used to track the trends in the complexity of structures as SNOMED CT changes over time. The measures were calculated for consecutive releases of five SNOMED CT hierarchies, including the Specimen hierarchy. The structural density measure shows that natural growth tends to move a hierarchy's structure toward a more complex state, whereas the accumulated structural measure shows that QA processes tend to move a hierarchy's structure toward a less complex state. It is also observed that both the structural density and accumulated structural measures are useful tools to track the evolution of an entire SNOMED CT hierarchy and reveal internal concept migration within it.

  12. Structural Measures to Track the Evolution of SNOMED CT Hierarchies

    PubMed Central

    Wei, Duo; Gu, Huanying (Helen); Perl, Yehoshua; Halper, Michael; Ochs, Christopher; Elhanan, Gai; Chen, Yan

    2015-01-01

    The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is an extensive reference terminology with an attendant amount of complexity. It has been updated continuously and revisions have been released semi-annually to meet users’ needs and to reflect the results of quality assurance (QA) activities. Two measures based on structural features are proposed to track the effects of both natural terminology growth and QA activities based on aspects of the complexity of SNOMED CT. These two measures, called the structural density measure and accumulated structural measure, are derived based on two abstraction networks, the area taxonomy and the partial-area taxonomy. The measures derive from attribute relationship distributions and various concept groupings that are associated with the abstraction networks. They are used to track the trends in the complexity of structures as SNOMED CT changes over time. The measures were calculated for consecutive releases of five SNOMED CT hierarchies, including the Specimen hierarchy. The structural density measure shows that natural growth tends to move a hierarchy’s structure toward a more complex state, whereas the accumulated structural measure shows that QA processes tend to move a hierarchy’s structure toward a less complex state. It is also observed that both the structural density and accumulated structural measures are useful tools to track the evolution of an entire SNOMED CT hierarchy and reveal internal concept migration within it. PMID:26260003

  13. Cortical tracking of hierarchical linguistic structures in connected speech.

    PubMed

    Ding, Nai; Melloni, Lucia; Zhang, Hang; Tian, Xing; Poeppel, David

    2016-01-01

    The most critical attribute of human language is its unbounded combinatorial nature: smaller elements can be combined into larger structures on the basis of a grammatical system, resulting in a hierarchy of linguistic units, such as words, phrases and sentences. Mentally parsing and representing such structures, however, poses challenges for speech comprehension. In speech, hierarchical linguistic structures do not have boundaries that are clearly defined by acoustic cues and must therefore be internally and incrementally constructed during comprehension. We found that, during listening to connected speech, cortical activity of different timescales concurrently tracked the time course of abstract linguistic structures at different hierarchical levels, such as words, phrases and sentences. Notably, the neural tracking of hierarchical linguistic structures was dissociated from the encoding of acoustic cues and from the predictability of incoming words. Our results indicate that a hierarchy of neural processing timescales underlies grammar-based internal construction of hierarchical linguistic structure.

  14. Cortical Tracking of Hierarchical Linguistic Structures in Connected Speech

    PubMed Central

    Ding, Nai; Melloni, Lucia; Zhang, Hang; Tian, Xing; Poeppel, David

    2016-01-01

    The most critical attribute of human language is its unbounded combinatorial nature: smaller elements can be combined into larger structures based on a grammatical system, resulting in a hierarchy of linguistic units, e.g., words, phrases, and sentences. Mentally parsing and representing such structures, however, poses challenges for speech comprehension. In speech, hierarchical linguistic structures do not have boundaries clearly defined by acoustic cues and must therefore be internally and incrementally constructed during comprehension. Here we demonstrate that during listening to connected speech, cortical activity of different time scales concurrently tracks the time course of abstract linguistic structures at different hierarchical levels, e.g. words, phrases, and sentences. Critically, the neural tracking of hierarchical linguistic structures is dissociated from the encoding of acoustic cues as well as from the predictability of incoming words. The results demonstrate that a hierarchy of neural processing timescales underlies grammar-based internal construction of hierarchical linguistic structure. PMID:26642090

  15. Detnex Project: Dispersion, Structure and Tracking of Exotic Nuclei

    NASA Astrophysics Data System (ADS)

    Alvarez, M. A. G.; Gómez-Camacho, J.; Espino, J. M.; Mukha, I.; Martel, I.

    2007-05-01

    Since 1970's when double-folding model, based on M3Y interaction, had to be renormalized to fit the elastic scattering of weakly bound 6,7Li and 9Be nuclei, we learned that preconceptions based on the highly successful experience of the optical model on stable nuclei could not be simply extrapolated to the scattering of exotic nuclei. Recently, we have shown some evidences of long range mechanisms in 6He induced reactions that lead to the loss of flux in the elastic channel at kinematic conditions that suggest the nuclei are well beyond the strong absorption radius [O. R. Kakuee, M. A. G. Alvarez, M. V. Andrés, S. Cherubini, T. Davinson, A. Di Pietro, W. Galster, J. Gómez-Camacho, A. M. Laird, M. Lamehi-Rachti, I. Martel, A. M. Moro, J. Rahighi, A. M. Sánchez-Benitez, A. C. Shotter, W. B. Smith, J. Vervier, P. J. Woods. Nucl. Phys. A 765, (2006) 294]. Even so, the use of nuclear reactions as an spectroscopic tool to investigate the nuclear structure of weakly bound nuclei requires a deep understanding of the reactions induced by these nuclei. Therefore, precise experimental measurements of the elastic scattering of exotic nuclei on a variety of targets, as well as the measurements of the main reaction channels are required in order to converge experimentally and theoretically to this understanding. With this aim a campaign of experiments involving different institutions and collaborations is being carefully established and going ahead at several radioactive ion beam (RIB) facilities: ISOLDE (CERN), CRC (Be), GSI (Ge) and TRIUMPH (Ca). The main idea is to measure the scattering of He, Li, and Be isotopes, and perform an intensive theoretical treatment, besides promoting some necessary instrumental development. In particular we participate in the low energy branch of the FAIR project where we take part in the tracking studies and developments.

  16. Ion-track membranes of fluoropolymers: Toward controlling the pore size and shape

    NASA Astrophysics Data System (ADS)

    Yamaki, T.; Nuryanthi, N.; Koshikawa, H.; Asano, M.; Sawada, S.; Hakoda, T.; Maekawa, Y.; Voss, K.-O.; Severin, D.; Seidl, T.; Trautmann, C.; Neumann, R.

    2013-11-01

    The possibility of varying the beam parameters and applying the effect of a pre-etching treatment for poly(vinylidene fluoride) (PVDF) ion-track membranes was investigated with the goal of achieving enhanced track etching for effective control of the pore size and shape. Commercially available 25 μm-thick PVDF films were irradiated at room temperature with swift heavy ions from the JAEA's TIARA cyclotron and GSI's UNILAC linear accelerator. Irradiation with a higher linear energy transfer (LET) beam gave faster track etching and larger pores, suggesting that the LET could be the most crucial factor determining the pore size. In-situ infra-red absorption and residual gas analyses shed light on the detailed chemistry of not only the ion-induced degradation, but also post-irradiation reactions. The pre-etching treatment effect involved oxidation of the unsaturated bonds within the latent track, which accelerated the chemical dissolution for efficient pore evolution. In other words, exposure to a gaseous oxidant, i.e., ozone, shortened the breakthrough time.

  17. Strain fields around high-energy ion tracks in {alpha}-quartz

    SciTech Connect

    Follstaedt, D. M.; Norman, A. K.; Doyle, B. L.; McDaniel, F. D.

    2006-09-15

    Transmission electron microscopy has been used to image the tracks of high-energy {sup 197}Au{sup +26} (374 MeV) and {sup 127}I{sup +18} (241 MeV) ions incident in a nonchanneling direction through a prethinned specimen of hexagonal {alpha}-quartz (SiO{sub 2}). These ions have high electronic stopping powers in quartz, 24 and 19 keV/nm, respectively, which are sufficient to produce a disordered latent track. When the tracks are imaged with diffraction contrast using several different reciprocal lattice vectors, they exhibit a radial strain extending outward from their disordered centerline approximately 16 nm into the crystalline surroundings. The images are consistent with a radial strain field with cylindrical symmetry around the amorphous track, like that found in models developed to account for the lateral expansion of amorphous SiO{sub 2} films produced by irradiation with high-energy ions. These findings provide an experimental basis for increased confidence in such modeling.

  18. Track membranes with embedded semiconductor nanocrystals: structural and optical examinations

    NASA Astrophysics Data System (ADS)

    Orlova, A. O.; Gromova, Yu A.; Savelyeva, A. V.; Maslov, V. G.; Artemyev, M. V.; Prudnikau, A.; Fedorov, A. V.; Baranov, A. V.

    2011-11-01

    We studied the optical properties of poly(ethylene terephthalate) ion track membranes of 1.5, 0.5 and 0.05 µm pores impregnated with luminescent semiconductor CdSe/ZnS nanocrystals of different diameters (2.5 and 5 nm). The nanocrystals were embedded from their colloidal solutions in toluene by the immersion of a membrane in a colloidal solution. Localization of quasi-isolated weakly interacting CdSe/ZnS nanocrystals in a loosened layer on the track pore wall surface along with the existence of empty pores was demonstrated. We observed also the spatial separation of nanocrystals of 2.5 and 5 nm in size along the 50 nm pores.

  19. 1. EXISTING TRASH RAKE STRUCTURE AND STEEL IBEAM TRACK, LOOKING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. EXISTING TRASH RAKE STRUCTURE AND STEEL I-BEAM TRACK, LOOKING EAST/NORTHEAST. - Washington Water Power Spokane River Upper Falls Hydroelectric Development, Gates & Gate-Lifting Mechanisms, Spokane River, approximately 0.5 mile northeast of intersection of Spokane Falls Boulevard & Post Street, Spokane, Spokane County, WA

  20. Tracking Coherent Structures and Source Localization in Geophysical Flows

    NASA Astrophysics Data System (ADS)

    Forgoston, Eric; Hsieh, Ani; Schwartz, Ira; Yecko, Philip

    There has been a steady increase in the deployment of autonomous underwater and surface vehicles for applications such as ocean monitoring, tracking of marine processes, and forecasting contaminant transport. The underwater environment poses unique challenges since robots must operate in a communication and localization-limited environment where their dynamics are tightly coupled with the environmental dynamics. This work presents current efforts in understanding the impact of geophysical fluid dynamics on underwater vehicle control and autonomy. The focus of the talk is on the use of collaborative vehicles to track Lagrangian coherent structures and to localize contaminant spills. Research supported by the National Science Foundation and the Office of Naval Research.

  1. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  2. Doping of Cn (N = 1, 3, 5, 8) cluster ion tracks in polyimide

    NASA Astrophysics Data System (ADS)

    Fink, D.; Klett, R.; Chung, W. H.; Grünwald, R.; Döbeli, M.; Ames, F.; Chadderton, L. T.; Vacik, J.; Hnatowicz, V.

    Cn+ cluster ions (n = 1, 3, 5, and 8) are implanted at 1 MeV/carbon atom and at fluences of 1010 to 1014 cluster ions/cm2 into thin polyimide foils. The ion-induced radiochemical changes are examined by infrared spectroscopy. The samples are then doped with either aqueous LiCl, or methylene blue dye solutions. The dopant uptake is determined by UV-Vis spectrometry in the first, and by NDP (neutron depth profiling) in the latter case. NDP examinations additionally give information about the depth distributions of the incorporated Li+ ions. Remarkable changes in the infrared signals and in the dopant uptake are found only at fluences when ion track overlapping sets in. For the same fluence, clusters with larger size show more efficient destruction than smaller ones. Also the dopant uptake capability is higher in cluster-irradiated polymers than in single-atomic C+ ion irradiated samples. The depth distribution of the incorporated dopant usually consists of both a pronounced surface-near, and a bulk dopant-enriched region. The surface-near dopant profile increases in height and width with increasing cluster size and fluence. The depth profile shape of the bulk component follows the one of the ion's energy transfer to the target via nuclear collisions. A rule of thumb to describe the action of such a cluster ion onto polymers is given.

  3. A thermalized ion explosion model for high energy sputtering and track registration

    NASA Technical Reports Server (NTRS)

    Seiberling, L. E.; Griffith, J. E.; Tombrello, T. A.

    1980-01-01

    A velocity spectrum of neutral sputtered particles as well as a low resolution mass spectrum of sputtered molecular ions was measured for 4.74 MeV F-19(+2) incident of UF4. The velocity spectrum is dramatically different from spectra taken with low energy (keV) bombarding ions, and is shown to be consistent with a hot plasma of atoms in thermal equilibrium inside the target. A thermalized ion explosion model is proposed for high energy sputtering which is expected to describe track formation in dielectric materials. The model is shown to be consistent with the observed total sputtering yield and the dependence of the yield on the primary ionization rate of the incident ion.

  4. Preparation of ion-track membranes of poly( p-phenylene terephthalamide): Control of pore shape by irradiation with different ion beams

    NASA Astrophysics Data System (ADS)

    Suzuki, Yasuyuki; Yamaki, Tetsuya; Koshikawa, Hiroshi; Asano, Masaharu; Voss, Kay-Obbe; Neumann, Reinhard; Yoshida, Masaru

    2007-07-01

    The preparation of ion-track membranes of thermally stable poly( p-phenylene terephthalamide) (PPTA) was performed by ion beam irradiation followed by chemical etching with a sodium hypochlorite solution. Cylindrical pores were observed in the membrane irradiated with 197Au and 238U ions at an energy of 11.1 MeV/n. In contrast, funnel shape pores appeared in the membrane irradiated with 84Kr, 102Ru and 129Xe ion at energies of 6.2, 3.6 and 3.5 MeV/n, respectively. The 197Au and 238U ion irradiation was found to exhibit more than four times larger sensitivity to the track etching under the same etching conditions. Consequently, the pore shape can be controlled by the masses and energies of the irradiated ions, in close relation to the etching sensitivity of the track.

  5. Toward an Automated Analysis of Slow Ions in Nuclear Track Emulsion

    NASA Astrophysics Data System (ADS)

    Mamatkulov, K. Z.; Kattabekov, R. R.; Ambrozova, I.; Artemenkov, D. A.; Bradnova, V.; Kamanin, D. V.; Majling, L.; Marey, A.; Ploc, O.; Rusakova, V. V.; Stanoeva, R.; Turek, K.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.

    Application of the nuclear track emulsion technique (NTE) in radioactivity and nuclear fission studies is discussed. It is suggested to use a HSP-1000 automated microscope for searching for a collinear cluster tri-partition of heavy nuclei implanted in NTE. Calibrations of α-particles and ion ranges in a novel NTE are carried out. Surface exposures of NTE samples to a 252Cf source started. Planar events containing fragments and long-range α-particles as well as fragment triples only are studied. NTE samples are calibrated by ions Kr and Xe of energy of 1.2 and 3 A MeV.

  6. Scanning force microscopy study of surface tracks induced in mica by 78.2-MeV 127I ions

    NASA Astrophysics Data System (ADS)

    Barlo Daya, D. D. N.; Hallén, A.; Håkansson, P.; Sundqvist, B. U. R.; Reimann, C. T.

    1995-12-01

    Tapping mode scanning force microscopy has been employed for the first time to image the radiation damage tracks on muscovite mica due to individual, normally incident 78.2-MeV 127I ions from the Uppsala EN tandem accelerator. Conical-shaped hillocks having nearly circularly-shaped bases with mean width 20 ± 2 nm and mean height 0.5 ± 0.2 nm have been observed. Similar types of hillocks have been observed in the contact mode both in air and under water. The absence of lattice structure on the tops of the hillocks indicates the formation of an amorphous region as a result of the expansion created by the passage of each ion. The presence of a crater beneath a hillock has been observed after the hillock was erased using strong interactions between the scanning force microscope probe tip and the surface.

  7. Impact of the track structure of heavy charged particles on cytogenetic damage in human blood lymphocytes

    NASA Astrophysics Data System (ADS)

    Lee, Ryonfa; Nasonova, Elena; Sommer, Sylwetster; Hartel, Carola; Durante, Marco; Ritter, Sylvia

    In space, astronauts are unavoidably exposed to charged particles from protons to irons. For a better estimate of the health risks of astronauts, further knowledge on the biological effects of charged particles, in particular the induction of cytogenetic damage is required. One im-portant factor that determines the biological response is the track structure of particles, i.e. their microscopic dose deposition in cells. The aim of the present study was to assess the influence of track structure of heavy ions on the yield and the quality of cytogenetic damage in human peripheral blood lymphocytes representing normal tissue. Cells were irradiated with 9.5 MeV/u C-ions or 990 MeV/u Fe-ions which have a comparable LET (175 keV/µm and 155 keV/µm, respectively) but a different track radius (2.3 and 6200 µm, respectively). When aberrations were analyzed in first cycle metaphases collected at different post-irradiation times (48-84 h) following fluorescence plus Giemsa staining, an increase in the aberration yield with sampling time was observed for both radiation qualities reflecting a damage dependent cell cycle progression delay to mitosis. The pronounced differences in the aberration frequency per cell are attributable to the stochastic distribution of particle traversals per cell nucleus (radius: 2.8 µm). Following C-ion exposure we found a high fraction of non-aberrant cells in samples collected at 48 h which represent cells not directly hit by a particle and slightly damaged cells that successfully repaired the induced lesions. In addition, at higher C-ion fluences the aberra-tion yield saturated, suggesting that a fraction of lymphocytes receiving multiple particle hits is not able to reach mitosis. On the other hand, at 48 h after Fe-ion exposure the proportion of non-aberrant cells is lower than after C-ion irradiation clearly reflecting the track structure of high energy particles (i.e. more homogeneous dose deposition compared to low energy C-ions

  8. Resonant structures in heavy-ion reactions

    SciTech Connect

    Sanders, S.J.; Henning, W.; Ernst, H.; Geesaman, D.F.; Jachcinski, C.; Kovar, D.G.; Paul, M.; Schiffer, J.P.

    1980-01-01

    An investigation of heavy-ion resonance structures using the /sup 24/Mg(/sup 16/O, /sup 12/C)/sup 28/Si reaction is presented. The data are analyzed in the context of Breit-Wigner resonances added to a direct-reaction background.

  9. Correlation of Particle Traversals with Clonogenic Survival Using Cell-Fluorescent Ion Track Hybrid Detector.

    PubMed

    Dokic, Ivana; Niklas, Martin; Zimmermann, Ferdinand; Mairani, Andrea; Seidel, Philipp; Krunic, Damir; Jäkel, Oliver; Debus, Jürgen; Greilich, Steffen; Abdollahi, Amir

    2015-01-01

    Development of novel approaches linking the physical characteristics of particles with biological responses are of high relevance for the field of particle therapy. In radiobiology, the clonogenic survival of cells is considered the gold standard assay for the assessment of cellular sensitivity to ionizing radiation. Toward further development of next generation biodosimeters in particle therapy, cell-fluorescent ion track hybrid detector (Cell-FIT-HD) was recently engineered by our group and successfully employed to study physical particle track information in correlation with irradiation-induced DNA damage in cell nuclei. In this work, we investigated the feasibility of Cell-FIT-HD as a tool to study the effects of clinical beams on cellular clonogenic survival. Tumor cells were grown on the fluorescent nuclear track detector as cell culture, mimicking the standard procedures for clonogenic assay. Cell-FIT-HD was used to detect the spatial distribution of particle tracks within colony-initiating cells. The physical data were associated with radiation-induced foci as surrogates for DNA double-strand breaks, the hallmark of radiation-induced cell lethality. Long-term cell fate was monitored to determine the ability of cells to form colonies. We report the first successful detection of particle traversal within colony-initiating cells at subcellular resolution using Cell-FIT-HD.

  10. Atom ejection from a fast-ion track: A molecular-dynamics study

    SciTech Connect

    Urbassek, H.M. ); Kafemann, H. ); Johnson, R.E. )

    1994-01-01

    As a model for atom ejection from fast-ion tracks, molecular-dynamics simulations of a cylindrical track of energized particles are performed. An idealized situation is studied where every atom in a cylindrical track of radius [ital R][sub 0] is energized with energy [ital E][sub 0]. The emission yield [ital Y]([ital E][sub 0],[ital R][sub 0]) shows the existence of two ejection regimes. If the particle energy [ital E][sub 0] is below the sublimation energy [ital U] of the material, a threshold regime is seen in which [ital Y] rises roughly like the third power of [ital E][sub 0]; for high-energy densities [ital E][sub 0][approx gt][ital U], the yield rises much more slowly, roughly linearly. In both cases, ejected particles mostly originate from the track, rather than from its surroundings, and from the first or the first few monolayers. The behavior found is interpreted here in terms of emission due to a pressure-driven jet (linear regime) or due to a pressure pulse (threshold regime). These both behave differently from the often-used thermal-spike sputtering model.

  11. Correlation of Particle Traversals with Clonogenic Survival Using Cell-Fluorescent Ion Track Hybrid Detector

    PubMed Central

    Dokic, Ivana; Niklas, Martin; Zimmermann, Ferdinand; Mairani, Andrea; Seidel, Philipp; Krunic, Damir; Jäkel, Oliver; Debus, Jürgen; Greilich, Steffen; Abdollahi, Amir

    2015-01-01

    Development of novel approaches linking the physical characteristics of particles with biological responses are of high relevance for the field of particle therapy. In radiobiology, the clonogenic survival of cells is considered the gold standard assay for the assessment of cellular sensitivity to ionizing radiation. Toward further development of next generation biodosimeters in particle therapy, cell-fluorescent ion track hybrid detector (Cell-FIT-HD) was recently engineered by our group and successfully employed to study physical particle track information in correlation with irradiation-induced DNA damage in cell nuclei. In this work, we investigated the feasibility of Cell-FIT-HD as a tool to study the effects of clinical beams on cellular clonogenic survival. Tumor cells were grown on the fluorescent nuclear track detector as cell culture, mimicking the standard procedures for clonogenic assay. Cell-FIT-HD was used to detect the spatial distribution of particle tracks within colony-initiating cells. The physical data were associated with radiation-induced foci as surrogates for DNA double-strand breaks, the hallmark of radiation-induced cell lethality. Long-term cell fate was monitored to determine the ability of cells to form colonies. We report the first successful detection of particle traversal within colony-initiating cells at subcellular resolution using Cell-FIT-HD. PMID:26697410

  12. Chitosan Hydrogel Structure Modulated by Metal Ions

    PubMed Central

    Nie, Jingyi; Wang, Zhengke; Hu, Qiaoling

    2016-01-01

    As one of the most important polysaccharide, chitosan (CS) has generated a great deal of interest for its desirable properties and wide applications. In the utilization of CS materials, hydrogel is a major and vital branch. CS has the ability to coordinate with many metal ions by a chelation mechanism. While most researchers focused on the applications of complexes between CS and metal ions, the complexes can also influence gelation process and structure of CS hydrogel. In the present work, such influence was studied with different metal ions, revealing two different kinds of mechanisms. Strong affinity between CS and metal ions leads to structural transition from orientation to multi-layers, while weak affinity leads to composite gel with in-situ formed inorganic particles. The study gave a better understanding of the gelation mechanism and provided strategies for the modulation of hydrogel morphology, which benefited the design of new CS-based materials with hierarchical structure and facilitated the utilization of polysaccharide resources. PMID:27777398

  13. Chitosan Hydrogel Structure Modulated by Metal Ions

    NASA Astrophysics Data System (ADS)

    Nie, Jingyi; Wang, Zhengke; Hu, Qiaoling

    2016-10-01

    As one of the most important polysaccharide, chitosan (CS) has generated a great deal of interest for its desirable properties and wide applications. In the utilization of CS materials, hydrogel is a major and vital branch. CS has the ability to coordinate with many metal ions by a chelation mechanism. While most researchers focused on the applications of complexes between CS and metal ions, the complexes can also influence gelation process and structure of CS hydrogel. In the present work, such influence was studied with different metal ions, revealing two different kinds of mechanisms. Strong affinity between CS and metal ions leads to structural transition from orientation to multi-layers, while weak affinity leads to composite gel with in-situ formed inorganic particles. The study gave a better understanding of the gelation mechanism and provided strategies for the modulation of hydrogel morphology, which benefited the design of new CS-based materials with hierarchical structure and facilitated the utilization of polysaccharide resources.

  14. Estimation of spatially restricted LET using track structure models

    NASA Technical Reports Server (NTRS)

    Kiefer, J.

    1994-01-01

    The spatial distribution of energy deposition is an important determinant in the formation of biologically significant lesions. It has been widely realized that Linear Energy Transfer (LET) being an average quantity is not sufficient to describe the situation at a submicroscopic scale. To remedy this to some extent 'energy-cut-off' values are sometimes used but since they are related to secondary electron energy and only indirectly to their range they are also not adequate although they may be easily calculated. 'Range-restricted LET' appears to be better but its determination is usually quite involved. Xapsos (1992) suggested a semi-empirical approximation based on a modified Bethe-formula which contains a number of assumption which are difficult to verify. A simpler and easier way is to use existing beam-models which describe energy deposition around an ion's path. They all agree that the energy density (i. e., energy deposited per unit mass) decreases with the inverse square of the distance from the track center. This simple dependence can be used to determine the fraction of total LET which is deposited in a cylinder of a given radius. As an example our own beam model. Energy density depends on distance x (measured in m) from the track center according to the presented formula.

  15. Robustness of target dose coverage to motion uncertainties for scanned carbon ion beam tracking therapy of moving tumors

    NASA Astrophysics Data System (ADS)

    Eley, John Gordon; Newhauser, Wayne David; Richter, Daniel; Lüchtenborg, Robert; Saito, Nami; Bert, Christoph

    2015-02-01

    Beam tracking with scanned carbon ion radiotherapy achieves highly conformal target dose by steering carbon pencil beams to follow moving tumors using real-time magnetic deflection and range modulation. The purpose of this study was to evaluate the robustness of target dose coverage from beam tracking in light of positional uncertainties of moving targets and beams. To accomplish this, we simulated beam tracking for moving targets in both water phantoms and a sample of lung cancer patients using a research treatment planning system. We modeled various deviations from perfect tracking that could arise due to uncertainty in organ motion and limited precision of a scanned ion beam tracking system. We also investigated the effects of interfractional changes in organ motion on target dose coverage by simulating a complete course of treatment using serial (weekly) 4DCTs from six lung cancer patients. For perfect tracking of moving targets, we found that target dose coverage was high ({{\\overline{V}}95} was 94.8% for phantoms and 94.3% for lung cancer patients, respectively) but sensitive to changes in the phase of respiration at the start of treatment and to the respiratory period. Phase delays in tracking the moving targets led to large degradation of target dose coverage (up to 22% drop for a 15° delay). Sensitivity to technical uncertainties in beam tracking delivery was minimal for a lung cancer case. However, interfractional changes in anatomy and organ motion led to large decreases in target dose coverage (target coverage dropped approximately 8% due to anatomy and motion changes after 1 week). Our findings provide a better understand of the importance of each of these uncertainties for beam tracking with scanned carbon ion therapy and can be used to inform the design of future scanned ion beam tracking systems.

  16. Robustness of Target Dose Coverage to Motion Uncertainties for Scanned Carbon Ion Beam Tracking Therapy of Moving Tumors

    PubMed Central

    Eley, John Gordon; Newhauser, Wayne David; Richter, Daniel; Lüchtenborg, Robert; Saito, Nami; Bert, Christoph

    2015-01-01

    Beam tracking with scanned carbon ion radiotherapy achieves highly conformal target dose by steering carbon pencil beams to follow moving tumors using real-time magnetic deflection and range modulation. The purpose of this study was to evaluate the robustness of target dose coverage from beam tracking in light of positional uncertainties of moving targets and beams. To accomplish this, we simulated beam tracking for moving targets in both water phantoms and a sample of lung cancer patients using a research treatment planning system. We modeled various deviations from perfect tracking that could arise due to uncertainty in organ motion and limited precision of a scanned ion beam tracking system. We also investigated the effects of interfractional changes in organ motion on target dose coverage by simulating a complete course of treatment using serial (weekly) 4DCTs from 6 lung cancer patients. For perfect tracking of moving targets, we found that target dose coverage was high (V̄95 was 94.8% for phantoms and 94.3% for lung cancer patients, respectively) but sensitive to changes in the phase of respiration at the start of treatment and to the respiratory period. Phase delays in tracking the moving targets led to large degradation of target dose coverage (up to 22% drop for a 15 degree delay). Sensitivity to technical uncertainties in beam tracking delivery was minimal for a lung cancer case. However, interfractional changes in anatomy and organ motion led to large decreases in target dose coverage (target coverage dropped approximately 8% due to anatomy and motion changes after 1 week). Our findings provide a better understand of the importance of each of these uncertainties for beam tracking with scanned carbon ion therapy and can be used to inform the design of future scanned ion beam tracking systems. PMID:25650520

  17. Robustness of target dose coverage to motion uncertainties for scanned carbon ion beam tracking therapy of moving tumors.

    PubMed

    Eley, John Gordon; Newhauser, Wayne David; Richter, Daniel; Lüchtenborg, Robert; Saito, Nami; Bert, Christoph

    2015-02-21

    Beam tracking with scanned carbon ion radiotherapy achieves highly conformal target dose by steering carbon pencil beams to follow moving tumors using real-time magnetic deflection and range modulation. The purpose of this study was to evaluate the robustness of target dose coverage from beam tracking in light of positional uncertainties of moving targets and beams. To accomplish this, we simulated beam tracking for moving targets in both water phantoms and a sample of lung cancer patients using a research treatment planning system. We modeled various deviations from perfect tracking that could arise due to uncertainty in organ motion and limited precision of a scanned ion beam tracking system. We also investigated the effects of interfractional changes in organ motion on target dose coverage by simulating a complete course of treatment using serial (weekly) 4DCTs from six lung cancer patients. For perfect tracking of moving targets, we found that target dose coverage was high ([Formula: see text] was 94.8% for phantoms and 94.3% for lung cancer patients, respectively) but sensitive to changes in the phase of respiration at the start of treatment and to the respiratory period. Phase delays in tracking the moving targets led to large degradation of target dose coverage (up to 22% drop for a 15° delay). Sensitivity to technical uncertainties in beam tracking delivery was minimal for a lung cancer case. However, interfractional changes in anatomy and organ motion led to large decreases in target dose coverage (target coverage dropped approximately 8% due to anatomy and motion changes after 1 week). Our findings provide a better understand of the importance of each of these uncertainties for beam tracking with scanned carbon ion therapy and can be used to inform the design of future scanned ion beam tracking systems.

  18. Ion track symmetric and asymmetric nanopores in polyethylene terephthalate foils for versatile applications

    NASA Astrophysics Data System (ADS)

    Apel, P. Yu.; Blonskaya, I. V.; Dmitriev, S. N.; Orelovich, O. L.; Sartowska, B. A.

    2015-12-01

    In this report we present several fabrication methods which allow production of ion track nanopore membranes with different pore configurations. Polymer foils, typically polyethylene terephthalate with a thickness of 5-23 μm, are irradiated with accelerated heavy ions (energy of 1-10 MeV/u) and then subjected to different physico-chemical treatments. Depending on the procedure, symmetric or asymmetric pores with nanoscale-sized narrowing are obtained. The asymmetric configurations include conical, funnel-like and bullet-like shapes. In electrolyte solutions the asymmetric nanopores exhibit diode-like properties which strongly depend on the pore shape. The peculiar features of such pores provide a basis for various applications.

  19. Intercomparison of experimental and theoretical ranges of heavy ions in plastic track detectors

    NASA Astrophysics Data System (ADS)

    Virk, H. S.; Randhawa, G. S.; Sharma, S. K.

    1996-01-01

    In the present study, CR-39 and Lexan polycarbonate plastic track detectors have been exposed to various heavy ion beams, i.e. ,238U, b,208Pb, u,197Au, a,139La, e132Xe and b93Nb (energy range from 5.6 to 18.0 MeV/u), from the UNILAC accelerator at GSI, Darmstadt. After exposure, the irradiated samples were etched under optimum etching conditions. The total etchable ranges of these heavy ions have been determined experimentally using a Carl Zeiss binocular microscope. In order to check the validity of the various stopping power and range formulations in this energy range, the experimentally determined range values have been compared with the theoretically computed values from the Benton and Henke, Mukherjee and Nayak, Ziegler et al. and Hubert et al. formulations.

  20. Latent tracks of swift heavy ions in Сr23C6 and Y-Ti-O nanoparticles in ODS alloys

    NASA Astrophysics Data System (ADS)

    Skuratov, V. A.; Sohatsky, A. S.; O'Connell, J. H.; Kornieieva, K.; Nikitina, A. A.; Uglov, V. V.; Neethling, J. H.; Ageev, V. S.

    2016-05-01

    The radiation stability of dielectric nanoparticles embedded into a metallic matrix is of considerable practical value due to the growing interest in oxide dispersion strengthened (ODS) steels as promising nuclear reactor materials. In this report the results of a TEM study of structural changes in Cr23C6 and Y-Ti-O nanoparticles in several ODS alloys irradiated with 1.2 MeV/amu Xe and 3.4 MeV/amu Bi ions is presented. It was found that swift heavy ion irradiation leads to the formation of amorphous latent tracks in both materials. The upper limit of the threshold electronic stopping power for track formation in carbides is estimated to be around 35 keV/nm. Multiple ion track overlapping leads to complete amorphization of carbide and Y-Ti oxide nanoparticles. Microstructural analysis have revealed a strong influence of the ferritic matrix on track morphology in Y2Ti2O7 nanoparticles in pre-thinned TEM targets after postradiation annealing and irradiation at elevated temperatures.

  1. Solar wind compressible structures at ion scales

    NASA Astrophysics Data System (ADS)

    Perrone, D.; Alexandrova, O.; Rocoto, V.; Pantellini, F. G. E.; Zaslavsky, A.; Maksimovic, M.; Issautier, K.; Mangeney, A.

    2014-12-01

    In the solar wind turbulent cascade, the energy partition between fluid and kinetic degrees of freedom, in the vicinity of plasma characteristic scales, i.e. ion and electron Larmor radius and inertial lengths, is still under debate. In a neighborhood of the ion scales, it has been observed that the spectral shape changes and fluctuations become more compressible. Nowadays, a huge scientific effort is directed to the comprehension of the link between macroscopic and microscopic scales and to disclose the nature of compressive fluctuations, meaning that if space plasma turbulence is a mixture of quasi-linear waves (as whistler or kinetic Alfvèn waves) or if turbulence is strong with formation of coherent structures responsible for dissipation. Here we present an automatic method to identify compressible coherent structures around the ion spectral break, using Morlet wavelet decomposition of magnetic signal from Cluster spacecraft and reconstruction of magnetic fluctuations in a selected scale range. Different kind of coherent structures have been detected: from soliton-like one-dimensional structures to current sheet- or wave-like two-dimensional structures. Using a multi-satellite analysis, in order to characterize 3D geometry and propagation in plasma rest frame, we recover that these structures propagate quasi-perpendicular to the mean magnetic field, with finite velocity. Moreover, without using the Taylor hypothesis, the spatial scales of coherent structures have been estimated. Our observations in the solar wind can provide constraints on theoretical modeling of small scale turbulence and dissipation in collisionless magnetized plasmas.

  2. Oligossacharide structure determination on an ion trap

    SciTech Connect

    Asam, M.R.; Glish, G.L.

    1995-12-31

    Oligosaccharides are important elements in intra- and inter-cellular/molecular recognition mechanisms. Linkage types are part of the information that determine the tertiary structure of oligosaccharides and the tertiary structure is what determines specific recognition, so easily obtained linkage sequences will provide valuable information for computer and other modeling of cellular signaling interactions. Hofmeister et al. have shown that lithium cationized oligosaccharides have specific MS/MS dissociation patterns indicative of the carbohydrate linkage under low energy CID conditions in a hybrid mass spectrometer. The authors have used electrospray ionization on a quadrupole ion trap mass spectrometer to examine MS/MS disaccharide dissociation patterns under ion trap conditions. These studies have concentrated on disaccharides complexed with lithium and sodium.

  3. Investigation of optical properties of Cu/Ni multilayer nanowires embedded in etched ion-track template

    NASA Astrophysics Data System (ADS)

    Xie, Lu; Yao, Huijun; Duan, Jinglai; Chen, Yonghui; Lyu, Shuangbao; Maaz, Khan; Mo, Dan; Liu, Jie; Sun, Youmei; Hou, Mingdong

    2016-12-01

    For understanding the interaction between light and noble/magnetism multilayer nanowires, Cu/Ni multilayer nanowires are fabricated by a multi-potential step deposition technique in etched ion-track polycarbonate template. The component and the corresponding layer thickness of multilayer nanowire are confirmed by TEM and EDS line-scan analysis. By tailoring the nanowire diameter, the Cu layer thickness and the periodicity of the nanowire, the extinction spectral of nanowire arrays exhibit an extra sensitivity to the change of structural parameters. The resonance wavelength caused by surface plasmon resonance increases obviously with increasing the nanowire diameter, the Cu layer thickness and the periodicity. The observations in our work can be explained by the "impurity effect" and coupled effect and can also be optimized for developing optical devices based on multilayer nanowires.

  4. Early stage of the electron kinetics in swift heavy ion tracks in dielectrics

    SciTech Connect

    Medvedev, N. A.; Rethfeld, B.; Volkov, A. E.; Shcheblanov, N. S.

    2010-09-15

    A Monte Carlo approach was applied for simulations of the early stage (first tens of femtosecond) of kinetics of the electronic subsystem of silica (SiO{sub 2}) in tracks of swift heavy ions (SHIs) decelerated in the electronic stopping regime. At the first step multiple ionizations of target atoms by a projectile (Ca{sup +19}, E=11.4 MeV/amu) were described that gave the initial spatial distributions of free electrons having different momenta as well as distributions of holes in different atomic shells. Spatial propagation of fast electrons results in secondary ionizations of target atoms as well as in energy transfer to the lattice at times much shorter than the times of atomic oscillations (phonons). The well detected front of excitation in the electronic and ionic subsystems is formed due to this propagation which cannot be described by models based on diffusion mechanisms (e.g., parabolic equations of heat diffusion). At times {approx}10 fs after the projectile passage, about {approx}0.1% of the energy is already transferred to the lattice. About 63% of the energy deposited by the ion is accumulated in holes at these times. Calculated distributions of these holes through the atomic shells are in excellent agreement with the spectroscopy experiments. Comparison with these experiments demonstrated also that relaxation of the electronic subsystem in SHI tracks in solids cannot be described adequately without taking into account intra-atomic and interatomic Auger (Knotek-Feibelman) processes.

  5. Swift heavy ions in insulating and conducting oxides: tracks and physical properties

    NASA Astrophysics Data System (ADS)

    Toulemonde, M.; Bouffard, S.; Studer, F.

    1994-06-01

    Damage induced in several oxide materials by swift heavy ions is presented. The discussion is based on results obtained on the following materials [Y3Fe5O12, AFe12O19 (A = Ba, Sr), BFe2O4 (B = Ni, Mg, Zn), ZrSi2O4, SiO2 quartz, Al2O3, high Tc superconductors (YBa2Cu3O7 - δ and Bi2Sr2CaCu2O8)] which have been irradiated by ions with atomic number ranging between 6 (12C) and 92 (238U) and energies between 0.05 GeV and 6 GeV. The damage cross section A has been deduced using several physical characterisations like Mössbauer spectrometry, saturation magnetisation measurements, channeling Rutherford backscattering, infrared absorption and electrical resistance measurements. Depending on the material and on the value of the electronic stopping power (dE/dx) the damage cross section varies between 10-17 and 10-12 cm2. Using medium and high resolution transmission electron microscopy and chemical etching of the latent track, an electronic stopping power evolution of the damage morphology has been observed leading to the definition of an effective radius Re of the latent track which can be linked to the damage (amorphous) cross section A by the relation Re = √A/π. Moreover there is a direct correlation between these values and the damage morphology: for Re > 3 nm the latent tracks are long and cylindrical, conversely for Re < 3 nm the damage is inhomogeneous along the latent track. The effect of the irradiation temperature, of the crystallographic orientation, of the initial electrical resistivity and of the oxygen stoichiometry will be presented. In opposition to what has been usually believed it will be shown that alumina (Al2O3) is indeed sensitive to the electronic stopping power. Moreover the velocity of the incident ion has a direct influence on the damage production: the lower the velocity, the higher the damage.

  6. Microdosimetric structure of HZE particle tracks in tissue

    NASA Technical Reports Server (NTRS)

    Schaefer, H. J.

    1975-01-01

    Heavy nuclei of the primary galactic radiation in space can have the same linear energy transfer yet greatly different lateral distribution patterns of the energy in the microstructure of tissue. Track structure thus presents itself as a new dosimetric parameter for HZE particles which is at present incompletely understood in its radiobiological significance. The theory of track structure distinguishes two regions: core and penumbra. The core is a narrow region with a radius far below 1 micron in tissue where energy deposition occurs mainly through excitations and collective oscillations of electrons. Energy density in the core accounts for slightly more than half the total LET. The penumbra surrounding the core extends laterally several to many microns depending on the energy of the primary. Energy density in the penumbra decreases steeply with the square of increasing radius. The relationships are illustrated with nuclear emulsion micrographs and plots of energy density profiles. The implications of the findings for a dosimetric system for HZE particles are discussed.

  7. Effects of model approximations for electron, hole, and photon transport in swift heavy ion tracks

    NASA Astrophysics Data System (ADS)

    Rymzhanov, R. A.; Medvedev, N. A.; Volkov, A. E.

    2016-12-01

    The event-by-event Monte Carlo code, TREKIS, was recently developed to describe excitation of the electron subsystems of solids in the nanometric vicinity of a trajectory of a nonrelativistic swift heavy ion (SHI) decelerated in the electronic stopping regime. The complex dielectric function (CDF) formalism was applied in the used cross sections to account for collective response of a matter to excitation. Using this model we investigate effects of the basic assumptions on the modeled kinetics of the electronic subsystem which ultimately determine parameters of an excited material in an SHI track. In particular, (a) effects of different momentum dependencies of the CDF on scattering of projectiles on the electron subsystem are investigated. The 'effective one-band' approximation for target electrons produces good coincidence of the calculated electron mean free paths with those obtained in experiments in metals. (b) Effects of collective response of a lattice appeared to dominate in randomization of electron motion. We study how sensitive these effects are to the target temperature. We also compare results of applications of different model forms of (quasi-) elastic cross sections in simulations of the ion track kinetics, e.g. those calculated taking into account optical phonons in the CDF form vs. Mott's atomic cross sections. (c) It is demonstrated that the kinetics of valence holes significantly affects redistribution of the excess electronic energy in the vicinity of an SHI trajectory as well as its conversion into lattice excitation in dielectrics and semiconductors. (d) It is also shown that induced transport of photons originated from radiative decay of core holes brings the excess energy faster and farther away from the track core, however, the amount of this energy is relatively small.

  8. Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames

    SciTech Connect

    Bremer, Peer-Timo; Weber, Gunther; Pascucci, Valerio; Day, Marc; Bell, John

    2009-06-01

    This paper presents topology-based methods to robustly extract, analyze, and track features defined as subsets of isosurfaces. First, we demonstrate how features identified by thresholding isosurfaces can be defined in terms of the Morse complex. Second, we present a specialized hierarchy that encodes the feature segmentation independent of the threshold while still providing a flexible multi-resolution representation. Third, for a given parameter selection we create detailed tracking graphs representing the complete evolution of all features in a combustion simulation over several hundred time steps. Finally, we discuss a user interface that correlates the tracking information with interactive rendering of the segmented isosurfaces enabling an in-depth analysis of the temporal behavior. We demonstrate our approach by analyzing three numerical simulations of lean hydrogen flames subject to different levels of turbulence. Due to their unstable nature, lean flames burn in cells separated by locally extinguished regions. The number, area, and evolution over time of these cells provide important insights into the impact of turbulence on the combustion process. Utilizing the hierarchy we can perform an extensive parameter study without re-processing the data for each set of parameters. The resulting statistics enable scientist to select appropriate parameters and provide insight into the sensitivity of the results wrt. to the choice of parameters. Our method allows for the first time to quantitatively correlate the turbulence of the burning process with the distribution of burning regions, properly segmented and selected. In particular, our analysis shows that counter-intuitively stronger turbulence leads to larger cell structures, which burn more intensely than expected. This behavior suggests that flames could be stabilized under much leaner conditions than previously anticipated.

  9. Intercomparison of experimental and theoretical ranges of heavy ions in plastic track detectors

    NASA Astrophysics Data System (ADS)

    Randhawa, G. S.; Sharma, S. K.; Virk, H. S.

    1996-01-01

    In the present study, CR-39 and Lexan polycarbonate plastic track detectors have been exposed to various heavy ion beams, i.e. 238U, 208Pb, 197Au, 139La, 132Xe and 93Nb (energy range from 5.6 to 18.0 MeV/u), from the UNILAC accelerator at GSI, Darmstadt. After exposure, the irradiated samples were etched under optimum etching conditions. The total etchable ranges of these heavy ions have been determined experimentally using a Carl Zeiss binocular microscope. In order to check the validity of the various stopping power and range formulations in this energy range, the experimentally determined range values have been compared with theoretically computed values from the Benton and Henke [Nucl. Instr. and Meth. 67 (1969) 87], Mukherjee and Nayak [Nucl. Instr. and Meth. 159 (1979) 421], Ziegler et al. [Stopping power and range of ions in solids, vol. 1 (Pergamon, New York, 1985); Nucl. Instr. and Meth. B 35 (1988) 215] and Hubert et al. [Nucl. Instr. and Meth. B 36 (1989) 357] formulations.

  10. 3D Visualization of Monte-Carlo Simulation's of HZE Track Structure and Initial Chemical Species

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2009-01-01

    Heavy ions biophysics is important for space radiation risk assessment [1] and hadron-therapy [2]. The characteristic of heavy ions tracks include a very high energy deposition region close to the track (<20 nm) denoted as the track core, and an outer penumbra region consisting of individual secondary electrons (6-rays). A still open question is the radiobiological effects of 6- rays relative to the track core. Of importance is the induction of double-strand breaks (DSB) [3] and oxidative damage to the biomolecules and the tissue matrix, considered the most important lesions for acute and long term effects of radiation. In this work, we have simulated a 56Fe26+ ion track of 1 GeV/amu with our Monte-Carlo code RITRACKS [4]. The simulation results have been used to calculate the energy depiction and initial chemical species in a "voxelized" space, which is then visualized in 3D. Several voxels with dose >1000 Gy are found in the penumbra, some located 0.1 mm from the track core. In computational models, the DSB induction probability is calculated with radial dose [6], which may not take into account the higher RBE of electron track ends for DSB induction. Therefore, these simulations should help improve models of DSB induction and our understanding of heavy ions biophysics.

  11. Grafting of acrylic acid on etched latent tracks induced by swift heavy ions on polypropylene films

    NASA Astrophysics Data System (ADS)

    Mazzei, R.; Fernández, A.; García Bermúdez, G.; Torres, A.; Gutierrez, M. C.; Magni, M.; Celma, G.; Tadey, D.

    2008-06-01

    In order to continue with a systematic study that include different polymers and monomers, the residual active sites produced by heavy ion beams, that remain after the etching process, were used to start the grafting process. To produce tracks, foils of polypropylene (PP) were irradiated with 208Pb of 25.62 MeV/n. Then, these were etched and grafted with acrylic acid (AA) monomers. Experimental curves of grafting yield as a function of grafting time with the etching time as a parameter were measured. Also, the grating yield as a function of the fluence and etching time was obtained. In addition, the permeation of solutions, with different pH, through PP grafted foils was measured.

  12. Sodium hypochlorite as a developer for heavy ion tracks in polyimide

    NASA Astrophysics Data System (ADS)

    Klintberg, Lena; Lindeberg, Mikael; Thornell, Greger

    2001-12-01

    The developing and etching of heavy ion tracks in polyimide with sodium hypochlorite have been studied to gain control over the parameters that affect the etch result. The shape of the resulting pores is a function of both alkalinity and hypochlorite content of the solution. Sodium hypochlorite decomposes during etching, and the rate constant has been determined as a function of the alkalinity at 62 °C. Polished cross-sections have been examined to determine the pore shape, and this method has shown to be a straightforward way to characterise the pores. Decreasing the alkalinity gives more cylindrical pores, but increases the decomposition rate of the hypochlorite solution and decreases the etch rate.

  13. Synergy of elastic and inelastic energy loss on ion track formation in SrTiO3

    SciTech Connect

    Weber, William J.; Zarkadoula, Eva; Pakarinen, Olli H.; Sachan, Ritesh; Chisholm, Matthew F.; Liu, Peng; Xue, Haizhou; Jin, Ke; Zhang, Yanwen

    2015-01-12

    While the interaction of energetic ions with solids is well known to result in inelastic energy loss to electrons and elastic energy loss to atomic nuclei in the solid, the coupled effects of these energy losses on defect production, nanostructure evolution and phase transformations in ionic and covalently bonded materials are complex and not well understood due to dependencies on electron-electron scattering processes, electron-phonon coupling, localized electronic excitations, diffusivity of charged defects, and solid-state radiolysis. Here we show that a colossal synergy occurs between inelastic energy loss and pre-existing atomic defects created by elastic energy loss in single crystal strontium titanate (SrTiO3), resulting in the formation of nanometer-sized amorphous tracks, but only in the narrow region with pre-existing defects. These defects locally decrease the electronic and atomic thermal conductivities and increase electron-phonon coupling, which locally increase the intensity of the thermal spike for each ion. This work identifies a major gap in understanding on the role of defects in electronic energy dissipation and electron-phonon coupling; it also provides insights for creating novel interfaces and nanostructures to functionalize thin film structures, including tunable electronic, ionic, magnetic and optical properties.

  14. Synergy of elastic and inelastic energy loss on ion track formation in SrTiO3

    PubMed Central

    Weber, William J.; Zarkadoula, Eva; Pakarinen, Olli H.; Sachan, Ritesh; Chisholm, Matthew F.; Liu, Peng; Xue, Haizhou; Jin, Ke; Zhang, Yanwen

    2015-01-01

    While the interaction of energetic ions with solids is well known to result in inelastic energy loss to electrons and elastic energy loss to atomic nuclei in the solid, the coupled effects of these energy losses on defect production, nanostructure evolution and phase transformations in ionic and covalently bonded materials are complex and not well understood due to dependencies on electron-electron scattering processes, electron-phonon coupling, localized electronic excitations, diffusivity of charged defects, and solid-state radiolysis. Here we show that a colossal synergy occurs between inelastic energy loss and pre-existing atomic defects created by elastic energy loss in single crystal strontium titanate (SrTiO3), resulting in the formation of nanometer-sized amorphous tracks, but only in the narrow region with pre-existing defects. These defects locally decrease the electronic and atomic thermal conductivities and increase electron-phonon coupling, which locally increase the intensity of the thermal spike for each ion. This work identifies a major gap in understanding on the role of defects in electronic energy dissipation and electron-phonon coupling; it also provides insights for creating novel interfaces and nanostructures to functionalize thin film structures, including tunable electronic, ionic, magnetic and optical properties. PMID:25578009

  15. Synergy of elastic and inelastic energy loss on ion track formation in SrTiO3

    DOE PAGES

    Weber, William J.; Zarkadoula, Eva; Pakarinen, Olli H.; ...

    2015-01-12

    While the interaction of energetic ions with solids is well known to result in inelastic energy loss to electrons and elastic energy loss to atomic nuclei in the solid, the coupled effects of these energy losses on defect production, nanostructure evolution and phase transformations in ionic and covalently bonded materials are complex and not well understood due to dependencies on electron-electron scattering processes, electron-phonon coupling, localized electronic excitations, diffusivity of charged defects, and solid-state radiolysis. Here we show that a colossal synergy occurs between inelastic energy loss and pre-existing atomic defects created by elastic energy loss in single crystal strontiummore » titanate (SrTiO3), resulting in the formation of nanometer-sized amorphous tracks, but only in the narrow region with pre-existing defects. These defects locally decrease the electronic and atomic thermal conductivities and increase electron-phonon coupling, which locally increase the intensity of the thermal spike for each ion. This work identifies a major gap in understanding on the role of defects in electronic energy dissipation and electron-phonon coupling; it also provides insights for creating novel interfaces and nanostructures to functionalize thin film structures, including tunable electronic, ionic, magnetic and optical properties.« less

  16. Structure and selectivity in bestrophin ion channels

    SciTech Connect

    Yang, Tingting; Liu, Qun; Kloss, Brian; Bruni, Renato; Kalathur, Ravi C.; Guo, Youzhong; Kloppmann, Edda; Rost, Burkhard; Colecraft, Henry M.; Hendrickson, Wayne A.

    2014-09-25

    Human bestrophin 1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where it can suffer mutations associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a subtle control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activation by mutations at the exit restriction. Lastly, a homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.

  17. Structure and selectivity in bestrophin ion channels

    DOE PAGES

    Yang, Tingting; Liu, Qun; Kloss, Brian; ...

    2014-09-25

    Human bestrophin 1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where it can suffer mutations associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a subtle control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activationmore » by mutations at the exit restriction. Lastly, a homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.« less

  18. Anomalous effect of ion velocity on track formation in GeS

    NASA Astrophysics Data System (ADS)

    Szenes, G.; Pécz, B.

    2016-12-01

    Systematic experiments were performed for studying the effect of the projectile velocity (velocity effect, VE) in GeS which has a highly anisotropic conductivity. The prethinned specimens were irradiated by Bi, Au, W, Xe, Ag, Kr, Ni and Fe ions of about E ≈ 1 MeV/nucleon energy. Track radii were measured by transmission electron microscopy. Compared to previous experiments performed with high velocity projectile, there is a marked VE for Se > 20 keV/nm (Se - electronic stopping power). However, the VE is gradually reduced and finally disappears as Se decreases. This effect is described for the first time. The predictions according to the Analytical Thermal Spike Model are in excellent quantitative agreement with the experiments in the range Se > 20 keV/nm. The anomalous behavior of track evolution at lower values of Se is attributed to the combination of semiconducting and insulating properties. An explanation of the VE is given based on the Coulomb explosion model.

  19. Tumor tracking based on correlation models in scanned ion beam therapy: an experimental study

    NASA Astrophysics Data System (ADS)

    Seregni, M.; Kaderka, R.; Fattori, G.; Riboldi, M.; Pella, A.; Constantinescu, A.; Saito, N.; Durante, M.; Cerveri, P.; Bert, C.; Baroni, G.

    2013-07-01

    Accurate dose delivery to extra-cranial lesions requires tumor motion compensation. An effective compensation can be achieved by real-time tracking of the target position, either measured in fluoroscopy or estimated through correlation models as a function of external surrogate motion. In this work, we integrated two internal/external correlation models (a state space model and an artificial neural network-based model) into a custom infra-red optical tracking system (OTS). Dedicated experiments were designed and conducted at GSI (Helmholtzzentrum für Schwerionenforschung). A robotic breathing phantom was used to reproduce regular and irregular internal target motion as well as external thorax motion. The position of a set of markers placed on the phantom thorax was measured with the OTS and used by the correlation models to infer the internal target position in real-time. Finally, the estimated target position was provided as input for the dynamic steering of a carbon ion beam. Geometric results showed that the correlation models transversal (2D) targeting error was always lower than 1.3 mm (root mean square). A significant decrease of the dosimetric error with respect to the uncompensated irradiation was achieved in four out of six experiments, demonstrating that phase shifts are the most critical irregularity for external/internal correlation models.

  20. The effect of track structure on the induction of chromosomal aberrations in murine cells

    NASA Technical Reports Server (NTRS)

    Durante, M.; Cella, L.; Furusawa, Y.; George, K.; Gialanella, G.; Grossi, G.; Pugliese, M.; Saito, M.; Yang, T. C.

    1998-01-01

    PURPOSE: To measure chromosome aberrations in C3H 10T1/2 mouse fibroblasts using FISH painting at the first mitosis following exposure to 30 keV/microm hydrogen or neon ions. MATERIALS AND METHODS: Cells in plateau-phase were irradiated with 0.86 MeV protons at the TTT-3 Tandem accelerator in Naples (Italy), or with 400 MeV/n Ne ions at the HIMAC accelerator in Chiba (Japan). Colcemid-blocked cells were harvested at the first mitosis following exposure, and chromosome spreads were hybridized in situ with a fluorescein-labelled composite mouse DNA probe specific for chromosomes 2 and 8. RESULTS: Protons were more efficient than neon ions at the same LET in the induction of chromosome interchanges and breaks. Yields of complex exchanges were similar for both particles at the same dose, but protons produced mostly insertions, while with Ne exposure non-reciprocal exchanges were the most frequent complex-type exchange. CONCLUSIONS: Charged particles with the same LET produce different yields of chromosome aberrations, and some observed differences can be explained based on the available track-structure models.

  1. Co-visualization of DNA damage and ion traversals in live mammalian cells using a fluorescent nuclear track detector.

    PubMed

    Kodaira, Satoshi; Konishi, Teruaki; Kobayashi, Alisa; Maeda, Takeshi; Ahmad, Tengku Ahbrizal Farizal Tengku; Yang, Gen; Akselrod, Mark S; Furusawa, Yoshiya; Uchihori, Yukio

    2015-03-01

    The geometric locations of ion traversals in mammalian cells constitute important information in the study of heavy ion-induced biological effect. Single ion traversal through a cellular nucleus produces complex and massive DNA damage at a nanometer level, leading to cell inactivation, mutations and transformation. We present a novel approach that uses a fluorescent nuclear track detector (FNTD) for the simultaneous detection of the geometrical images of ion traversals and DNA damage in single cells using confocal microscopy. HT1080 or HT1080-53BP1-GFP cells were cultured on the surface of a FNTD and exposed to 5.1-MeV/n neon ions. The positions of the ion traversals were obtained as fluorescent images of a FNTD. Localized DNA damage in cells was identified as fluorescent spots of γ-H2AX or 53BP1-GFP. These track images and images of damaged DNA were obtained in a short time using a confocal laser scanning microscope. The geometrical distribution of DNA damage indicated by fluorescent γ-H2AX spots in fixed cells or fluorescent 53BP1-GFP spots in living cells was found to correlate well with the distribution of the ion traversals. This method will be useful for evaluating the number of ion hits on individual cells, not only for micro-beam but also for random-beam experiments.

  2. Tracks to therapy

    NASA Technical Reports Server (NTRS)

    Katz, R.; Cucinotta, F. A.

    1999-01-01

    Studies of the structure of particle tracks have led to models of track effects based on radial dose and radiobiological target theory that have been very successful in describing and predicting track effects in physical, chemical, and biological systems. For describing mammalian cellular inactivation two inactivation modes are required, called gamma-kill and ion-kill, the first due to synergistic effects of delta rays from adjacent ion paths thus resembling the effects from gamma rays, and the second to the effects of single ion transits through a cell nucleus. The ion-kill effect is more severe, where the fraction of cells experiencing ion kill is responsible for a decrease in the oxygen enhancement ratio, and an increase in relative biological effectiveness, but these are accompanied by loss of repair, hence to a reduction in the efficiency of fractionation in high LET therapy, as shown by our calculations for radiobiological effects in the "spread out Bragg Peak".

  3. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  4. A new method for measuring ion clusters produced by charged particles in nanometre track sections of DNA size

    NASA Astrophysics Data System (ADS)

    Pszona, S.; Kula, J.; Marjanska, S.

    2000-06-01

    A new method is presented for measuring the frequency distribution of ion clusters, formed in nanometre sections of track, by charged particles. The simulated nanometer-size sites are produced in a device, called the Jet Counter. It consists of a pulse-operated valve which injects an expanding jet of nitrogen gas into an interaction chamber. The resulting distributions of ion clusters produced by alpha particle tracks (from 241Am) in sections ranging from 2 to around 10 nm at unit density in nitrogen gas have been measured. Analysis of the experimental results confirm that the primary ionisation distributions produced in the nanometer sections comply with the Poisson distribution. The ionisation cluster distributions produced in the 2-10 nm track-segments are the first ever to be determined experimentally.

  5. Electrical conduction of ion tracks in tetrahedral amorphous carbon: temperature, field and doping dependence and comparison with matrix data

    NASA Astrophysics Data System (ADS)

    Krauser, J.; Gehrke, H.-G.; Hofsäss, H.; Amani, J.; Trautmann, C.; Weidinger, A.

    2015-12-01

    This paper gives an extended overview of the electrical properties of ion tracks in hydrogen-free tetrahedral amorphous carbon (ta-C) with a sp3 bond fraction of about 80%. The films were grown by mass selected ion beam deposition of 100 eV 12C+ ions. The ion tracks are generated by irradiation of ta-C films with uranium ions of 1 GeV kinetic energy. Along the ion path a conversion from diamond-like (sp3) carbon to graphite-like (sp2) carbon takes place. Topography and current measurements of individual ion tracks were performed by atomic force microscopy at ambient temperature. The temperature dependence of the electric conductivity was studied between 15 and 390 K by means of 0.28 mm2 large contact pads averaging over about 107 tracks. For each sample and at each temperature the conductivity as a function of the applied electrical field (non-ohmic behaviour) was measured separately and the data were extrapolated to field zero. In this way, the zero-field conductivity was determined independent from the field dependence. In spite of large differences in the absolute values, the temperature dependence of the zero-field conductivities is found to be very similar in shape for all samples. The conductivities follow a {T}-{1/4} law up to temperatures slightly below room temperature. At higher temperatures a transport mechanism based on over-barrier hopping dominates with an activation energy of about 220 meV for tracks and 260 meV for the ta-C matrix. The field dependence measurements show that the deviation of the I-V characteristics from ohmic behaviour decreases with increasing zero-field conductivity. We also tested Cu-doped ta-C samples and found that they conduct significantly better than pure ta-C. However, the doping also increases the zero-field conductivity resulting in a weaker contrast between the track and matrix. The data are interpreted within the so-called ‘barrier model’ where the electrons are assumed to move fairly freely in well-conducting sp2

  6. Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations.

    PubMed

    Allen, Samuel J; Eaton, Rachel M; Bush, Matthew F

    2016-09-20

    Ion mobility separation of native-like protein and protein complex ions expands the structural information available through native mass spectrometry analysis. Here, we implement Structures for Lossless Ion Manipulations (SLIM) for the analysis of native-like ions. SLIM has been shown previously to operate with near lossless transmission of ions up to 3000 Da in mass. Here for the first time, SLIM was used to separate native-like protein and protein complex ions ranging in mass from 12 to 145 kDa. The resulting arrival-time distributions were monomodal and were used to determine collision cross section values that are within 3% of those determined from radio-frequency-confining drift cell measurements. These results are consistent with the retention of native-like ion structures throughout these experiments. The apparent resolving powers of native-like ions measured using SLIM are as high as 42, which is the highest value reported directly from experimental data for the native-like ion of a protein complex. Interestingly, the apparent resolving power depends strongly on the identity of the analyte, suggesting that the arrival-time distributions of these ions may have contributions from an ensemble of structures in the gas phase that is unique to each analyte. These results suggest that the broad range of emerging SLIM technologies may all be adaptable to the analysis of native-like ions, which will enable future applications in the areas of structural biology, biophysics, and biopharmaceutical characterization.

  7. A Phase-tracking Snow Micro-structure Model

    NASA Astrophysics Data System (ADS)

    Slaughter, A. E.; Zabaras, N.

    2012-12-01

    Utilizing a methodology derived from models for phase transitions in alloy solidification [1], a 3D finite element (FE) model for snow metamorphism was developed. Avalanches are known to occur due to the existence of a weak-layer of faceted crystals, which form due to temperature gradients within the snow through a process known as kinetic metamorphism [2]. In general, snow models are limited in their ability to model these microstructural changes, especially in three dimensions, and rely on effective properties. To enhance the tools available to avalanche researchers a finite element model was developed capable of tracking vapor deposition within the snow. This is accomplished using a fixed-domain, stabilized finite element solution for the energy, mass, momentum, and transport equations. Using a level-set parameter the domain is separated into either solid or fluid components and along the phase-change boundary a "mushy-zone" is establish [1, 3]. This zone is modeled as porous media that includes the effects of shrinkage and density changes [1]. The basis of the model is the open-source C++ libMesh FE library, as such the model includes adaptive mesh coarsening and refinement and relies on domain decomposition for optimum parallel performance. This work is the initial phase of an ongoing research project that aims to demonstrate the ability to model snow at the micro-structural level and move away from the common coarse, effective property modeling techniques. It will serve as the deterministic basis for a multi-scale, stochastic model of snow that will account for uncertainties such as poorly understood growth properties and measurement variability. Future applications may include the inclusion of liquid melt and include external forces, yielding a comprehensive thermo-mechanical model that could evolve and fracture. [1] D. Samanta, N. Zabaras (2005), Modelling convection in solidification processes using stabilized finite element techniques, J. Numer. Meth. Eng

  8. Gas-phase transformation of phosphatidylcholine cations to structurally informative anions via ion/ion chemistry.

    PubMed

    Stutzman, John R; Blanksby, Stephen J; McLuckey, Scott A

    2013-04-02

    Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/18:1)) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC(18:1/16:0)), were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, [PC + PDPA - H](-). Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating [PC - CH3](-). Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low-abundance acyl neutral losses as free acids and ketenes. Product ion spectra of [PC - CH3](-) suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry.

  9. Defect induced modification of structural, topographical and magnetic properties of zinc ferrite thin films by swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Raghavan, Lisha; Joy, P. A.; Vijaykumar, B. Varma; Ramanujan, R. V.; Anantharaman, M. R.

    2017-04-01

    Swift heavy ion irradiation provides unique ways to modify physical and chemical properties of materials. In ferrites, the magnetic properties can change significantly as a result of swift heavy ion irradiation. Zinc ferrite is an antiferromagnet with a Neel temperature of 10 K and exhibits anomalous magnetic properties in the nano regime. Ion irradiation can cause amorphisation of zinc ferrite thin films; thus the role of crystallinity on magnetic properties can be examined. The influence of surface topography in these thin films can also be studied. Zinc ferrite thin films, of thickness 320 nm, prepared by RF sputtering were irradiated with 100 MeV Ag ions. Structural characterization showed amorphisation and subsequent reduction in particle size. The change in magnetic properties due to irradiation was correlated with structural and topographical effects of ion irradiation. A rough estimation of ion track radius is done from the magnetic studies.

  10. Active structured learning for cell tracking: algorithm, framework, and usability.

    PubMed

    Lou, Xinghua; Schiegg, Martin; Hamprecht, Fred A

    2014-04-01

    One distinguishing property of life is its temporal dynamics, and it is hence only natural that time lapse experiments play a crucial role in modern biomedical research areas such as signaling pathways, drug discovery or developmental biology. Such experiments yield a very large number of images that encode complex cellular activities, and reliable automated cell tracking emerges naturally as a prerequisite for further quantitative analysis. However, many existing cell tracking methods are restricted to using only a small number of features to allow for manual tweaking. In this paper, we propose a novel cell tracking approach that embraces a powerful machine learning technique to optimize the tracking parameters based on user annotated tracks. Our approach replaces the tedious parameter tuning with parameter learning and allows for the use of a much richer set of complex tracking features, which in turn affords superior prediction accuracy. Furthermore, we developed an active learning approach for efficient training data retrieval, which reduces the annotation effort to only 17%. In practical terms, our approach allows life science researchers to inject their expertise in a more intuitive and direct manner. This process is further facilitated by using a glyph visualization technique for ground truth annotation and validation. Evaluation and comparison on several publicly available benchmark sequences show significant performance improvement over recently reported approaches. Code and software tools are provided to the public.

  11. Local structures of ions at ion-exchange resin/solution interface.

    PubMed

    Harada, Makoto; Okada, Tetsuo

    2005-08-26

    The local structures of Cl- and Br- in anion-exchange resins have been studied by X-ray absorption fine structure (XAFS), and separation selectivity is discussed on the basis of results. When two different anion-exchange resins having trimethylammonium and dimethylammonium groups as anion-exchange groups are employed for ion-exchange experiments, slightly higher Br- selectivity has been obtained with the former. XAFS has indicated that the average hydration numbers for a given anion is not affected by the structure of the ion-exchange group, but that the extent of ion-association between the anion and the ion-exchange groups depends on the type of the ion-exchange group. Shorter interaction distance (and in turn stronger ion-association) has been confirmed for the dimethylammonium-type resin, and is consistent with lower Br- selectivity of this resin.

  12. Helical Pulse Line Structures for Ion Acceleration

    SciTech Connect

    Briggs, R.J.; Reginato, L.L.; Waldron, W.L.

    2005-05-01

    The basic concept of the ''Pulse Line Ion Accelerator'' is presented, where pulse power sources create a ramped traveling wave voltage pulse on a helical pulse line. Ions can surf on this traveling wave and achieve energy gains much larger than the peak applied voltage. Tapered and untapered lines are compared, and a transformer coupling technique for launching the wave is described.

  13. Analysis and design of on-grade reinforced concrete track support structures

    NASA Technical Reports Server (NTRS)

    Mclean, F. G.; Williams, R. D.; Greening, L. R.

    1972-01-01

    For the improvement of rail service, the Department of Transportation, Federal Rail Administration, is sponsoring a test track on the Atchison, Topeka, and Santa Fe Railway. The test track will contain nine separate rail support structures, including one conventional section for control and three reinforced concrete structures on grade, one slab and two beam sections. The analysis and design of these latter structures was accomplished by means of the finite element method, NASTRAN, and is presented.

  14. Ion aggregation in high salt solutions. II. Spectral graph analysis of water hydrogen-bonding network and ion aggregate structures.

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2014-10-21

    Graph theory in mathematics and computer science is the study of graphs that are structures with pairwise connections between any objects. Here, the spectral graph theory and molecular dynamics simulation method are used to describe both morphological variation of ion aggregates in high salt solutions and ion effects on water hydrogen-bonding network structure. From the characteristic value analysis of the adjacency matrices that are graph theoretical representations of ion clusters, ion networks, and water H-bond structures, we obtained the ensemble average eigenvalue spectra revealing intricate connectivity and topology of ion aggregate structure that can be classified as either ion cluster or ion network. We further show that there is an isospectral relationship between the eigenvalue spectra of ion networks in high KSCN solutions and those of water H-bonding networks. This reveals the isomorphic relationship between water H-bond structure and ion-ion network structure in KSCN solution. On the other hand, the ion clusters formed in high NaCl solutions are shown to be graph-theoretically and morphologically different from the ion network structures in KSCN solutions. These observations support the bifurcation hypothesis on large ion aggregate growth mechanism via either ion cluster or ion network formation. We thus anticipate that the present spectral graph analyses of ion aggregate structures and their effects on water H-bonding network structures in high salt solutions can provide important information on the specific ion effects on water structures and possibly protein stability resulting from protein-water interactions.

  15. Whole cell structural imaging at 20 nanometre resolutions using MeV ions

    NASA Astrophysics Data System (ADS)

    Watt, F.; Chen, X.; Chen, C.-B.; Udalagama, CNB; van Kan, J. A.; Bettiol, A. A.

    2013-07-01

    MeV proton and alpha (helium ion) particle beams can now be focused to 20 nm spot sizes, and ion/matter simulations using the DEEP computer code show that these resolutions are maintained through the top micrometre or so of organic material. In addition, the energy deposition profiles of the transmitted ions are laterally constrained to a few nanometers from the initial ion path. This paves the way for high resolution structural imaging of relatively thick biological material, e.g. biological cells. Examples are shown of high resolution structural imaging of whole biological cells (MRC5) using on-axis scanning transmission ion microscopy (STIM). Nanoparticles have the ability to cross the cell membrane, and may therefore prove useful as drug delivery probes. We show that the combination of on-axis STIM for imaging the cell interior, and off-axis STIM for imaging gold nanoparticles with enhanced contrast within the cell, represents a powerful set of ion beam techniques for tracking gold nanoparticles in biological cells. Whole cell imaging at high spatial resolutions represents a new area for nuclear microprobes.

  16. Design and Construction of Optimized Electrochemical Cell and Data Analysis System for Etching of Ion Tracks and Electro Deposition of Nano and Micro Wires in Porous Ion Tracks Foils

    NASA Astrophysics Data System (ADS)

    ShakeriJooybari, B.; Moghimi, R.; Golgiri, D.; Afarideh, H.; Lamehi-Rachti, M.; Ghergherehchi, M.

    In this work, an optimized computer controlled electrochemical cell were designed and constructed. This Electrolytic cell was used for etching latent ion tracks and electrochemical deposition of wires in pores of etched-ion tracks foils. The applied voltage and current through the electrochemical cell during the etching and electrodeposition were measured and monitored in real time by a Data Analysis system. Monitoring the current time curve during the filling of pores and growth of micro and nano wires allows one to stop the deposition process after a given time to obtain nano- and micro wire of a predefined length. In this work, Design and manufacture of a sealed electrochemical cell was done in a manner that one can change distance between electrodes and geometry of cathodes. Data analysis system was used to measuring and monitoring of applied voltage and current through the cell consists of three parts: Amplifier, Data acquisition (DAQ) system and Software. A current amplifier that used in data analysis system is a log ratio amplifier. A log ratio amplifier provides an output voltage proportional to the log base 10 of the ratio input current I1 (current during the electrodeposition of wire in cell) and Input current I2(flexible current of precision current source). A DAQ reading output voltage of amplifier and send to Computer. With lab view software analyzed the voltage and converted to the current corresponding to the electrodeposition of wires. Current amplifier designed and built in this work is a noise suppression that can measure small current through the cell with high accuracy. Advantage of proposed log ratio amplifier is one can used this amplifier for measuring and monitoring of current during the filling of pores and growth of wires in the etched ion track foils with various track density.

  17. Fission track-secondary ion mass spectrometry as a tool for detecting the isotopic signature of individual uranium containing particles.

    PubMed

    Esaka, Fumitaka; Lee, Chi-Gyu; Magara, Masaaki; Kimura, Takaumi

    2012-04-06

    A fission track technique was used as a sample preparation method for subsequent isotope abundance ratio analysis of individual uranium containing particles with secondary ion mass spectrometry (SIMS) to measure the particles with higher enriched uranium efficiently. A polycarbonate film containing particles was irradiated with thermal neutrons and etched with 6M NaOH solution. Each uranium containing particle was then identified by observing fission tracks created and a portion of the film having a uranium containing particle was cut out and put onto a glassy carbon planchet. The polycarbonate film, which gave the increases of background signals on the uranium mass region in SIMS analysis, was removed by plasma ashing with 200 W for 20 min. In the analysis of swipe samples having particles containing natural (NBL CRM 950a) or low enriched uranium (NBL CRM U100) with the fission track-SIMS method, uranium isotope abundance ratios were successfully determined. This method was then applied to the analysis of a real inspection swipe sample taken at a nuclear facility. As a consequence, the range of (235)U/(238)U isotope abundance ratio between 0.0276 and 0.0438 was obtained, which was higher than that measured by SIMS without using a fission track technique (0.0225 and 0.0341). This indicates that the fission track-SIMS method is a powerful tool to identify the particle with higher enriched uranium in environmental samples efficiently.

  18. Simulations of DSB Yields and Radiation-induced Chromosomal Aberrations in Human Cells Based on the Stochastic Track Structure iIduced by HZE Particles

    NASA Technical Reports Server (NTRS)

    Ponomarev, Artem; Plante, Ianik; George, Kerry; Wu, Honglu

    2014-01-01

    The formation of double-strand breaks (DSBs) and chromosomal aberrations (CAs) is of great importance in radiation research and, specifically, in space applications. We are presenting a new particle track and DNA damage model, in which the particle stochastic track structure is combined with the random walk (RW) structure of chromosomes in a cell nucleus. The motivation for this effort stems from the fact that the model with the RW chromosomes, NASARTI (NASA radiation track image) previously relied on amorphous track structure, while the stochastic track structure model RITRACKS (Relativistic Ion Tracks) was focused on more microscopic targets than the entire genome. We have combined chromosomes simulated by RWs with stochastic track structure, which uses nanoscopic dose calculations performed with the Monte-Carlo simulation by RITRACKS in a voxelized space. The new simulations produce the number of DSBs as function of dose and particle fluence for high-energy particles, including iron, carbon and protons, using voxels of 20 nm dimension. The combined model also calculates yields of radiation-induced CAs and unrejoined chromosome breaks in normal and repair deficient cells. The joined computational model is calibrated using the relative frequencies and distributions of chromosomal aberrations reported in the literature. The model considers fractionated deposition of energy to approximate dose rates of the space flight environment. The joined model also predicts of the yields and sizes of translocations, dicentrics, rings, and more complex-type aberrations formed in the G0/G1 cell cycle phase during the first cell division after irradiation. We found that the main advantage of the joined model is our ability to simulate small doses: 0.05-0.5 Gy. At such low doses, the stochastic track structure proved to be indispensable, as the action of individual delta-rays becomes more important.

  19. Simulations of DSB Yields and Radiation-induced Chromosomal Aberrations in Human Cells Based on the Stochastic Track Structure Induced by HZE Particles

    NASA Technical Reports Server (NTRS)

    Ponomarev, Artem; Plante, Ianik; George, Kerry; Wu, Honglu

    2014-01-01

    The formation of double-strand breaks (DSBs) and chromosomal aberrations (CAs) is of great importance in radiation research and, specifically, in space applications. We are presenting a new particle track and DNA damage model, in which the particle stochastic track structure is combined with the random walk (RW) structure of chromosomes in a cell nucleus. The motivation for this effort stems from the fact that the model with the RW chromosomes, NASARTI (NASA radiation track image) previously relied on amorphous track structure, while the stochastic track structure model RITRACKS (Relativistic Ion Tracks) was focused on more microscopic targets than the entire genome. We have combined chromosomes simulated by RWs with stochastic track structure, which uses nanoscopic dose calculations performed with the Monte-Carlo simulation by RITRACKS in a voxelized space. The new simulations produce the number of DSBs as function of dose and particle fluence for high-energy particles, including iron, carbon and protons, using voxels of 20 nm dimension. The combined model also calculates yields of radiation-induced CAs and unrejoined chromosome breaks in normal and repair deficient cells. The joined computational model is calibrated using the relative frequencies and distributions of chromosomal aberrations reported in the literature. The model considers fractionated deposition of energy to approximate dose rates of the space flight environment. The joined model also predicts of the yields and sizes of translocations, dicentrics, rings, and more complex-type aberrations formed in the G0/G1 cell cycle phase during the first cell division after irradiation. We found that the main advantage of the joined model is our ability to simulate small doses: 0.05-0.5 Gy. At such low doses, the stochastic track structure proved to be indispensable, as the action of individual delta-rays becomes more important.

  20. The structure of the stable negative ion of calcium

    SciTech Connect

    Pegg, D.J.; Thompson, J.S.; Compton, R.N.; Alton, G.D.

    1988-01-01

    The structure of the Ca/sup /minus// ion has been determined using a crossed laser-ion beams apparatus. The photoelectron detachment spectrum shows that, contrary to earlier expectations, the Ca/sup /minus// ion is stably bound in the (4s/sup 2/4p)/sup 2/p state. The electron affinity of Ca was measured to be 0.043 /sup + -/ 0.007 eV.

  1. Experimental impact features in Stardust aerogel: How track morphology reflects particle structure, composition, and density

    NASA Astrophysics Data System (ADS)

    Kearsley, Anton T.; Burchell, Mark J.; Price, Mark C.; Cole, Michael J.; Wozniakiewicz, Penelope J.; Ishii, Hope A.; Bradley, John P.; Fries, Marc; Foster, Nicholas J.

    2012-04-01

    The Stardust collector shows diverse aerogel track shapes created by impacts of cometary dust. Tracks have been classified into three broad types (A, B, and C), based on relative dimensions of the elongate "stylus" (in Type A "carrots") and broad "bulb" regions (Types B and C), with occurrence of smaller "styli" in Type B. From our experiments, using a diverse suite of projectile particles shot under Stardust cometary encounter conditions onto similar aerogel targets, we describe differences in impactor behavior and aerogel response resulting in the observed range of Stardust track shapes. We compare tracks made by mineral grains, natural and artificial aggregates of differing subgrain sizes, and diverse organic materials. Impacts of glasses and robust mineral grains generate elongate, narrow Type A tracks (as expected), but with differing levels of abrasion and lateral branch creation. Aggregate particles, both natural and artificial, of a wide range of compositions and volatile contents produce diverse Type B or C shapes. Creation of bulbous tracks is dependent upon impactor internal structure, grain size distribution, and strength, rather than overall grain density or content of volatile components. Nevertheless, pure organic particles do create Type C, or squat Type A* tracks, with length to width ratios dependent upon both specific organic composition and impactor grain size. From comparison with the published shape data for Stardust aerogel tracks, we conclude that the abundant larger Type B tracks on the Stardust collector represent impacts by particles similar to our carbonaceous chondrite meteorite powders.

  2. Ion heating in an auroral potential structure

    NASA Astrophysics Data System (ADS)

    Anastasiadis, A.; Daglis, I. A.; Tsironis, C.

    2004-06-01

    We investigate the interaction of O+ ions with a one-dimensional potential well, using Hamiltonian formulation. Heating of plasma originating in the terrestrial ionosphere plays a catalytic role in solar-driven magnetic storms, which dissipate energy globally within the magnetosphere of the earth. An interesting candidate for ionospheric plasma heating is a potential well located at auroral arcs in the high-latitude magnetosphere. We consider a potential with an exponential form, having a characteristic length Lx. The oxygen ions drift towards the auroral arc in the presence of a constant magnetic field Bz and a constant electric field Ey. The orbits of individual ions for different initial conditions - phase angle and kinetic energy - are traced. Our results show that, depending upon the initial conditions, test particles can be either accelerated or decelerated. Furthermore, we perform a parametric study for the interactions of mono-energetic and Maxwellian type of initial ion distribution - using random phase angle injection of the particles - with respect to our main model parameter, the characteristic length of the potential Lx. We conclude that for characteristic lengths comparable to twice the ion gyroradius, the O+ population is accelerated.

  3. Simulation analysis for ion assisted fast ignition using structured targets

    NASA Astrophysics Data System (ADS)

    Sakagami, H.; Johzaki, T.; Sunahara, A.; Nagatomo, H.

    2016-05-01

    As the heating efficiency by fast electrons in the fast ignition scheme is estimated to be very low due to their large divergence angle and high energy. To mitigate this problem, low-density plastic foam, which can generate not only proton (H+) but also carbon (C6+) beams, can be introduced to currently used cone-guided targets and additional core heating by ions is expected. According to 2D PIC simulations, it is found that the ion beams also diverge by the static electric field and concave surface deformation. Thus structured targets are suggested to optimize ion beam characteristics, and their improvement and core heating enhancement by ion beams are confirmed.

  4. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    PubMed Central

    Zhang, Xinyu; Garimella, Sandilya V. B.; Prost, Spencer A; Webb, Ian K; Chen, Tsung-Chi; Tang, Keqi; Tohnachev, Aleksey V.; Norheim, Randolph V.; Baker, Erin S.; Anderson, Gordon A; Ibrahim, Yehia M.; Smith, Richard D.

    2015-01-01

    A new Structures for Lossless lon Manipulations (SUM) module, having electrode arrays patterned on a pair of parallel printed circuit boards (PCB), was constructed and utilized to investigate capabilities for ion trapping at a pressure of 4 Torr. Positive ions were confined by application of RF voltages to a series of inner rung electrodes with alternating phase on adjacent electrodes, in conjunction with positive DC potentials on surrounding guard electrodes on each PCB. An axial DC :field was also introduced by stepwise varying the DC potentials applied to the inner rung electrodes to control the ion transport and accumulation inside the ion trapping region. We show that ions can be trapped and accumulated with up to 100% efficiency, stored for at least 5 h with no significant losses, and then could be rapidly ejected from the SUM trap. The present results provide a foundation for the development of much more complex SUM devices that facilitate extended ion manipulations. PMID:25971536

  5. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    SciTech Connect

    Zhang, Xinyu; Garimella, Venkata BS; Prost, Spencer A.; Webb, Ian K.; Chen, Tsung-Chi; Tang, Keqi; Tolmachev, Aleksey V.; Norheim, Randolph V.; Baker, Erin Shammel; Anderson, Gordon A.; Ibrahim, Yehia M.; Smith, Richard D.

    2015-06-16

    A structure for lossless ion manipulation (SLIM) module was constructed with electrode arrays patterned on a pair of parallel printed circuit boards (PCB) separated by 5 mm and utilized to investigate capabilities for ion trapping at 4 Torr. Positive ions were confined by application of RF having alternating phases on a series of inner rung electrodes and by positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potential of the inner rung electrodes so as to control the ion transport and accumulation inside the ion trap. We show that ions could be trapped and accumulated with 100% efficiency, stored for at least 5 hours with no losses, and could be rapidly ejected from the SLIM trap.

  6. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations.

    PubMed

    Hamid, Ahmed M; Ibrahim, Yehia M; Garimella, Sandilya V B; Webb, Ian K; Deng, Liulin; Chen, Tsung-Chi; Anderson, Gordon A; Prost, Spencer A; Norheim, Randolph V; Tolmachev, Aleksey V; Smith, Richard D

    2015-11-17

    We report on the development and characterization of a traveling wave (TW)-based Structures for Lossless Ion Manipulations (TW-SLIM) module for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters are reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200-2500) utilizing a confining rf waveform (∼1 MHz and ∼300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ∼32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. The combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.

  7. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations

    DOE PAGES

    Hamid, Ahmed M.; Ibrahim, Yehia M.; Garimella, Venkata BS; ...

    2015-10-28

    We report on the development and characterization of a new traveling wave-based Structure for Lossless Ion Manipulations (TW-SLIM) for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters aremore » reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200–2500) utilizing a confining rf waveform (~1 MHz and ~300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ~32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. In conclusion, the combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.« less

  8. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations

    SciTech Connect

    Hamid, Ahmed M.; Ibrahim, Yehia M.; Garimella, Venkata BS; Webb, Ian K.; Deng, Liulin; Chen, Tsung-Chi; Anderson, Gordon A.; Prost, Spencer A.; Norheim, Randolph V.; Tolmachev, Aleksey V.; Smith, Richard D.

    2015-10-28

    We report on the development and characterization of a new traveling wave-based Structure for Lossless Ion Manipulations (TW-SLIM) for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters are reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200–2500) utilizing a confining rf waveform (~1 MHz and ~300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ~32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. In conclusion, the combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.

  9. Method for fabricating MNOS structures utilizing hydrogen ion implantation

    NASA Astrophysics Data System (ADS)

    Saks, N. S.

    1984-05-01

    An improved method for reducing the density of electronic trapping states and fixed insulator charge in the thin oxide layer of an MNOS structure is discussed. The method includes the steps of implanting hydrogen ions in field region of the oxide layer and annealing the MNOS structure at 400 deg C to cause the ions to diffuse laterally into the gate region of the oxide layer.

  10. Robotic Manifold Tracking of Coherent Structures in Flows

    DTIC Science & Technology

    2012-05-01

    analysis techniques to derive a tracking strategy for a team of robots. The cooperative control strategy leverages the spatio-temporal sensing capa...Ĵt‖ chosen to be in the interval [2dMin,2dMax]. IV. ANALYSIS In this section, we discuss the theoretical feasibility of the proposed saddle straddle...turbulence,” Phys. D, vol. 147, pp. 352–370, Dec 2000. [2] S. C. Shadden, F. Lekien, and J. E. Marsden , “Definition and properties of lagrangian coherent

  11. Computational Model Tracking Primary Electrons, Secondary Electrons, and Ions in the Discharge Chamber of an Ion Engine

    NASA Technical Reports Server (NTRS)

    Mahalingam, Sudhakar; Menart, James A.

    2005-01-01

    Computational modeling of the plasma located in the discharge chamber of an ion engine is an important activity so that the development and design of the next generation of ion engines may be enhanced. In this work a computational tool called XOOPIC is used to model the primary electrons, secondary electrons, and ions inside the discharge chamber. The details of this computational tool are discussed in this paper. Preliminary results from XOOPIC are presented. The results presented include particle number density distributions for the primary electrons, the secondary electrons, and the ions. In addition the total number of a particular particle in the discharge chamber as a function of time, electric potential maps and magnetic field maps are presented. A primary electron number density plot from PRIMA is given in this paper so that the results of XOOPIC can be compared to it. PRIMA is a computer code that the present investigators have used in much of their previous work that provides results that compare well to experimental results. PRIMA only models the primary electrons in the discharge chamber. Modeling ions and secondary electrons, as well as the primary electrons, will greatly increase our ability to predict different characteristics of the plasma discharge used in an ion engine.

  12. Ion nose spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

    2016-12-01

    We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  13. Atomistic simulation of defects formation and structure transitions in U-Mo alloys at swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Kolotova, L. N.; Starikov, S. V.

    2017-01-01

    At irradiation of swift heavy ions, the track formation frequently takes place in nuclear materials. There is a large interest to understanding of the mechanisms of defects/track formation at this phenomenon. In this work, the atomistic simulation of defects formation and melting in U-Mo alloys at irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes at irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation at irradiation in the various conditions are calculated.

  14. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

    DOE PAGES

    Chen, Tsung-Chi; Ibrahim, Yehia M.; Webb, Ian K.; ...

    2016-01-11

    The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in a more reliable and cost-effective manner, while opening opportunities for much more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolationmore » and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. Lastly, we observed a linear increase in ion intensity with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.« less

  15. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    SciTech Connect

    Garimella, Sandilya V. B; Ibrahim, Yehia M.; Webb, Ian K.; Tolmachev, Aleksey V.; Zhang, Xinyu; Prost, Spencer A.; Anderson, Gordon A.; Smith, Richard D.

    2014-09-26

    Here we report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g. turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also feasible. Lastly, the performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which agree closely with experimental and theoretical IMS performance for a conventional drift tube design.

  16. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    PubMed Central

    Garimella, Sandilya V.B.; Ibrahim, Yehia M.; Webb, Ian K.; Tolmachev, Aleksey V.; Zhang, Xinyu; Prost, Spencer A.; Anderson, Gordon A.; Smith, Richard D.

    2014-01-01

    We report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining and manipulating ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g. turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also shown feasible. The performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which are also shown to agree closely with experimental and theoretical IMS performance for a conventional drift tube design. PMID:25257188

  17. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    DOE PAGES

    Garimella, Sandilya V. B; Ibrahim, Yehia M.; Webb, Ian K.; ...

    2014-09-26

    Here we report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g.more » turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also feasible. Lastly, the performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which agree closely with experimental and theoretical IMS performance for a conventional drift tube design.« less

  18. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

    SciTech Connect

    Chen, Tsung-Chi; Ibrahim, Yehia M.; Webb, Ian K.; Garimella, Sandilya V. B.; Zhang, Xing; Hamid, Ahmed M.; Deng, Liulin; Karnesky, William E.; Prost, Spencer A.; Sandoval, Jeremy A.; Norheim, Randolph V.; Anderson, Gordon A.; Tolmachev, Aleksey V.; Baker, Erin Shammel; Smith, Richard D.

    2016-01-11

    The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in a more reliable and cost-effective manner, while opening opportunities for much more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolation and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. Lastly, we observed a linear increase in ion intensity with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.

  19. Structural resolution of 4-substituted proline diastereomers with ion mobility spectrometry via alkali metal ion cationization.

    PubMed

    Flick, Tawnya G; Campuzano, Iain D G; Bartberger, Michael D

    2015-03-17

    The chirality of substituents on an amino acid can significantly change its mode of binding to a metal ion, as shown here experimentally by traveling wave ion mobility spectrometry-mass spectrometry (TWIMS-MS) of different proline isomeric molecules complexed with alkali metal ions. Baseline separation of the cis- and trans- forms of both hydroxyproline and fluoroproline was achieved using TWIMS-MS via metal ion cationization (Li(+), Na(+), K(+), and Cs(+)). Density functional theory calculations indicate that differentiation of these diastereomers is a result of the stabilization of differing metal-complexed forms adopted by the diastereomers when cationized by an alkali metal cation, [M + X](+) where X = Li, Na, K, and Cs, versus the topologically similar structures of the protonated molecules, [M + H](+). Metal-cationized trans-proline variants exist in a linear salt-bridge form where the metal ion interacts with a deprotonated carboxylic acid and the proton is displaced onto the nitrogen atom of the pyrrolidine ring. In contrast, metal-cationized cis-proline variants adopt a compact structure where the carbonyl of the carboxylic acid, nitrogen atom, and if available, the hydroxyl and fluorine substituent solvate the metal ion. Experimentally, it was observed that the resolution between alkali metal-cationized cis- and trans-proline variants decreases as the size of the metal ion increases. Density functional theory demonstrates that this is due to the decreasing stability of the compact charge-solvated cis-proline structure with increased metal ion radius, likely a result of steric hindrance and/or weaker binding to the larger metal ion. Furthermore, the unique structures adopted by the alkali metal-cationized cis- and trans-proline variants results in these molecules having significantly different quantum mechanically calculated dipole moments, a factor that can be further exploited to improve the diastereomeric resolution when utilizing a drift gas with a

  20. The Biological Effectiveness of Accelerated Particles for the Induction of Chromosome Damage: Track Structure Effects and Cytogenetic Signatures of High-LET Exposure

    NASA Technical Reports Server (NTRS)

    George, K.; Hada, M.; Chappell, L.; Cucinotta, F. A.

    2012-01-01

    Track structure models predict that at a fixed value of LET, particles with lower charge number, Z will have a higher biological effectiveness compared to particles with a higher Z. In this report we investigated how track structure effects induction of chromosomal aberration in human cells. Human lymphocytes were irradiated in vitro with various energies of accelerated iron, silicon, neon, or titanium ions and chromosome damage was assessed in using three color FISH chromosome painting in chemically induced PCC samples collected a first cell division post irradiation. The LET values for these ions ranged from 30 to 195 keV/micrometers. Of the particles studied, Neon ions have the highest biological effectiveness for induction of total chromosome damage, which is consistent with track structure model predictions. For complex-type exchanges 64 MeV/ u Neon and 450 MeV/u Iron were equally effective and induced the most complex damage. In addition we present data on chromosomes exchanges induced by six different energies of protons (5 MeV/u to 2.5 GeV/u). The linear dose response term was similar for all energies of protons suggesting that the effect of the higher LET at low proton energies is balanced by the production of nuclear secondaries from the high energy protons. All energies of protons have a much higher percentage of complex-type chromosome exchanges than gamma rays, signifying a cytogenetic signature for proton exposures.

  1. Online State-Based Structured SVM Combined With Incremental PCA for Robust Visual Tracking.

    PubMed

    Yin, Yingjie; Xu, De; Wang, Xingang; Bai, Mingran

    2015-09-01

    In this paper, we propose a robust state-based structured support vector machine (SVM) tracking algorithm combined with incremental principal component analysis (PCA). Different from the current structured SVM for tracking, our method directly learns and predicts the object's states and not the 2-D translation transformation during tracking. We define the object's virtual state to combine the state-based structured SVM and incremental PCA. The virtual state is considered as the most confident state of the object in every frame. The incremental PCA is used to update the virtual feature vector corresponding to the virtual state and the principal subspace of the object's feature vectors. In order to improve the accuracy of the prediction, all the feature vectors are projected onto the principal subspace in the learning and prediction process of the state-based structured SVM. Experimental results on several challenging video sequences validate the effectiveness and robustness of our approach.

  2. Track structure: time evolution from physics to chemistry.

    PubMed

    Dingfelder, M

    2006-01-01

    This review discusses interaction cross sections of charged particles (electrons, protons, light ions) with atoms and molecules. The focus is on biological relevant targets like liquid water which serves as a substitute of soft tissue in most Monte Carlo codes. The spatial distribution of energy deposition patterns by different radiation qualities and their importance to the time evolution from the physical to the chemical stage or radiation response is discussed. The determination of inelastic interaction cross sections for charged particles in condensed matter is discussed within the relativistic plane-wave Born approximation and semi-empirical models. The dielectric-response-function of liquid water is discussed.

  3. Ion Beam Synthesis Of Metal - Silicon Carbide - Si Multilayer Structures

    NASA Astrophysics Data System (ADS)

    Lindner, J. K. N.; Tsang, W. M.; Stritzker, B.; Wong, S. P.

    2003-08-01

    High doses of Ti, Ni, Mo, or W ions were implanted at elevated temperatures either conventionally or using a MEVVA ion source into ion beam synthesized Si/SiC/Si or SiC/Si layer structures in order to create metallic layers contacting the SiC. The depth distribution of metal atoms and the formation of silicide and carbide phases as well as the formation of cavities at the lower SiC/Si interface are studied by Rutherford backscattering spectroscopy (RBS) and cross-sectional transmission electron microscopy (XTEM). A brief survey of the effects ocurring in the ion beam metallization of SiC films is given and the benefit of using ion beams for metallization of thin films is elucidated.

  4. Time-domain analysis of neural tracking of hierarchical linguistic structures.

    PubMed

    Zhang, Wen; Ding, Nai

    2017-02-01

    When listening to continuous speech, cortical activity measured by MEG concurrently follows the rhythms of multiple linguistic structures, e.g., syllables, phrases, and sentences. This phenomenon was previously characterized in the frequency domain. Here, we investigate the waveform of neural activity tracking linguistic structures in the time domain and quantify the coherence of neural response phases over subjects listening to the same stimulus. These analyses are achieved by decomposing the multi-channel MEG recordings into components that maximize the correlation between neural response waveforms across listeners. Each MEG component can be viewed as the recording from a virtual sensor that is spatially tuned to a cortical network showing coherent neural activity over subjects. This analysis reveals information not available from previous frequency-domain analysis of MEG global field power: First, concurrent neural tracking of hierarchical linguistic structures emerges at the beginning of the stimulus, rather than slowly building up after repetitions of the same sentential structure. Second, neural tracking of the sentential structure is reflected by slow neural fluctuations, rather than, e.g., a series of short-lasting transient responses at sentential boundaries. Lastly and most importantly, it shows that the MEG responses tracking the syllabic rhythm are spatially separable from the MEG responses tracking the sentential and phrasal rhythms.

  5. Structure Change of PTFE by Low Energy Ion Irradiation

    NASA Astrophysics Data System (ADS)

    Watari, Kunio; Iwao, Toru; Yumoto, Motoshige

    The authors irradiate low energy nitrogen ion (100eV) on PTFE (poly-tetra-fluoro-ethylene) for surface modification. However, PTFE cannot anticipate adhesive strength improvement because it is collapse type polymer and weariness of surface occurs by ion irradiation. We paid attention to cross-linked structure to solve this problem. By this study introduce below, PTFE was changed collapse type polymer into cross-linked type polymer by rising temperature above the glass transition in the case of ion irradiation. As a result, the formation of the CF3 combination was restrained and collapse phenomenon was prevented by ion irradiation above the glass transition. In addition, it was suggested that cross-linked structure is effective for adhesive strength improvement by convolution of C1s spectrum and density profile.

  6. Ion Structure Near a Core-Shell Dielectric Nanoparticle

    NASA Astrophysics Data System (ADS)

    Ma, Manman; Gan, Zecheng; Xu, Zhenli

    2017-02-01

    A generalized image charge formulation is proposed for the Green's function of a core-shell dielectric nanoparticle for which theoretical and simulation investigations are rarely reported due to the difficulty of resolving the dielectric heterogeneity. Based on the formulation, an efficient and accurate algorithm is developed for calculating electrostatic polarization charges of mobile ions, allowing us to study related physical systems using the Monte Carlo algorithm. The computer simulations show that a fine-tuning of the shell thickness or the ion-interface correlation strength can greatly alter electric double-layer structures and capacitances, owing to the complicated interplay between dielectric boundary effects and ion-interface correlations.

  7. Dynamic ion structure factor of warm dense matter.

    PubMed

    Vorberger, J; Donko, Z; Tkachenko, I M; Gericke, D O

    2012-11-30

    The dynamics of the ion structure in warm dense matter is determined by molecular dynamics simulations using an effective ion-ion potential. This potential is obtained from ab initio simulations and has a strong short-range repulsion added to a screened Coulomb potential. Models based on static or dynamic local field corrections are found to be insufficient to describe the data. An extended Mermin approach, a hydrodynamic model, and the method of moments with local constraints are capable of reproducing the numerical results but have rather limited predictive powers as they all need some numerical data as input. The method of moments is found to be the most promising.

  8. Structural Modification of Nanocrystalline Ceria using Ion Beams

    SciTech Connect

    Zhang, Yanwen; Edmondson, Philip D; Varga, Tamas; Moll, Sandra; Namavar, Fereydoon; Weber, William J

    2011-01-01

    Exceptional size-dependent electronic-ionic conductivity of nanostructured ceria can significantly alter materials properties in chemical, physical, electronic and optical applications. Using energetic ions, we have demonstrated effective modification of interface volume and grain size in nanocrystalline ceria from a few nm up to ~ 25 nm, which is the critical region for controlling size-dependent material property. The unique self-healing response of radiation damage at grain boundaries is applied to control the grain size at nanoscale as a function of ion dose and irradiation temperature. Structural modification by energetic ions is proposed to achieve disirable electronic-ionic conductivity.

  9. Instrumentation by accelerometers and distributed optical fiber sensors of a real ballastless track structure

    NASA Astrophysics Data System (ADS)

    Chapeleau, Xavier; Cottineau, Louis-Marie; Sedran, Thierry; Cailliau, Joël; Gueguen, Ivan; Dumoulin, Jean

    2015-04-01

    While relatively expensive to build, ballastless track structures are presently seen as an attractive alternative to conventional ballast. Firstly, they are built quickly since the slabs can be cast in place in an automated fashion by a slipform paver. Secondly, with its service life of at least 60 years, they requires little maintenance and hence they offers great availability. Other reasons for using ballastless tracks instead of ballasted tracks are the lack of suitable ballast material and the need of less noise and vibration for high-speed, in particularly. In the framework of a FUI project (n° 072906053), a new ballastless track structure based on concrete slabs was designed and its thermal-mechanical behavior in fatigue under selected mechanical and thermal conditions was tested on a real scale mockup in our laboratory [1,2]. By applying to the slabs both together mechanical stresses and thermal gradients, finite elements simulation and experimental results show that the weather conditions influence significantly the concrete slabs curvatures and by the way, the contact conditions with the underlaying layers. So it is absolutely necessary to take into account this effect in the design of the ballastless track structures in order to guarantee a long target life of at least of 50 years. After design and experimental tests in laboratory, a real ballastless track structure of 1km was built in France at the beginning of year 2013. This structure has 2 tracks on which several trains circulate every day since the beginning of year 2014. Before the construction, it was decided to monitor this structure to verify that the mechanical behavior is conform to the simulations. One part of the instrumentation is dedicated to monitor quasi-continuously the evolution of the curvature of a concrete slab. For this, 2 accelerometers were fixed on the slab under the track. One was placed on the edge and the other in the middle of the slab. The acquisition of the signals by a

  10. Combining structured light and ladar for pose tracking in THz sensor management

    NASA Astrophysics Data System (ADS)

    Engström, Philip; Axelsson, Maria; Karlsson, Mikael

    2013-05-01

    Stand-off 3D THz imaging to detect concealed treats is currently under development. The technology can provide high resolution 3D range data of a passing subject showing layers of clothes and if there are concealed items. However, because it is a scanning sensor technology with a narrow field of view, the subjects pose and position need to be accurately tracked in real time to focus the system and map the imaged THz data to specific body parts. Structured light is a technique to obtain 3D range information. It is, for example, used in the Microsoft Kinect for pose tracking of game players in real time. We demonstrate how structured light can contribute to a THz sensor management system and track subjects in real time. The main advantage of structured light is its simplicity, the disadvantages are the sensitivity to lighting conditions and material properties as well as a relatively low accuracy. Time of flight laser scanning is a technique that complements structured light well, the accuracy is usually much higher and it is less sensitive to lighting conditions. We show that by combining the techniques it is possible to create a robust real time pose tracking system for THz sensor management. We present a concept system based on the Microsoft Kinect and a SICK LMS-511 laser scanner. The laser scanner is used for 2D tracking of the subjects, this tracking is then used to initialize and validate the Microsoft Kinect pose tracking. We have evaluated the sensors individually in both static and dynamic scenes and present their advantages and drawbacks.

  11. 200 MeV silver ion irradiation induced structural modification in YBa{sub 2}Cu{sub 3}O{sub 7-y} thin films at 89 K: An in situ x-ray diffraction study

    SciTech Connect

    Biswal, R.; Dash, B. N.; Mishra, N. C.; John, J.; Raychaudhuri, P.; Mallick, P.; Kulriya, P. K.; Avasthi, D. K.; Kanjilal, D.; Behera, D.; Mohanty, T.

    2009-09-01

    We report in situ x-ray diffraction (XRD) study of 200 MeV Ag ion irradiation induced structural modification in c-axis oriented YBa{sub 2}Cu{sub 3}O{sub 7-y} (YBCO) thin films at 89 K. The films remained c-axis oriented up to a fluence of 2x10{sup 13} ions cm{sup -2}, where complete amorphization sets in. The amorphous ion tracks, the strained region around these tracks, and irradiation induced point defects are shown to control the evolution of the structure with ion fluence. Secondary electrons emanating from the ion paths are shown to create point defects in a cylindrical region of 97 nm radius, which corresponds to their maximum range in the YBCO medium. The point defects are created exclusively in the CuO basal planes of fully oxygenated YBCO, which has not been possible, by other techniques including low energy ion irradiation and thermal quenching. The point defects led to a faster decrease in the integral intensity of XRD peaks at very low fluences of irradiation (PHI<=3x10{sup 10} ions cm{sup -2}) than what can be expected from amorphous tracks. The radius of amorphous ion tracks, estimated from the fluence dependence of integral XRD peak intensity beyond this fluence, was found to be 1.9 nm. Both point defect and the strained region around amorphous ion tracks are shown to contribute to the increase in the c-parameter at 89 K. The full width at half maximum (FWHM) of XRD peaks arising mostly due to the strained region around the ion tracks showed an incubation effect up to 10{sup 12} ions cm{sup -2}, before increasing at higher fluences. Fluence dependence of FWHM gives the cross section of the strained region as 37.9 nm{sup 2}, which is more than three times the cross section of the amorphous ion tracks.

  12. PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

    PubMed Central

    Agarwal, Vatsal; Remmert, Michael; Biegert, Andreas; Söding, Johannes

    2008-01-01

    Background During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When no homologs can be found in the protein structure database (PDB), the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available. Results PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models. Conclusion PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest. PMID:19025670

  13. Ion track based tunable device as humidity sensor: a neural network approach

    NASA Astrophysics Data System (ADS)

    Sharma, Mamta; Sharma, Anuradha; Bhattacherjee, Vandana

    2013-01-01

    Artificial Neural Network (ANN) has been applied in statistical model development, adaptive control system, pattern recognition in data mining, and decision making under uncertainty. The nonlinear dependence of any sensor output on the input physical variable has been the motivation for many researchers to attempt unconventional modeling techniques such as neural networks and other machine learning approaches. Artificial neural network (ANN) is a computational tool inspired by the network of neurons in biological nervous system. It is a network consisting of arrays of artificial neurons linked together with different weights of connection. The states of the neurons as well as the weights of connections among them evolve according to certain learning rules.. In the present work we focus on the category of sensors which respond to electrical property changes such as impedance or capacitance. Recently, sensor materials have been embedded in etched tracks due to their nanometric dimensions and high aspect ratio which give high surface area available for exposure to sensing material. Various materials can be used for this purpose to probe physical (light intensity, temperature etc.), chemical (humidity, ammonia gas, alcohol etc.) or biological (germs, hormones etc.) parameters. The present work involves the application of TEMPOS structures as humidity sensors. The sample to be studied was prepared using the polymer electrolyte (PEO/NH4ClO4) with CdS nano-particles dispersed in the polymer electrolyte. In the present research we have attempted to correlate the combined effects of voltage and frequency on impedance of humidity sensors using a neural network model and results have indicated that the mean absolute error of the ANN Model for the training data was 3.95% while for the validation data it was 4.65%. The corresponding values for the LR model were 8.28% and 8.35% respectively. It was also demonstrated the percentage improvement of the ANN Model with respect to the

  14. Observations of the latent track structure in polymers by diffusion measurements

    NASA Astrophysics Data System (ADS)

    Bacmeister, G. U.; Enge, W.

    1997-08-01

    The diffusion constants of ion irradiated Makrofol KG polycarbonate (PC) sheets have been measured with argon and nitrogen as diffusion gas. In order to determine the characteristics of the original latent tracks the material was not etched. The polymers were irradiated with uranium, gold, lead and selen ions at energies of about 10 MeV/u and different fluences in the range of 10 11 ions/cm 2. We used stacks with layers of 8 μm thickness for the irradiation. This allowed us to relate a definite energy loss to each layer and to examine the dependence of the diffusion constant on the energy loss. Additionally we irradiated polymers with 180 keV electrons. The irradiation there was performed with constant energy and current. As reference the diffusion constant of pristine material (i.e. the untreated material) was also measured. Thus the results found with Makrofol KG were checked under different conditions. The ion irradiated probes show two quite different dependencies of the diffusion constant on the ion energy loss. These effects are strongly related to the fluence and the flux of the irradiation. In case of low fluences the diffusion constant is up to 8 times higher than that of the pristine material. In the probes irradiated with high fluences we observed a decrease of the diffusion constant down to half the value of the pristine material. All probes irradiated with high fluences have visibly changed to a brittle material. The electron irradiated probes only show the decrease of the diffusion constant. The material has also visibly changed. To understand the dependence of the diffusion constant on the energy loss we suggest a model. As a result of this model we achieve an average radius of the latent track. Its values show a strong dependence on the ion energy loss. The calculated values vary from 9 to 25 nm.

  15. Computer simulation of structural modifications induced by highly energetic ions in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Sasajima, Y.; Osada, T.; Ishikawa, N.; Iwase, A.

    2013-11-01

    The structural modification caused by the high-energy-ion irradiation of single-crystalline uranium dioxide was simulated by the molecular dynamics method. As the initial condition, high kinetic energy was supplied to the individual atoms within a cylindrical region of nanometer-order radius located in the center of the specimen. The potential proposed by Basak et al. [C.B. Basak, A.K. Sengupta, H.S. Kamath, J. Alloys Compd. 360 (2003) 210-216] was utilized to calculate interaction between atoms. The supplied kinetic energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it dissipated in the specimen. The amorphous track radius Ra was determined as a function of the effective stopping power gSe, i.e., the kinetic energy of atoms per unit length created by ion irradiation (Se: electronic stopping power, g: energy transfer ratio from stopping power to lattice vibration energy). It was found that the relationship between Ra and gSe follows the relation Ra2=aln(gS)+b. Compared to the case of Si and β-cristobalite single crystals, it was harder to produce amorphous track because of the long range interaction between U atoms.

  16. Ion mobility–mass spectrometry for structural proteomics

    PubMed Central

    Zhong, Yueyang; Hyung, Suk-Joon; Ruotolo, Brandon T

    2012-01-01

    Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility– mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility–mass spectrometry data with more classical (e.g., ‘bottom-up’) proteomics approaches for the rapid structural characterization of protein networks. PMID:22292823

  17. Ion nose spectral structures observed by the Van Allen Probes

    DOE PAGES

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

  18. Ion nose spectral structures observed by the Van Allen Probes

    SciTech Connect

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; Kistler, L. M.; Larsen, Brian Arthur; Reeves, Geoffrey D.; Skoug, Ruth M.; Funsten, Herbert O.

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  19. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, R.; Scheiner, B.; Baalrud, S. D.; Hopkins, M. M.; Barnat, E. V.; Yee, B. T.; Merlino, R. L.; Skiff, F.

    2016-11-01

    What effect does a dielectric material surrounding a small positively biased electrode have on the ion flow and sheath structure near the electrode? Measurements of the ion velocity distribution function and plasma potential near positively biased electrodes were made using laser-induced fluorescence and an emissive probe. The results were compared with 2D particle-in-cell simulations. Both measurements and simulations showed that when the positive electrode was surrounded by the dielectric material, ions were accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier of the electrode. The axial potential profile in this case contained a virtual cathode. In comparison, when the dielectric material was removed from around the electrode, both the ion flow and virtual cathode depth near the electrode were dramatically reduced. These measurements suggest that the ion presheath from the dielectric material surrounding the electrode may enclose the electron sheath of the electrode, resulting in a virtual cathode that substantially influences the ion flow profile in the region.

  20. Solitary structures with ion and electron thermal anisotropy

    NASA Astrophysics Data System (ADS)

    Khusroo, Murchana; Bora, Madhurjya P.

    2015-11-01

    The formation of electrostatic solitary structures is analysed for a magnetised plasma with ion and electron thermal anisotropies. The ion thermal anisotropy is modelled with the help of the Chew-Goldberger-Low (CGL) double adiabatic equations of state while the electrons are treated as inertia-less species with an anisotropic bi-Maxwellian velocity distribution function. A negative electron thermal anisotropy ≤ft({{T}e\\bot}/{{T}e\\parallel}>1\\right) is found to help form large amplitude solitary structures which are in agreement with observational data.

  1. Tracking recurrence of correlation structure in neuronal recordings

    PubMed Central

    Neymotin, Samuel A.; Talbot, Zoe N.; Jung, Jeeyune Q.; Fenton, André A.; Lytton, William W.

    2017-01-01

    Background Correlated neuronal activity in the brain is hypothesized to contribute to information representation, and is important for gauging brain dynamics in health and disease. Due to high dimensional neural datasets, it is difficult to study temporal variations in correlation structure. New Method We developed a multiscale method, Population Coordination (PCo), to assess neural population structure in multiunit single neuron ensemble and multi-site local field potential (LFP) recordings. PCo utilizes population correlation (PCorr) vectors, consisting of pair-wise correlations between neural elements. The PCo matrix contains the correlations between all PCorr vectors occurring at different times. Results We used PCo to interpret dynamics of two electrophysiological datasets: multisite LFP and single unit ensemble. In the LFP dataset from an animal model of medial temporal lobe epilepsy, PCo isolated anomalous brain states, where particular brain regions broke off from the rest of the brain’s activity. In a dataset of rat hippocampal single-unit recordings, PCo enabled visualizing neuronal ensemble correlation structure changes associated with changes of animal environment (place-cell remapping). Comparison with Existing Method(s) PCo allows directly visualizing high dimensional data. Dimensional reduction techniques could also be used to produce dynamical snippets that could be examined for recurrence. PCo allows intuitive, visual assessment of temporal recurrence in correlation structure directly in the high dimensionality dataset, allowing for immediate assessment of relevant dynamics at a single site. Conclusions PCo can be used to investigate how neural correlation structure occurring at multiple temporal and spatial scales reflect underlying dynamical recurrence without intermediate reduction of dimensionality. PMID:27746231

  2. Cellular parameters for track structure modelling of radiation hazard in space

    NASA Astrophysics Data System (ADS)

    Hollmark, M.; Lind, B.; Gudowska, I.; Waligorski, M.

    Based on irradiation with 45 MeV/u N and B ions and with Co-60 gamma rays, track structure cellular parameters have been fitted for V 79-379A Chinese hamster lung fibroblasts and for human melanoma cells (AA wtp53). These sets of parameters will be used to develop a calculation of radiation hazard in deep space, based on the system for evaluating, summing and reporting occupational exposures proposed in 1967 by subcommittee of the NCRP, but never issued as an NCRP report. The key concepts of this system were: i) expression of the risk from all radiation exposures relative to that from a whole-body exposure to Co-60 radiation; ii) relating the risk from any exposure to that of the standard (Co-60) radiation through an "effectiveness factor" (ef), a product of sub-factors representing radiation quality, body region irradiated, and depth of penetration of radiation; the product of absorbed dose by ef being termed the "exposure record unit" (eru); iii) development of ef values and a cumulative eru record for external and internal emitters. Application of this concept should provide a better description of the Gy -equivalent presently in use by NASA for evaluating risk in deep space than the equivalent dose, following ICRP-60 recommendations. Dose and charged particle fluence levels encountered in space, particularly after Solar Particle Events, require that deterministic rather than stochastic effects be considered. Also, synergistic effects due to simultaneous multiple charged particle transfers, may have to be considered. Thus, models applicable in radiotherapy, where the Gy -equivalent is also applied, in conjunction with transport calculations performed using, e.g. the ADAM and EVA phantoms, along the concepts of the 1967 NCRP system, may be more appropriate for evaluating the radiation hazard from external fields with a large flux and a major high-LET component.

  3. Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

    SciTech Connect

    Liu, Wei; Chun, Eugene; Thompson, Aaron A.; Chubukov, Pavel; Xu, Fei; Katritch, Vsevolod; Han, Gye Won; Roth, Christopher B.; Heitman, Laura H.; IJzerman, Adriaan P.; Cherezov, Vadim; Stevens, Raymond C.

    2012-08-31

    Pharmacological responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resolution of GPCR structures. We reengineered the human A{sub 2A} adenosine receptor by replacing its third intracellular loop with apocytochrome b{sub 562}RIL and solved the structure at 1.8 angstrom resolution. The high-resolution structure allowed us to identify 57 ordered water molecules inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp{sup 2.50}. Additionally, two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resolution details shed light on the potential role of structured water molecules, sodium ions, and lipids/cholesterol in GPCR stabilization and function.

  4. Structural dynamic interaction with solar tracking control for evolutionary Space Station concepts

    NASA Technical Reports Server (NTRS)

    Lim, Tae W.; Cooper, Paul A.; Ayers, J. Kirk

    1992-01-01

    The sun tracking control system design of the Solar Alpha Rotary Joint (SARJ) and the interaction of the control system with the flexible structure of Space Station Freedom (SSF) evolutionary concepts are addressed. The significant components of the space station pertaining to the SARJ control are described and the tracking control system design is presented. Finite element models representing two evolutionary concepts, enhanced operations capability (EOC) and extended operations capability (XOC), are employed to evaluate the influence of low frequency flexible structure on the control system design and performance. The design variables of the control system are synthesized using a constrained optimization technique to meet design requirements, to provide a given level of control system stability margin, and to achieve the most responsive tracking performance. The resulting SARJ control system design and performance of the EOC and XOC configurations are presented and compared to those of the SSF configuration. Performance limitations caused by the low frequency of the dominant flexible mode are discussed.

  5. Robust object tracking based on structural local sparsity via a global L2 norm constraint

    NASA Astrophysics Data System (ADS)

    Li, Meihui; Peng, Zhenming; Zhang, Ping

    2016-10-01

    In the structural local sparse model, every candidate derived from the particle filter framework is divided into several overlapping image patches. However, in the tracking process, the structural characteristics of the target may change due to alterations in appearance, resulting in unstable pooled features and therefore drifting and false tracking. We propose a method to correct the changed part of the target using atoms in the patched dictionary by adding a global constraint. If the target is corrupted, this constraint term will weaken the influence of variation and strengthen the stability of the pooled features. Otherwise, the method is based on the whole target and will protect its spatial continuity. Both qualitative and quantitative evaluations on challenging benchmark image sequences demonstrate that the proposed algorithm has excellent tracking behavior, displaying robustness and stability with little drifting on a target with altering appearance and partial occlusion.

  6. Structure and dynamics of aqueous solution of uranyl ions

    SciTech Connect

    Chopra, Manish; Choudhury, Niharendu

    2014-04-24

    The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.

  7. Investigations on the structure of the extracted ion beam from an electron cyclotron resonance ion source

    SciTech Connect

    Spaedtke, P.; Lang, R.; Maeder, J.; Rossbach, J.; Tinschert, K.; Maimone, F.

    2012-02-15

    Using improved beam diagnostic tools, the structure of an ion beam extracted from an electron cyclotron resonance ion source (ECRIS) becomes visible. Especially viewing targets to display the beam profile and pepper pot devices for emittance measurements turned out to be very useful. On the contrary, diagnostic tools integrating over one space coordinate like wire harps for profile measurements or slit-slit devices, respectively slit-grid devices to measure the emittance might be applicable for beam transport investigations in a quadrupole channel, but are not very meaningful for investigations regarding the given ECRIS symmetry. Here we try to reproduce the experimentally found structure on the ion beam by simulation. For the simulation, a certain model has to be used to reproduce the experimental results. The model is also described in this paper.

  8. Eye tracking detects disconjugate eye movements associated with structural traumatic brain injury and concussion.

    PubMed

    Samadani, Uzma; Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H; McStay, Christopher; Todd, S Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-04-15

    Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury.

  9. Eye Tracking Detects Disconjugate Eye Movements Associated with Structural Traumatic Brain Injury and Concussion

    PubMed Central

    Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H.; McStay, Christopher; Todd, S. Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-01-01

    Abstract Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury. PMID:25582436

  10. Three-dimensional tracking and analysis of ion channel signals across dendritic arbors

    PubMed Central

    Ginger, Melanie; Broser, Philip; Frick, Andreas

    2013-01-01

    Most neuron types possess elaborate dendritic arbors that receive and integrate excitatory and inhibitory inputs from numerous other neurons to give rise to cell-type specific firing patterns. The computational properties of these dendrites are therefore crucial for neuronal information processing, and are strongly determined by the expression of many types of voltage-gated ion channels in their membrane. The dendritic distribution patterns of these ion channels are characteristic for each ion channel type, are dependent on the neuronal identity, and can be modified in a plastic or pathophysiological manner. We present a method that enables us to semi-automatically map and quantify in 3D the expression levels of specific ion channel types across the entire dendritic arbor. To achieve this, standard immunohistochemistry was combined with reconstruction and quantification procedures for the localization and relative distribution of ion channels with respect to dendritic morphology. This method can, in principle, be applied to any fluorescent signal, including fluorescently tagged membrane proteins, RNAs, or intracellular signaling molecules. PMID:23576958

  11. Enhanced Ion Acceleration from Micro-tube Structured Targets

    NASA Astrophysics Data System (ADS)

    Snyder, Joseph; Ji, Liangliang; Akli, Kramer

    2015-11-01

    We present an enhanced ion acceleration method that leverages recent advancements in 3D printing for target fabrication. Using the three-dimensional Particle-in-Cell simulation code Virtual Laser-Plasma Lab (VLPL), we model the interaction of a short pulse, high intensity laser with a micro-tube plasma (MTP) structured target. When compared to flat foils, the MTP target enhances the maximum proton energy by a factor of about 4. The ion enhancement is attributed to two main factors: high energy electrons extracted from the tube structure enhancing the accelerating field and light intensification within the MTP target increasing the laser intensity at the location of the foil. We also present results on ion energy scaling with micro-tube diameter and incident laser pulse intensity. This work was supported by the AFOSR under contract No. FA9550-14-1-0085.

  12. FAST TRACK COMMUNICATION: Neodymium ion diffusion during sintering of Nd : YAG transparent ceramics

    NASA Astrophysics Data System (ADS)

    Hollingsworth, Joel P.; Kuntz, Joshua D.; Soules, Thomas F.

    2009-03-01

    Using an electron microprobe, we measured and characterized the Nd3+ ion diffusion across a boundary between Nd doped and undoped ceramic yttrium aluminium garnet (YAG) for different temperature ramps and hold times and temperatures. The results show significant Nd ion diffusion on the order of micrometres to tens of micrometres depending on the time and temperature of sintering. The data fit well a model including bulk diffusion, grain boundary diffusion and grain growth. Grain boundary diffusion dominates and grain growth limits grain boundary diffusion by reducing the total cross-sectional area of grain boundaries.

  13. The gas phase structure of coulombically stretched polyethylene glycol ions.

    PubMed

    Larriba, Carlos; de la Mora, Juan Fernandez

    2012-01-12

    Prior ion-mobility mass-spectrometry (IMS-MS) studies of polyethylene glycol (PEG) ions have identified only two out of many sharply different observed structures: Linear shapes with several individually solvated singly charged cations at high charge states z (beads on a string), and single multiply charged globules at low z. The present study is devoted to assign all other existing structures of PEG ions, for the first time reaching masses of 100 kDa and charge states up to z = 10. There are at most z different structures at charge state z. All involve a single globule carrying n charges, tied to one or several appendices bearing z - n separate charges in a beads-on-a-string configuration. All sharp shape transitions observed at decreasing ion mass involve ejection of one elementary charge (sometimes two) from the shrinking globule into the growing linear appendage. This picture is supported by molecular dynamics simulations and approximate calculations of electrical mobilities for computed structures.

  14. A New Ion Implant Monitor Electrical Test Structure.

    DTIC Science & Technology

    1986-01-01

    In this paper, a new Ion Implant Monitor test structure and measurement method is reported. A direct measurement of the sheet resistance of the...probe measurements. Voltage measurements are directly converted to sheet resistance , thus measurements may be performed rapidly.

  15. Structure and dynamics of ion transport through gramicidin A.

    PubMed Central

    Mackay, D H; Berens, P H; Wilson, K R; Hagler, A T

    1984-01-01

    Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed. PMID:6206901

  16. Prompt Gas Desorption Due to Ion Impact on Accelerator Structures

    NASA Astrophysics Data System (ADS)

    Vijay, Sagar; Seidl, Peter A.; Faltens, Andy; Lidia, Steven M.

    2011-10-01

    The repetition rate and peak current of high intensity ion accelerators for inertial fusion or other applications may be limited under certain conditions by the desorption of gas molecules and atoms due to stray ions striking the accelerator structure. We have measured the prompt yield of atoms in close proximity to the point of impact of the ions on a surface. Using the 300-keV, K+ ion beam of the Neutralized Drift Compression Experiment (NDCX-I), ions strike a metal target in a 5-10 microsecond bunch. The collector of a Bayert-Alpert style ionization gauge is used to detect the local pressure burst several centimeters away. Pressure transients are observed on a micro-second time scale due to the initial burst of desorbed gas, and on a much longer (~1 second) timescale, corresponding to the equilibration of the pressure after many ``bounces'' of atoms in the vacuum chamber. We report on these time dependent pressure measurements, modeling of the pressure transient, and implications for high-intensity ion accelerators. Work performed under auspices of U.S. DOE by LBNL under Contract DE-AC02-05CH1123.

  17. Trajectory tracking and vibration control in a space frame flexible structure with a PZT stack actuator

    NASA Astrophysics Data System (ADS)

    Garcia-Perez, Oscar A.; Silva-Navarro, G.; Peza-Solís, J. F.; Trujillo-Franco, L. G.

    2015-04-01

    This work deals with the robust asymptotic output tracking control problem of the tip position of a space frame flexible structure, mounted on a rigid revolute servomechanism actuated and controlled with a dc motor. The structure is also affected by undesirable vibrations due to excitation of its first lateral vibration modes and possible variations of the tip mass. The overall flexible structure is modeled by using finite element methods and this is validated via experimental modal analysis techniques. The tip position of the structure is estimated from acceleration and strain gauge measurements. The asymptotic output tracking problem is formulated and solved by means of Passivity-Based and Sliding-Mode Control techniques, applied to the dc motor coupled to the rigid part of the structure, and those undesirable vibrations are simultaneously attenuated by an active vibration control using Positive Position Feedback control schemes implemented on a PZT stack actuator properly located into the mechanical structure. The investigation also addresses the trajectory tracking problem of fast motions, with harmonic excitations close to the first vibration modes of the structure. The overall dynamic performance is evaluated and validated by numerical and experimental results.

  18. The structure and regulation of magnesium selective ion channels.

    PubMed

    Payandeh, Jian; Pfoh, Roland; Pai, Emil F

    2013-11-01

    The magnesium ion (Mg(2+)) is the most abundant divalent cation within cells. In man, Mg(2+)-deficiency is associated with diseases affecting the heart, muscle, bone, immune, and nervous systems. Despite its impact on human health, little is known about the molecular mechanisms that regulate magnesium transport and storage. Complete structural information on eukaryotic Mg(2+)-transport proteins is currently lacking due to associated technical challenges. The prokaryotic MgtE and CorA magnesium transport systems have recently succumbed to structure determination by X-ray crystallography, providing first views of these ubiquitous and essential Mg(2+)-channels. MgtE and CorA are unique among known membrane protein structures, each revealing a novel protein fold containing distinct arrangements of ten transmembrane-spanning α-helices. Structural and functional analyses have established that Mg(2+)-selectivity in MgtE and CorA occurs through distinct mechanisms. Conserved acidic side-chains appear to form the selectivity filter in MgtE, whereas conserved asparagines coordinate hydrated Mg(2+)-ions within the selectivity filter of CorA. Common structural themes have also emerged whereby MgtE and CorA sense and respond to physiologically relevant, intracellular Mg(2+)-levels through dedicated regulatory domains. Within these domains, multiple primary and secondary Mg(2+)-binding sites serve to staple these ion channels into their respective closed conformations, implying that Mg(2+)-transport is well guarded and very tightly regulated. The MgtE and CorA proteins represent valuable structural templates to better understand the related eukaryotic SLC41 and Mrs2-Alr1 magnesium channels. Herein, we review the structure, function and regulation of MgtE and CorA and consider these unique proteins within the expanding universe of ion channel and transporter structural biology.

  19. Ion Bombardment of Microprotrusions in High Gradient Accelerating Structures

    SciTech Connect

    Nusinovich, Gregory S.; Kashyn, Dmytro; Antonsen, Thomas Jr.; Haber, Irving

    2010-11-04

    This paper starts from a brief overview of theoretical studies of high-gradient accelerating structures at the University of Maryland. The rest of the paper is devoted to the analysis of ion bombardment of small protrusions in such structures. First, this problem is studied analytically. Then, some results of particle-in-cell simulations performed with the use of code WARP are presented and discussed.

  20. Passive radar tracking of a maneuvering target using variable structure multiple-model algorithm

    NASA Astrophysics Data System (ADS)

    Mao, Yunxiang; Zhou, Xiaohui; Zhang, Jin

    2013-03-01

    The variable structure multiple-model (VSMM) algorithm to passive radar maneuvering target tracking problem is considered. A new VSMM design, expected mode augmentation based on likely model set (LMS-EMA) algorithm is presented. The LMS-EMA algorithm adaptively determines the fixed grid model set using likely model set (LMS) algorithm, and generates the expected mode based on this set. Then, the union of fixed grid model set and expected model is used to perform multiple-model estimation. The performance of the LMS-EMA algorithm is evaluated via simulation of a highly maneuvering target tracking problem.

  1. Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study

    PubMed Central

    Serec, Kristina; Babić, Sanja Dolanski; Podgornik, Rudolf; Tomić, Silvia

    2016-01-01

    Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO2 stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92–94%, DNA may undergo a structural transition into a more compact form. PMID:27484473

  2. Monte-Carlo simulations of electronic excitations in swift heavy ion tracks in SiO{sub 2}

    SciTech Connect

    Medvedev, N. A.; Volkov, A. E.

    2008-04-10

    Monte-Carlo simulations were applied for investigation of the initial electronic kinetics ({<=}10{sup -14} s) in tracks of Ca{sup +19} (11.4 MeV/u) in SiO{sub 2}. The spatial and temporal distributions of the volume and excess energy densities of free electrons, electronic vacancies in different atomic shells and the lattice were obtained. It was demonstrated that at 10{sup -14} s an essential part ({approx}55%) of the energy deposited by the ion is trapped in electronic vacancies. The energy transferred to the lattice at times shorter than the characteristic time of electron-phonon coupling was determined. It was found that only {approx}6% of the excess energy of delocalized electrons near the projectile trajectory ({approx}6 nm) may be thermalized on the time 10{sup -14} s from the projectile passage. Ballistic spatial propagation of excess energy cannot be described by thermal diffusion.

  3. Surface pressure profiles, vortex structure and initialization for hurricane prediction. Part II: numerical simulations of track, structure and intensity

    NASA Astrophysics Data System (ADS)

    Davidson, Noel E.; Ma, Yimin

    2012-07-01

    In part 1 of this study, an assessment of commonly used surface pressure profiles to represent TC structures was made. Using the Australian tropical cyclone model, the profiles are tested in case studies of high-resolution prediction of track, structure and intensity. We demonstrate that: (1) track forecasts are mostly insensitive to the imposed structure; (2) in some cases [here Katrina (2005)], specification of vortex structure can have a large impact on prediction of structure and intensity; (3) the forecast model mostly preserves the characteristics of the initial structure and so correct structure at t = 0 is a requirement for improved structure forecasting; and (4) skilful prediction of intensity does not guarantee skilful prediction of structure. It is shown that for Ivan (2004) the initial structure from each profile is preserved during the simulations, and that markedly different structures can have similar intensities. Evidence presented suggests that different initial profiles can sometimes change the timing of intensification. Thus, correct initial vortex structure is an essential ingredient for more accurate intensity and structure prediction.

  4. Soft-tissue motion tracking and structure estimation for robotic assisted MIS procedures.

    PubMed

    Stoyanov, Danail; Mylonas, George P; Deligianni, Fani; Darzi, Ara; Yang, Guang Zhong

    2005-01-01

    In robotically assisted laparoscopic surgery, soft-tissue motion tracking and structure recovery are important for intraoperative surgical guidance, motion compensation and delivering active constraints. In this paper, we present a novel method for feature based motion tracking of deformable soft-tissue surfaces in totally endoscopic coronary artery bypass graft (TECAB) surgery. We combine two feature detectors to recover distinct regions on the epicardial surface for which the sparse 3D surface geometry may be computed using a pre-calibrated stereo laparoscope. The movement of the 3D points is then tracked in the stereo images with stereo-temporal constrains by using an iterative registration algorithm. The practical value of the technique is demonstrated on both a deformable phantom model with tomographically derived surface geometry and in vivo robotic assisted minimally invasive surgery (MIS) image sequences.

  5. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  6. Cumulative approaches to track formation under swift heavy ion (SHI) irradiation: Phenomenological correlation with formation energies of Frenkel pairs

    NASA Astrophysics Data System (ADS)

    Crespillo, M. L.; Agulló-López, F.; Zucchiatti, A.

    2017-03-01

    An extensive survey for the formation energies of Frenkel pairs, as representative candidates for radiation-induced point defects, is presented and discussed in relation to the cumulative mechanisms (CM) of track formation in dielectric materials under swift heavy ion (SHI) irradiation. These mechanisms rely on the generation and accumulation of point defects during irradiation followed by collapse of the lattice once a threshold defect concentration is reached. The physical basis of those approaches has been discussed by Fecht as a defect-assisted transition to an amorphous phase. Although a first quantitative analysis of the CM model was previously performed for LiNbO3 crystals, we have, here, adopted a broader phenomenological approach. It explores the correlation between track formation thresholds and the energies for Frenkel pair formation for a broad range of materials. It is concluded that the threshold stopping powers can be roughly scaled with the energies required to generate a critical Frenkel pair concentration in the order of a few percent of the total atomic content. Finally, a comparison with the predictions of the thermal spike model is discussed within the analytical Szenes approximation.

  7. Ion aggregation in high salt solutions. V. Graph entropy analyses of ion aggregate structure and water hydrogen bonding network

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2016-05-01

    Dissolved ions in water tend to form polydisperse ion aggregates such as ion pairs, relatively compact ion clusters, and even spatially extended ion networks with increasing salt concentration. Combining molecular dynamics simulation and graph theoretical analysis methods, we recently studied morphological structures of ion aggregates with distinctively different characteristics. They can be distinguished from each other by calculating various spectral graph theoretical properties such as eigenvalues and eigenvectors of adjacency matrices of ion aggregates and water hydrogen-bonding networks, minimum path lengths, clustering coefficients, and degree distributions. Here, we focus on percolation and graph entropic properties of ion aggregates and water hydrogen-bonding networks in high salt solutions. Ion network-forming K+ and SCN- ions at high concentrations show a percolating behavior in their aqueous solutions, but ion cluster-forming ions in NaCl solutions do not show such a transition from isolated ion aggregates to percolating ion-water mixture morphology. Despite that the ion aggregate structures are strikingly different for either cluster- or network-forming ions in high salt solutions, it is interesting that the water structures remain insensitive to the electrostatic properties, such as charge densities and polydentate properties, of dissolved ions, and morphological structures of water H-bonding networks appear to be highly robust regardless of the nature and concentration of salt. We anticipate that the present graph entropy analysis results would be of use in understanding a variety of anomalous behaviors of interfacial water around biomolecules as well as electric conductivities of high electrolyte solutions.

  8. Radiation-induced grafting of styrene onto polyimide ion track membranes

    NASA Astrophysics Data System (ADS)

    Friese, K.; Mehnert, R.; Placek, V.; Trautmann, C.; Angert, N.; Spohr, R.; Trautmann, Ch.

    1995-11-01

    The radiation induced grafting of styrene onto polyimide was carried out by applying the method of preirradiation as well as the simultaneous irradiation of polymer and monomer. The polymerization was initiated by gamma irradiation and by swift heavy ions. The result of these experiments was that no grafting occurs by applying the preirradiation method but grafting (up to 30%) is obtained by using the simultaneous method. For an explanation some ESR-experiments were carried out. We found that even the non-irradiated polyimide has a clear ESR signal with two different lines, probably as a result of absorbed oxygen and thermally formed radicals. The preirradiation method was not successful, because no peroxy-radicals are formed after irradiation. Grafting by initiation with heavy ions results in small grafting yields, but etching of the membranes is markedly reduced.

  9. Metal ion influence on eumelanin fluorescence and structure

    NASA Astrophysics Data System (ADS)

    Sutter, Jens-Uwe; Birch, David J. S.

    2014-06-01

    Melanin has long been thought to have an unworkably weak and complex fluorescence, but here we study its intrinsic fluorescence in order to demonstrate how metal ions can be used to control the rate of formation, constituents and structure of eumelanin formed from the well-known laboratory auto-oxidation of 3,4-dihydroxy-L-phenylalanine (L-DOPA). The effect on eumelanin absorption and fluorescence of a range of solvated metal ions is reported including Cu, Zn, Ni, Na and K. Monovalent cations and Zn have little effect, but the effect of transition metal cations can be considerable. For example, at pH 10, copper ions are shown to accelerate the onset of eumelanin formation, but not the rate of formation once it commences, and simplify the usual complex structure and intrinsic fluorescence of eumelanin in a way that is consistent with an increased abundance of 5,5-dihydroxyindole-2-carboxylic acid (DHICA). The presence of a dominant 6 ns fluorescence decay time at 480 nm, when excited at 450 nm describes a distinct photophysical species, which we tentatively assign to small oligomers. Copper is well-known to normally quench fluorescence, but increasing amounts of copper surprisingly leads to an increase in the fluorescence decay time of eumelanin, while reducing the fluorescence intensity, suggesting copper modification of the excited state. Such results have bearing on diverse areas. The most accepted morphology for melanin is that of a graphite-like sheet structure, and one which readily binds metal ions, an interaction that is thought to have an important, though as yet unclear bearing on several areas of medicine including neurology. There is also increasing interest in bio-mimicry by preparing and labelling sheet structures with metal ions for new electronic and photonic materials.

  10. Quantitative tracking of grain structure evolution in a nanocrystalline metal during cyclic loading

    NASA Astrophysics Data System (ADS)

    Panzarino, Jason F.; Ramos, Jesus J.; Rupert, Timothy J.

    2015-02-01

    Molecular dynamics simulations were used to quantify mechanically induced structural evolution in nanocrystalline Al with an average grain size of 5 nm. A polycrystalline sample was cyclically strained at different temperatures, while a recently developed grain tracking algorithm was used to measure the relative contributions of novel deformation mechanisms such as grain rotation and grain sliding. Sample texture and grain size were also tracked during cycling, to show how nanocrystalline plasticity rearranges overall grain structure and alters the grain boundary network. While no obvious texture is developing during cycling, the processes responsible for plasticity act collectively to alter the interfacial network. Cyclic loading led to the formation of many twin boundaries throughout the sample as well as the occasional coalescence of neighboring grains, with higher temperatures causing more evolution. A temperature-dependent cyclic strengthening effect was observed, demonstrating that both the structure and properties of nanocrystalline metals can be dynamic during loading.

  11. Reduction and structural modification of zirconolite on He+ ion irradiation

    NASA Astrophysics Data System (ADS)

    Gupta, Merry; Kulriya, P. K.; Shukla, Rishabh; Dhaka, R. S.; Kumar, Raj; Ghumman, S. S.

    2016-07-01

    The immobilization of minor actinides and alkaline-earth metal is a major concern in nuclear industry due to their long-term radioactive contribution to the high level waste (HLW). Materials having zirconolite, pyrochlore, and perovskite structure are promising candidates for immobilization of HLW. The zirconolite which exhibits high radiation stability and corrosion resistance behavior is investigated for its radiation stability against alpha particles in the present study. CaZrTi2O7 pellets prepared using solid state reaction techniques, were irradiated with 30 keV He+ ions for the ion fluence varying from 1 × 1017 to 1 × 1021 ions/m2. Scanning electron microscopy (SEM) images of the un-irradiated sample exhibited well separated grains with average size of about 6.8 μm. On the ion irradiation, value of the average grains size was about 7.1 μm, and change in the microstructure was insignificant. The X-ray photoelectron spectroscopy (XPS) studies showed a shift in the core level peak position (of Ca 2p, Ti 2p and Zr 3d) towards lower binding energy with respect to pristine sample as well as loss of oxygen was also observed for sample irradiated with the ion fluence of 1 × 1020 ions/m2. These indicate a decrease in co-ordination number and the ionic character of Msbnd O bond. Moreover, core level XPS signal was not detected for sample irradiated with ion fluence of 1 × 1021 ions/m2, suggesting surface damage of the sample at this ion fluence. However, X-ray diffraction (XRD) studies showed that zirconolite was not amorphized even on irradiation up to a fluence order of 1 × 1021 ion/m2. But, significant decrease in peak intensity due to creation of defects and a marginal positive peak shift due to tensile strain induced by irradiation, were observed. Thus, XRD along with XPS investigation suggests that reduction, decrease in co-ordination number, and increase in covalency are responsible for the radiation damage in zirconolite.

  12. Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming

    SciTech Connect

    Garimella, Venkata BS; Hamid, Ahmed M.; Deng, Liulin; Ibrahim, Yehia M.; Webb, Ian K.; Baker, Erin M.; Prost, Spencer A.; Norheim, Randolph V.; Anderson, Gordon A.; Smith, Richard D.

    2016-11-02

    In this work, we report an approach for spatial and temporal gas phase ion population manipulation, and demonstrate its application for the collapse of the ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventionally traveling wave (TW)-driven region to a region where the TW is intermittently halted or ‘stuttered’. This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllable and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using Structures for Lossless Ion Manipulations (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved S/N ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multi-pass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening due to increasing peak widths.

  13. Stable Ion Beam Analysis (RBS and PIXE) Study of Photocatalytic Track-Etched Membranes

    NASA Astrophysics Data System (ADS)

    Rossouw, A.; Artoshina, O. V.; Nechaev, A. N.; Apel, P. Yu.; Petrik, L.; Perold, W. J.; Pineda-Vargas, C. A.

    2015-11-01

    In microfiltration, caking is a major problem. Organic molecules get absorbed on the track-etched membrane TM surface during water purification. This leads to a loss of efficiency and changes in TM selectivity. A solution devised to solve this problem is the creation of self-cleaning, low-absorptive TM coatings. The TM surface was modified by depositing a thin-film photocatalytic semiconductor, titanium dioxide (TiO2). Strong oxidizing agents appear on the TiO2 surface in the presence of water, dissolved oxygen and UV irradiation. This results in the mineralization of the organic compounds present, By applying the use of exotic beams in the material research, it becomes possible to investigate properties regarding the layer thickness, homogeneity and purity of the modified TMs, not otherwise attainable.

  14. Calibration of solid state nuclear track detectors at high energy ion beams for cosmic radiation measurements: HAMLET results

    NASA Astrophysics Data System (ADS)

    Szabó, J.; Pálfalvi, J. K.

    2012-12-01

    The MATROSHKA experiments and the related HAMLET project funded by the European Commission aimed to study the dose burden of the crew working on the International Space Station (ISS). During these experiments a human phantom equipped with several thousands of radiation detectors was exposed to cosmic rays inside and outside the ISS. Besides the measurements realized in Earth orbit, the HAMLET project included also a ground-based program of calibration and intercomparison of the different detectors applied by the participating groups using high-energy ion beams. The Space Dosimetry Group of the Centre for Energy Research (formerly Atomic Energy Research Institute) participated in these experiments with passive solid state nuclear track detectors (SSNTDs). The paper presents the results of the calibration experiments performed in the years 2008-2011 at the Heavy Ion Medical Accelerator (HIMAC) of the National Institute of Radiological Sciences (NIRS), Chiba, Japan. The data obtained serve as update and improvement for the previous calibration curves which are necessary for the evaluation of the SSNTDs exposed in unknown space radiation fields.

  15. Investigation of Semiconductor Surface Structure by Transmission Ion Channeling.

    NASA Astrophysics Data System (ADS)

    Lyman, Paul Francis

    The primary thrust of this dissertation is the investigation of the composition and structure of two important surface systems on Si, and the study of how this structure evolves under the influence of ion bombardment or film growth. I have studied the initial stages of oxidation of Si immediately following removal of a surface oxide by an HF etch. I have also studied the structure of Ge deposited on clean Si(100) at low temperatures. These systems are of considerable technological interest, but were chosen because they naturally pose fundamental questions regarding physical and chemical processes at surfaces. In the study of the oxidation of Si, I have focused on the influence of the bombarding ion beam in altering the structure and composition of the surface layer. Thus, the system then provides a natural vehicle to study ion-induced chemistry. In the study of low-temperature growth of Ge, I have focused on the structure of the Ge layer and the evolution of that structure upon further deposition or upon heating. This simple system is a model one for observing strained semiconductor heteroepitaxial growth. The primary probe for these studies was transmission channeling of MeV ions. The sensitivity of this technique to correlations between the substrate and an overlayer allowed us to make the following observations. The O, Si and H bound in the thin oxide formed after an HF etch and H_2O rinse occupy preferred positions with respect to the Si matrix. Upon ion bombardment, the O further reacts with the Si (the reaction proceeds linearly with the ion fluence) and the portion of the H that is uncorrelated to the substrate is preferentially desorbed. For the case of Ge growth on Si(100)-(2 x 1) at room temperature, a substantial fraction of the Ge films is strained to occupy sites having the lattice constant of the Si substrate (pseudomorphic growth). A model for film growth is proposed in which pseudomorphic domains constitute roughly half of the Ge films up to a

  16. Spectrum of Radiation-Induced Clustered Non-DSB Damage - A Monte Carlo Track Structure Modeling and Calculations.

    PubMed

    Watanabe, Ritsuko; Rahmanian, Shirin; Nikjoo, Hooshang

    2015-05-01

    The aim of this report is to present the spectrum of initial radiation-induced cellular DNA damage [with particular focus on non-double-strand break (DSB) damage] generated by computer simulations. The radiation types modeled in this study were monoenergetic electrons (100 eV-1.5 keV), ultrasoft X-ray photons Ck, AlK and TiK, as well as some selected ions including 3.2 MeV/u proton; 0.74 and 2.4 MeV/u helium ions; 29 MeV/u nitrogen ions and 950 MeV/u iron ions. Monte Carlo track structure methods were used to simulate damage induction by these radiation types in a cell-mimetic condition from a single-track action. The simulations took into account the action of direct energy deposition events and the reaction of hydroxyl radicals on atomistic linear B-DNA segments of a few helical turns including the water of hydration. Our results permitted the following conclusions: a. The absolute levels of different types of damage [base damage, simple and complex single-strand breaks (SSBs) and DSBs] vary depending on the radiation type; b. Within each damage class, the relative proportions of simple and complex damage vary with radiation type, the latter being higher with high-LET radiations; c. Overall, for both low- and high-LET radiations, the ratios of the yields of base damage to SSBs are similar, being about 3.0 ± 0.2; d. Base damage contributes more to the complexity of both SSBs and DSBs, than additional SSB damage and this is true for both low- and high-LET radiations; and e. The average SSB/DSB ratio for low-LET radiations is about 18, which is about 5 times higher than that for high-LET radiations. The hypothesis that clustered DNA damage is more difficult for cells to repair has gained currency among radiobiologists. However, as yet, there is no direct in vivo experimental method to validate the dependence of kinetics of DNA repair on DNA damage complexity (both DSB and non-DSB types). The data on the detailed spectrum of DNA damage presented here, in particular

  17. Automatic tracking of vessel-like structures from a single starting point.

    PubMed

    Oliveira, Dário Augusto Borges; Leal-Taixé, Laura; Feitosa, Raul Queiroz; Rosenhahn, Bodo

    2016-01-01

    The identification of vascular networks is an important topic in the medical image analysis community. While most methods focus on single vessel tracking, the few solutions that exist for tracking complete vascular networks are usually computationally intensive and require a lot of user interaction. In this paper we present a method to track full vascular networks iteratively using a single starting point. Our approach is based on a cloud of sampling points distributed over concentric spherical layers. We also proposed a vessel model and a metric of how well a sample point fits this model. Then, we implement the network tracking as a min-cost flow problem, and propose a novel optimization scheme to iteratively track the vessel structure by inherently handling bifurcations and paths. The method was tested using both synthetic and real images. On the 9 different data-sets of synthetic blood vessels, we achieved maximum accuracies of more than 98%. We further use the synthetic data-set to analyze the sensibility of our method to parameter setting, showing the robustness of the proposed algorithm. For real images, we used coronary, carotid and pulmonary data to segment vascular structures and present the visual results. Still for real images, we present numerical and visual results for networks of nerve fibers in the olfactory system. Further visual results also show the potential of our approach for identifying vascular networks topologies. The presented method delivers good results for the several different datasets tested and have potential for segmenting vessel-like structures. Also, the topology information, inherently extracted, can be used for further analysis to computed aided diagnosis and surgical planning. Finally, the method's modular aspect holds potential for problem-oriented adjustments and improvements.

  18. Correlation of ion dynamics and structure of superionic tellurite glasses

    SciTech Connect

    Dutta, D.; Ghosh, A.

    2008-01-28

    Ion dynamics and structure of a series of superionic AgI-doped silver tellurite glasses have been investigated in this paper. The composition dependence of the dc conductivity and the activation energy of these glasses has been compared with those of AgI-doped silver phosphate and borate glasses. We have observed that the conductivity increases and the activation energy decreases with increase of AgI content and that the tellurite glasses have higher conductivity than those for phosphate or borate glasses. We have analyzed the ac electrical data in the framework of the power law and the electric modulus formalisms. We have established a correlation between the crossover rate of the mobile silver ions and the rearrangement of the structural units in tellurite glasses. The scaling of the conductivity spectra has been used to interpret the temperature and composition dependence of the relaxation dynamics. Analysis of the dielectric relaxation in the framework of modulus formalism indicates an increase in the ion-ion cooperation in the glass compositions with increasing AgI content.

  19. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

  20. Studying Radiation Damage in Structural Materials by Using Ion Accelerators

    NASA Astrophysics Data System (ADS)

    Hosemann, Peter

    2011-02-01

    Radiation damage in structural materials is of major concern and a limiting factor for a wide range of engineering and scientific applications, including nuclear power production, medical applications, or components for scientific radiation sources. The usefulness of these applications is largely limited by the damage a material can sustain in the extreme environments of radiation, temperature, stress, and fatigue, over long periods of time. Although a wide range of materials has been extensively studied in nuclear reactors and neutron spallation sources since the beginning of the nuclear age, ion beam irradiations using particle accelerators are a more cost-effective alternative to study radiation damage in materials in a rather short period of time, allowing researchers to gain fundamental insights into the damage processes and to estimate the property changes due to irradiation. However, the comparison of results gained from ion beam irradiation, large-scale neutron irradiation, and a variety of experimental setups is not straightforward, and several effects have to be taken into account. It is the intention of this article to introduce the reader to the basic phenomena taking place and to point out the differences between classic reactor irradiations and ion irradiations. It will also provide an assessment of how accelerator-based ion beam irradiation is used today to gain insight into the damage in structural materials for large-scale engineering applications.

  1. Effect of LET and track structure on the statistical distribution of chromosome aberrations

    NASA Astrophysics Data System (ADS)

    Gudowska-Nowak, E.; Lee, R.; Nasonova, E.; Ritter, S.; Scholz, M.

    Chromosome aberration data obtained for various types of mammalian cells after exposure to low and high LET radiation clearly demonstrate differences in the energy deposition pattern of both radiation qualities. In the present study we focus on the distributions of chromosome aberrations induced in human peripheral blood lymphocytes after exposure to 990 MeV/u Fe ions (LET = 155 keV/μm) or X-rays. For the analysis three different types of distributions were applied, namely a Poisson distribution, a compound Poisson-Poisson (Neyman type A) distribution and a convoluted Poisson-Neyman distribution. The analysis showed that after low LET radiation the distribution of aberrations can be well described by Poisson statistics, reflecting a simple random distribution of damages as expected according to the homogeneous pattern of energy depositions. In contrast, for particles the energy is deposited spatially very inhomogeneous and concentrated along the ion trajectories. After exposure to high energy, high LET particles where the track radius is much larger than the cell nucleus, best fits to the data were achieved by a convoluted Poisson-Neyman statistics. The analysis indicates that, under this exposure condition, the distribution of aberrations is determined by two independent components. The first component is determined by the damage induced by a center of the tracks and follows the Neyman distribution. The second component is determined by the overlapping part of tracks which in the case of very high energetic particles leads to a "photon-like" background dose and is thus characterized by a Poisson distribution.

  2. Study of heavy ion range in different solid state nuclear track detector materials

    NASA Astrophysics Data System (ADS)

    Diwan, P. K.; Singh, Lakhwant; Singh, Gurinder; Kumar, Shyam

    2000-03-01

    The range of several heavy ions as 238U, 208Pb, 197Au, 139La, 58Ni and 56Fe in sodalime glass; 197Au and 58Ni in muscovite mica and Lexan polycarbonate; 209Bi and 197Au in CR-39 have been determined experimentally. The calculations of range for these projectile-target combinations have been made using the Benton and Henke [10], Mukherjee and Nayak [11], Ziegler et al. [12] and Hubert et al. [14] semiempirical formulations. Finally a comparison has been made with the experimental results.

  3. Instrumentation by distributed optical fiber sensors of a new ballastless track structure

    NASA Astrophysics Data System (ADS)

    Chapeleau, Xavier; Cottineau, Louis-Marie; Sedran, Thierry; Gueguen, Ivan; Cailliau, Joël

    2013-04-01

    While relatively expensive to build, ballastless track structures are presently seen as an attractive alternative to conventional ballast. With its service life of at least 60 years, they require little maintenance and hence they offer great availability. Other reasons for using ballastless tracks instead of ballasted tracks are the lack of suitable ballast material and the need of less noise and vibration for high-speed, in particularly. A new ballastless track structure has been designed to be circulated up to 300km/h, with a target life of 100 years. It is an interoperable way on concrete slabs that are cast-in-place and slip formed. This structure has been built and tested at the scale one in our laboratory. Indeed, ten millions cyclic loads were applied at 2.5Hz to evaluate the fatigue behaviour under selected mechanical and thermal conditions. To monitor the thermo-mechanical behavior of this new structure and to verify the numerical simulations used for its design, a lot of sensors have been embedded. In particularly, we have tested an optical fiber as distributed sensors to measure strain distribution in the railway model. This sensor can also be used to detect, localize and monitor cracks in concrete slabs. The optical fiber sensing technique ("Rayleigh technique") used in this experimentation has a centimetric spatial resolution which allows to measure complex strain profiles unlike electrical strain gauges which only give local information. Firstly, optical cables used as sensors have been successfully embedded and attached to the reinforcing steel bars in the structure. We have noted that they are resistant enough to resist concrete pouring and working activities. Secondly, strains measured by conventional strain gauges has confirmed the quality of the strain profiles measurements obtained by optical fiber sensors. Moreover, we have found a good agreement between experimental profiles measurements and those obtained by numerical simulations. Early

  4. Performance optimized, small structurally integrated ion thruster system

    NASA Technical Reports Server (NTRS)

    Hyman, J., Jr.

    1973-01-01

    A 5-cm structurally integrated ion thruster has been developed for attitude control and stationkeeping of synchronous satellites. As optimized with a conventional ion extraction system, the system demonstrates a thrust T = 0.47 mlb at a beam voltage of 1600 V, total mass efficiency of 76%, and electrical efficiency of 56%. Under the subject contract effort, no significant performance change was noted for operation with two dimensional electrostatic thrust-vectoring grids. Structural integrity with the vectoring grids was demonstrated for shock (+ or - 30 G), sinusoidal (9 G), and random (19.9 G rms) accelerations. System envelope is 31.2 cm long by 13.4 cm flange bolt circle, with a mass of 9.0 Kg, including 6.8 Kg mercury propellant.

  5. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Glover, Matthew S.; Dilger, Jonathan M.; Acton, Matthew D.; Arnold, Randy J.; Radivojac, Predrag; Clemmer, David E.

    2016-05-01

    Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/ trans orientation of Xaa-Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

  6. Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network.

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2015-09-14

    Ions in high salt solutions form a variety of ion aggregates, from ion pairs to clusters and networks. Their influences on water hydrogen bonding (H-bonding) network structures have long been of great interest. Recently, we have shown that the morphological structures of ion aggregates can be analyzed by using a spectral graph analysis theory, where each ion cluster or ion network is represented by a properly defined graph with edges and vertices. Here, to further examine the network properties of ion aggregates and water H-bonding networks in high salt solutions, we consider a few representative graph-theoretical descriptors: clustering coefficient, minimum path length, global efficiency, and degree distribution of ion aggregates. From the molecular dynamics trajectories, these graph theoretical properties of ion aggregates and water structures in NaCl and kosmotropic solutions are calculated and shown to be strongly dependent on the two types of ion aggregate structures, i.e., ion cluster and ion network. Ion clusters in high NaCl solutions exhibit typical behaviors of scale free network. The corresponding graph theoretical properties of ion networks in high KSCN solutions are notably different from those of NaCl ion clusters and furthermore they are very similar to those of water hydrogen-bonding network. The present graph-theoretical analysis results indicate that the high solubility limits of KSCN and other ion-network-forming salts might originate from their ability to form a large scale morphological network that can be intertwined with co-existing water H-bonding network. Furthermore, it is shown that the graph-theoretical properties of water H-bonding network structures do not strongly depend on the nature of dissolved ions nor on the morphological structures of ion aggregates, indicating that water's H-bonding interaction and network-forming capability are highly robust. We anticipate that the present graph-theoretical analysis results of high salt

  7. Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2015-09-01

    Ions in high salt solutions form a variety of ion aggregates, from ion pairs to clusters and networks. Their influences on water hydrogen bonding (H-bonding) network structures have long been of great interest. Recently, we have shown that the morphological structures of ion aggregates can be analyzed by using a spectral graph analysis theory, where each ion cluster or ion network is represented by a properly defined graph with edges and vertices. Here, to further examine the network properties of ion aggregates and water H-bonding networks in high salt solutions, we consider a few representative graph-theoretical descriptors: clustering coefficient, minimum path length, global efficiency, and degree distribution of ion aggregates. From the molecular dynamics trajectories, these graph theoretical properties of ion aggregates and water structures in NaCl and kosmotropic solutions are calculated and shown to be strongly dependent on the two types of ion aggregate structures, i.e., ion cluster and ion network. Ion clusters in high NaCl solutions exhibit typical behaviors of scale free network. The corresponding graph theoretical properties of ion networks in high KSCN solutions are notably different from those of NaCl ion clusters and furthermore they are very similar to those of water hydrogen-bonding network. The present graph-theoretical analysis results indicate that the high solubility limits of KSCN and other ion-network-forming salts might originate from their ability to form a large scale morphological network that can be intertwined with co-existing water H-bonding network. Furthermore, it is shown that the graph-theoretical properties of water H-bonding network structures do not strongly depend on the nature of dissolved ions nor on the morphological structures of ion aggregates, indicating that water's H-bonding interaction and network-forming capability are highly robust. We anticipate that the present graph-theoretical analysis results of high salt

  8. Ion transport in a model gramicidin channel. Structure and thermodynamics.

    PubMed Central

    Roux, B; Karplus, M

    1991-01-01

    The potential of mean force for Na+ and K+ ions as a function of position in the interior of a periodic poly(L,D)-alanine model for the gramicidin beta-helix is calculated with a detailed atomic model and realistic interactions. The calculated free energy barriers are 4.5 kcal/mol for Na+ and 1.0 kcal/mol for K+. A decomposition of the free energy demonstrates that the water molecules make a significant contribution to the free energy of activation. There is an increase in entropy at the transition state associated with greater fluctuations. Analysis reveals that the free energy profile of ions in the periodic channel is controlled not by the large interaction energy involving the ion but rather by the weaker water-water, water-peptide and peptide-peptide hydrogen bond interactions. The interior of the channel retains much of the solvation properties of a liquid in its interactions with the cations. Of particular importance is the flexibility of the helix, which permits it to respond to the presence of an ion in a fluidlike manner. The distortion of the helix is local (limited to a few carbonyls) because the structure is too flexible to transmit a perturbation to large distances. The plasticity of the structure (i.e., the property to deform without generating a large energy stress) appears to be an essential factor in the transport of ions, suggesting that a rigid helix model would be inappropriate. Images FIGURE 1 FIGURE 10 PMID:1714305

  9. Last ion engine thrust puts ESA's SMART-1 on the right track for its Moon encounter

    NASA Astrophysics Data System (ADS)

    2004-10-01

    SMART-1, on its way to the Moon, has now covered more than 80 million kilometres. Its journey started on 27 September 2003, when the spacecraft was launched on board an Ariane 5 rocket from Europe’s spaceport in Kourou, French Guiana. Since then, it has been spiralling in progressively larger orbits around Earth, to eventually be captured by the lunar gravity and enter into orbit around the Moon in November this year. The SMART-1 mission was designed to pursue two main objectives. The first is purely technological: to demonstrate and test a number of space techniques to be applied to future interplanetary exploration missions. The second goal is scientific, mainly dedicated to lunar science. It is the technology demonstration goal, in particular the first European flight test of a solar-powered ion engine as a spacecraft’s main propulsion system, that gave shape to the peculiar route and duration (13 months) of the SMART-1 journey to the Moon. The long spiralling orbit around Earth, which is bringing the spacecraft closer and closer to the Moon, is needed for the ion engine to function and be tested over a distance comparable to that a spacecraft would travel during a possible interplanetary trip. The SMART-1 mission is also testing the response of a spacecraft propelled by such an engine during gravity-assisted manoeuvres. These are techniques currently used on interplanetary journeys, which make use of the gravitational pull of celestial objects (e.g. planets) for the spacecraft to gain acceleration and reach its final target while saving fuel. In SMART-1’s case, the Moon’s gravitational pull has been exploited in three “lunar resonance” manoeuvres. The first two successfully took place in August and September 2004. The last resonance manoeuvre was on 12 October, during the last major ion engine thrust, which lasted nearly five days, from 10 to 14 October. Thanks to this final thrust, SMART-1 will make two more orbits around Earth without any further

  10. Structure, dynamics, and ion conductance of the phospholamban pentamer.

    PubMed

    Maffeo, Christopher; Aksimentiev, Aleksei

    2009-06-17

    A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5'-triphosphate-driven calcium pump, the Ca2+-ATPase. Although the inhibition of Ca2+-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 A in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.

  11. Impact of tracking station distribution structure on BeiDou satellite orbit determination

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Zhang, Qin; Huang, Guanwen; Wang, Le; Qu, Wei

    2015-11-01

    The racking station distribution structure plays an important role in GNSS satellite orbit determination. Due to the current satellite distribution of the BeiDou satellite navigation system (BDS), the problem how to construct a reasonable distribution of tracking stations to obtain BDS satellite orbits with high precision has become a highly imperative issue. Based on the theory of dynamic orbit determination, two different station distributions were analyzed to study their impact on BDS precise and real-time orbit determination. Subsequently, the impact of Satellite Position Dilution of Precision (SPDOP) values on orbit determination was analyzed. Finally, an improved scheme for the tracking station distribution was designed based on the original scheme. The numerical results show that the SPDOP value can be used to evaluate the contribution of the tracking stations distribution on the BDS IGSO and MEO satellites orbit determination. In addition, the tracking stations which focus on the Asia-Pacific region play a key role in current BDS orbit determination.

  12. Structural evolution of zirconium carbide under ion irradiation

    NASA Astrophysics Data System (ADS)

    Gosset, D.; Dollé, M.; Simeone, D.; Baldinozzi, G.; Thomé, L.

    2008-02-01

    Zirconium carbide is one of the candidate materials to be used for some fuel components of the high temperature nuclear reactors planned in the frame of the Gen-IV project. Few data exist regarding its behaviour under irradiation. We have irradiated ZrC samples at room temperature with slow heavy ions (4 MeV Au, fluence from 10 11 to 5 × 10 15 cm -2) in order to simulate neutron irradiations. Grazing incidence X-Ray diffraction (GIXRD) and transmission electron microscopy (TEM) analysis have been performed in order to study the microstructural evolution of the material versus ion fluence. A high sensitivity to oxidation is observed with the formation of zirconia precipitates during the ion irradiations. Three damage stages are observed. At low fluence (<10 12 cm -2), low modifications are observed. At intermediate fluence, high micro-strains appear together with small faulted dislocation loops. At the highest fluence (>10 14 cm -2), the micro-strains saturate and the loops coalesce to form a dense dislocation network. No other structural modification is observed. The material shows a moderate cell parameter increase, corresponding to a 0.6 vol.% swelling, which saturates around 10 14 ions/cm 2, i.e., a few Zr dpa. As a result, in spite of a strong covalent bonding component, ZrC seems to have a behaviour under irradiation close to cubic metals.

  13. Opto-structural and dielectric properties of 80 MeV oxygen ion irradiated natural phlogopite mica

    NASA Astrophysics Data System (ADS)

    Kaur, Sukhnandan; Singh, Surinder; Singh, Lakhwant; Lochab, S. P.

    2013-04-01

    Ion beams of MeV energies produce latent tracks in most dielectrics. These ion tracks in turn produce various modifications in their structural, optical and dielectric properties. These modifications are monitored using various techniques such as Ultraviolet-visible spectrometry, X-ray Diffraction, LCR meter and Fourier Transform Infra red spectroscopy in natural phlogopite mica. Thin sheets (˜20 μm) of phlogopite mica were exposed to 80 MeV oxygen ions. A systematic decrease of the optical band gap with ion fluence was observed. An increase in the Urbach energy indicates an increase in the disorder in phlogopite mica. The dielectric constant was found to decrease with increasing fluence while measurements of tan δ, a.c. conductivity and dielectric loss show an increase. The measured data revealed that the value of a.c. conductivity depends linearly on the frequency, with slope n ranging between 0.62 and 0.77. X-ray Diffraction analysis of pristine and irradiated phlogopite mica demonstrated that the crystallite size decreases while strain and dislocation density increases with increasing fluence. Fourier Transform Infra red spectra showed the shifting of the OH stretching band and the disappearance of Si-H bands due to irradiation. Different causes of these modifications are discussed here.

  14. The effect of track structure on cell inactivation and chromosome damage at a constant let of 120 keV/mum

    NASA Astrophysics Data System (ADS)

    Goodwin, E. H.; Bailey, S. M.; Chen, D. J.; Cornforth, M. N.

    The influence of track structure on chromosome damage and cell inactivation are being investigated. Plateau-phase normal human fibroblast cultures were irradiated with gamma rays, and He, Ne and Ar ions. Particle velocities were chosen so that all beams had an LET of 120 keV/mum. In this constant-LET experimental design, the radial distribution of excitations and ionizations about the particle track is the most significant variable. Using premature chromosome condensation, chromatin breaks were measured at two time points, promptly after irradiation and after a prolonged incubation to allow for repair. These measurements give an indication of both initial chromosomal damage and also residual damage that is either not repaired or is misrepaired. Survival was measured under the same conditions. Results indicate that the RBEs for both cell inactivation and, to a lesser extent, chromosome damage decrease as particle energy increases.

  15. Defect engineering in the MOSLED structure by ion implantation

    NASA Astrophysics Data System (ADS)

    Prucnal, S.; Wójtowicz, A.; Pyszniak, K.; Drozdziel, A.; Zuk, J.; Turek, M.; Rebohle, L.; Skorupa, W.

    2009-05-01

    When amorphous SiO2 films are bombarded with energetic ions, various types of defects are created as a consequence of ion-solid interaction (peroxy radicals POR, oxygen deficient centres (ODC), non-bridging oxygen hole centres (NBOHC), E‧ centres, etc.). The intensity of the electroluminescence (EL) from oxygen deficiency centres at 2.7 eV, non-bridging oxygen hole centres at 1.9 eV and defect centres with emission at 2.07 eV can be easily modified by the ion implantation of the different elements (H, N, O) into the completely processed MOSLED structure. Nitrogen implanted into the SiO2:Gd layer reduces the concentration of the ODC and NBOHC while the doping of the oxygen increases the EL intensity observed from POR defect and NBOHC. Moreover, after oxygen or hydrogen implantation into the SiO2:Ge structure fourfold or fifth fold increase of the germanium related EL intensity was observed.

  16. Structures and physical properties of gaseous metal cationized biological ions.

    PubMed

    Burt, Michael B; Fridgen, Travis D

    2012-01-01

    Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

  17. Spontaneous nucleation of structural defects in inhomogeneous ion chains

    NASA Astrophysics Data System (ADS)

    De Chiara, Gabriele; del Campo, Adolfo; Morigi, Giovanna; Plenio, Martin B.; Retzker, Alex

    2010-11-01

    Structural defects in ion crystals can be formed during a linear quench of the transverse trapping frequency across the mechanical instability from a linear chain to a zigzag structure. The density of defects after the sweep can be conveniently described by the Kibble-Zurek mechanism (KZM). In particular, the number of kinks in the zigzag ordering can be derived from a time-dependent Ginzburg-Landau equation for the order parameter, here the zigzag transverse size, under the assumption that the ions are continuously laser cooled. In a linear Paul trap, the transition becomes inhomogeneous, since the charge density is larger in the center and more rarefied at the edges. During the linear quench, the mechanical instability is first crossed in the center of the chain, and a front, at which the mechanical instability is crossed during the quench, is identified that propagates along the chain from the center to the edges. If the velocity of this front is smaller than the sound velocity, the dynamics become adiabatic even in the thermodynamic limit and no defect is produced. Otherwise, the nucleation of kinks is reduced with respect to the case in which the charges are homogeneously distributed, leading to a new scaling of the density of kinks with the quenching rate. The analytical predictions are verified numerically by integrating the Langevin equations of motion of the ions, in the presence of a time-dependent transverse confinement. We argue that the non-equilibrium dynamics of an ion chain in a Paul trap constitutes an ideal scenario to test the inhomogeneous extension of the KZM, which lacks experimental evidence to date.

  18. Microdosimetry of the full slowing down of protons using Monte Carlo track structure simulations.

    PubMed

    Liamsuwan, T; Uehara, S; Nikjoo, H

    2015-09-01

    The article investigates two approaches in microdosimetric calculations based on Monte Carlo track structure (MCTS) simulations of a 160-MeV proton beam. In the first approach, microdosimetric parameters of the proton beam were obtained using the weighted sum of proton energy distributions and microdosimetric parameters of proton track segments (TSMs). In the second approach, phase spaces of energy depositions obtained using MCTS simulations in the full slowing down (FSD) mode were used for the microdosimetric calculations. Targets of interest were water cylinders of 2.3-100 nm in diameters and heights. Frequency-averaged lineal energies ([Formula: see text]) obtained using both approaches agreed within the statistical uncertainties. Discrepancies beyond this level were observed for dose-averaged lineal energies ([Formula: see text]) towards the Bragg peak region due to the small number of proton energies used in the TSM approach and different energy deposition patterns in the TSM and FSD of protons.

  19. Automatic PSO-Based Deformable Structures Markerless Tracking in Laparoscopic Cholecystectomy

    NASA Astrophysics Data System (ADS)

    Djaghloul, Haroun; Batouche, Mohammed; Jessel, Jean-Pierre

    An automatic and markerless tracking method of deformable structures (digestive organs) during laparoscopic cholecystectomy intervention that uses the (PSO) behavour and the preoperative a priori knowledge is presented. The associated shape to the global best particles of the population determines a coarse representation of the targeted organ (the gallbladder) in monocular laparoscopic colored images. The swarm behavour is directed by a new fitness function to be optimized to improve the detection and tracking performance. The function is defined by a linear combination of two terms, namely, the human a priori knowledge term (H) and the particle's density term (D). Under the limits of standard (PSO) characteristics, experimental results on both synthetic and real data show the effectiveness and robustness of our method. Indeed, it outperforms existing methods without need of explicit initialization (such as active contours, deformable models and Gradient Vector Flow) on accuracy and convergence rate.

  20. Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations

    SciTech Connect

    Deng, Liulin; Ibrahim, Yehia M.; Garimella, Sandilya V. B.; Webb, Ian K.; Hamid, Ahmed M.; Norheim, Randolph V.; Prost, Spencer A.; Sandoval, Jeremy A.; Baker, Erin S.; Smith, Richard D.

    2016-10-18

    The initial use of traveling waves (TW) for ion mobility (IM) separations using a structures for lossless ion manipulations (SLIM) employed an ion funnel trap (IFT) to accumulate ions from a continuous electrospray ionization source, and limited to injected ion populations of ~106 charges due to the onset of space charge effects in the trapping region. Additional limitations arise due to the loss of resolution for the injection of ions over longer periods (e.g. in extended pulses). In this work a new SLIM ‘flat funnel’ (FF) module has been developed and demonstrated to enable the accumulation of much larger ion populations and their injection for IM separations. Ion current measurements indicate a capacity of ~3.2×108 charges for the extended trapping volume, over an order of magnitude greater than the IFT. The orthogonal ion injection into a funnel shaped separation region can greatly reduce space charge effects during the initial IM separation stage, and the gradually reduced width of the path allows the ion packet to be increasingly compressed in the lateral dimension as the separation progresses, allowing e.g. efficient transmission through conductance limits or compatibility with subsequent ion manipulations. This work examined the TW, RF, and DC confining field SLIM parameters involved in ion accumulation, injection, transmission and separation in the FF IM module using both direct ion current and MS measurements. Wide m/z range ion transmission is demonstrated, along with significant increases in signal to noise (S/N) ratios due to the larger ion populations injected. Additionally, we observed a reduction in the chemical background, which was attributed to more efficient desolvation of solvent related clusters over the extended ion accumulation periods. The TW SLIM FF IM module is anticipated to be especially effective as a front end for long path SLIM IM separation modules.

  1. Time-resolved X-ray Tracking of Expansion and Compression Dynamics in Supersaturating Ion-Networks

    PubMed Central

    Matsushita, Y.; Sekiguchi, H.; Ichiyanagi, K.; Ohta, N.; Ikezaki, K.; Goto, Y.; Sasaki, Y. C.

    2015-01-01

    Supersaturation of a solution system is a metastable state containing more solute than can be normally solubilized. Moreover, this condition is thermodynamically important for a system undergoing a phase transition. This state plays critical roles in deposition morphology in inorganic, organic, polymer and protein solution systems. In particular, microscopic solution states under supersaturated conditions have recently received much attention. In this report, we observed the dynamic motion of individual ion-network domains (INDs) in a supersaturated sodium acetate trihydrate solution (6.4 M) by using microsecond time-resolved and high accuracy (picometre scale) X-ray observations (diffracted X-ray tracking; DXT). We found that there are femto-Newton (fN) anisotropic force fields in INDs that correspond to an Angstrom-scale relaxation process (continuous expansion and compression) of the INDs at 25 μs time scale. The observed anisotropic force-field (femto-Newton) from DXT can lead to new explanations of how material crystallization is triggered. This discovery could also influence the interpretation of supercooling, bio-polymer and protein aggregation processes, and supersaturated systems of many other materials. PMID:26658326

  2. Time-resolved X-ray Tracking of Expansion and Compression Dynamics in Supersaturating Ion-Networks

    NASA Astrophysics Data System (ADS)

    Matsushita, Y.; Sekiguchi, H.; Ichiyanagi, K.; Ohta, N.; Ikezaki, K.; Goto, Y.; Sasaki, Y. C.

    2015-12-01

    Supersaturation of a solution system is a metastable state containing more solute than can be normally solubilized. Moreover, this condition is thermodynamically important for a system undergoing a phase transition. This state plays critical roles in deposition morphology in inorganic, organic, polymer and protein solution systems. In particular, microscopic solution states under supersaturated conditions have recently received much attention. In this report, we observed the dynamic motion of individual ion-network domains (INDs) in a supersaturated sodium acetate trihydrate solution (6.4 M) by using microsecond time-resolved and high accuracy (picometre scale) X-ray observations (diffracted X-ray tracking; DXT). We found that there are femto-Newton (fN) anisotropic force fields in INDs that correspond to an Angstrom-scale relaxation process (continuous expansion and compression) of the INDs at 25 μs time scale. The observed anisotropic force-field (femto-Newton) from DXT can lead to new explanations of how material crystallization is triggered. This discovery could also influence the interpretation of supercooling, bio-polymer and protein aggregation processes, and supersaturated systems of many other materials.

  3. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch

    DOE PAGES

    Garimella, Sandilya V. B.; Ibrahim, Yehia. M.; Webb, Ian K.; ...

    2015-08-19

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated using theoretical and simulation methods at 4 Torr pressure. SIMION simulations were used to optimize and evaluate conditions for performing turns without loss of signal intensity or ion mobility resolving power. Fundamental considerations indicated that the “race track” effect during ion turns may incur only small losses to the ion mobility resolving power at 4 Torr pressure for the typical plume widths predicted in an optimized SLIM ‘tee’ switch design. The dynamic switching of ions into orthogonal channels was alsomore » evaluated using SIMION ion trajectory simulations, and achieved similar performance. Simulation results were in close agreement with experimental results and were used to refine SLIM designs and applied potentials for their use.« less

  4. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch

    SciTech Connect

    Garimella, Sandilya V. B.; Ibrahim, Yehia. M.; Webb, Ian K.; Ipsen, Andreas B.; Chen, Tsung-Chi; Tolmachev, Aleksey V.; Baker, Erin S.; Anderson, Gordon A.; Smith, Richard D.

    2015-08-19

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated using theoretical and simulation methods at 4 Torr pressure. SIMION simulations were used to optimize and evaluate conditions for performing turns without loss of signal intensity or ion mobility resolving power. Fundamental considerations indicated that the “race track” effect during ion turns may incur only small losses to the ion mobility resolving power at 4 Torr pressure for the typical plume widths predicted in an optimized SLIM ‘tee’ switch design. The dynamic switching of ions into orthogonal channels was also evaluated using SIMION ion trajectory simulations, and achieved similar performance. Simulation results were in close agreement with experimental results and were used to refine SLIM designs and applied potentials for their use.

  5. Coherent structures in ion temperature gradient turbulence-zonal flow

    SciTech Connect

    Singh, Rameswar; Singh, R.; Kaw, P.; Gürcan, Ö. D.; Diamond, P. H.

    2014-10-15

    Nonlinear stationary structure formation in the coupled ion temperature gradient (ITG)-zonal flow system is investigated. The ITG turbulence is described by a wave-kinetic equation for the action density of the ITG mode, and the longer scale zonal mode is described by a dynamic equation for the m = n = 0 component of the potential. Two populations of trapped and untrapped drift wave trajectories are shown to exist in a moving frame of reference. This novel effect leads to the formation of nonlinear stationary structures. It is shown that the ITG turbulence can self-consistently sustain coherent, radially propagating modulation envelope structures such as solitons, shocks, and nonlinear wave trains.

  6. Emerging models of glutamate receptor ion channel structure and function.

    PubMed

    Mayer, Mark L

    2011-10-12

    Excitatory synaptic transmission in the brain is mediated by ligand-gated ion channels (iGluRs) activated by glutamate. Distinct from other neurotransmitter receptors, the extracellular domains of iGluRs are loosely packed assemblies with two clearly distinct layers, each of which has both local and global 2-fold axes of symmetry. By contrast, the iGluR transmembrane segments have 4-fold symmetry and share a conserved pore loop architecture found in tetrameric voltage-gated ion channels. The striking layered architecture of iGluRs revealed by the 3.6 Å resolution structure of an AMPA receptor homotetramer likely arose from gene fusion events that occurred early in evolution. Although this modular design has greatly facilitated biophysical and structural studies on individual iGluR domains, and suggested conserved mechanisms for iGluR gating, recent work is beginning to reveal unanticipated diversity in the structure, allosteric regulation, and assembly of iGluR subtypes.

  7. Development and fabrication of a two-axis tracking structure and baseline module improvement

    SciTech Connect

    Sanders, J.A.; Cass, D.C.

    1987-03-01

    The design improvement objectives of this project were to further enhance the performance and reduce cost of the second-generation low-profile point-focus Fresnel lens concentrator. The primary objective was to redesign a two-axis drive mechanism and structure that overcomes the failure modes of the first-generation design and increases collector aperture area without detriment to performance. A secondary objective was to develop secondary optics and grid obscuration techniques to improve module electrical performance and increase tracking error tolerance. The drive mechanism and structure design resulted in a significant reduction in the number of parts and improved structural integrity. The tracking structure is capable of supporting 70 square meters of flat-plate modules and 41 square meters of second-generation point-focus Fresnel lens modules. A total internal reflector (TIR) with cell grid obscuration grooves was designed. The TIR had superior offtracking performance over secondary reflectors but, without grid obscuration, was unable to achieve operating efficiencies equal to the earlier designs. Grid obscuration designs were evolved and proof of concept established. Further development is necessary to evaluate the actual application of grid obscuration techniques under high concentration.

  8. Ion structure in dense plasmas: MSA versus HNC

    NASA Astrophysics Data System (ADS)

    Wünsch, K.; Vorberger, J.; Gregori, G.; Gericke, D. O.

    2009-05-01

    We present results for the ionic structure in dense, moderately to strongly coupled plasmas using two models: the mean spherical approximation (MSA) and the hypernetted chain (HNC) approach. While the first method allows for an analytical solution, the latter has to be solved iteratively. Independent of the coupling strength, the results show only small differences when the ions are considered to form an unscreened one-component plasma (OCP) system. If the electrons are treated as a polarizable background, the different ways to incorporate the screening yield, however, large discrepancies between the models, particularly for more strongly coupled plasmas.

  9. Real-time tracking the Li+-ion transition behavior and dynamics in solid Poly(vinyl alcohol)/LiClO4 electrolytes

    PubMed Central

    Bao, Lixia; Zou, Xin; Luo, Xin; Pu, Yanlei; Wang, Jiliang; Lei, Jingxin

    2017-01-01

    To delicately track the Li-ion transport in SPEs under an external electric field (EF) is a big challenge, considering the limitation of most spectroscopic methods to monitor the real-time conformational changes and track the dynamic process. Herein, real-time Li-ion transition behavior and transport dynamics in typical poly(vinyl alcohol)/LiClO4 electrolytes under an external EF have been studied by combining time-resolved Fourier transform infrared (FTIR) with two-dimensional correlation FTIR spectroscopy. Results show that no migration of Li-ions has been detected when the time scale of the EF loading is at nanosecond (less than 200 ns). However, for the first time, Li-ions have been found to significantly transfer along the EF direction as the time scale enhances to microsecond order of magnitude and the migration period is less than 10 microseconds. The Li+ migration in the SPEs under an EF is a complicated process including quasi-periodic dissociation and coordination effects between Li-ion carriers and polymeric chains. PMID:28378837

  10. Real-time tracking the Li(+)-ion transition behavior and dynamics in solid Poly(vinyl alcohol)/LiClO4 electrolytes.

    PubMed

    Bao, Lixia; Zou, Xin; Luo, Xin; Pu, Yanlei; Wang, Jiliang; Lei, Jingxin

    2017-04-05

    To delicately track the Li-ion transport in SPEs under an external electric field (EF) is a big challenge, considering the limitation of most spectroscopic methods to monitor the real-time conformational changes and track the dynamic process. Herein, real-time Li-ion transition behavior and transport dynamics in typical poly(vinyl alcohol)/LiClO4 electrolytes under an external EF have been studied by combining time-resolved Fourier transform infrared (FTIR) with two-dimensional correlation FTIR spectroscopy. Results show that no migration of Li-ions has been detected when the time scale of the EF loading is at nanosecond (less than 200 ns). However, for the first time, Li-ions have been found to significantly transfer along the EF direction as the time scale enhances to microsecond order of magnitude and the migration period is less than 10 microseconds. The Li(+) migration in the SPEs under an EF is a complicated process including quasi-periodic dissociation and coordination effects between Li-ion carriers and polymeric chains.

  11. DUAL HEATED ION SOURCE STRUCTURE HAVING ARC SHIFTING MEANS

    DOEpatents

    Lawrence, E.O.

    1959-04-14

    An ion source is presented for calutrons, particularly an electrode arrangement for the ion generator of a calutron ion source. The ion source arc chamber is heated and an exit opening with thermally conductive plates defines the margins of the opening. These plates are electrically insulated from the body of the ion source and are connected to a suitable source of voltage to serve as electrodes for shaping the ion beam egressing from the arc chamber.

  12. Tracking "apolar" NMe4+ ions within two polyoxothiomolybdates that have the same pores: smaller clathrate and larger highly porous clusters in action.

    PubMed

    Korenev, Vladimir S; Boulay, Antoine G; Haouas, Mohamed; Bannani, Fatma; Fedin, Vladimir P; Sokolov, Maxim N; Terazzi, Emmanuel; Garai, Somenath; Müller, Achim; Taulelle, Francis; Marrot, Jérôme; Leclerc, Nathalie; Floquet, Sébastien; Cadot, Emmanuel

    2014-03-10

    Two nanosized polyoxothiometalates were synthesized based on linking oxomolybdate building blocks with {Mo2O2S2}(2+) groups. Remarkably, both compounds are formed selectively primarily upon changing the related concentrations in a logical way; they exhibit common structural features based on the same {Mo9O6S3}-type pores, which result in connections between {Mo6O21} pentagons and {Mo2O2S2}(2+) linkers. Whereas the much larger spherical Mo132-type Keplerate contains twenty pores, the smaller Mo63 -type cluster remarkably contains only two. The two compounds and a similar Keplerate exhibit interesting supramolecular properties related to interactions with the unusual predominantly apolar NMe4(+) cations. Structural characterization of the Mo63 -type compound reveals in the solid state a clathrate-like species that contains four NMe4(+) cations embedded in two types of structurally well-adapted pockets. Related NMR spectroscopic investigations in solution using NMe4(+) as the NMR spectroscopic probe are in agreement with the solid-state description. (1)H NMR spectroscopic experiments (1D variable-temperature, 2D total correlation spectroscopy (TOCSY), exchange spectroscopy (EXSY), and diffusion-ordered spectroscopy (DOSY)) feature firmly immobilized and mobile NMe4(+) ions in relationship with the type of host-guest arrangements. The use of the (1)H NMR DOSY spectroscopic methodology has been successfully applied to track the interactions of the NMe4(+) cations with the {Mo9O6S3} pores of a sulfurated Keplerate, thereby allowing the first quantitative analysis of this type of plugging process. The stability constant K=(210±20) mol(-1)  L is discussed related to the character of the process.

  13. Magnetic force microscopy and spinstand testing of multi-row-per-track discrete bit patterned media fabricated by focused ion beam

    NASA Astrophysics Data System (ADS)

    Chen, Y. J.; Huang, T. L.; Leong, S. H.; Hu, S. B.; Ng, K. W.; Yuan, Z. M.; Zong, B. Y.; Shi, J. Z.; Hendra, S. K.; Liu, B.; Ng, V.

    2009-04-01

    Multi-row-per-track discrete bit patterned media with interleaved bits have been fabricated on granular perpendicular media disks by focused ion beam and tested by magnetic force microscopy and spinstand tester. It was found that sub-100 nm patterned magnetic islands showed single domain behavior and narrowed switching field distribution. We further demonstrate from captured spinstand readback waveforms the concept of recording two rows of interleaved dot bits as one track. In addition to overcoming the down track patterning resolution limit, the proposed concept patterned media provide many other advantages including higher data rate for read/write, a flexible bit aspect ratio (BAR)≥2 design for better integration with head design and servo control, as well as allowing the use of wider write pole to improve writing efficiency for high density recording.

  14. The real structure of columnar pinning centers in heavy-ion-irradiated cuprate superconductors

    SciTech Connect

    Welch, D.O.; Zhu, Y.; Budhani, R.C.

    1995-12-31

    There has been considerable recent interest in the use of columnar defects produced by irradiation with energetic heavy ions to raise the irreversibility line and improve the critical current density of cuprate superconductors. In the interpretation and theoretical modeling of the flux-pinning characteristics of heavy-ion tracks, it is generally assumed that they are simply columns of non-superconducting material. In this paper we present a more realistic description, based both on resistivity measurements and on detailed, quantitative transmission electron microscope methods (both imaging and analytical studies), of the nature of heavy-ion damage, including defects, disorder, strain fields, and oxygen deficiencies in the matrix of the superconductor surrounding the amorphous columns. The presence of such disorder appears to be a consequence of the mechanism of track formation, which involves partial epitaxial regrowth of a molten region which follows the passage of sufficiently energetic ions.

  15. Characterization and properties of micro- and nanowires of controlled size, composition, and geometry fabricated by electrodeposition and ion-track technology

    PubMed Central

    2012-01-01

    Summary The combination of electrodeposition and polymeric templates created by heavy-ion irradiation followed by chemical track etching provides a large variety of poly- and single-crystalline nanowires of controlled size, geometry, composition, and surface morphology. Recent results obtained by our group on the fabrication, characterization and size-dependent properties of nanowires synthesized by this technique are reviewed, including investigations on electrical resistivity, surface plasmon resonances, and thermal instability. PMID:23365800

  16. Sugar-metal ion interactions: the complicated coordination structures of cesium ion with D-ribose and myo-inositol.

    PubMed

    Hu, Haijian; Xue, Junhui; Wen, Xiaodong; Li, Weihong; Zhang, Chao; Yang, Limin; Xu, Yizhuang; Zhao, Guozhong; Bu, Xiaoxia; Liu, Kexin; Chen, Jia'er; Wu, Jinguang

    2013-11-18

    The novel cesium chloride-D-ribose complex (CsCl·C5H10O5; Cs-R) and cesium chloride-myo-inositol complex (CsCl·C6H12O6; Cs-I) have been synthesized and characterized using X-ray diffraction and FTIR, FIR, THz, and Raman spectroscopy. Cs(+) is eight-coordinated to three chloride ions, O1 and O2 from one D-ribose molecule, O1 from another D-ribose molecule, and O4 and O5 from the third D-ribose molecule in Cs-R. For one D-ribose molecule, the oxygen atom O1 in the ring is coordinated to two cesium ions as an oxygen bridge, O2 is cocoordinated with O1 to one of the two cesium ions, and O4 and O5 are coordinated to the third cesium ion, respectively. O3 does not coordinate to metal ions and only takes part in forming hydrogen bonds. One chloride ion is connected to three cesium ions. Thus, a complicated structure of Cs-D-ribose forms. For Cs-I, Cs(+) is 10-coordinated to three chloride ions, O1 and O2 from one myo-inositol molecule, O3 and O4 from another myo-inositol molecule, O5 and O6 from the third myo-inositol molecule, and O6 from the fourth myo-inositol molecule. One metal ion is connected to four ligands, and one myo-inositol is coordinated to four Cs(+) ions, which is also a complicated coordination structure. Crystal structure results, FTIR, FIR, THz, and Raman spectra provide detailed information on the structure and coordination of hydroxyl groups to metal ions in the cesium chloride-D-ribose and cesium chloride-myo-inositol complexes.

  17. Poles tracking of weakly nonlinear structures using a Bayesian smoothing method

    NASA Astrophysics Data System (ADS)

    Stephan, Cyrille; Festjens, Hugo; Renaud, Franck; Dion, Jean-Luc

    2017-02-01

    This paper describes a method for the identification and the tracking of poles of a weakly nonlinear structure from its free responses. This method is based on a model of multichannel damped sines whose parameters evolve over time. Their variations are approximated in discrete time by a nonlinear state space model. States are estimated by an iterative process which couples a two-pass Bayesian smoother with an Expectation-Maximization (EM) algorithm. The method is applied on numerical and experimental cases. As a result, accurate frequency and damping estimates are obtained as a function of amplitude.

  18. Glutamate Receptor Ion Channels: Structure, Regulation, and Function

    PubMed Central

    Wollmuth, Lonnie P.; McBain, Chris J.; Menniti, Frank S.; Vance, Katie M.; Ogden, Kevin K.; Hansen, Kasper B.; Yuan, Hongjie; Myers, Scott J.; Dingledine, Ray

    2010-01-01

    The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors. PMID:20716669

  19. Crystal structures of a double-barrelled fluoride ion channel

    PubMed Central

    Stockbridge, Randy B.; Kolmakova-Partensky, Ludmila; Shane, Tania; Koide, Akiko; Koide, Shohei; Miller, Christopher; Newstead, Simon

    2016-01-01

    To contend with hazards posed by environmental fluoride, microorganisms export this anion through F--specific ion channels of the Fluc family1–4. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been unearthed, including extreme selectivity for F- over Cl- and dual-topology dimeric assembly5–6. To understand the chemical basis for F- permeation and how the antiparallel subunits convene to form a F--selective pore, we solved crystal structures of two bacterial Fluc homologues in complex with three different monobody inhibitors, with and without F- present, to a maximum resolution of 2.1 Å. The structures reveal a surprising “double-barrelled” channel architecture in which two F- ion pathways span the membrane and the dual-topology arrangement includes a centrally coordinated cation, most likely Na+. F- selectivity is proposed to arise from the very narrow pores and an unusual anion coordination that exploits the quadrupolar edges of conserved phenylalanine rings. PMID:26344196

  20. Complete structural characterization of ceramides as [M-H](-) ions by multiple-stage linear ion trap mass spectrometry.

    PubMed

    Hsu, Fong-Fu

    2016-11-01

    Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MS(n)) towards complete structural determination of ceramides in ten major families characterized as the [M-H](-) ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS(2) spectrum, while the sequential MS(3) and MS(4) spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail.

  1. Combining ion mobility spectrometry with hydrogen-deuterium exchange and top-down MS for peptide ion structure analysis.

    PubMed

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Maleki, Hossein; Arndt, James R; Donohoe, Gregory C; Valentine, Stephen J

    2014-12-01

    The gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined by ion mobility spectrometry (IMS) and hydrogen deuterium exchange (HDX)-tandem mass spectrometry (MS/MS) techniques. [M+4H](4+) ions exhibit two conformers with collision cross sections of 418 Å(2) and 471 Å(2). [M+3H](3+) ions exhibit a predominant conformer with a collision cross section of 340 Å(2) as well as an unresolved conformer (shoulder) with a collision cross section of ~367 Å(2). Maximum HDX levels for the more compact [M+4H](4+) ions and the compact and partially-folded [M+3H](3+) ions are ~12.9, ~15.5, and ~14.9, respectively. Ion structures obtained from molecular dynamics simulations (MDS) suggest that this ordering of HDX level results from increased charge-site/exchange-site density for the more compact ions of lower charge. Additionally, a new model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) for the computer-generated structures is shown to better correlate to the experimentally determined per-residue deuterium uptake. Future comparisons of IMS-HDX-MS data with structures obtained from MDS are discussed with respect to novel experiments that will reveal the HDX rates of individual residues.

  2. Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Maleki, Hossein; Arndt, James R.; Donohoe, Gregory C.; Valentine, Stephen J.

    2014-12-01

    The gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined by ion mobility spectrometry (IMS) and hydrogen deuterium exchange (HDX)-tandem mass spectrometry (MS/MS) techniques. [M+4H]4+ ions exhibit two conformers with collision cross sections of 418 Å2 and 471 Å2. [M+3H]3+ ions exhibit a predominant conformer with a collision cross section of 340 Å2 as well as an unresolved conformer (shoulder) with a collision cross section of ~367 Å2. Maximum HDX levels for the more compact [M+4H]4+ ions and the compact and partially-folded [M+3H]3+ ions are ~12.9, ~15.5, and ~14.9, respectively. Ion structures obtained from molecular dynamics simulations (MDS) suggest that this ordering of HDX level results from increased charge-site/exchange-site density for the more compact ions of lower charge. Additionally, a new model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) for the computer-generated structures is shown to better correlate to the experimentally determined per-residue deuterium uptake. Future comparisons of IMS-HDX-MS data with structures obtained from MDS are discussed with respect to novel experiments that will reveal the HDX rates of individual residues.

  3. Online in situ x-ray diffraction setup for structural modification studies during swift heavy ion irradiation.

    PubMed

    Grygiel, C; Lebius, H; Bouffard, S; Quentin, A; Ramillon, J M; Madi, T; Guillous, S; Been, T; Guinement, P; Lelièvre, D; Monnet, I

    2012-01-01

    The high energy density of electronic excitations due to the impact of swift heavy ions can induce structural modifications in materials. We present an x-ray diffractometer called ALIX ("Analyse en Ligne sur IRRSUD par diffraction de rayons X"), which has been set up at the low-energy beamline (IRRadiation SUD - IRRSUD) of the Grand Accélérateur National d'Ions Lourds facility, to allow the study of structural modification kinetics as a function of the ion fluence. The x-ray setup has been modified and optimized to enable irradiation by swift heavy ions simultaneously to x-ray pattern recording. We present the capability of ALIX to perform simultaneous irradiation-diffraction by using energy discrimination between x-rays from diffraction and from ion-target interaction. To illustrate its potential, results of sequential or simultaneous irradiation-diffraction are presented in this article to show radiation effects on the structural properties of ceramics. Phase transition kinetics have been studied during xenon ion irradiation of polycrystalline MgO and SrTiO(3). We have observed that MgO oxide is radiation-resistant to high electronic excitations, contrary to the high sensitivity of SrTiO(3), which exhibits transition from the crystalline to the amorphous state during irradiation. By interpreting the amorphization kinetics of SrTiO(3), defect overlapping models are discussed as well as latent track characteristics. Together with a transmission electron microscopy study, we conclude that a single impact model describes the phase transition mechanism.

  4. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

    PubMed

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

    2017-03-17

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

  5. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J.

    2017-03-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

  6. Linear Quadratic Tracking Design for a Generic Transport Aircraft with Structural Load Constraints

    NASA Technical Reports Server (NTRS)

    Burken, John J.; Frost, Susan A.; Taylor, Brian R.

    2011-01-01

    When designing control laws for systems with constraints added to the tracking performance, control allocation methods can be utilized. Control allocations methods are used when there are more command inputs than controlled variables. Constraints that require allocators are such task as; surface saturation limits, structural load limits, drag reduction constraints or actuator failures. Most transport aircraft have many actuated surfaces compared to the three controlled variables (such as angle of attack, roll rate & angle of side slip). To distribute the control effort among the redundant set of actuators a fixed mixer approach can be utilized or online control allocation techniques. The benefit of an online allocator is that constraints can be considered in the design whereas the fixed mixer cannot. However, an online control allocator mixer has a disadvantage of not guaranteeing a surface schedule, which can then produce ill defined loads on the aircraft. The load uncertainty and complexity has prevented some controller designs from using advanced allocation techniques. This paper considers actuator redundancy management for a class of over actuated systems with real-time structural load limits using linear quadratic tracking applied to the generic transport model. A roll maneuver example of an artificial load limit constraint is shown and compared to the same no load limitation maneuver.

  7. Time-dependent cylindrical and spherical ion-acoustic solitary structures in relativistic degenerate multi-ion plasmas with positively-charged heavy ions

    NASA Astrophysics Data System (ADS)

    Hossen, M. R.; Nahar, L.; Mamun, A. A.

    2014-12-01

    The properties of time-dependent cylindrical and spherical, modified ion-acoustic (mIA) solitary structures in relativistic degenerate multi-ion plasmas (containing degenerate electron fluids, inertial positively-, as well as negatively-, charged light ions, and positively-charged static heavy ions) have been investigated theoretically. This investigation is valid for both non-relativistic and ultra-relativistic limits. The well-known reductive perturbation method has been used to derive the Korteweg-de Vries (K-dV) and the mK-dV equations for studying the basic features of solitary waves. The fundamental characteristics of mIA solitary waves are found to be significantly modified by the effects of the degenerate pressures of the electron and the ion fluids, their number densities, and the various charge states of heavy ions. The relevance of our results in astrophysical compact objects like white dwarfs and neutron stars, which are of scientific interest, is briefly discussed.

  8. Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins

    PubMed Central

    Mealman, Tiffany D.; McEvoy, Megan M.; Blackburn, Ninian J.

    2014-01-01

    Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli. However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. Here, we use selenomethionine (SeM) active site labels in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm. PMID:25313055

  9. Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins

    DOE PAGES

    Chacon, Kelly N.; Mealman, Tiffany D.; McEvoy, Megan M.; ...

    2014-10-13

    Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli. However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. In this paper, we use selenomethionine (SeM) active site labelsmore » in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Finally, our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm.« less

  10. Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins

    SciTech Connect

    Chacon, Kelly N.; Mealman, Tiffany D.; McEvoy, Megan M.; Blackburn, Ninian J.

    2014-10-13

    Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli. However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. In this paper, we use selenomethionine (SeM) active site labels in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Finally, our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm.

  11. Near real-time tracking of dynamic properties for standalone structural health monitoring systems

    NASA Astrophysics Data System (ADS)

    Rainieri, C.; Fabbrocino, G.; Cosenza, E.

    2011-11-01

    Automated modal parameter identification of civil engineering structures has been analyzed in a previous paper. An original algorithm, named LEONIDA, working in frequency domain, has been presented and a number of test cases have been discussed in order to point out advantages and drawbacks. It has been demonstrated that LEONIDA represents a promising and reliable tool, in particular for modal testing. Conversely, integration of such a procedure into a fully automated structural health monitoring (SHM) system has shown that it can be used as modal information engine, but length of record durations, amount of computational burden and response time lead to recognize that serious drawbacks and limitations exist for a class of applications, such as continuous monitoring of structures in seismically prone areas. In fact, a fast assessment of relevant structure health conditions in the early post-earthquake phase is becoming of interest in different European areas. In such a context, the statistical treatment of measured dynamic properties could be certainly useful, but it requires the collection of an extensive amount of local and global data in a short time. As a consequence, availability of reliable, robust and fairly fast data processing procedures for modal tracking is fundamental whenever really effective and useful SHM systems are adopted to support civil protection activities during seismic sequences. This applies mainly to strategic structures, whose health conditions must be rapidly assessed after any seismic event, in order to securely manage rescue operations. In the present paper, the main issues related to a fast, robust and reliable modal tracking for emergency management are outlined. Then, an automated modal tracking strategy for SHM applications in earthquake prone regions is described. It is based on the knowledge of the experimental mode shapes and a revised concept of spatial filtering. Results of sample applications of the proposed procedure refer

  12. Crystallization of ultrathin W-Si multilayer structures by high-energy heavy ion irradiations

    SciTech Connect

    Marfaing, J.; Marine, W. ); Vidal, B. ); Toulemonde, M. ); Hage Ali, M.; Stoquert, J.P. )

    1990-10-22

    Ultrathin amorphous multilayers structures (1.55 nm bilayer period) were irradiated by high-energy heavy ion ({sup 127}I and {sup 238}U ions). Transmission electron microscopy study shows that the ion-material interaction in such a configuration leads to an irreversible transformation of the initial amorphous structures. In this letter, we report the first observation of the crystallization of the multilayers induced by the heavy ion irradiations with a subsequent formation of a new WSi structure. The crucial role of the electronic effects in the crystallization process is discussed relatively to the other phenomena induced under the ion irradiation.

  13. Ion induced changes in the structure of bordered pit membranes.

    PubMed

    Lee, Jinkee; Holbrook, N Michele; Zwieniecki, Maciej A

    2012-01-01

    Ion-mediated changes in xylem hydraulic resistance are hypothesized to result from hydrogel like properties of pectins located in the bordered pit membranes separating adjacent xylem vessels. Although the kinetics of the ion-mediated changes in hydraulic resistance are consistent with the swelling/deswelling behavior of pectins, there is no direct evidence of this activity. In this report we use atomic force microscopy (AFM) to investigate structural changes in bordered pit membranes associated with changes in the ionic concentration of the surrounding solution. When submerged in de-ionized water, AFM revealed bordered pit membranes as relatively smooth, soft, and lacking any sharp edges surface, in contrast to pictures from scanning electron microscope (SEM) or AFM performed on air-dry material. Exposure of the bordered pit membranes to 50 mM KCl solution resulted in significant changes in both surface physical properties and elevation features. Specifically, bordered pit membranes became harder and the fiber edges were clearly visible. In addition, the membrane contracted and appeared much rougher due to exposed microfibers. In neither solution was there any evidence of discrete pores through the membrane whose dimensions were altered in response to the ionic composition of the surrounding solution. Instead the variable hydraulic resistance appears to involve changes in the both the permeability and the thickness of the pit membrane.

  14. Some electronic and magnetic properties of Fluoride ion in Fluoride structure nanocrystals

    NASA Astrophysics Data System (ADS)

    Imtani, Ali Nasir

    2012-01-01

    We have investigated the effects of the environment potential around Fluoride ion on some important electronic and magnetic properties such as dipole polarisability, moment of oscillator strengths S(k) and magnetic susceptibility. The theoretical procedure is based on the variational-perturbation theory with two parameter trial functions incorporated in an ionic model. We estimate these properties in four cases for Fluoride ion; free ion, ion under different potentials, ion in the crystals and ion in nanocrystal, CdF2, CaF2, PbF2, SrF2 and BaF2. Our results indicate that these properties vary with ion environments and the free state of Fluoride ion has higher values and there is linearity behaviour of these properties with lattice constant. For Fluoride ion in nanocrystal, we have found that there is an extra parameter that can also affect the dipole polarisability, the number of ions in the structure.

  15. Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

    SciTech Connect

    Hamid, Ahmed M.; Garimella, Sandilya V. B.; Ibrahim, Yehia M.; Deng, Liulin; Zheng, Xueyun; Webb, Ian K.; Anderson, Gordon A.; Prost, Spencer A.; Norheim, Randolph V.; Tolmachev, Aleksey V.; Baker, Erin S.; Smith, Richard D.

    2016-09-20

    We report on ion mobility separations (IMS) achievable using traveling waves in a Structures for Lossless Ion Manipulations (TW-SLIM) module having a 44-cm path length and sixteen 90º turns. The performance of the TW-SLIM module was evaluated for ion transmission, and ion mobility separations with different RF, TW parameters and SLIM surface gaps in conjunction with mass spectrometry. In this work TWs were created by the transient and dynamic application of DC potentials. The TW-SLIM module demonstrated highly robust performance and the ion mobility resolution achieved even with sixteen close spaced turns was comparable to a similar straight path TW-SLIM module. We found an ion mobility peak capacity of ~ 31 and peak generation rate of 780 s-1 for TW speeds of <210 m/s using the current multi-turn TW-SLIM module. The separations achieved for isomers of peptides and tetrasaccharides were found to be comparable to those from a ~ 0.9-m drift tube-based IMS-MS platform operated at the same pressure (4 torr). The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater ion mobility resolutions via greatly extended ion path lengths and compact serpentine designs that do not significantly impact the instrumentation profile, a direction described in a companion manuscript.

  16. Status of structural analysis of 30 cm diameter ion optics

    NASA Technical Reports Server (NTRS)

    Macrae, Gregory S.; Hering, Gary T.

    1990-01-01

    Three structural finite element programs are compared with theory, experimental data, and each other to evaluate their usefulness for modeling the thermomechanical deflection of ion engine electrodes. Two programs, NASTRAN and MARC, used a Cray XMP and the third, Algor, used an IBM compatible personal computer. The shape of the applied temperature gradient greatly affects off-axis displacement, implying that an accurate temperature distribution is required to analyze new designs. The use of bulk material constants to model the perforated electrodes was investigated. The stress and displacement predictions are shown to be sensitive to the temperature gradient and the Young's modulus, and insensitive to number of nodes, above some minimum value, and the Poisson ratio used. The models are shown to be useful tools for evaluating designs. Experimental measurements of temperatures and displacements was identified as the most critical area.

  17. Conformal SiO2 coating of sub-100 nm diameter channels of polycarbonate etched ion-track channels by atomic layer deposition.

    PubMed

    Sobel, Nicolas; Hess, Christian; Lukas, Manuela; Spende, Anne; Stühn, Bernd; Toimil-Molares, M E; Trautmann, Christina

    2015-01-01

    Polycarbonate etched ion-track membranes with about 30 µm long and 50 nm wide cylindrical channels were conformally coated with SiO2 by atomic layer deposition (ALD). The process was performed at 50 °C to avoid thermal damage to the polymer membrane. Analysis of the coated membranes by small angle X-ray scattering (SAXS) reveals a homogeneous, conformal layer of SiO2 in the channels at a deposition rate of 1.7-1.8 Å per ALD cycle. Characterization by infrared and X-ray photoelectron spectroscopy (XPS) confirms the stoichiometric composition of the SiO2 films. Detailed XPS analysis reveals that the mechanism of SiO2 formation is based on subsurface crystal growth. By dissolving the polymer, the silica nanotubes are released from the ion-track membrane. The thickness of the tube wall is well controlled by the ALD process. Because the track-etched channels exhibited diameters in the range of nanometres and lengths in the range of micrometres, cylindrical tubes with an aspect ratio as large as 3000 have been produced.

  18. Quantitative evaluation of image processing algorithms for ill-structured road detection and tracking

    NASA Astrophysics Data System (ADS)

    Dufourd, Delphine; Dalgalarrondo, Andre

    2003-09-01

    In a previous presentation at AeroSense 2002, we described a methodology to assess the results of image processing algorithms for ill-structured road detection and tracking. In this paper, we present our first application of this methodology on sixedge detectors and a database counting about 20,000 images. Our evaluation approach is based on the use of video image sequences, ground truth - reference results established by human experts - and assessment metrics which measure the quality of the image processing results. We need a quantitative, comparative and repetitive evaluation of many algorithms in order to direct future developments. The main scope of this paper consists in presenting the lessons learned from applying our methodology. More precisely, we describe the assessment metrics, the algorithms and the database. Then we describe how we manage to extract the qualities and weaknesses of each algorithm and to establish a global scoring. The insight we gain for the definition of assessment metrics is also presented. Finally, we suggest some promising directions for the development of road tracking algorithms and complementarities that must be sought after. To conclude, we describe future improvements for the database constitution, the assessment tools and the overall methodology.

  19. Structural transitions in ion coordination driven by changes in competition for ligand binding.

    PubMed

    Varma, Sameer; Rempe, Susan B

    2008-11-19

    Transferring Na(+) and K(+) ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical theory of solutions, quantum chemical simulations, classical mechanics simulations, and structural informatics to understand this aspect of ion partitioning. Our studies lead to the identification of a specific role of the solvation environment in driving transitions in ion coordination structures. Although ion solvation in liquid media is an exergonic reaction overall, we find it is also associated with considerable free energy penalties for extracting ligands from their solvation environments to form coordinated ion complexes. Reducing these penalties increases the stabilities of higher-order coordinations and brings down the energetic cost to partition ions from water into overcoordinated binding sites in biomolecules. These penalties can be lowered via a reduction in direct favorable interactions of the coordinating ligands with all atoms other than the ions themselves. A significant reduction in these penalties can, in fact, also drive up ion coordination preferences. Similarly, an increase in these penalties can lower ion coordination preferences, akin to a Hofmeister effect. Since such structural transitions are effected by the properties of the solvation phase, we anticipate that they will also occur for other ions. The influence of other factors, including ligand density, ligand chemistry, and temperature, on the stabilities of ion coordination structures are also explored.

  20. A graphical approach to tracking and reporting target status in structural genomics.

    PubMed

    Pan, Xiaokang; Wesenberg, Gary E; Markley, John L; Fox, Brian G; Phillips, George N; Bingman, Craig A

    2007-12-01

    Determination of a protein structure requires a series of decisions and processes, starting with target selection, through cloning, expression, purification, and finally structure determination. Structural genomics projects may distribute these steps among several different groups of researchers. Although this division may achieve a lower cost per solved structure, it creates a unique set of challenges for integrating and passing information on the progress of a given target across several functional divisions. Laboratory information management systems (LIMS) are essential for gathering this information, but may not display the progress of a given target in an intuitive way. In addition, structural genomics projects funded by the Protein Structure Initiative (PSI) are obliged to disseminate data regularly to the TargetDB and PepcDB data repositories, and this requires the creation of specialized views of the data. We report here how the flow of a target through a structural genomics pipeline and reports to TargetDB and PepcDB can be abstracted as directed acyclic graphs or trees. To implement this kind of display, we created software that tracks the flow of activity leading toward protein structure determination and prepares XML reports as input to TargetDB and PepcDB. The target tracing software consists of a set of Perl CGI scripts that integrate with the Graphviz visualization system to provide a graphical, user-friendly Web interface. The database reporting software, also coded in Perl, transfers large-scale genomics data from our LIMS into a PepcDB reportable XML file. This software package has facilitated inter-group communication, improved the quality and accuracy of information in our LIMS, and increased the efficiency and accuracy of our reports to PepcDB.

  1. Magnetic and structural properties of manganese ion implanted silicon

    NASA Astrophysics Data System (ADS)

    Awo-Affouda, Chaffra A.

    2007-12-01

    This thesis focuses on semiconductor based spin electronics. The integration of ferromagnetic regions into semiconductor "spintronic" devices to produce spin polarized current is a dynamic research area. One avenue is to make conventional semiconductors ferromagnetic by doping with a transition metal impurity such as Mn. For this, we first investigated the magnetic properties of Mn-implanted Si. We were able to measure above room temperature ferromagnetic hysteresis loops. The high Curie temperature obtained (>400 K), indicated that the synthesis of a technologically useful Si-based magnetic semiconductor is possible. We then focused on studying the structure of the implanted samples in order to establish a correlation between the magnetic and structural properties. The structural investigation involved secondary ion mass spectrometry, Rutherford backscattering, and transmission electron microscopy (TEM) as the main characterization techniques. The combination of the structural and magnetic studies allowed us to isolate an "active" region from which the ferromagnetism originates. We then found that the magnetic properties of the samples are strongly dependant on the interaction of the Mn atoms with the residual implant damage. The evolution of the Mn concentration profiles was also found to be closely related to the distribution of the Si lattice defects. We also observed the formation of Mn rich secondary phases at high enough annealing temperatures >800°C. However, we argued that theses crystallites cannot account for all the observed magnetic properties due to the low Curie temperature of these compounds in bulk form. We concluded that achieving a room temperature Si-based DMS has great potential but careful synthesis of this material system is needed to prevent secondary phase formation.

  2. Three-scale structure of diffusion region in the presence of cold ions

    NASA Astrophysics Data System (ADS)

    Divin, A.; Khotyaintsev, Yu. V.; Vaivads, A.; André, M.; Toledo-Redondo, S.; Markidis, S.; Lapenta, G.

    2016-12-01

    Kinetic simulations and spacecraft observations typically display the two-scale structure of collisionless diffusion region (DR), with electron and ion demagnetization scales governing the spatial extent of the DR. Recent in situ observations of the nightside magnetosphere, as well as investigation of magnetic reconnection events at the Earth's magnetopause, discovered the presence of a population of cold (tens of eV) ions of ionospheric origin. We present two-dimensional particle-in-cell simulations of collisionless magnetic reconnection in multicomponent plasma with ions consisting of hot and cold populations. We show that a new cold ion diffusion region scale is introduced in between that of hot ions and electrons. Demagnetization scale of cold ion population is several times (˜4-8) larger than the initial cold ion gyroradius. Cold ions are accelerated and thermalized during magnetic reconnection and form ion beams moving with velocities close to the Alfvén velocity.

  3. Highly charged ions for atomic clocks and search for variation of the fine structure constant

    NASA Astrophysics Data System (ADS)

    Dzuba, V. A.; Flambaum, V. V.

    2015-11-01

    We review a number of highly charged ions which have optical transitions suitable for building extremely accurate atomic clocks. This includes ions from Hf 12+ to U 34+, which have the 4 f 12 configuration of valence electrons, the Ir 17+ ion, which has a hole in almost filled 4 f subshell, the Ho 14+, Cf 15+, Es 17+ and Es 16+ ions. Clock transitions in most of these ions are sensitive to variation of the fine structure constant, α (α = e2/hbar c). E.g., californium and einsteinium ions have largest known sensitivity to α-variation while holmium ion looks as the most suitable ion for experimental study. We study the spectra of the ions and their features relevant to the use as frequency standards.

  4. FINE-SCALE STRUCTURES OF FLUX ROPES TRACKED BY ERUPTING MATERIAL

    SciTech Connect

    Li Ting; Zhang Jun E-mail: zjun@nao.cas.cn

    2013-06-20

    We present Solar Dynamics Observatory observations of two flux ropes tracked out by material from a surge and a failed filament eruption on 2012 July 29 and August 4, respectively. For the first event, the interaction between the erupting surge and a loop-shaped filament in the east seems to 'peel off' the filament and add bright mass into the flux rope body. The second event is associated with a C-class flare that occurs several minutes before the filament activation. The two flux ropes are, respectively, composed of 85 {+-} 12 and 102 {+-} 15 fine-scale structures, with an average width of about 1.''6. Our observations show that two extreme ends of the flux rope are rooted in opposite polarity fields and each end is composed of multiple footpoints (FPs) of fine-scale structures. The FPs of the fine-scale structures are located at network magnetic fields, with magnetic fluxes from 5.6 Multiplication-Sign 10{sup 18} Mx to 8.6 Multiplication-Sign 10{sup 19} Mx. Moreover, almost half of the FPs show converging motion of smaller magnetic structures over 10 hr before the appearance of the flux rope. By calculating the magnetic fields of the FPs, we deduce that the two flux ropes occupy at least 4.3 Multiplication-Sign 10{sup 20} Mx and 7.6 Multiplication-Sign 10{sup 20} Mx magnetic fluxes, respectively.

  5. Applications of a New Tropical Cyclone Initialization Scheme on Improving TC Track, Intensity and Structure Forecasts

    NASA Astrophysics Data System (ADS)

    Chen, C. Y.; Chen, Y. L.

    2015-12-01

    The TC initialization scheme developed by Nguyen and Chen (2011) (NC2011) was used to produce the initial TC structure and intensity in the model for 18 TCs (2004-2013) over the Northwestern Pacific using the Weather and Research Forecast Model (WRF). For these storms, the initial storm structure and intensity in the model agrees well with observations. These results attest that the environment, including SST, in which the storm is embedded has a significant impact on the intensity and rainband patterns of these well-developed TCs. Recently, the scheme was used throughout the entire life cycle of super typhoon Jelawat (2012), which underwent a rapid intensification (RI) stage, and a few other storms including Haiyan (2013) and Iniki (1992). The NC2014 scheme was also tested in a real-time experiment forecast for a Category 1 hurricane (Ana 2014) over the Hawaiian Islands and compared with the performance of the Hurricane WRF model (HWRF) and the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS). For all cases considered, the scheme works well in predicting track, intensity and structure for storms with different intensities at different stages of their life cycle. This is because at the model initial time, the initial storm intensity and structure are well adjusted to the environmental conditions in which it is embedded and well adapted to the model employed.

  6. Ion etching of human adenovirus 2: structure of the core

    SciTech Connect

    Newcomb, W.W.; Boring, J.W.; Brown, J.C.

    1984-07-01

    The surface of human adenovirus 2 was etched by irradiating intact virions with low-energy (1-keV) Ar/sup +/ ions in a Technics Hummer V sputter coater. Viral structures exposed by the etching process were shadowed and then examined in the electron microscope. Periods of etching that were sufficient to reduce the viral diameter by 20 to 30 nm revealed distinct substructural elements in the virion core. Cores were found to consist of a cluster of 12 large, uniformly sized spheres which abutted one another in the intact virion. The spheres, for which we suggest the name adenosomes, had a diameter of 23.0 +/- 2.3 nm, and they were related to each other by two-, three-, and fivefold axes of rotational symmetry. The results support the view, originally suggested by Brown et al. that the adenovirus 2 core is composed of 12 large spheres packed tightly together in such a way that each is directed toward the vertex of an icosahedron. Such a structure, constructed of 23.0-nm-diameter spheres, would have an outside diameter (vertex-to-vertex distance) of 67.0 nm and a face-to-face distance of 58.2 nm. It could be accommodated inside the icosahedral adenovirus capsid if each large sphere were located beneath a capsid vertex.

  7. Ion-Scale Structure in Mercury's Magnetopause Reconnection Diffusion Region

    NASA Technical Reports Server (NTRS)

    Gershman, Daniel J.; Dorelli, John C.; DiBraccio, Gina A.; Raines, Jim M.; Slavin, James A.; Poh, Gangkai; Zurbuchen, Thomas H.

    2016-01-01

    The strength and time dependence of the electric field in a magnetopause diffusion region relate to the rate of magnetic reconnection between the solar wind and a planetary magnetic field. Here we use approximately 150 milliseconds measurements of energetic electrons from the Mercury Surface, Space Environment, GEochemistry, and Ranging (MESSENGER) spacecraft observed over Mercury's dayside polar cap boundary (PCB) to infer such small-scale changes in magnetic topology and reconnection rates. We provide the first direct measurement of open magnetic topology in flux transfer events at Mercury, structures thought to account for a significant portion of the open magnetic flux transport throughout the magnetosphere. In addition, variations in PCB latitude likely correspond to intermittent bursts of approximately 0.3 to 3 millivolts per meter reconnection electric fields separated by approximately 5 to10 seconds, resulting in average and peak normalized dayside reconnection rates of approximately 0.02 and approximately 0.2, respectively. These data demonstrate that structure in the magnetopause diffusion region at Mercury occurs at the smallest ion scales relevant to reconnection physics.

  8. Investigation of structural mimetics of natural phosphate ion binding motifs.

    PubMed

    Kataev, Evgeny A; Shumilova, Tatiana A

    2015-02-16

    Phosphates are ubiquitous in biology and nearly half of all proteins interact with their partners by means of recognition of phosphate residues. Therefore, a better understanding of the phosphate ion binding by peptidic structures is highly desirable. Two new receptors have been designed and synthesized and their anion binding properties in an acetonitrile solution have been determined. The structure of hosts mimics a part of the kinase active site that is responsible for the recognition of the phosphate residue. New hosts contain additional free amino groups with the aim to facilitate coordination of protonated anions, such as dihydrogen phosphate. According to spectrophotometric measurements, stepwise 1:1 and 1:2 binding modes have been observed for both receptors in the presence of acetate, hydrogen sulfate and dihydrogen phosphate. Compared with the acyclic receptor, the macrocyclic receptor has demonstrated a remarkably enhanced selectivity for dihydrogen phosphate over other anions. Fluorometric measurements have revealed different responses of the acyclic and macrocyclic receptors towards anions. However, in both cases, a 5-8 nm hypsochromic shift of fluorescence maximum has been observed upon interaction of acetate and dihydrogen phosphate with receptors.

  9. Understanding chlorophylls: central magnesium ion and phytyl as structural determinants.

    PubMed

    Fiedor, Leszek; Kania, Agnieszka; Myśliwa-Kurdziel, Beata; Orzeł, Łukasz; Stochel, Grazyna

    2008-12-01

    Phytol, a C20 alcohol esterifying the C-17(3) propionate, and Mg2+ ion chelated in the central cavity, are conservative structural constituents of chlorophylls. To evaluate their intramolecular structural effects we prepared a series of metal- and phytyl-free derivatives of bacteriochlorophyll a and applied them as model chlorophylls. A detailed spectroscopic study on the model pigments reveals meaningful differences in the spectral characteristics of the phytylated and non-phytylated pigments. Their analysis in terms of solvatochromism and axial coordination shows how the central Mg and phytyl residue shape the properties of the pigment. Surprisingly, the presence/absence of the central Mg has no effect on the solvatochromism of (bacterio)chlorophyll pi-electron system and the hydrophobicity of phytyl does not interfere with the first solvation shell of the chromophore. However, both residues significantly influence the conformation of the pigment macrocycle and the removal of either residue increases the macrocycle flexibility. The chelation of Mg has a flattening effect on the macrocycle whereas bulky phytyl residue seems to control the conformation of the chromophore via steric interactions with ring V and its substituents. The analysis of spectroscopic properties of bacteriochlorophyllide (free acid) shows that esterification of the C-17(3) propionate is necessary in chlorophylls because the carboxyl group may act as a strong chelator of the central Mg. These observations imply that the truncated chlorophylls used in theoretical studies are not adequate as models of native chromophores, especially when fine effects are to be modeled.

  10. Optimal structural design of a 5-kW CPV tracking system by considering the ISO 4017/4762 standard through structure and flow simulations

    NASA Astrophysics Data System (ADS)

    Lee, Hyo Geun; Kim, Sang Suk; Kim, Sung Jo; Park, Su-Jin; Yun, Chang-wuk; Im, Gil-pyeong

    2015-09-01

    Photovoltaic generation systems have disadvantage in that they are usually installed outdoors and are exposed to extreme environments such as wind, snow and rain loadings. The structure of a photovoltaic generation system should be designed to have sufficient stiffness and strength against such loads. Especially, electric power generation by a concentrator photovoltaic(CPV) system can produce enough power if a right angle is main fained between the solar and the CPV panel within 90° ± 1°. To make the CPV tracking system in this study, we designed the structure by calculating the variations in and the strees applied to the structure by the wind load when the CPV tracking was influenced by the wind load. In this study, a 5-kW CPV tracking structure was designed through a structural analysis and a finiteelement analysis for a wind speed of 65 m/s by using ANSYS. The simulation of the structural design showed that the, structure of the 5-kW CPV tracking system corresponded with the ISO4017/ISO4762 standard. Based on this research, we will produce a 5-kW CPV tracking system and proceed to field test.

  11. Flight parameters monitoring system for tracking structural integrity of rotary-wing aircraft

    NASA Technical Reports Server (NTRS)

    Mohammadi, Jamshid; Olkiewicz, Craig

    1994-01-01

    Recent developments in advanced monitoring systems used in conjunction with tracking structural integrity of rotary-wing aircraft are explained. The paper describes: (1) an overview of rotary-wing aircraft flight parameters that are critical to the aircraft loading conditions and each parameter's specific requirements in terms of data collection and processing; (2) description of the monitoring system and its functions used in a survey of rotary-wing aircraft; and (3) description of the method of analysis used for the data. The paper presents a newly-developed method in compiling flight data. The method utilizes the maneuver sequence of events in several pre-identified flight conditions to describe various flight parameters at three specific weight ranges.

  12. Structured light-based motion tracking in the limited view of an MR head coil

    NASA Astrophysics Data System (ADS)

    Erikshøj, M.; Olesen, O. V.; Conradsen, K.; Højgaard, L.; Larsen, R.

    2013-02-01

    A markerless motion tracking (MT) system developed for use in PET brain imaging has been tested in the limited field of view (FOV) of the MR head coil from the Siemens Biograph mMR. The system is a 3D surface scanner that uses structured light (SL) to create point cloud reconstructions of the facial surface. The point clouds are continuously realigned to a reference scan to obtain pose estimates. The system has been tested on a mannequin head performing controlled rotational and translational axial movements within the head coil outside the range of the magnetic field. The RMS of the residual error of the rotation was 0.11° and the RMS difference in the translation with the control system was 0.17 mm, within the trackable range of movement.

  13. Using particle filter to track horizontal variations of atmospheric duct structure from radar sea clutter

    NASA Astrophysics Data System (ADS)

    Zhao, X. F.; Huang, S. X.; Wang, D. X.

    2012-11-01

    This paper addresses the problem of estimating range-varying parameters of the height-dependent refractivity over the sea surface from radar sea clutter. In the forward simulation, the split-step Fourier parabolic equation (PE) is used to compute the radar clutter power in the complex refractive environments. Making use of the inherent Markovian structure of the split-step Fourier PE solution, the refractivity from clutter (RFC) problem is formulated within a nonlinear recursive Bayesian state estimation framework. Particle filter (PF), which is a technique for implementing a recursive Bayesian filter by Monte Carlo simulations, is used to track range-varying characteristics of the refractivity profiles. Basic ideas of employing PF to solve RFC problem are introduced. Both simulation and real data results are presented to confirm the feasibility of PF-RFC performances.

  14. Using particle filter to track horizontal variations of atmospheric duct structure from radar sea clutter

    NASA Astrophysics Data System (ADS)

    Zhao, X. F.; Huang, S. X.

    2012-08-01

    This paper addresses the problem of estimating range-varying parameters of the height-dependent refractivity over the sea surface from radar sea clutter. In the forward simulation, the split-step Fourier parabolic equation (PE) is used to compute the radar clutter power in the complex refractive environments. Making use of the inherent Markovian structure of the split-step Fourier PE solution, the refractivity from clutter (RFC) problem is formulated within a nonlinear recursive Bayesian state estimation framework. Particle filter (PF) that is a technique for implementing a recursive Bayesian filter by Monte Carlo simulations is used to track range-varying characteristics of the refractivity profiles. Basic ideas of employing PF to solve RFC problem are introduced. Both simulation and real data results are presented to check up the feasibility of PF-RFC performances.

  15. Ion Spectral Structures Observed by the Van Allen Probes and Cluster

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

    2014-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

  16. Markerless rat head motion tracking using structured light for brain PET imaging of unrestrained awake small animals

    NASA Astrophysics Data System (ADS)

    Miranda, Alan; Staelens, Steven; Stroobants, Sigrid; Verhaeghe, Jeroen

    2017-03-01

    Preclinical positron emission tomography (PET) imaging in small animals is generally performed under anesthesia to immobilize the animal during scanning. More recently, for rat brain PET studies, methods to perform scans of unrestrained awake rats are being developed in order to avoid the unwanted effects of anesthesia on the brain response. Here, we investigate the use of a projected structure stereo camera to track the motion of the rat head during the PET scan. The motion information is then used to correct the PET data. The stereo camera calculates a 3D point cloud representation of the scene and the tracking is performed by point cloud matching using the iterative closest point algorithm. The main advantage of the proposed motion tracking is that no intervention, e.g. for marker attachment, is needed. A manually moved microDerenzo phantom experiment and 3 awake rat [18F]FDG experiments were performed to evaluate the proposed tracking method. The tracking accuracy was 0.33 mm rms. After motion correction image reconstruction, the microDerenzo phantom was recovered albeit with some loss of resolution. The reconstructed FWHM of the 2.5 and 3 mm rods increased with 0.94 and 0.51 mm respectively in comparison with the motion-free case. In the rat experiments, the average tracking success rate was 64.7%. The correlation of relative brain regional [18F]FDG uptake between the anesthesia and awake scan reconstructions was increased from on average 0.291 (not significant) before correction to 0.909 (p  <  0.0001) after motion correction. Markerless motion tracking using structured light can be successfully used for tracking of the rat head for motion correction in awake rat PET scans.

  17. Atomistic simulation of track formation by energetic recoils in zircon.

    PubMed

    Moreira, Pedro A F P; Devanathan, Ram; Weber, William J

    2010-10-06

    We have performed classical molecular dynamics simulations of fission track formation in zircon. We simulated the passage of a swift heavy ion through crystalline zircon using cylindrical thermal spikes with energy deposition (dE/dx) of 2.5-12.8 keV nm( - 1) and a radius of 3 nm. At a low dE/dx of 2.55 keV nm( - 1), the structural damage recovered almost completely and a damage track was not produced. At higher values of dE/dx, tracks were observed and the radius of the track increased with increasing dE/dx. Our structural analysis shows amorphization in the core of the track and phase separation into Si-rich regions near the center of the track and Zr-rich regions near the periphery. These simulations establish a threshold dE/dx for fission track formation in zircon that is relevant to thermochronology and nuclear waste immobilization.

  18. Perspectives in radiation biophysics: From radiation track structure simulation to mechanistic models of DNA damage and repair

    NASA Astrophysics Data System (ADS)

    Nikjoo, H.; Taleei, R.; Liamsuwan, T.; Liljequist, D.; Emfietzoglou, D.

    2016-11-01

    In radiation targeted therapy and genetic risk estimation of low dose radiation protection there is a crucial need for full description of DNA damage response and repair (DDR) leading to cell death and cell mutation. We propose such a description can be arrived through realistic track-structure simulations together with mechanistic mathematical formulation of DDR and the availability of experimental data for testing the proof of principle. In this paper we review briefly first the state of the art in DNA damage and repair, and then the recent advances in the physics of track structure which represents an essential tool in radiation biophysics.

  19. New frontiers for mass spectrometry based upon structures for lossless ion manipulations.

    PubMed

    Ibrahim, Yehia M; Hamid, Ahmed M; Deng, Liulin; Garimella, Sandilya V B; Webb, Ian K; Baker, Erin S; Smith, Richard D

    2017-03-06

    Structures for lossless ion manipulations (SLIM) provide a new paradigm for efficient, complex and extended gas phase ion manipulations. SLIM are created from electric fields generated by the application of DC and RF potentials to arrays of electrodes patterned on two parallel surfaces. The electric fields provide lossless ion manipulations, including effective ion transport and storage. SLIM modules have been developed using both constant and oscillatory electric fields (e.g. traveling waves) to affect the ion motion. Ion manipulations demonstrated to date with SLIM include: extended trapping, ion selection, ion dissociation, and ion mobility spectrometry (IMS) separations achieving unprecedented ultra high resolution. SLIM thus provide the basis for previously impractical manipulations, such as very long path length ion mobility separations where ions traverse a serpentine path multiple times, as well as new capabilities that extend the utility of these developments based on temporal and spatial compression of ion mobility separations and other ion distributions. The evolution of SLIM devices developed over the last three years is reviewed and we provide examples of various ion manipulations performed, and briefly discuss potential applications and new directions.

  20. Vibronic-structure tracking: A shortcut for vibrationally resolved UV/Vis-spectra calculations

    SciTech Connect

    Barton, Dennis; König, Carolin; Neugebauer, Johannes

    2014-10-28

    The vibrational coarse structure and the band shapes of electronic absorption spectra are often dominated by just a few molecular vibrations. By contrast, the simulation of the vibronic structure even in the simplest theoretical models usually requires the calculation of the entire set of normal modes of vibration. Here, we exploit the idea of the mode-tracking protocol [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] in order to directly target and selectively calculate those normal modes which have the largest effect on the vibronic band shape for a certain electronic excitation. This is achieved by defining a criterion for the importance of a normal mode to the vibrational progressions in the absorption band within the so-called “independent mode, displaced harmonic oscillator” (IMDHO) model. We use this approach for a vibronic-structure investigation for several small test molecules as well as for a comparison of the vibronic absorption spectra of a truncated chlorophyll a model and the full chlorophyll a molecule. We show that the method allows to go beyond the often-used strategy to simulate absorption spectra based on broadened vertical excitation peaks with just a minimum of computational effort, which in case of chlorophyll a corresponds to about 10% of the cost for a full simulation within the IMDHO approach.

  1. Structure Modulates Similarity-Based Interference in Sluicing: An Eye Tracking study

    PubMed Central

    Harris, Jesse A.

    2015-01-01

    In cue-based content-addressable approaches to memory, a target and its competitors are retrieved in parallel from memory via a fast, associative cue-matching procedure under a severely limited focus of attention. Such a parallel matching procedure could in principle ignore the serial order or hierarchical structure characteristic of linguistic relations. I present an eye tracking while reading experiment that investigates whether the sentential position of a potential antecedent modulates the strength of similarity-based interference, a well-studied effect in which increased similarity in features between a target and its competitors results in slower and less accurate retrieval overall. The manipulation trades on an independently established Locality bias in sluiced structures to associate a wh-remnant (which ones) in clausal ellipsis with the most local correlate (some wines), as in The tourists enjoyed some wines, but I don't know which ones. The findings generally support cue-based parsing models of sentence processing that are subject to similarity-based interference in retrieval, and provide additional support to the growing body of evidence that retrieval is sensitive to both the structural position of a target antecedent and its competitors, and the specificity or diagnosticity of retrieval cues. PMID:26733893

  2. Quadrupole ion trap studies of the structure and reactivity of transition metal ion pair complexes

    PubMed

    Vachet; Callahan

    2000-03-01

    Ion pairs are common species observed in the electrospray mass spectra of transition metal coordination complexes. To understand the nature of these ion pairs, a systematic study of the gas-phase chemistry of these species using ion-molecule reactions and collision-induced dissociation (CID) was carried out. Ion pair complexes of the type MLnX+ (where M is Mn(II), Fe(II), Co(II), Ni(II), Cu(II) or Zn(II), L is 1,10-phenanthroline, 2,2'-bipyridine, ethylenediamine, diethylenetriamine or 1,4,8,11-tetraazacyclotetradecane and X is Cl-, NO3-, acetylacetonate, ClO4-, acetate or SCN-) were studied. Ion-molecule reactions can distinguish whether the counterion in an ion pair is an inner- or outer-sphere ligand and can determine the coordination mode of the counterion. In addition, CID and ion-molecule reactions reveal some interesting chemistry of these complexes and unique coordination modes for some of the anions studied here were inferred from the ion-molecule reactions. For example, the thiocyanate ion is found to coordinate in a bidentate fashion in Zn(II) and Ni(II) complexes, contrasting behavior typically observed in solution. Also, certain Co(II) and Fe(II) ion pair complexes undergo oxidation reactions in which species such as dioxygen and nitric oxide from the counterions ClO4- and NO3- are transferred to the Co(II) and Fe(II) complexes, showing the inherent affinity of these metals for these molecules. These complexes were also studied by ion-molecule reactions and CID. Dioxygen in complexes formed by CID is demonstrated to be bidentate, suggesting the formation of a peroxo ligand with concurrent oxidation of the metal.

  3. The importance of phenological tracking to plant community structure under stationary versus nonstationary environments

    NASA Astrophysics Data System (ADS)

    Wolkovich, E. M.; Donahue, M. J.

    2014-12-01

    Recent work has found links between how a species' phenology shifts with climate change and its changes in performance with climate change. Species that appear to 'track' climate change, for example North American temperate plant species that shift leafing or flowering earlier with warmer springs, also tend to increase in abundance or other metrics of plant performance, while the reverse is generally seen for species that delay phenology with warming. This correlation between phenological tracking and performance has been implicated in plant invasions and appears to be an important factor in predicting future plant populations and communities under climate change scenarios. We have, however, little theory on why--or why not--species may phenologically track the start of spring. Early-season phenology gives priority access to light and soil resources and thus, in a simplistic model where the start of season varies between years, all species should strongly track the start of season, yet communities are always a mix of phenological tracking strategies (from species that do not track the start of season to strong trackers). Using a stochastic community assembly model we examined how phenological tracking influences species abundances across time under two different environmental scenarios: one with a stationary environment and one with a nonstationary environment where the start of season shifts earlier over time. Our model shows that trade-offs are required between phenological tracking and parameters related to species-specific resource use to maintain a community with a diversity of phenological tracking strategies and that nonstationary environments strongly favor species that track the start of season. Our results suggest that trade-offs established under a stationary climate that allow a diversity of phenological tracking strategies across species in a community may not hold under non-stationary environments to maintain the same diversity of species. Instead

  4. Long-Term Tracking of Corotating Density Structures Using Heliospheric Imaging

    NASA Astrophysics Data System (ADS)

    Plotnikov, I.; Rouillard, A. P.; Davies, J. A.; Bothmer, V.; Eastwood, J. P.; Gallagher, P.; Harrison, R. A.; Kilpua, E.; Möstl, C.; Perry, C. H.; Rodriguez, L.; Lavraud, B.; Génot, V.; Pinto, R. F.; Sanchez-Diaz, E.

    2016-08-01

    stream interface measured in situ by an average of 55 km s^{-1} at ST-A and 84 km s^{-1} at STEREO-B (ST-B). We show that the speeds of the corotating density structures derived using our fitting technique track well the long-term variation of the radial speed of the slow solar wind during solar minimum years (2007 - 2008). Furthermore, we demonstrate that these features originate near the coronal neutral line that eventually becomes the heliospheric current sheet.

  5. Method and system for detecting polygon boundaries of structures in images as particle tracks through fields of corners and pixel gradients

    DOEpatents

    Paglieroni, David W.; Manay, Siddharth

    2011-12-20

    A stochastic method and system for detecting polygon structures in images, by detecting a set of best matching corners of predetermined acuteness .alpha. of a polygon model from a set of similarity scores based on GDM features of corners, and tracking polygon boundaries as particle tracks using a sequential Monte Carlo approach. The tracking involves initializing polygon boundary tracking by selecting pairs of corners from the set of best matching corners to define a first side of a corresponding polygon boundary; tracking all intermediate sides of the polygon boundaries using a particle filter, and terminating polygon boundary tracking by determining the last side of the tracked polygon boundaries to close the polygon boundaries. The particle tracks are then blended to determine polygon matches, which may be made available, such as to a user, for ranking and inspection.

  6. Fast Variable Structure Stochastic Automaton for Discovering and Tracking Spatiotemporal Event Patterns.

    PubMed

    Zhang, Junqi; Wang, Yuheng; Wang, Cheng; Zhou, MengChu

    2017-04-05

    Discovering and tracking spatiotemporal event patterns have many applications. For example, in a smart-home project, a set of spatiotemporal pattern learning automata are used to monitor a user's repetitive activities, by which the home's automaticity can be promoted while some of his/her burdens can be reduced. Existing algorithms for spatiotemporal event pattern recognition in dynamic noisy environment are based on fixed structure stochastic automata whose state transition function is fixed and predesigned to guarantee their immunity to noise. However, such design is conservative because it needs continuous and identical feedbacks to converge, thus leading to its very low convergence rate. In many real-life applications, such as ambient assisted living, consecutive nonoccurrences of an elder resident's routine activities should be treated with an alert as quickly as possible. On the other hand, no alert should be output even for some occurrences in order to diminish the effects caused by noise. Clearly, confronting a pattern's change, slow speed and low accuracy may degrade a user's life security. This paper proposes a fast and accurate leaning automaton based on variable structure stochastic automata to satisfy the realistic requirements for both speed and accuracy. Bias toward alert is necessary for elder residents while the existing method can only support the bias toward ``no alert.'' This paper introduces a method to allow bias toward alert or no alert to meet a user's specific bias requirement. Experimental results show its better performance than the state-of-the-art methods.

  7. Tracking molecular structure deformation of nitrobenzene and its torsion-vibration coupling by intense pumping CARS

    NASA Astrophysics Data System (ADS)

    Wang, Chang; Wu, Hong-Lin; Song, Yun-Fei; He, Xing; Yang, Yan-Qiang; Tan, Duo-Wang

    2016-11-01

    The structural deformation induced by intense laser field of liquid nitrobenzene (NB) molecule, a typical molecule with restricting internal rotation, is tracked by time- and frequency-resolved coherent anti-Stokes. Raman spectroscopy (CARS) technique with an intense pump laser. The CARS spectra of liquid NB show that the NO2 torsional mode couples with the NO2 symmetric stretching mode, and the NB molecule undergoes ultrafast structural deformation with a relaxation time of 265 fs. The frequency of NO2 torsional mode in liquid NB (42 cm-1) at room temperature is found from the sum and difference combination bands involving the NO2 symmetric stretching mode and torsional mode in time- and frequency-resolved CARS spectra. Project supported by the National Natural Science Foundation of China (Grant Nos. 21173063 and 21203047), the Foundation of Heilongjiang Bayi Agricultural University, China (Grant No. XZR2014-16), NSAF (Grant No. U1330106), and the Special Research Project of National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics (Grant No. 2012-S-07).

  8. On the consistency of Monte Carlo track structure DNA damage simulations

    SciTech Connect

    Pater, Piotr Seuntjens, Jan; El Naqa, Issam; Bernal, Mario A.

    2014-12-15

    Purpose: Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies. Methods: The MCTS code Geant4-DNA was used to compare radial dose profiles in a nanometer-scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV–220 keV were superimposed on a geometric DNA model composed of 2.7 × 10{sup 6} nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy E{sub TH}. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter-SB distances and on the number of affected strands. Results: Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer-based SB definitions give similar SB yields as the one based on energy deposit when E{sub TH} ≈ 10.79 eV, but deviate significantly for higher E{sub TH} values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their

  9. Crustal and uppermost mantle structure variation beneath La Réunion hotspot track

    NASA Astrophysics Data System (ADS)

    Fontaine, Fabrice R.; Barruol, Guilhem; Tkalčić, Hrvoje; Wölbern, Ingo; Rümpker, Georg; Bodin, Thomas; Haugmard, Méric

    2015-10-01

    The Piton de la Fournaise basaltic volcano, on La Réunion Island in the western Indian Ocean, is one of the most active volcanoes in the world. This volcano is classically considered as the surface expression of an upwelling mantle plume and its activity is continuously monitored, providing detailed information on its superficial dynamics and on the edifice structure. Deeper crustal and upper mantle structure under La Réunion Island is surprisingly poorly constrained, motivating this study. We used receiver function techniques to determine a shear wave velocity profile through the crust and uppermost mantle beneath La Réunion, but also at other seismic stations located on the hotspot track, to investigate the plume and lithosphere interaction and its evolution through time. Receiver functions (RFs) were computed at permanent broad-band seismic stations from the GEOSCOPE network (on La Réunion and Rodrigues), at IRIS stations MRIV and DGAR installed on Mauritius and Diego Garcia islands, and at the GEOFON stations KAAM and HMDM on the Maldives. We performed non-linear inversions of RFs through modelling of P-to-S conversions at various crustal and upper mantle interfaces. Joint inversion of RF and surface wave dispersion data suggests a much deeper Mohorovičić discontinuity (Moho) beneath Mauritius (˜21 km) compared to La Réunion (˜12 km). A magmatic underplated body may be present under La Réunion as a thin layer (≤3 km thick), as suggested by a previous seismic refraction study, and as a much thicker layer beneath other stations located on the hotspot track, suggesting that underplating is an important process resulting from the plume-lithosphere interaction. We find evidence for a strikingly low velocity layer starting at about 33 km depth beneath La Réunion that we interpret as a zone of partial melt beneath the active volcano. We finally observe low velocities below 70 km beneath La Réunion and below 50 km beneath Mauritius that could represent

  10. Structure and mechanism of formation of an important ion in doping control

    NASA Astrophysics Data System (ADS)

    Borges, Chad R.; Taccogno, James; Crouch, Dennis J.; Le, Ly; Truong, Thanh N.

    2005-12-01

    An ion with m/z 143 serves as a biomarker that is often continuously monitored in urine samples undergoing screening by electron ionization gas chromatography/mass spectrometry (EI GC/MS) for banned anabolic agents. The ion is known to arise from trimethylsilyl (TMS)-derivatized synthetic 17-hydroxy, 17-methyl steroids. The purpose of this work was to characterize, in detail, the origin(s), structure(s), and mechanism(s) of formation of such ions with m/z 143. High resolution mass spectrometry (HRMS) data revealed the elemental composition of the D-ring derived m/z 143 ion to be C7H15OSi. Analysis of dihydrotestosterone (DHT) and its 2-methyl substituted analog dromostanolone by HRMS revealed that an elementally equivalent ion of m/z 143 could be derived from the A-ring of TMS-derivatized 3-keto-enol steroids demonstrating that an abnormally intense peak in the m/z 143 extracted ion chromatogram of urine samples undergoing screening for banned anabolic agents does not necessarily indicate the presence of a 17-hydroxy, 17-methyl steroid. To gain information on ion structure, breakdown curves for the most abundant product ions of the m/z 143 ion were generated using both native and perdeutero-TMS derivatives, providing structures for second, third, and fourth generation product ions. An EI-mass spectrum of [16,16,17-2H3]-DHT (DHT-d3) demonstrated that one of the C-16 hydrogen atoms is removed prior to the formation of an ion that is highly analogous to the ion with m/z 143 strongly suggesting, in accord with all other evidence, one particular fragmentation pathway and resulting product: a resonance stabilized 3-(O-trimethylsilyl)but-1-ene ion.

  11. Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

    PubMed Central

    Ibrahim, Yehia M.; Deng, Liulin; Zheng, Xueyun; Webb, Ian K.; Anderson, Gordon A.; Prost, Spencer A.; Norheim, Randolph V.; Tolmachev, Aleksey V.; Baker, Erin S.; Smith, Richard D.

    2017-01-01

    We report on ion mobility (IM) separations achievable using traveling waves (TW) in a Structures for Lossless Ion Manipulations (SLIM) module having a 44 cm path length and 16 90° turns. The performance of the TW-SLIM module was evaluated for ion transmission and IM separations with different RF, TW parameters, and SLIM surface gaps in conjunction with mass spectrometry. In this work, TWs were created by the transient and dynamic application of DC potentials. The module demonstrated highly robust performance and, even with 16 closely spaced turns, achieving IM resolution performance and ion transmission comparable to a similar straight path module. We found an IM peak capacity of ~31 and peak generation rate of 780 s−1 for TW speeds of ~80 m/s using the current multi-turn TW-SLIM module. The separations achieved for isomers of peptides and tetrasaccharides were found to be comparable to those from a ~0.9-m drift tube-based IM-MS platform operated at the same pressure (4 Torr). The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater IM resolution via greatly extended ion path lengths and using compact serpentine designs. PMID:27479234

  12. Ion Dynamics and Field Structure of Quasi-perpendicular Collisionless Shocks near the Critical Mach Number

    NASA Astrophysics Data System (ADS)

    Balikhin, M. A.; Malkov, M.; Sagdeev, R.; Dudnikova, G.

    2015-12-01

    The structure of subcritical (laminar) collisionless shocks has been understood long time ago. When the Mach number exceeds a critical value, some of the incident ions are reflected. This needs to be included into the description of the shock structure and entropy production at the shock front. We present an analytical model of ion reflection from a quasi-perpendicular collisionless shock and the formation of the foot region associated with this reflection. Reflected ions perturb the electrostatic and magnetic fields in the foot region which we self-consistently include in determining the fraction of reflected ions, depending on the Mach number of the shock. The subsequent motion of the shock reflected ions downstream and formation of the downstream field structure is analyzed. Models for thermalization of the downstream plasma and approaches to Rankine-Hugoniot relations will also be discussed. The obtained overall shock structure is compared with the Cluster observations.

  13. Nanocomposites with embedded structures for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Yang, Zichao

    Lithium-ion batteries (LIBs) have been widely employed in portable electronics and are rapidly expanding into emerging markets such as hybrid and electric vehicles and potentially electric grid storage. These new opportunities create new challenges for LIBs and further improvement of specific energy, cycling performance and rate capability are required. A major strategy in performance enhancement for the electrode materials involves the creation of carbon composites to provide mechanical buffering of active material and to improve electrical conductivity. In the current work, a platform is developed for creating functional hybrid materials by copolymerization of organic molecules and inorganic compounds followed by thermal pyrolysis, and the approach yields nanostructured composites in which nanoparticles are uniformly embedded in a porous, partially graphitic carbon matrix. Depending upon the chemistry of the starting materials, nanocomposites with embedded structures created using the approach are attractive as anode or cathode materials for next-generation rechargeable lithium battery systems. The platform is very versatile and through ex situ conversion or utilization of multiple precursors, can be applied to various classes of materials including metal oxides (single or mixed), metals, metal sulfides, alloys, metalloids, phosphates, etc. The approach also lends itself to the development of scalable processes for production of nanostructured battery materials. Mechanistic analysis was performed and reveals that the performance enhancement of the embedded nanocomposite configuration is mainly brought about by the mechanical buffering effect offered by the carbon matrix. The active material loading was shown to be an important factor in the design of the composites as electrode materials. In addition to the polymerization-based approach, other in situ methods such as one based on spray pyrolysis are also explored and demonstrate the versatility of the in situ

  14. Anode-electrolyte double-layer of Li-ion batteries: Structure and Li-ion intercalation

    NASA Astrophysics Data System (ADS)

    Wipf, David O.; Abou Hamad, Ibrahim; Rikvold, Per Arne; Novotny, Mark A.

    2011-03-01

    The electrochemical double-layer structure plays an important role in Li-ion intercalation during charging of Li-ion batteries with a graphite anode. In our recent Molecular Dynamics studies of a proposed accelerated charging method [I. Abou Hamad~et al., Phys. Chem. Chem. Phys. 12, 2740-2743 (2010)], we notice that ethylene carbonate and propylene carbonate molecules of the electrolyte assemble themselves in a preferred orientation at the electrode-electrolyte interface. On the other hand, they are randomly oriented in the bulk electrolyte. We show that the structure of the double layer is affected by the intercalating Li-ion: while the dipole moments of double-layer molecules far from the intercalating Li-ion point toward the graphite sheets of the anode, they point away from the intercalation site close to the intercalating Li-ion. This observation should contribute to a better understanding of the intercalation process. This work was supported in part by NSF Grant No. DMR-0802288.

  15. Effect of ion irradiation on the surface, structural and mechanical properties of brass

    NASA Astrophysics Data System (ADS)

    Ahmad, Shahbaz; Bashir, Shazia; Ali, Nisar; Umm-i-Kalsoom; Yousaf, Daniel; Faizan-ul-Haq; Naeem, Athar; Ahmad, Riaz; Khlaeeq-ur-Rahman, M.

    2014-04-01

    Modifications to the surface, structural and mechanical properties of brass after ion irradiation have been investigated. Brass targets were bombarded by carbon ions of 2 MeV energy from a Pelletron linear accelerator for various fluences ranging from 56 × 1012 to 26 × 1013 ions/cm2. A scanning electron microscope and X-ray diffractometer were utilized to analyze the surface morphology and crystallographic structure respectively. To explore the mechanical properties e.g., yield stress, ultimate tensile strength and microhardness of irradiated brass, an universal tensile testing machine and Vickers microhardness tester were used. Scanning electron microscopy results revealed an irregular and randomly distributed sputter morphology for a lower ion fluence. With increasing ion fluence, the incoherently shaped structures were transformed into dendritic structures. Nano/micro sized craters and voids, along with the appearance of pits, were observed at the maximum ion fluence. From X-ray diffraction results, no new phases were observed to be formed in the brass upon irradiation. However, a change in the peak intensity and higher and lower angle shifting were observed, which represents the generation of ion-induced defects and stresses. Analyses confirmed modifications in the mechanical properties of irradiated brass. The yield stress, ultimate tensile strength and hardness initially decreased and then increased with increasing ion fluence. The changes in the mechanical properties of irradiated brass are well correlated with surface and crystallographic modifications and are attributed to the generation, augmentation, recombination and annihilation of the ion-induced defects.

  16. Solid Electrolytes: Alkali-Ion Transport in Skeleton Structures

    DTIC Science & Technology

    1976-06-30

    side if necessary and identify by block number) solid electrolytes alkali -ion transport sodium -sulfur batteries fast -ion transport O ABSTRACT...molten Na 2 S4 for 10 days at 400’C indicated chemical stability, similar testing i-1 molten sodium was initiated, and it has been established that...tests under dynamic conditions are necessary before long-term stability of tile material can be established. Tests for stability in molten sodium have

  17. Structural Modification of Nanocrystalline Ceria by Ion Beams

    SciTech Connect

    Zhang, Yanwen; Edmondson, Philip D.; Varga, Tamas; Moll, Sandra J.; Namavar, Fereydoon; Lan, Chune; Weber, William J.

    2011-05-25

    Using energetic ions, we have demonstrated effective modification of grain size in nanocrystalline ceria in the critical region for controlling exceptional size-dependent electronicionic conductivity. The grain size increases and follows an exponential law as a function of ion fluence that increases with temperature, while the cubic phase is stable under the irradiation. The unique self-healing response of radiation damage at grain boundaries is utilized to control the grain size at the nanoscale.

  18. Improving accuracy of overhanging structures for selective laser melting through reliability characterization of single track formation on thick powder beds

    NASA Astrophysics Data System (ADS)

    Mohanty, Sankhya; Hattel, Jesper H.

    2016-04-01

    Repeatability and reproducibility of parts produced by selective laser melting is a standing issue, and coupled with a lack of standardized quality control presents a major hindrance towards maturing of selective laser melting as an industrial scale process. Consequently, numerical process modelling has been adopted towards improving the predictability of the outputs from the selective laser melting process. Establishing the reliability of the process, however, is still a challenge, especially in components having overhanging structures. In this paper, a systematic approach towards establishing reliability of overhanging structure production by selective laser melting has been adopted. A calibrated, fast, multiscale thermal model is used to simulate the single track formation on a thick powder bed. Single tracks are manufactured on a thick powder bed using same processing parameters, but at different locations in a powder bed and in different laser scanning directions. The difference in melt track widths and depths captures the effect of changes in incident beam power distribution due to location and processing direction. The experimental results are used in combination with numerical model, and subjected to uncertainty and reliability analysis. Cumulative probability distribution functions obtained for melt track widths and depths are found to be coherent with observed experimental values. The technique is subsequently extended for reliability characterization of single layers produced on a thick powder bed without support structures, by determining cumulative probability distribution functions for average layer thickness, sample density and thermal homogeneity.

  19. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, Ryan; Scheiner, Brett; Baalrud, Scott; Hopkins, Matthew; Barnat, Ed; Yee, Benjamin; Merlino, Robert; Skiff, Fred

    2016-10-01

    Measurements of the ion velocity distribution function (IVDF) and plasma potential were made near small positively biased electrodes using laser-induced fluorescence (LIF) and an emissive probe. The effect of dielectric around the electrode was tested and compared with a 2D particle-in-cell (PIC) simulation. Both measurements and simulation reveal that if the electrode is embedded within a surrounding dielectric, ions are accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier. The axial potential profile in this case contains a virtual cathode. In comparison, when the surrounding dielectric is removed, both the ion flow and virtual cathode depth are dramatically reduced. These measurements suggest that the ion presheath from the dielectric may enclose the electron sheath of the electrode resulting in a virtual cathode that substantially influences the local ion flow profile. This research was supported by the Office of Fusion Energy Sciences at the U.S. Department of Energy under contract DE-AC04-94SL85000.

  20. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-05-01

    A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  1. Differential time scales of change to learning frequency structures of isometric force tracking.

    PubMed

    Studenka, Breanna E; King, Adam C; Newell, Karl M

    2014-08-01

    Multiple processes support the persistent (learning) and transient (adaptive) change in behavior over time. We investigated whether practice and rest influence similarly the learning and adaptation of slow and fast frequency structures in isometric force tracking of pathways that varied in their regularity. Participants practiced 25 trials on each of 5 days in either a constant force target or 1 with the 1/f distributional properties of brown or pink noise. There was a reduction in root mean squared error (RMSE) as well as an increasing positive correlation between force output and the target pathway for all noise conditions over days. The spectral frequency analysis of force output and RMSE revealed task dependent outcomes of learning and adaptation as a function of the relatively slow (0-4 Hz) and fast (8-12 Hz) oscillatory time scales. These contrasting findings show that the persistent and transient properties of learning occur across different timescales and dimensions of behavior (force output and outcome-RMSE).

  2. Annealing kinetics of latent particle tracks in Durango apatite

    SciTech Connect

    Afra, B.; Rodriguez, M. D.; Giulian, R.; Kluth, P.; Lang, M.; Zhang, J.; Ewing, R. C.; Kirby, N.; Trautmann, C.; Toulemonde, M.

    2011-02-01

    Using synchrotron small-angle x-ray scattering we determine the ''latent'' track morphology and the track annealing kinetics in the Durango apatite. The latter, measured during ex situ and in situ annealing experiments, suggests structural relaxation followed by recrystallization of the damaged material. The resolution of fractions of a nanometer with which the track radii are determined, as well as the nondestructive, artefact-free measurement methodology shown here, provides an effective means for in-depth studies of ion-track formation in natural minerals under a wide variety of geological conditions.

  3. Precise small-angle X-ray scattering evaluation of the pore structures in track-etched membranes: Comparison with other convenient evaluation methods

    NASA Astrophysics Data System (ADS)

    Miyazaki, Tsukasa; Takenaka, Mikihito

    2017-03-01

    Poly(ethylene terephthalate) (PET)-based track-etched membranes (TMs) with pore sizes ranging from few nanometers to approximately 1 μm are used in various applications in the biological field, and their pore structures are determined by small-angle X-ray scattering (SAXS). These TMs with the nanometer-sized cylindrical pores aligned parallel to the film thickness direction are produced by chemical etching of the track in the PET films irradiated by heavy ions with the sodium hydroxide aqueous solution. It is well known that SAXS allows us to precisely and statistically estimate the pore size and the pore size distribution in the TMs by using the form factor of a cylinder with the extremely long pore length relative to the pore diameter. The results obtained were compared with those estimated with scanning electron microscopy and gas permeability measurements. The result showed that the gas permeability measurement is convenient to evaluate the pore size of TMs within a wide length scale, and the SEM observation is also suited to estimate the pore size, although SEM observation is usually limited above approximately 30 nm.

  4. Structural transitions in ion coordination driven by changes in competition for ligand binding

    PubMed Central

    Varma, Sameer; Rempe, Susan B.

    2009-01-01

    Transferring Na+ and K+ ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical theory of solutions, quantum chemical simulations, classical mechanics simulations and structural informatics to understand this aspect of ion partitioning. Our studies lead to the identification of a specific role of the solvation environment in driving transitions in ion coordination structures. Although ion solvation in liquid media is an exergonic reaction overall, we find it is also associated with considerable free energy penalties for extracting ligands from their solvation environments to form coordinated ion complexes. Reducing these penalties increases the stabilities of higher-order coordinations and brings down the energetic cost to partition ions from water into over-coordinated binding sites in biomolecules. These penalties can be lowered via a reduction in direct favorable interactions of the coordinating ligands with all atoms other than the ions themselves. A significant reduction in these penalties can, in fact, also drive up ion coordination preferences. Similarly, an increase in these penalties can lower ion coordination preferences, akin to a Hofmeister effect. Since such structural transitions are effected by the properties of the solvation phase, we anticipate that they will also occur for other ions. The influence of other factors, including ligand density, ligand chemistry and temperature, on the stabilities of ion coordination structures are also explored. PMID:18954053

  5. Surface ion trap structures with excellent optical access for quantum information processing

    NASA Astrophysics Data System (ADS)

    Maunz, P.; Blain, M.; Benito, F.; Chou, C.; Clark, C.; Descour, M.; Ellis, R.; Haltli, R.; Heller, E.; Kemme, S.; Sterk, J.; Tabakov, B.; Tigges, C.; Stick, D.

    2013-05-01

    Microfabricated surface electrode ion traps are necessary for the advancement of trapped ion quantum information processing as it offers a scalable way for realizing complex trap structures capable of storing and controlling many ions. The most promising way of performing two-qubit quantum gates in a chain of trapped ions is to focus laser beams on individual ions of the chain to drive gates. However, in surface ion traps the close proximity of the ions to the surface and the size of the chips usually cannot accommodate the tightly focused laser beams necessary to address individual ions parallel to the chip surface. Here we present a surface electrode ion trap monolithically fabricated in standard silicon technology that implements a linear quadrupole trap on a bowtie shaped chip with a narrow section that is only 1.2 mm wide. Laser beams parallel to the surface can be focused down to a waist of 4 μm with enough separation from the trap chip to prevent light scattering. The trap structure incorporates two Y-junctions for reordering ions and is optimized for quantum information processing. This work was supported by the Intelligence Advanced Research Projects Activity (IARPA). Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  6. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    DOE PAGES

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; ...

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5more » to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.« less

  7. "Trunk-like" heavy ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.-C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. We report "trunk-like" ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L = 3.6-2.6, magnetic local time (MLT) = 9.1-10.5, and magnetic latitude (MLAT) = -2.4-0.09°, vary monotonically from 3.5 to 0.04 keV. The values at the two end points of the O+ trunk are energy = 4.5-0.7 keV, L = 3.6-2.5, MLT = 9.1-10.7, and MLAT = -2.4-0.4°. Results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  8. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    SciTech Connect

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5 to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  9. Performance analysis of continuous tracking laser Doppler vibrometry applied to rotating structures in coast-down

    NASA Astrophysics Data System (ADS)

    Martarelli, M.; Castellini, P.

    2012-06-01

    In this paper a performance analysis of the so-called tracking continuous scanning laser Doppler vibrometry (TCSLDV) exploited in coast-down has been performed. This non-contact measurement system is able to scan continuously over a rotating surface during coast-down and to determine vibration operational deflection shapes (ODSs) and natural frequencies in short time, i.e. the temporal extent of the coast-down. The method is based on a laser Doppler vibrometer (LDV) whose laser beam is driven to scan continuously over the whole rotor surface synchronously with its rotation, so that the LDV output is modulated by the structure's ODSs. This technique has a full-field nature that enables it to measure simultaneously the time and spatial dependence of the vibration in a unique measurement. However, the TCSLDV presents some criticalities in practical applications, especially when applied to rotary transient and fast processes. In fact, if the vibration is transient and decays very fast, then the laser beam could not have had the time to scan the complete structure surface and the modulation of the ODS could be partial. An analytical model reproducing a representative experiment has been developed in order to evaluate the sensitivity of results to testing conditions. The laser beam trajectory in both the fixed and rotating reference systems has been synthesized showing its dependence on experimental parameters as the rotation speed variation during coast-down. It has been demonstrated the decrease in speed induces the deformation of the laser trajectory influencing the LDV output time history, spectrum and consequently the recovered ODS.

  10. Impact of ion irradiation on the thermal, structural, and mechanical properties of metallic glasses

    SciTech Connect

    Mayr, S.G.

    2005-04-01

    The impact of ion-beam irradiation on the thermal, structural, and mechanical properties of metallic glasses is investigated using the model glass, CuTi, in molecular dynamics computer simulations. It is found that ion-beam bombardment successively modifies the compositional and structural order toward a universal steady state, which proves to be independent of the initial relaxation state and thermal history of the unirradiated sample. This is reflected by key materials properties, including enthalpy, structural and compositional short-range order, as well as Young's modulus and fracture behavior. The results are interpreted within the framework of competing dynamics, where radiation-induced plastic relaxation counteracts ion-beam disordering.

  11. Irradiation effects on secondary structure of protein induced by keV ions

    NASA Astrophysics Data System (ADS)

    Cui, F. Z.; Lin, Y. B.; Zhang, D. M.; Tian, M. B.

    2001-01-01

    Protein secondary structure changes by low-energy ion irradiation are reported for the first time. The selected system is 30 keV N + irradiation on bovine serum albumin (BSA). After irradiation at increasing fluences from 1.0×10 15 to 2.5×10 16 ion/cm 2, Fourier transform infrared spectra analysis was conducted. It was found that the secondary structures of BSA molecules were very sensitive to ion irradiation. Secondary conformations showed different trends of change during irradiation. With the increase of ion fluence from 0 to 2.5×10 16 ion/cm 2, the fraction of α-helix and β-turns decreased from 17 to 12%, and from 40 to 31%, respectively, while that of random coil and β-sheet structure increased from 18 to 27%, and from 25 to 30%, respectively. Possible explanations for the secondary conformational changes of protein are proposed.

  12. Carbohydrate Structure Characterization by Tandem Ion Mobility Mass Spectrometry (IMMS)2

    PubMed Central

    Li, Hongli; Bendiak, Brad; Siems, William F.; Gang, David R.; Hill, Herbert H.

    2013-01-01

    A high resolution ion mobility spectrometer was interfaced to a Synapt G2 high definition mass spectrometer (HDMS) to produce IMMS-IMMS analysis. The hybrid instrument contained an electro-spray ionization source, two ion gates, an ambient pressure linear ion mobility drift tube, a quadrupole mass filter, a traveling wave ion mobility spectrometer (TWIMS) and a time of flight mass spectrometer. The dual gate drift tube ion mobility spectrometer (DTIMS) could be used to acquire traditional IMS spectra, but also could selectively transfer specific mobility selected precursor ions to the Synapt G2 HDMS for mass filtration (quadrupole). The mobility and mass selected ions could then be introduced into a collision cell for fragmentation followed by mobility separation of the fragment ions with the traveling wave ion mobility spectrometer. These mobility separated fragment ions are finally mass analyzed using a time-of-flight mass spectrometer. This results in an IMMS-IMMS analysis and provides a method to evaluate the isomeric heterogeneity of precursor ions by both DTIMS and TWIMS, to acquire a mobility-selected and mass-filtered fragmentation pattern and to additionally obtain traveling wave ion mobility spectra of the corresponding product ions. This new IMMS2 instrument enables the structural diversity of carbohydrates to be studied in greater detail. The physical separation of isomeric oligosaccharide mixtures was achieved by both DTIMS and TWIMS, with DTIMS demonstrating higher resolving power (70~80) than TWIMS (30~40). Mobility selected MS/MS spectra were obtained, and TWIMS evaluation of product ions showed that isomeric forms of fragment ions existed for identical m/z values. PMID:23330948

  13. Carbohydrate structure characterization by tandem ion mobility mass spectrometry (IMMS)2.

    PubMed

    Li, Hongli; Bendiak, Brad; Siems, William F; Gang, David R; Hill, Herbert H

    2013-03-05

    A high resolution ion mobility spectrometer was interfaced to a Synapt G2 high definition mass spectrometer (HDMS) to produce IMMS-IMMS analysis. The hybrid instrument contained an electrospray ionization source, two ion gates, an ambient pressure linear ion mobility drift tube, a quadrupole mass filter, a traveling wave ion mobility spectrometer (TWIMS), and a time-of-flight mass spectrometer. The dual gate drift tube ion mobility spectrometer (DTIMS) could be used to acquire traditional IMS spectra but also could selectively transfer specific mobility selected precursor ions to the Synapt G2 HDMS for mass filtration (quadrupole). The mobility and mass selected ions could then be introduced into a collision cell for fragmentation followed by mobility separation of the fragment ions with the traveling wave ion mobility spectrometer. These mobility separated fragment ions are finally mass analyzed using a time-of-flight mass spectrometer. This results in an IMMS-IMMS analysis and provides a method to evaluate the isomeric heterogeneity of precursor ions by both DTIMS and TWIMS to acquire a mobility-selected and mass-filtered fragmentation pattern and to additionally obtain traveling wave ion mobility spectra of the corresponding product ions. This new IMMS(2) instrument enables the structural diversity of carbohydrates to be studied in greater detail. The physical separation of isomeric oligosaccharide mixtures was achieved by both DTIMS and TWIMS, with DTIMS demonstrating higher resolving power (70-80) than TWIMS (30-40). Mobility selected MS/MS spectra were obtained, and TWIMS evaluation of product ions showed that isomeric forms of fragment ions existed for identical m/z values.

  14. Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry

    SciTech Connect

    Deng, Liulin; Ibrahim, Yehia M.; Baker, Erin S.; Aly, Noor A.; Hamid, Ahmed M.; Zhang, Xing; Zheng, Xueyun; Garimella, Sandilya V. B.; Webb, Ian K.; Prost, Spencer A.; Sandoval, Jeremy A.; Norheim, Randolph V.; Anderson, Gordon A.; Tolmachev, Aleksey V.; Smith, Richard D.

    2016-07-01

    Mass spectrometry (MS)-based multi-omic measurements, including proteomics, metabolomics, lipidomics, and glycomics, are increasingly transforming our ability to characterize and understand biological systems, but, presently have limitations due to the chemical diversity and range of abundances of biomolecules in complex samples. Advances addressing these challenges increasingly are based upon the ability to quickly separate, react and otherwise manipulate sample components for analysis by MS. Here we report on a new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses. This approach provides previously unachieved mobility biomolecule isomer separations for biomolecular species, in conjunction with more effective ion utilization, and producing a basis for the improved characterization of very small samples.

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

    SciTech Connect

    Colby, Ralph H.; Maranas, Janna K.; Mueller, Karl T.; Runt, James; Winey, Karen I.

    2015-03-01

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

  16. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core

    SciTech Connect

    Stahley,M.; Adams, P.; Wang, J.; Strobel, S.

    2007-01-01

    Metal ions play key roles in the folding and function for many structured RNAs, including group I introns. We determined the X-ray crystal structure of the Azoarcus bacterial group I intron in complex with its 5' and 3' exons. In addition to 222 nucleotides of RNA, the model includes 18 Mg2+ and K+ ions. Five of the metals bind within 12 Angstroms of the scissile phosphate and coordinate the majority of the oxygen atoms biochemically implicated in conserved metal-RNA interactions. The metals are buried deep within the structure and form a multiple metal ion core that is critical to group I intron structure and function. Eight metal ions bind in other conserved regions of the intron structure, and the remaining five interact with peripheral structural elements. Each of the 18 metals mediates tertiary interactions, facilitates local bends in the sugar-phosphate backbone or binds in the major groove of helices. The group I intron has a rich history of biochemical efforts aimed to identify RNA-metal ion interactions. The structural data are correlated to the biochemical results to further understand the role of metal ions in group I intron structure and function.

  17. Types and concentrations of metal ions affect local structure and dynamics of RNA

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Xiao, Yi

    2016-10-01

    The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the pre Q1 riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.

  18. Structural phase transitions and topological defects in ion Coulomb crystals

    SciTech Connect

    Partner, Heather L.; Nigmatullin, Ramil; Burgermeister, Tobias; Keller, Jonas; Pyka, Karsten; Plenio, Martin B.; Retzker, Alex; Zurek, Wojciech Hubert; del Campo, Adolfo; Mehlstaubler, Tanja E.

    2014-11-19

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed non-adiabatically. For a second order phase transition, the Kibble-Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  19. Ion streaming instabilities with application to collisionless shock wave structure

    NASA Technical Reports Server (NTRS)

    Golden, K. I.; Linson, L. M.; Mani, S. A.

    1973-01-01

    The electromagnetic dispersion relation for two counterstreaming ion beams of arbitrary relative strength flowing parallel to a dc magnetic field is derived. The beams flow through a stationary electron background and the dispersion relation in the fluid approximation is unaffected by the electron thermal pressure. The dispersion relation is solved with a zero net current condition applied and the regions of instability in the k-U space (U is the relative velocity between the two ion beams) are presented. The parameters are then chosen to be applicable for parallel shocks. It was found that unstable waves with zero group velocity in the shock frame can exist near the leading edge of the shock for upstream Alfven Mach numbers greater than 5.5. It is suggested that this mechanism could generate sufficient turbulence within the shock layer to scatter the incoming ions and create the required dissipation for intermediate strength shocks.

  20. Ion streaming instabilities with application to collisionless shock wave structure

    NASA Technical Reports Server (NTRS)

    Golden, K. I.; Linson, L. M.; Mani, S. A.

    1973-01-01

    The electromagnetic dispersion relation for two counterstreaming ion beams of arbitrary relative strength flowing parallel to a dc magnetic field is derived. The beams flow through a stationary electron background and the dispersion relation in the fluid approximation is unaffected by the electron thermal pressure. Magnetic effects on the ion beams are included, but the electrons are treated as a magnetized fluid. The dispersion relation is solved with a zero net current condition applied and the regions of instability in the k-U space (U is the relative velocity between the two ion beams) are presented. These results are extensions of Kovner's analysis for weak beams. The parameters are then chosen to be applicable for parallel shocks. It is found that unstable waves with zero group velocity in the shock frame can exist near the leading edge of the shock for upstream Alfven Mach numbers greater than 5.5.

  1. Fine structures and ion images on fresh frozen dried ultrathin sections by transmission electron and scanning ion microscopy

    NASA Astrophysics Data System (ADS)

    Takaya, K.; Okabe, M.; Sawataishi, M.; Takashima, H.; Yoshida, T.

    2003-01-01

    Ion microscopy (IM) of air-dried or freeze-dried cryostat and semi-thin cryosections has provided ion images of elements and organic substances in wide areas of the tissue. For reproducible ion images by a shorter time of exposure to the primary ion beam, fresh frozen dried ultrathin sections were prepared by freezing the tissue in propane chilled with liquid nitrogen, cryocut at 60 nm, mounted on grids and silicon wafer pieces, and freeze-dried. Rat Cowper gland and sciatic nerve, bone marrow of the rat administered of lithium carbonate, tree frog and African toad spleen and buffy coat of atopic dermatitis patients were examined. Fine structures and ion images of the corresponding areas in the same or neighboring sections were observed by transmission electron microscopy (TEM) followed by sector type and time-of-flight type IM. Cells in the buffy coat contained larger amounts of potassium and magnesium while plasma had larger amounts of sodium and calcium. However, in the tissues, lithium, sodium, magnesium, calcium and potassium were distributed in the cell and calcium showed a granular appearance. A granular cell of the tree frog spleen contained sodium and potassium over the cell and magnesium and calcium were confined to granules.

  2. Effects of ion dynamics on kinetic structures of the diffusion region during magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Chen, L. J.; Shuster, J. R.; Bessho, N.; Li, G.; Torbert, R. B.; Daughton, W. S.

    2014-12-01

    Based on results from Particle-in-cell (PIC) simulations, we report how ion dynamics influencethe Hall electric field and electron velocity distributions in the diffusion region of magnetic reconnection.The Hall electric field is due to charge imbalance in the diffusion region. At early times, within a few ion cyclotron oscillations from the peak reconnection,electron orbit dynamics dominate, and the Hall electric field layer assumes the width of the electron current layer.As the pre-existing current sheet ions are accelerated and jetted away, inflowing ions form an ion phase space hole structure.The ion hole structure is self-consistently supported by the Hall electric field. The ion meandering orbit width increasesover the course of about 10 ion cyclotron oscillations from several to approximately 40 electron skin depths (two ion skin depths,where the skin depth is based on the initial current sheet density), and theHall electric field layer widens in the same manner to become much broader than the electron diffusion region.The electron velocity distributions upstream of the electron diffusion region and within the regionof counter streaming ions become fragmented as the ion hole establishes itself.The fragmentation is carried into the electron diffusion region, and through the electron outflow jet, leading to a multitude of arcs in the electron distributions at the end of the jet. The broadening of the Hall electric field layer resolves a longstanding discrepancy concerning whether the narrowest width of the layer is of the electron [Chen et al., 2008] or ion [Mozer et al., 2002] scale. The fragmentation of the electron distributions may be due to an electron-ion instability, and is underinvestigation.

  3. A micro-structured ion-implanted magnonic crystal

    SciTech Connect

    Obry, Bjoern; Pirro, Philipp; Chumak, Andrii V.; Ciubotaru, Florin; Serga, Alexander A.; Hillebrands, Burkard; Braecher, Thomas; Osten, Julia; Fassbender, Juergen

    2013-05-20

    We investigate spin-wave propagation in a microstructured magnonic-crystal waveguide fabricated by localized ion implantation. The irradiation caused a periodic variation in the saturation magnetization along the waveguide. As a consequence, the spin-wave transmission spectrum exhibits a set of frequency bands, where spin-wave propagation is suppressed. A weak modification of the saturation magnetization by 7% is sufficient to decrease the spin-wave transmission in the band gaps by a factor of 10. These results evidence the applicability of localized ion implantation for the fabrication of efficient micron- and nano-sized magnonic crystals for magnon spintronic applications.

  4. Nanoscale surface structuring during ion bombardment of elemental semiconductors

    NASA Astrophysics Data System (ADS)

    Anzenberg, Eitan

    2013-01-01

    Nano-patterning of surfaces with uniform ion bombardment yields a rich phase-space of topographic patterns. Particle irradiation can cause surface ultra-smoothing or self-organized nanoscale pattern formation in surface topography. Topographic pattern formation has previously been attributed to the effects of the removal of target atoms by sputter erosion. In this thesis, the surface morphology evolution of Si(100) and Ge(100) during low energy ion bombardment of Ar+ and Kr+ ions, respectively, is studied. Our facilities for studies of surface processes at the National Synchrotron Light Source (NSLS) allow in-situ characterization of surface morphology evolution during ion bombardment using grazing incidence small angle x-ray scattering (GISAXS). This technique is used to measure in reciprocal space the kinetics of formation or decay of correlated nanostructures on the surface, effectively measuring the height-height correlations. A linear model is used to characterize the early time kinetic behavior during ion bombardment as a function of ion beam incidence angle. The curvature coefficients predicted by the widely used erosive model of Bradley and Harper are quantitatively negligible and of the wrong sign when compared to the observed effect in both Si and Ge. A mass-redistribution model explains the observed ultra-smoothing at low angles, exhibits an instability at higher angles, and predicts the observed 45° critical angle separating these two regimes in Si. The Ge surface evolution during Kr+ irradiation is qualitatively similar to that observed for Ar+ irradiation of Si at the same ion energy. However, the critical angle for Ge cannot be quantitatively reproduced by the simple mass redistribution model. Crater function theory, as developed by Norris et al., incorporates both mass redistributive and erosive effects, and predicts constraining relationships between curvature coefficients. These constraints are compared to experimental data of both Si and Ge

  5. Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

    2017-01-01

    Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

  6. Analysis of ion-implanted surface and interface structures by computer-simulated backscattering spectra

    NASA Astrophysics Data System (ADS)

    Kido, Y.; Kakeno, M.; Yamada, K.; Kawamoto, J.; Ohsawa, H.

    1985-10-01

    Computer codes for synthesizing random and channeling backscattering spectra have been elaborated to characterize the surface and interface structures formed or modified by ion implantation. Both effects of isotopes and energy fluctuation are taken into account in the spectrum simulation. This backscattering measurement combined with the simulation method is applied to characterization of the N(+)-implanted Al films and to quantitative analysis of chemical reaction and interdiffusion induced by ion-beam mixing. An ion-beam-induced damage profile and its epitaxial recovery of crystallinity are analyzed by the simulation of channeling spectra from ion-implanted Al2O3 substrates.

  7. Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

    PubMed Central

    Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

    2016-01-01

    The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

  8. A structural health monitoring fastener for tracking fatigue crack growth in bolted metallic joints

    NASA Astrophysics Data System (ADS)

    Rakow, Alexi Schroder

    Fatigue cracks initiating at fastener hole locations in metallic components are among the most common form of airframe damage. The fastener hole site has been surveyed as the second leading initiation site for fatigue related accidents of fixed wing aircraft. Current methods for inspecting airframes for these cracks are manual, whereby inspectors rely on non-destructive inspection equipment or hand-held probes to scan over areas of a structure. Use of this equipment often demands disassembly of the vehicle to search appropriate hole locations for cracks, which elevates the complexity and cost of these maintenance inspections. Improved reliability, safety, and reduced cost of such maintenance can be realized by the permanent integration of sensors with a structure to detect this damage. Such an integrated system of sensors would form a structural health monitoring (SHM) system. In this study, an Additive, Interleaved, Multi-layer Electromagnetic (AIME) sensor was developed and integrated with the shank of a fastener to form a SHM Fastener, a new SHM technology targeted at detection of fastener hole cracks. The major advantages of the SHM Fastener are its installation, which does not require joint layer disassembly, its capability to detect inner layer cracks, and its capability to operate in a continuous autonomous mode. Two methods for fabricating the proposed SHM Fastener were studied. The first option consisted of a thin flexible printed circuit film that was bonded around a thin metallic sleeve placed around the fastener shank. The second option consisted of coating sensor materials directly to the shank of a part in an effort to increase the durability of the sensor under severe loading conditions. Both analytical and numerical models were developed to characterize the capability of the sensors and provide a design tool for the sensor layout. A diagnostic technique for crack growth monitoring was developed to complete the SHM system, which consists of the

  9. Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.

    PubMed

    Hosaka, Toshiaki; Yoshizawa, Susumu; Nakajima, Yu; Ohsawa, Noboru; Hato, Masakatsu; DeLong, Edward F; Kogure, Kazuhiro; Yokoyama, Shigeyuki; Kimura-Someya, Tomomi; Iwasaki, Wataru; Shirouzu, Mikako

    2016-08-19

    The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.

  10. Probing the nuclear structure with heavy-ion reactions

    SciTech Connect

    Broglia, R.A.

    1982-01-01

    Nuclei display distortions in both ordinary space and in gauge space. It is suggested that it is possible to learn about the spatial distribution of the Nilsson orbitals and about the change of the pairing gap with the rotational frequency through the analysis of one- and two-nucleon transfer reactions induced in heavy-ion collisions.

  11. Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water.

    PubMed

    Draper, David E

    2013-12-01

    The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water.

  12. Relativistic Calculating the Spectral Lines Hyperfine Structure Parameters for Heavy Ions

    SciTech Connect

    Khetselius, O. Yu.

    2008-10-22

    The energies and constants of the hyperfine structure, derivatives of the one-electron characteristics on nuclear radius, nuclear electric quadrupole, magnetic dipole moments for some Li-like multicharged ions are calculated.

  13. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  14. Probing the defect nanostructure of helium and proton tracks in LiF:Mg,Ti using optical absorption: Implications to track structure theory calculations of heavy charged particle relative efficiency

    NASA Astrophysics Data System (ADS)

    Eliyahu, I.; Horowitz, Y. S.; Oster, L.; Weissman, L.; Kreisel, A.; Girshevitz, O.; Marino, S.; Druzhyna, S.; Biderman, S.; Mardor, I.

    2015-04-01

    A major objective of track structure theory (TST) is the calculation of heavy charged particle (HCP) induced effects. Previous calculations have been based exclusively on the radiation action/dose response of the released secondary electrons during the HCP slowing down. The validity of this presumption is investigated herein using optical absorption (OA) measurements on LiF:Mg,Ti (TLD-100) samples following irradiation with 1.4 MeV protons and 4 MeV He ions at levels of fluence from 1010 cm-2 to 2 × 1014 cm-2. The major bands in the OA spectrum are the 5.08 eV (F band), 4.77 eV, 5.45 eV and the 4.0 eV band (associated with the trapping structure leading to composite peak 5 in the thermoluminescence (TL) glow curve). The maximum intensity of composite peak 5 occurs at a temperature of ∼200 °C in the glow curve and is the glow peak used for most dosimetric applications. The TST calculations use experimentally measured OA dose response following low ionization density (LID) 60Co photon irradiation over the dose-range 10-105 Gy for the simulation of the radiation action of the HCP induced secondary electron spectrum. Following proton and He irradiation the saturation levels of concentration for the F band and the 4.77 eV band are approximately one order of magnitude greater than following LID irradiation indicating enhanced HCP creation of the relevant defects. Relative HCP OA efficiencies, ηHCP, are calculated by TST and are compared with experimentally measured values, ηm, at levels of fluence from 1010 cm-2 to 1011 cm-2 where the response is linear due to negligible track overlap. For the F band, values of ηm/ηHCP = 2.0 and 2.6 for the He ions and protons respectively arise from the neglect of enhanced Fluorine vacancy/F center creation by the HCPs in the TST calculations. It is demonstrated that kinetic analysis simulating LID F band dose response with enhanced Fluorine vacancy creation, and incorporated into the TST calculation, can lead to values of

  15. Critical issues in the formation of quantum computer test structures by ion implantation

    SciTech Connect

    Schenkel, T.; Lo, C. C.; Weis, C. D.; Schuh, A.; Persaud, A.; Bokor, J.

    2009-04-06

    The formation of quantum computer test structures in silicon by ion implantation enables the characterization of spin readout mechanisms with ensembles of dopant atoms and the development of single atom devices. We briefly review recent results in the characterization of spin dependent transport and single ion doping and then discuss the diffusion and segregation behaviour of phosphorus, antimony and bismuth ions from low fluence, low energy implantations as characterized through depth profiling by secondary ion mass spectrometry (SIMS). Both phosphorus and bismuth are found to segregate to the SiO2/Si interface during activation anneals, while antimony diffusion is found to be minimal. An effect of the ion charge state on the range of antimony ions, 121Sb25+, in SiO2/Si is also discussed.

  16. Tracking nuclear wave-packet dynamics in molecular oxygen ions with few-cycle infrared laser pulses

    SciTech Connect

    De, S.; Bocharova, I. A.; Magrakvelidze, M.; Ray, D.; Cao, W.; Thumm, U.; Cocke, C. L.; Bergues, B.; Kling, M. F.; Litvinyuk, I. V.

    2010-07-15

    We have tracked nuclear wave-packet dynamics in doubly charged states of molecular oxygen using few-cycle infrared laser pulses. Bound and dissociating wave packets were launched and subsequently probed via a pair of 8-fs pulses of 790 nm radiation. Ionic fragments from the dissociating molecules were monitored by velocity-map imaging. Pronounced oscillations in the delay-dependent kinetic energy release spectra were observed. The occurrence of vibrational revivals permits us to identify the potential curves of the O{sub 2} dication which are most relevant to the molecular dynamics. These studies show the accessibility to the dynamics of such higher-charged molecules.

  17. Coupled ion Binding and Structural Transitions Along the Transport Cycle of Glutamate Transporters

    SciTech Connect

    Verdon, Gregory; Oh, SeCheol; Serio, Ryan N.; Boudker, Olga

    2014-05-19

    Membrane transporters that clear the neurotransmitter glutamate from synapses are driven by symport of sodium ions and counter-transport of a potassium ion. Previous crystal structures of a homologous archaeal sodium and aspartate symporter showed that a dedicated transport domain carries the substrate and ions across the membrane. We report new crystal structures of this homologue in ligand-free and ions-only bound outward- and inward-facing conformations. We then show that after ligand release, the apo transport domain adopts a compact and occluded conformation that can traverse the membrane, completing the transport cycle. Sodium binding primes the transport domain to accept its substrate and triggers extracellular gate opening, which prevents inward domain translocation until substrate binding takes place. Moreover, we describe a new cation-binding site ideally suited to bind a counter-transported ion. We suggest that potassium binding at this site stabilizes the translocation-competent conformation of the unloaded transport domain in mammalian homologues.

  18. Spiking structure of amplitude characteristics for ion trajectories in hyperboloidal mass spectrometers: the theory.

    PubMed

    Sheretov, Ernst P; Philippov, Igor V; Karnav, Tatiana B; Kolotilin, Boris I; Ivanov, Vladimir W

    2002-01-01

    We present a theory that describes a 'spiking' structure of the amplitude characteristics for trajectories of ions within a hyperboloidal mass spectrometer (HMS) discovered and reported recently. This effect, as well as modulation parametric resonance, relates directly to a fine structure of the stability diagram for a HMS. A method of extremum characteristic solutions of the Hill equation (developed in our laboratory earlier) has been used in this work. Simple expressions determined the shape of narrow dips (or reversed peaks) in the amplitude of ion oscillation versus stability parameter curves and conditions of their appearance are presented. The results that were calculated from analytical expressions are compared with those obtained from direct computations of ion trajectories in a HMS. This effect with respect to a nature of 'black holes' or 'black canyons' observed earlier in investigations of trapping efficiency and ion trapping within ion traps is discussed.

  19. Evolution of structural and magnetic properties of Co-doped TiO2 thin films irradiated with 100 MeV Ag7+ ions

    NASA Astrophysics Data System (ADS)

    Mohanty, P.; Singh, V. P.; Mishra, N. C.; Ojha, S.; Kanjilal, D.; Rath, Chandana

    2014-08-01

    In continuation to our earlier studies where we have shown room temperature ferromagnetism observed in TiO2 and Co-doped TiO2 (CTO) thin films independent of their phase (Mohanty et al 2012 J. Phys. D: Appl. Phys. 45 325301), here the modifications in structure and magnetic properties in CTO thin films using 100 MeV Ag7+ ion irradiation are reported. Owing to the important role of defects in tailoring the magnetic properties of the material, we vary the ion fluence from 5 × 1011 to 1 × 1012 ions cm-2 to create post-deposition defects. While the film deposited under 0.1 mTorr oxygen partial pressure retains its crystallinity showing radiation-resistant behaviour even at a fluence of 1 × 1012 ions cm-2, films deposited under 1 to 300 mTorr oxygen partial pressure becomes almost amorphous at the same fluence. Using Poisson's law, the diameter of the amorphized region surrounding the ion path is calculated to be ˜4.2 nm from the x-ray diffraction peak intensity ((1 1 0) for rutile phase) as a function of ion fluence. The saturation magnetization (Ms) decreases exponentially similar to the decrease in x-ray peak intensity with fluence, indicating magnetic disordered region surrounding the ion path. The diameter of the magnetic disordered region is found to be ˜6.6 nm which is larger than the diameter of the amorphized latent track. Therefore, it is confirmed that swift heavy ion irradiation induces a more significant magnetic disorder than the structural disorder.

  20. Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

    DOE PAGES

    Sachan, Ritesh; Cooper, Valentino R.; Liu, Bin; ...

    2016-12-19

    Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd2Ti2O7) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effectmore » on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiOx polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd2Ti2O7. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.« less

  1. Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

    SciTech Connect

    Sachan, Ritesh; Cooper, Valentino R.; Liu, Bin; Aidhy, Dilpuneet S.; Voas, Brian K.; Lang, Maik; Ou, Xin; Trautmann, Christina; Zhang, Yanwen; Chisholm, Matthew F.; Weber, William J.

    2016-12-19

    Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd2Ti2O7) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effect on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiOx polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd2Ti2O7. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.

  2. Chromosome Damage in Human Cells by γ Rays, α Particles and Heavy Ions: Track Interactions in Basic Dose-Response Relationships

    PubMed Central

    Loucas, Bradford D.; Durante, Marco; Bailey, Susan M.; Cornforth, Michael N.

    2013-01-01

    We irradiated normal human lymphocytes and fibroblasts with 137Cs γ rays, 3.5 MeV α particles and 1 GeV/amu 56Fe ions and measured the subsequent formation of chromosome-type aberrations by mFISH at the first mitosis following irradiation. This was done for the purposes of characterizing the shape of dose-response relationships and determining the frequency distribution of various aberration types with respect to the parameters of dose, radiation quality and cell type. Salient results and conclusions include the following. For low-LET γ rays, lymphocytes showed a more robust dose response for overall damage and a higher degree of upward curvature compared to fibroblasts. For both sources of high-LET radiation, and for both cell types, the response for simple and complex exchanges was linear with dose. Independent of all three parameters considered, the most likely damage outcome was the formation of a simple exchange event involving two breaks. However, in terms of the breakpoints making up exchange events, the majority of damage registered following HZE particle irradiation was due to complex aberrations involving multiple chromosomes. This adds a decidedly nonlinear component to the overall breakpoint response, giving it a significant degree of positive curvature, which we interpret as being due to interaction between ionizations of the primary HZE particle track and long-range δ rays produced by other nearby tracks. While such track interaction had been previously theorized, to the best of our knowledge, it has never been demonstrated experimentally. PMID:23198992

  3. Chromosome damage in human cells by γ rays, α particles and heavy ions: track interactions in basic dose-response relationships.

    PubMed

    Loucas, Bradford D; Durante, Marco; Bailey, Susan M; Cornforth, Michael N

    2013-01-01

    We irradiated normal human lymphocytes and fibroblasts with (137)Cs γ rays, 3.5 MeV α particles and 1 GeV/amu (56)Fe ions and measured the subsequent formation of chromosome-type aberrations by mFISH at the first mitosis following irradiation. This was done for the purposes of characterizing the shape of dose-response relationships and determining the frequency distribution of various aberration types with respect to the parameters of dose, radiation quality and cell type. Salient results and conclusions include the following. For low-LET γ rays, lymphocytes showed a more robust dose response for overall damage and a higher degree of upward curvature compared to fibroblasts. For both sources of high-LET radiation, and for both cell types, the response for simple and complex exchanges was linear with dose. Independent of all three parameters considered, the most likely damage outcome was the formation of a simple exchange event involving two breaks. However, in terms of the breakpoints making up exchange events, the majority of damage registered following HZE particle irradiation was due to complex aberrations involving multiple chromosomes. This adds a decidedly nonlinear component to the overall breakpoint response, giving it a significant degree of positive curvature, which we interpret as being due to interaction between ionizations of the primary HZE particle track and long-range δ rays produced by other nearby tracks. While such track interaction had been previously theorized, to the best of our knowledge, it has never been demonstrated experimentally.

  4. A comparison between track-structure, condensed-history Monte Carlo simulations and MIRD cellular S-values.

    PubMed

    Tajik-Mansoury, M A; Rajabi, H; Mozdarani, H

    2017-03-07

    The S-value is a standard measure in cellular dosimetry. S-values are calculated by applying analytical methods or by Monte Carlo simulation. In Monte Carlo simulation, particles are either tracked individually event-by-event or close events are condensed and processed collectively in different steps. Both of these methods have been employed for estimation of cellular S-values, but there is no consistency between the published results. In the present paper, we used the Geant4-DNA track-structure physics model as the reference to estimate the cellular S-values. We compared the results with the corresponding values obtained from the following three condensed-history physics models of Geant4: Penelope, Livermore and standard. The geometry and source were exactly the same in all the simulations. We utilized mono-energetic electrons with an initial kinetic energy in the range 1-700 keV as the source of radiation. We also compared our results with the MIRD S-values. We first drew an overall comparison between different data series and then compared the dependence of results on the energy of particles and the size of scoring compartments. The overall comparison indicated a very good linear correlation (R (2)  >  91%) and small bias (3%) between the results of the track-structure model and the condensed-history physics model. The bias between MIRD and the results of Monte Carlo track-structure simulation was considerable (-8%). However, the point-by-point comparison revealed differences of up to 28% between the condensed-history and the track-structure MC codes for self-absorption S-values in the 10-50 keV energy range. For the cross-absorption S-values, the difference was up to 34%. In this energy range, the difference between the MIRD S-values and the Geant4-DNA results was up to 68%. Our findings suggest that the consistency/inconsistency of the results obtained with different MC simulations depends on the size of the scoring volumes, the energy of the

  5. A comparison between track-structure, condensed-history Monte Carlo simulations and MIRD cellular S-values

    NASA Astrophysics Data System (ADS)

    Tajik-Mansoury, M. A.; Rajabi, H.; Mazdarani, H.

    2017-03-01

    The S-value is a standard measure in cellular dosimetry. S-values are calculated by applying analytical methods or by Monte Carlo simulation. In Monte Carlo simulation, particles are either tracked individually event-by-event or close events are condensed and processed collectively in different steps. Both of these methods have been employed for estimation of cellular S-values, but there is no consistency between the published results. In the present paper, we used the Geant4-DNA track-structure physics model as the reference to estimate the cellular S-values. We compared the results with the corresponding values obtained from the following three condensed-history physics models of Geant4: Penelope, Livermore and standard. The geometry and source were exactly the same in all the simulations. We utilized mono-energetic electrons with an initial kinetic energy in the range 1–700 keV as the source of radiation. We also compared our results with the MIRD S-values. We first drew an overall comparison between different data series and then compared the dependence of results on the energy of particles and the size of scoring compartments. The overall comparison indicated a very good linear correlation (R 2  >  91%) and small bias (3%) between the results of the track-structure model and the condensed-history physics model. The bias between MIRD and the results of Monte Carlo track-structure simulation was considerable (‑8%). However, the point-by-point comparison revealed differences of up to 28% between the condensed-history and the track-structure MC codes for self-absorption S-values in the 10–50 keV energy range. For the cross-absorption S-values, the difference was up to 34%. In this energy range, the difference between the MIRD S-values and the Geant4-DNA results was up to 68%. Our findings suggest that the consistency/inconsistency of the results obtained with different MC simulations depends on the size of the scoring volumes, the energy of the

  6. Stripline fast faraday cup for measuring GHz structure of ion beams

    DOEpatents

    Bogaty, John M.

    1992-01-01

    The Stripline Fast Faraday Cup is a device which is used to quantitatively and qualitatively measure gigahertz time structure characteristics of ion beams with energies up to at least 30 Mev per nucleon. A stripline geometry is employed in conjunction with an electrostatic screen and a Faraday cup to provide for analysis of the structural characteristics of an ion beam. The stripline geometry allows for a large reduction in the size of the instrument while the electrostatic screen permits measurements of the properties associated with low speed ion beams.

  7. Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

    NASA Astrophysics Data System (ADS)

    Manojkumar, P. A.; Chirayath, V. A.; Balamurugan, A. K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A. K.; Raj, Baldev

    2016-09-01

    Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  8. Ion-beam induced domain structure in piezoelectric PMN-PT single crystal

    SciTech Connect

    Kim, Kyou-Hyun; Payne, David A.; Zuo Jianmin

    2010-12-27

    We report an investigation of the domain structure in Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-30%PbTiO{sub 3} single crystals after ion milling. We show that ion milling induces microdomains, typically 0.1-1 {mu}m in size. The induced microdomains disappear after temperature annealing or electric poling, leaving behind nanodomains of a few nanometers in size. We attribute the microdomains to surface stress induced by ion milling. The results demonstrate the general importance of separating sample preparation artifacts from the true domain structure in the study of ferroic materials.

  9. Electronic structure ‘engineering’ in the development of materials for Li-ion and Na-ion batteries

    NASA Astrophysics Data System (ADS)

    Molenda, Janina

    2017-03-01

    Transition metal oxides with a general formula A x M a O b (A  =  Li, Na, M  =  transition metal) constitute a group of potential electrode materials for a new generation of alkaline batteries. This application is related to the fact that these compounds can reversibly intercalate high amounts of alkaline ions (1 or more moles per mole of M a O b ) already at room temperature, without significant changes in their crystallographic structure. The author of this work basing on her own investigations of A x M a O b (A  =  Li, Na; M  =  3d, 4d, 5d) has demonstrated that the electronic structure of these materials plays an important role in the intercalation process. Electronic model of intercalation process is presented. Author’s studies show that electronic structure ‘engineering’ is an excellent method of controlling properties of the cathode materials for Li-ion and Na-ion batteries, changing their unfavorable character of the discharge curve, from step-like to monotonic, through modification and control density of states function of a cathode material. Keynote talk at 8th International Workshop on Advanced Materials Science and Nanotechnology (IWAMSN2016), 8–12 November 2016, Ha Long City, Vietnam.

  10. Magnetosheath Filamentary Structures Formed by Ion Acceleration at the Quasi-Parallel Bow Shock

    NASA Technical Reports Server (NTRS)

    Omidi, N.; Sibeck, D.; Gutynska, O.; Trattner, K. J.

    2014-01-01

    Results from 2.5-D electromagnetic hybrid simulations show the formation of field-aligned, filamentary plasma structures in the magnetosheath. They begin at the quasi-parallel bow shock and extend far into the magnetosheath. These structures exhibit anticorrelated, spatial oscillations in plasma density and ion temperature. Closer to the bow shock, magnetic field variations associated with density and temperature oscillations may also be present. Magnetosheath filamentary structures (MFS) form primarily in the quasi-parallel sheath; however, they may extend to the quasi-perpendicular magnetosheath. They occur over a wide range of solar wind Alfvénic Mach numbers and interplanetary magnetic field directions. At lower Mach numbers with lower levels of magnetosheath turbulence, MFS remain highly coherent over large distances. At higher Mach numbers, magnetosheath turbulence decreases the level of coherence. Magnetosheath filamentary structures result from localized ion acceleration at the quasi-parallel bow shock and the injection of energetic ions into the magnetosheath. The localized nature of ion acceleration is tied to the generation of fast magnetosonic waves at and upstream of the quasi-parallel shock. The increased pressure in flux tubes containing the shock accelerated ions results in the depletion of the thermal plasma in these flux tubes and the enhancement of density in flux tubes void of energetic ions. This results in the observed anticorrelation between ion temperature and plasma density.

  11. Void structure of O+ ions in the inner magnetosphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Nakayama, Y.; Ebihara, Y.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.; Kistler, L. M.; Tanaka, T.

    2016-12-01

    The Van Allen Probes Helium Oxygen Proton Electron instrument observed a new type of enhancement of O+ ions in the inner magnetosphere during substorms. As the satellite moved outward in the premidnight sector, the flux of the O+ ions with energy 10 keV appeared first in the energy-time spectrograms. Then, the enhancement of the flux spread toward high and low energies. The enhanced flux of the O+ ions with the highest energy remained, whereas the flux of the ions with lower energy vanished near apogee, forming what we call the void structure. The structure cannot be found in the H+ spectrogram. We studied the generation mechanism of this structure by using numerical simulation. We traced the trajectories of O+ ions in the electric and magnetic fields from the global magnetohydrodynamics simulation and calculated the flux of O+ ions in the inner magnetosphere in accordance with the Liouville theorem. The simulated spectrograms are well consistent with the ones observed by Van Allen Probes. We suggest the following processes. (1) When magnetic reconnection starts, an intensive equatorward and tailward plasma flow appears in the plasma lobe. (2) The flow transports plasma from the lobe to the plasma sheet where the radius of curvature of the magnetic field line is small. (3) The intensive dawn-dusk electric field transports the O+ ions earthward and accelerates them nonadiabatically to an energy threshold; (4) the void structure appears at energies below the threshold.

  12. Magnetosheath filamentary structures formed by ion acceleration at the quasi-parallel bow shock

    NASA Astrophysics Data System (ADS)

    Omidi, N.; Sibeck, D.; Gutynska, O.; Trattner, K. J.

    2014-04-01

    Results from 2.5-D electromagnetic hybrid simulations show the formation of field-aligned, filamentary plasma structures in the magnetosheath. They begin at the quasi-parallel bow shock and extend far into the magnetosheath. These structures exhibit anticorrelated, spatial oscillations in plasma density and ion temperature. Closer to the bow shock, magnetic field variations associated with density and temperature oscillations may also be present. Magnetosheath filamentary structures (MFS) form primarily in the quasi-parallel sheath; however, they may extend to the quasi-perpendicular magnetosheath. They occur over a wide range of solar wind Alfvénic Mach numbers and interplanetary magnetic field directions. At lower Mach numbers with lower levels of magnetosheath turbulence, MFS remain highly coherent over large distances. At higher Mach numbers, magnetosheath turbulence decreases the level of coherence. Magnetosheath filamentary structures result from localized ion acceleration at the quasi-parallel bow shock and the injection of energetic ions into the magnetosheath. The localized nature of ion acceleration is tied to the generation of fast magnetosonic waves at and upstream of the quasi-parallel shock. The increased pressure in flux tubes containing the shock accelerated ions results in the depletion of the thermal plasma in these flux tubes and the enhancement of density in flux tubes void of energetic ions. This results in the observed anticorrelation between ion temperature and plasma density.

  13. The Structure and Transport of Water and Hydrated Ions Within Hydrophobic, Nanoscale Channels

    SciTech Connect

    Holt, J K; Herberg, J L; Wu, Y; Schwegler, E; Mehta, A

    2009-06-15

    The purpose of this project includes an experimental and modeling investigation into water and hydrated ion structure and transport at nanomaterials interfaces. This is a topic relevant to understanding the function of many biological systems such as aquaporins that efficiently shuttle water and ion channels that permit selective transport of specific ions across cell membranes. Carbon nanotubes (CNT) are model nanoscale, hydrophobic channels that can be functionalized, making them artificial analogs for these biological channels. This project investigates the microscopic properties of water such as water density distributions and dynamics within CNTs using Nuclear Magnetic Resonance (NMR) and the structure of hydrated ions at CNT interfaces via X-ray Absorption Spectroscopy (XAS). Another component of this work is molecular simulation, which can predict experimental measurables such as the proton relaxation times, chemical shifts, and can compute the electronic structure of CNTs. Some of the fundamental questions this work is addressing are: (1) what is the length scale below which nanoscale effects such as molecular ordering become important, (2) is there a relationship between molecular ordering and transport?, and (3) how do ions interact with CNT interfaces? These are questions of interest to the scientific community, but they also impact the future generation of sensors, filters, and other devices that operate on the nanometer length scale. To enable some of the proposed applications of CNTs as ion filtration media and electrolytic supercapacitors, a detailed knowledge of water and ion structure at CNT interfaces is critical.

  14. Experimental study of adaptive pointing and tracking for large flexible space structures

    NASA Technical Reports Server (NTRS)

    Boussalis, D.; Bayard, D. S.; Ih, C.; Wang, S. J.; Ahmed, A.

    1991-01-01

    This paper describes an experimental study of adaptive pointing and tracking control for flexible spacecraft conducted on a complex ground experiment facility. The algorithm used in this study is based on a multivariable direct model reference adaptive control law. Several experimental validation studies were performed earlier using this algorithm for vibration damping and robust regulation, with excellent results. The current work extends previous studies by addressing the pointing and tracking problem. As is consistent with an adaptive control framework, the plant is assumed to be poorly known to the extent that only system level knowledge of its dynamics is available. Explicit bounds on the steady-state pointing error are derived as functions of the adaptive controller design parameters. It is shown that good tracking performance can be achieved in an experimental setting by adjusting adaptive controller design weightings according to the guidelines indicated by the analytical expressions for the error.

  15. Ion trap mass spectrometry in the structural analysis of haemoglobin peptides modified by epichlorohydrin and diepoxybutane.

    PubMed

    Miraglia, Nadia; Basile, Adriana; Pieri, Maria; Acampora, Antonio; Malorni, Livia; De Giulio, Beatrice; Sannolo, Nicola

    2002-01-01

    Ion trap mass spectrometry has been shown to be particularly suitable for the structural analysis of high molecular weight peptides directly fragmented in the mass analyser without needing further sub-digestion reactions. Here we report the advantages of using multi-stage ion trap mass spectrometry in the structural characterisation of haemoglobin alkylated with epichlorohydrin and diepoxybutane. Alkylated globins were digested with trypsin and the peptide mixtures were analysed by MS(3). This technique allows the sequential fragmentation of peptides under analysis, giving rise to MS(3) product ion spectra with additional information with respect to MS(2) mass spectra. The results obtained complete the previously reported structural characterisation of alkylated haemoglobin, demonstrating the potential of ion trap mass spectrometry.

  16. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

    SciTech Connect

    Qiu, Xiayang; Janson, Cheryl A.

    2010-11-16

    A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.

  17. On the influence of ion exchange on the local structure of the titanosilicate ETS-10.

    PubMed

    Pavel, Claudiu C; Zibrowius, Bodo; Löffler, Elke; Schmidt, Wolfgang

    2007-07-14

    The effect of ion exchange with different monovalent cations (NH(4)(+), K(+), Na(+) and Cs(+)) on the local structure of the titanosilicate ETS-10 has been studied by (29)Si MAS NMR and Raman spectroscopy. Although X-ray diffraction shows no significant influence of ion exchange on the long range order, ammonium exchange is found to result in substantial damage to the local structure. Ion exchange experiments with alkali cations under significantly more acidic conditions clearly show that the structural damage brought about by ammonium exchange is not caused by the low pH of the exchange solution. The exchange with potassium and caesium ions also leads to significant changes in the (29)Si NMR and Raman spectra. However, these changes can largely be reversed by sodium back-exchange.

  18. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification.

    PubMed

    Zinnel, Nathanael F; Russell, David H

    2014-05-20

    Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

  19. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    DOE PAGES

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

  20. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  1. Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

    PubMed

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D

    2015-05-01

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  2. Lanthanide ion probes of structure in biology. Environmentally sensitive fine structure in laser-induced terbium(III) luminescence.

    PubMed

    Sudnick, D R; Horrocks, W D

    1979-05-23

    The 488 nm line of the CW argon ion laser provides a convenient visible source for the direct excitation of the emissive 5D4 state of the Tb(III) ion. Room temperature emission spectra of Tb(III) in a variety of environments have been examined under relatively high resolution. The samples studied include structurally well-characterized crystalline solids, model chelate complexes in solution and Tb(III) bound to the enzyme thermolysin and the protein parvalbumin. The fine structure in the emissions is caused by ligand field splittings of both ground and excited state J manifolds. These spectra provide signatures sensitive to the immediate coordination environment of the Tb(III) ion. Solid state/solution state structural comparisons are made. The emission fine structure reveal differences between the EF side calcium-binding sites of parvalbumin and the calcium site 1 of thermolysin.

  3. Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

    PubMed

    Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

    2016-02-18

    Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

  4. Identification of ion-pair structures in solution by vibrational stark effects

    DOE PAGES

    Hack, John; Mani, Tomoyasu; Grills, David C.; ...

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

  5. Identification of ion-pair structures in solution by vibrational stark effects

    SciTech Connect

    Hack, John; Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

  6. Li-Ion Localization and Energetics as a Function of Anode Structure.

    PubMed

    McNutt, Nicholas W; McDonnell, Marshall; Rios, Orlando; Keffer, David J

    2017-03-01

    In this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes. The edges of the crystalline and amorphous fragments of aromatic carbon that exist in these composites are terminated by hydrogen atoms, which play a crucial role in adsorption. In this work, we demonstrate how differences in composite structure due to changes in the processing conditions alter the type and extent of the interface between the amorphous and crystalline domains, thus impacting the nature of Li-ion storage. The effects of structural properties are evaluated using a suite of pair distribution functions as well as an original technique to extract archetypal structures, in the form of three-dimensional atomic density distributions, from highly disordered systems. The energetics of Li-ion binding are understood by relating changes in the energy and charge distributions to changes in structural properties. The distribution of Li-ion energies reveals that some structures lead to greater chemisorption, while others have greater physisorption. Carbon composites with a high volume fraction of small crystallites demonstrate the highest ion storage capacity because of the high interfacial area between the crystalline and amorphous domains. At these interfaces, stable H atoms, terminating the graphitic crystallites, provide favorable sites for reversible Li adsorption.

  7. Sheath structure in plasmas with nonextensively distributed electrons and thermal ions

    SciTech Connect

    Hatami, M. M.

    2015-02-15

    Sheath region of an electropositive plasma consisting of q-nonextensive electrons and singly charged positive ions with finite temperature is modeled. Using Sagdeev's pseudo potential technique to derive the modified sheath formation criterion, it is shown that the velocity of ions at the sheath edge is directly proportional to the ion temperatures and inversely proportional to the degree of nonextensivity of electrons (q-parameter). Using the modified Bohm criterion, effect of degree of nonextensivity of electrons and temperature of positive ions on the characteristics of the sheath region are investigated numerically. It is shown that an increase in the ion temperature gives rise to an increase in the electrostatic potential and the velocity of ions in the sheath regardless of the value of q. Furthermore, it is seen that the sheath width and the density distribution of the charged particles decrease by increasing the temperature of positive ions. In addition, it is found that the positive ion temperature is less effective on the sheath structure for higher values of the q-parameter. Finally, the results obtained for a thermal plasma with nonextensively distributed electrons are compared with the results of a cold plasma with nonextensive electrons and an extensive (Maxwellian) plasma with thermal ions.

  8. Effect of calcium/sodium ion exchange on the osmotic properties and structure of polyelectrolyte gels.

    PubMed

    Horkay, Ferenc; Basser, Peter J; Hecht, Anne-Marie; Geissler, Erik

    2015-12-01

    We discuss the main findings of a long-term research program exploring the consequences of sodium/calcium ion exchange on the macroscopic osmotic and elastic properties, and the microscopic structure of representative synthetic polyelectrolyte (sodium polyacrylate, (polyacrylic acid)) and biopolymer gels (DNA). A common feature of these gels is that above a threshold calcium ion concentration, they exhibit a reversible volume phase transition. At the macroscopic level, the concentration dependence of the osmotic pressure shows that calcium ions influence primarily the third-order interaction term in the Flory-Huggins model of polymer solutions. Mechanical tests reveal that the elastic modulus is practically unaffected by the presence of calcium ions, indicating that ion bridging does not create permanent cross-links. At the microscopic level, small-angle neutron scattering shows that polyacrylic acid and DNA gels exhibit qualitatively similar structural features in spite of important differences (e.g. chain flexibility and chemical composition) between the two polymers. The main effect of calcium ions is that the neutron scattering intensity increases due to the decrease in the osmotic modulus. At the level of the counterion cloud around dissolved macroions, anomalous small-angle X-ray scattering measurements made on DNA indicate that divalent ions form a cylindrical sheath enveloping the chain, but they are not localized. Small-angle neutron scattering and small-angle X-ray scattering provide complementary information on the structure and interactions in polymer solutions and gels.

  9. Structural Changes in Polymer Films by Fast Ion Implantation

    NASA Astrophysics Data System (ADS)

    Parada, M. A.; Minamisawa, R. A.; Muntele, C.; Muntele, I.; De Almeida, A.; Ila, D.

    2006-11-01

    In applications from food wrapping to solar sails, polymers films can be subjected to intense charged panicle bombardment and implantation. ETFE (ethylenetetrafluoroethylene) with high impact resistance is used for pumps, valves, tie wraps, and electrical components. PFA (tetrafluoroethylene-per-fluoromethoxyethylene) and FEP (tetrafluoroethylene-hexa-fluoropropylene) are sufficiently biocompatible to be used as transcutaneous implants since they resist damage from the ionizing space radiation, they can be used in aerospace engineering applications. PVDC (polyvinyllidene-chloride) is used for food packaging, and combined with others plastics, improves the oxygen barrier responsible for the food preservation. Fluoropolymers are also known for their radiation dosimetry applications, dependent on the type and energy of the radiation, as well as of the beam intensity. In this work ETFE, PFA, FEP and PVDC were irradiated with ions of keV and MeV energies at several fluences and were analyzed through techniques as RGA, OAP, FTIR, ATR and Raman spectrophotometry. CF3 is the main specie emitted from PFA and FEP when irradiated with MeV protons. H and HF are released from ETFE due to the broken C-F and C-H bonds when the polymer is irradiated with keV Nitrogen ions and protons. At high fluence, especially for keV Si and N, damage due to carbonization is observed with the formation of hydroperoxide and polymer dehydroflorination. The main broken bonds in PVDC are C-O and C-Cl, with the release of Cl and the formation of double carbon bonds. The ion fluence that causes damage, which could compromise fluoropolymer film applications, has been determined.

  10. From one to one million: How does community structure track disturbance across time and space?

    NASA Astrophysics Data System (ADS)

    Webb, A. E.

    2012-12-01

    The rate and severity of disturbances to the biosphere have been increasing over the last millennium due in part to anthropogenic effects, and the results of these disturbances are of increasing interest to the scientific and public communities. This project examines the impact of acidification and global warming on communities across a spectrum of temporal and spatial scales in both modern and fossil systems. Twenty datasets were selected from published zoo- and phyto-plankton literature to represent a temporal and spatial gradient, from small lakes to the open ocean, and from one year to one million years. Each dataset is associated with a proxy for an environmental disturbance (isotopes, pH, sedimentology, etc.) and consists of 15-300 samples across the interval of disturbance. To test the biotic changes induced by disturbance, community structure is measured by quantifying species-abundance distributions using rank-abundance curves and ordinations. A community consists of the individuals present in a given location at a given time, and the relative abundance of different species serves as a proxy for resource-partitioning. Disturbances cause a change in resource-partitioning, either by changing resource availability or by removing/adding species which compete for those resources. Therefore, shifts in resource-partitioning resulting from disturbance can be tracked by changes in community composition. Prior to an environmental disturbance, communities typically consist of many species that evenly partition resources and thereby abundance. After a disturbance, communities are dominated by a few species that can tolerate or thrive in the new conditions. Non-metric multi-dimensional scaling and Bray-Curtis polar ordinations reveal a progression from pre-disturbance communities, through the disturbance, and into the eventual recovery, which may or may not resemble the pre-disturbance communities. Larger disturbances (in terms of spatial extent or temporal duration

  11. Study of structural and spectroscopic behavior of Sm3+ ions in lead-zinc borate glasses containing alkali metal ions

    NASA Astrophysics Data System (ADS)

    Sasi Kumar, M. V.; Babu, S.; Rajeswara Reddy, B.; Ratnakaram, Y. C.

    2017-02-01

    High luminescence behavior of rare earth inorganic glasses have a variety of uses in the industry. In the past few decades, rare earth ions with characteristic photonics applications are being hosted by heavy metal oxide glasses. Among the rare earth ions Sm3+ ion has features which make it apt for high density optical storage. The authors of the paper have experimented to synthesize Sm3+ doped glasses. In this regard a new series of borate glasses doped with 1 mol% Sm3+ ion are developed by using melt-quenching technique. XRD, FTIR, optical absorption, luminescence techniques are used to study the various characteristics of Sm3+ ion in the present glass matrices. The XRD spectra confirms the amorphous nature of glasses. Further, the researchers have used differential thermal analysis to study the glass transition temperature. The structural groups in the prepared glasses are studied using Fourier transform infrared spectra. From the measurement of its optical absorption, three phenomenological Judd-Ofelt intensity parameters (Ω2, Ω4 and Ω6) have been computed. Based on these Judd-Ofelt intensity parameters, radiative properties such as radiative probabilities (Arad), branching ratios (β), and radiative life time (τR) are calculated. The excitation spectra of Sm3+ doped lithium heavy metal borate glass matrix is recorded under the emission wavelength of 600 nm. The emission spectra are recorded under 404 nm excitation wavelength. From various emission transitions, 4G5/2 → 6H7/2 and 4G5/2 → 6H9/2 bands could be of interest for various applications. The decay profiles of 4G5/2 level exhibit single exponential nature in all the prepared glass matrices. The potassium glass matrix exhibits higher quantum efficiency than the other glass matrices. Finally, by going through these several spectroscopic characterizations, it is concluded that the prepared Sm3+ doped lead-zinc borate glasses might be useful for visible light applications.

  12. Linguistic Complexity and Information Structure in Korean: Evidence from Eye-Tracking during Reading

    ERIC Educational Resources Information Center

    Lee, Yoonhyoung; Lee, Hanjung; Gordon, Peter C.

    2007-01-01

    The nature of the memory processes that support language comprehension and the manner in which information packaging influences online sentence processing were investigated in three experiments that used eye-tracking during reading to measure the ease of understanding complex sentences in Korean. All three experiments examined reading of embedded…

  13. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization.

    PubMed

    Pepin, Robert; Laszlo, Kenneth J; Marek, Aleš; Peng, Bo; Bush, Matthew F; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.

  14. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

    NASA Astrophysics Data System (ADS)

    Pepin, Robert; Laszlo, Kenneth J.; Marek, Aleš; Peng, Bo; Bush, Matthew F.; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions.

  15. Controlled deposition of sulphur-containing semiconductor and dielectric nano-structured films on metals in SF{sub 6} ion-ion plasma

    SciTech Connect

    Rafalskyi, Dmytro; Bredin, Jérôme; Aanesland, Ane

    2013-12-07

    In the present paper, the deposition processes and formation of films in SF{sub 6} ion-ion plasma, with positive and negative ion flows accelerated to the surface, are investigated. The PEGASES (acronym for Plasma Propulsion with Electronegative GASES) source is used as an ion-ion plasma source capable of generating almost ideal ion-ion plasma with negative ion to electron density ratio more than 2500. It is shown that film deposition in SF{sub 6} ion-ion plasma is very sensitive to the polarity of the incoming ions. The effect is observed for Cu, W, and Pt materials. The films formed on Cu electrodes during negative and positive ion assisted deposition were analyzed. Scanning electron microscope analysis has shown that both positive and negative ion fluxes influence the copper surface and leads to film formation, but with different structures of the surface: the low-energy positive ion bombardment causes the formation of a nano-pored film transparent for ions, while the negative ion bombardment leads to a continuous smooth insulating film. The transversal size of the pores in the porous film varies in the range 50–500 nm, and further analysis of the film has shown that the film forms a diode together with the substrate preventing positive charge drain, and positive ions are neutralized by passing through the nano-pores. The film obtained with the negative ion bombardment has an insulating surface, but probably with a multi-layer structure: destroying the top surface layer allows to measure similar “diode” IV-characteristics as for the nano-pored film case. Basing on results, practical conclusions for the probes and electrodes cleaning in ion-ion SF{sub 6} plasmas have been made. Different applications are proposed for the discovered features of the controlled deposition from ion-ion plasmas, from Li-sulphur rechargeable batteries manufacturing and nanofluidics issues to the applications for microelectronics, including low-k materials formation.

  16. Near-complete structural characterization of phosphatidylcholines using electron impact excitation of ions from organics.

    PubMed

    Campbell, J Larry; Baba, Takashi

    2015-06-02

    Although lipids are critical components of many cellular assemblies and biological pathways, accurate descriptions of their molecular structures remain difficult to obtain. Many benchtop characterization methods require arduous and time-consuming procedures, and multiple assays are required whenever a new structural feature is probed. Here, we describe a new mass-spectrometry-based workflow for enhanced structural lipidomics that, in a single experiment, can yield almost complete structural information for a given glycerophospholipid (GPL) species. This includes the lipid's sum (Brutto) composition from the accurate mass measured for the intact lipid ion and the characteristic headgroup fragment, the regioisomer composition from fragment ions unique to the sn-1 and sn-2 positions, and the positions of carbon-carbon double bonds in the lipid acyl chains. Here, lipid ions are fragmented using electron impact excitation of ions from organics (EIEIO)--a technique where the singly charged lipid ions are irradiated by an electron beam, producing diagnostic product ions. We have evaluated this methodology on various lipid standards, as well as on a biological extract, to demonstrate this new method's utility.

  17. Structure and dynamics of hydrated ion pairs in a hydrophobic environment.

    PubMed

    Benjamin, Ilan

    2010-10-28

    The structure, energetics, and dynamics of different alkali halide ion pairs hydrated in a hydrophobic medium are studied using molecular dynamics computer simulations. One or two water molecules hydrating NaCl, NaI, KCl, KI, and KF in bulk carbon tetrachloride are considered. The ion pairs remain in contact throughout the simulations, so the structure of the hydration complex is well characterized. The ions' interaction energy and hydration structure are examined and correlated with the ion sizes and charges. For the first four salts, the stronger interaction of the water molecules with the cation than with the anion of the ion pair is in agreement with recent experiments. However, when the anion is significantly smaller than the cation (as in the case of KF, which was not studied experimentally), the opposite behavior is found. The asymmetry of interaction with the cation and the anion are further elucidated by examining hypothetical ion pairs made from equal-sized cations and anions and by defining an asymmetry hydration parameter, which is found to correlate well with the structural characteristics, as well as with the water molecules' reorientation dynamics.

  18. Comparison of Solar Surface Flows Inferred from Time-Distance Helioseismology and Coherent Structure Tracking Using HMI/SDO Observations

    NASA Astrophysics Data System (ADS)

    Švanda, Michal; Roudier, Thierry; Rieutord, Michel; Burston, Raymond; Gizon, Laurent

    2013-07-01

    We compare measurements of horizontal flows on the surface of the Sun using helioseismic time-distance inversions and coherent structure tracking of solar granules. Tracking provides two-dimensional horizontal flows on the solar surface, whereas the time-distance inversions estimate the full three-dimensional velocity flows in the shallow near-surface layers. Both techniques use Helioseismic and Magnetic Imager observations as input. We find good correlations between the various measurements resulting from the two techniques. Further, we find a good agreement between these measurements and the time-averaged Doppler line-of-sight velocity, and also perform sanity checks on the vertical flow that resulted from the three-dimensional time-distance inversion.

  19. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels.

    PubMed

    Jang, Hyunbum; Arce, Fernando Teran; Lee, Joon; Gillman, Alan L; Ramachandran, Srinivasan; Kagan, Bruce L; Lal, Ratnesh; Nussinov, Ruth

    2016-01-01

    Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.

  20. Superconducting accelerating structures for very low velocity ion beams

    SciTech Connect

    Xu, J.; Shepard, K.W.; Ostroumov, P.N.; Fuerst, J.D.; Waldschmidt, G.; Gonin, I.V.; /Fermilab

    2008-01-01

    This paper presents designs for four types of very-low-velocity superconducting accelerating cavity capable of providing several MV of accelerating potential per cavity, and suitable for particle velocities in the range 0.006 < v/c < 0.06. Superconducting TEM-class cavities have been widely applied to CW acceleration of ion beams. SC linacs can be formed as an array of independently-phased cavities, enabling a variable velocity profile to maximize the output energy for each of a number of different ion species. Several laboratories in the US and Europe are planning exotic beam facilities based on SC linacs. The cavity designs presented here are intended for the front-end of such linacs, particularly for the post-acceleration of rare isotopes of low charge state. Several types of SC cavities have been developed recently to cover particle velocities above 0.06c. Superconducting four-gap quarter-wave resonators for velocities 0.008 < {beta} = v/c < 0.05 were developed about two decades ago and have been successfully operated at the ATLAS SC linac at Argonne National Laboratory. Since that time, progress in simulation tools, cavity fabrication and processing have increased SC cavity gradients by a factor of 3-4. This paper applies these tools to optimize the design of a four-gap quarter-wave resonator for exotic beam facilities and other low-velocity applications.

  1. High-spin nuclear structure studies with radioactive ion beams

    SciTech Connect

    Baktash, C.

    1992-12-31

    Two important developments in the sixties, namely the advent of heavy-ion accelerators and fabrication of Ge detectors, opened the way for the experimental studies of nuclear properties at high angular momentum. Addition of a new degree of freedom, namely spin, made it possible to observe such fascinating phenomena as occurrences and coexistence of a variety of novel shapes, rise, fall and occasionally rebirth of nuclear collectivity, and disappearance of pairing correlations. Today, with the promise of development of radioactive ion beams (RIB) and construction of the third-generation Ge-detection systems (GAMMASPHERE and EUROBALL), the authors are poised to explore new and equally fascinating phenomena that have been hitherto inaccessible. With the addition of yet another dimension, namely the isospin, they will be able to observe and verify predictions for exotic shapes as varied as rigid triaxiality, hyperdeformation and triaxial octupole shapes, or to investigate the T = 0 pairing correlations. In this paper, they shall review, separately for neutron-deficient and neutron-rich nuclei, these and a few other new high-spin physics opportunities that may be realized with RIB. Following this discussion, they shall present a list of the beam species, intensities and energies that are needed to fulfill these goals. The paper will conclude with a description of the experimental techniques and instrumentations that are required for these studies.

  2. Fine Structural Detection of Calcium Ions by Photoconversion

    PubMed Central

    Poletto, V.; Galimberti, V.; Guerra, G.; Rosti, V.; Moccia, F.; Biggiogera, M.

    2016-01-01

    We propose a tool for a rapid high-resolution detection of calcium ions which can be used in parallel with other techniques. We have applied a new approach by photo-oxidation of diaminobenzidine in presence of the emission of an excited fluorochrome specific for calcium detection. This method combines the selectivity of available fluorophores to the high spatial resolution offered by transmission electron microscopy to detect fluorescing molecules even when present in low amounts in membrane-bounded organelles. We show in this paper that Mag-Fura 2 photoconversion via diaminobenzidine oxidation is an efficient way for localizing Ca2+ ions at electron microscopy level, is easily carried out and reproducible, and can be obtained on a good amount of cells, since the exposure in our conditions is not limited to the direct irradiation of the sample via an objective but obtained with a germicide lamp. The end product is sufficiently electron dense to be detected clearly when present in sufficient amount within a membrane boundary. PMID:27734989

  3. Enhancing Target Normal Sheath Accelerated Ions with Micro-structured Targets

    NASA Astrophysics Data System (ADS)

    George, Kevin; Snyder, Joseph; Ji, Liangliang; Rubin, Trevor; Handler, Abraham; Poole, Patrick; Willis, Christopher; Daskalova, Rebecca; Cochran, Ginevra; Schumacher, Douglass

    2016-10-01

    Laser driven target normal sheath acceleration (TNSA) of ions has been widely studied due to its fundamental importance, use as a probe, and for possible applications such as cancer therapy and neutron generation. Much of this work has been conducted on thin foils with peak ion energy and yield optimized using laser parameters such as energy and spot size. Micro-structured targets, however, have demonstrated increased peak ion energy and yield by controlling and enhancing mechanisms preferential to TNSA. Novel micro-structured targets were developed using optical lithography techniques on thin substrates at the OSU NanoSystem Laboratory. Variable structure height (0.5-2 micron) and transverse patterning (up to 1 micron resolution) permit the survey of a range of structured target variables in the study of ion acceleration. We describe the development of these targets and an experiment investigating the enhancement of TNSA ions from lithography produced micro-structured targets conducted at the Scarlet Laser Facility. Experimental results show increased proton and Carbon yield >2 MeV and higher peak Carbon energy from structured targets. This work was supported by the Air Force Office of Scientific Research.

  4. Fabrication of submicron structures in nanoparticle/polymer composite by holographic lithography and reactive ion etching

    NASA Astrophysics Data System (ADS)

    Zhang, A. Ping; He, Sailing; Kim, Kyoung Tae; Yoon, Yong-Kyu; Burzynski, Ryszard; Samoc, Marek; Prasad, Paras N.

    2008-11-01

    We report on the fabrication of nanoparticle/polymer submicron structures by combining holographic lithography and reactive ion etching. Silica nanoparticles are uniformly dispersed in a (SU8) polymer matrix at a high concentration, and in situ polymerization (cross-linking) is used to form a nanoparticle/polymer composite. Another photosensitive SU8 layer cast upon the nanoparticle/SU8 composite layer is structured through holographic lithography, whose pattern is finally transferred to the nanoparticle/SU8 layer by the reactive ion etching process. Honeycomb structures in a submicron scale are experimentally realized in the nanoparticle/SU8 composite.

  5. CR-39 track detector calibration for H, He, and C ions from 0.1-0.5 MeV up to 5 MeV for laser-induced nuclear fusion product identification.

    PubMed

    Baccou, C; Yahia, V; Depierreux, S; Neuville, C; Goyon, C; Consoli, F; De Angelis, R; Ducret, J E; Boutoux, G; Rafelski, J; Labaune, C

    2015-08-01

    Laser-accelerated ion beams can be used in many applications and, especially, to initiate nuclear reactions out of thermal equilibrium. We have experimentally studied aneutronic fusion reactions induced by protons accelerated by the Target Normal Sheath Acceleration mechanism, colliding with a boron target. Such experiments require a rigorous method to identify the reaction products (alpha particles) collected in detectors among a few other ion species such as protons or carbon ions, for example. CR-39 track detectors are widely used because they are mostly sensitive to ions and their efficiency is near 100%. We present a complete calibration of CR-39 track detector for protons, alpha particles, and carbon ions. We give measurements of their track diameters for energy ranging from hundreds of keV to a few MeV and for etching times between 1 and 8 h. We used these results to identify alpha particles in our experiments on proton-boron fusion reactions initiated by laser-accelerated protons. We show that their number clearly increases when the boron fuel is preformed in a plasma state.

  6. Nonlinear ion-acoustic structures in dusty plasma with superthermal electrons and positrons

    SciTech Connect

    El-Tantawy, S. A.; El-Bedwehy, N. A.; Moslem, W. M.

    2011-05-15

    Nonlinear ion-acoustic structures are investigated in an unmagnetized, four-component plasma consisting of warm ions, superthermal electrons and positrons, as well as stationary charged dust impurities. The basic set of fluid equations is reduced to modified Korteweg-de Vries equation. The latter admits both solitary waves and double layers solutions. Numerical calculations indicate that these nonlinear structures cannot exist for all physical parameters. Therefore, the existence regions for both solitary and double layers excitations have been defined precisely. Furthermore, the effects of temperature ratios of ions-to-electrons and electrons-to-positrons, positrons and dust concentrations, as well as superthermal parameters on the profiles of the nonlinear structures are investigated. Also, the acceleration and deceleration of plasma species have been highlight. It is emphasized that the present investigation may be helpful in better understanding of nonlinear structures which propagate in astrophysical environments, such as in interstellar medium.

  7. Influence of Si ion implantation on structure and morphology of g-C3N4

    NASA Astrophysics Data System (ADS)

    Varalakshmi, B.; Sreenivasulu, K. V.; Asokan, K.; Srikanth, V. V. S. S.

    2016-07-01

    Effect of Si ion implantation on structural and morphological features of graphite-like carbon nitride (g-C3N4) was investigated. g-C3N4 was prepared by using a simple atmospheric thermal decomposition process. The g-C3N4 pellets were irradiated with a Si ion beam of energy 200 keV with different fluencies. Structural, morphological and elemental, and phase analysis of the implanted samples in comparison with the pristine samples was carried out by using X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM) with energy dispersive spectroscopy (EDS) and Fourier transform infrared spectroscopy (FTIR) techniques, respectively. The observations revealed that Si ion implantation results in a negligible change in the crystallite size and alteration of the network-like to the sheet-like morphology of g-C3N4 and Si ions in the g-C3N4 network.

  8. Structure of the hydrated and dimethyl sulfoxide solvated rubidium ions in solution.

    PubMed

    D'Angelo, Paola; Persson, Ingmar

    2004-05-31

    The structure of the hydrated and the dimethyl sulfoxide solvated rubidium ions in solution has been determined by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) studies. The models of the hydrated and dimethyl sulfoxide solvated rubidium ions fitting the experimental data best are square antiprisms with Rb-O bond distances of 2.98(2) and 2.98(3) A, respectively. The EXAFS data show a significant asymmetry in the Rb-O bond distance distribution with C(3) values of 0.0076 and 0.015 A(3), respectively. No second hydration sphere is observed around the hydrated rubidium ion. The dimethyl sulfoxide solvated rubidium ion displays a Rb-O-S bond angle of ca. 130 degrees, which is typical for a medium hard electron acceptor such as rubidium.

  9. Metal Ion Induced Pairing of Cytosine Bases: Formation of I-Motif Structures Identified by IR Ion Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gao, Juehan; Berden, Giel; Oomens, J.

    2015-06-01

    While the Watson-Crick structure of DNA is among the most well-known molecular structures of our time, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or presence of cations. Pairing of two cytosine (C) bases induced by the sharing of a single proton (C-H^+-C) gives rise to the so-called i-motif, occurring particularly in the telomeric region of DNA, and particularly at low pH. At physiological pH, silver cations were recently suggested to form cytosine dimers in a C-Ag^+-C structure analogous to the hemiprotonated cytosine dimer, which was later confirmed by IR spectroscopy.^1 Here we investigate whether Ag^+ is unique in this behavior. Using infrared action spectroscopy employing the free-electron laser FELIX and a tandem mass spectrometer in combination with quantum-chemical computations, we investigate a series of C-M^+-C complexes, where M is Cu, Li and Na. The complexes are formed by electrospray ionization (ESI) from a solution of cytosine and the metal chloride salt in acetonitrile/water. The complexes of interest are mass-isolated in the cell of a FT ion cyclotron resonance mass spectrometer, where they are irradiated with the tunable IR radiation from FELIX in the 600 - 1800 wn range. Spectra in the H-stretching range are obtained with a LaserVision OPO. Both experimental spectra as well as theoretical calculations indicate that while Cu behaves as Ag, the alkali metal ions induce a clearly different dimer structure, in which the two cytosine units are parallelly displaced. In addition to coordination to the ring nitrogen atom, the alkali metal ions coordinate to the carbonyl oxygen atoms of both cytosine bases, indicating that the alkali metal ion coordination favorably competes with hydrogen bonding between the two cytosine sub-units of the i-motif like structure. 1. Berdakin, Steinmetz, Maitre, Pino, J. Phys. Chem. A 2014, 118, 3804

  10. Solitary and double-layer structures in quantum bi-ion plasma

    NASA Astrophysics Data System (ADS)

    Shahmansouri, Mehran; Tribeche, Mouloud

    2016-06-01

    Weak ion-acoustic solitary waves (IASWs) in an unmagnetized quantum plasmas having two-fluid ions and fluid electrons are considered. Using the one-dimensional quantum hydrodynamics model and then the reductive perturbation technique, a generalized form of nonlinear quantum Korteweg-de Vries (KdV) equation governing the dynamics of weak ion acoustic solitary waves is derived. The effects of ion population, warm ion temperature, quantum diffraction, and polarity of ions on the nonlinear properties of these IASWs are analyzed. It is found that our present plasma model may support compressive as well as rarefactive solitary structures. Furthermore, formation and characteristics properties of IA double layers in the present bi-ion plasma model are investigated. The results of this work should be useful and applicable in understanding the wide relevance of nonlinear features of localized electro-acoustic structures in laboratory and space plasma, such as in super-dense astrophysical objects [24] and in the Earth's magnetotail region (Parks [43]. The implications of our results in some space plasma situations are discussed.

  11. Ion-beam-induced modifications in the structural and electrical properties of copper oxide selenite nanowires

    NASA Astrophysics Data System (ADS)

    Rana, Pallavi; Chauhan, R. P.

    2015-04-01

    Irradiation with swift heavy ions (SHIs) with energy in the MeV range is a unique tool for engineering the properties of materials. In this context, the objective of the present work is to study the conduction of charge carriers in pre- and post-ion-irradiated semiconducting nanowires. Copper oxide selenite nanowires were synthesized using a template-assisted electrodeposition technique from an aqueous solution of 0.8 M CuSO4·5H2O and 8 mM SeO2. The synthesized nanowires were observed to have a monoclinic structure with linear I-V characteristics (IVC). The effect of irradiation with 160 MeV Ni+12 ions on the properties of the copper oxide selenite nanowires was investigated for fluences varying from 1011 to 1013 ions/cm2. XRD spectra confirmed no change in the phase of the swift-heavy-ion-irradiated nanowires, but a modification in the orientation of the planes was observed that depended on the ion fluence. The electrical resistivity of the semiconducting nanowires also varied with the ion fluence. Simultaneous irradiation-induced modifications to the electro-chemical potential gradient and the granular properties of the material may have been the origin of the alteration in the structural and electrical properties of the nanowires.

  12. Modification of the crystal structure of gadolinium gallium garnet by helium ion irradiation

    SciTech Connect

    Ostafiychuk, B. K.; Yaremiy, I. P. Yaremiy, S. I.; Fedoriv, V. D.; Tomyn, U. O.; Umantsiv, M. M.; Fodchuk, I. M.; Kladko, V. P.

    2013-12-15

    The structure of gadolinium gallium garnet (GGG) single crystals before and after implantation by He{sup +} ions has been investigated using high-resolution X-ray diffraction methods and the generalized dynamic theory of X-ray scattering. The main types of growth defects in GGG single crystals and radiation-induced defects in the ion-implanted layer have been determined. It is established that the concentration of dislocation loops in the GGG surface layer modified by ion implantation increases and their radius decreases with an increase in the implantation dose.

  13. Hollow structure formation of intense ion beams with sharp edge in background plasmas

    SciTech Connect

    Hu, Zhang-Hu; Wang, You-Nian

    2016-02-15

    The transport of intense ion beams with sharp radial beam edge in plasmas has been studied with two-dimensional electromagnetic particle simulations. The initial solid beam evolves into a hollow beam due to the nonlinear sharp transverse force peak in the regions of beam edge. The magnitude and nonlinearity of this peak are enhanced as the ion beam travels further into the plasma, due to the self-consistent interactions between the beam ions and the plasma electrons. This structure formation is shown to be independent on the beam radius.

  14. Computer simulations of helium-solvated ions: solid-like versus liquid-like defect structures

    NASA Astrophysics Data System (ADS)

    Paolini, Stefano; Ancilotto, Francesco; Toigo, Flavio

    2007-03-01

    The local order around several alkali (Li^+ and Na^+) and alkali-earth (Be^+, Mg^+ and Ca^+) ions in ^4He clusters has been studied using ground-state path integral Monte Carlo simulations. We apply a criterion based on multipole dynamical correlations to discriminate between solid-like versus liquid-like behavior of the He solvent surrounding the impurity-ion. In agreement with existing experimental measurements in bulk helium, our findings suggest that Be^+ produces a solid-(``snowball'')-like structure, similarly to alkali ions and in contrast to heavier alkali-earth ones, for which a liquid-like environment is predicted.

  15. Tribological properties and surface structures of ion implanted 9Cr18Mo stainless steels

    NASA Astrophysics Data System (ADS)

    Fengbin, Liu; Guohao, Fu; Yan, Cui; Qiguo, Sun; Min, Qu; Yi, Sun

    2013-07-01

    The polished quenched-and-tempered 9Cr18Mo steels were implanted with N ions and Ti ions respectively at a fluence of 2 × 1017 ions/cm2. The mechanical properties of the samples were investigated by using nanoindenter and tribometer. The results showed that the ion implantations would improve the nanohardness and tribological property, especially N ion implantation. The surface analysis of the implanted samples was carried out by using XRD, XPS and AES. It indicated that the surface exhibits graded layers after ion implantation. For N ion implantation, the surface about 20 nm thickness is mainly composed of supersaturated interstitial N solid solution, oxynitrides, CrxCy phase and metal nitrides. In the subsurface region, the metal nitrides dominate and the other phases disappear. For Ti ion implantation, the surface of about 20 nm thickness is mainly composed of titanium oxides and carbon amorphous phase, the interstitial solid solution of Ti in Fe is abundant in the subsurface region. The surface components and structures have significant contributions to the improved mechanical properties.

  16. A review of nanofibrous structures in lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Pampal, Esra Serife; Stojanovska, Elena; Simon, Bálint; Kilic, Ali

    2015-12-01

    Materials for harvesting and storing energy have been extensively studied in the last decade. Many inorganic materials have already been developed and utilized in products for electrochemical energy-storage systems. The nature of these complex materials requires further investigation from several approaches in order to improve specific characteristics of batteries, such as storage capacity and environmental impact. Fiber scientists have also introduced original solutions using mostly inorganic novel materials. Nanofibers and nanofibrous materials have found applications in the three battery components of anodes, cathodes, and separators. Many methods produce nanofibers; out of these, electrospinning is seen as the most adaptable technique because of the versatility and scalability of the process. The present review collates recent studies on nanofibers for applications in Li-ion batteries, with a focus on the electrospinning technique. The advantages of the investigated fibrous materials are explored in detail.

  17. Multi-beam RFQ linac structure for heavy ion fusion

    NASA Astrophysics Data System (ADS)

    Hayashizaki, Noriyosu; Ishibashi, Takuya; Ito, Taku; Hattori, Toshiyuki

    2009-07-01

    Both the RF linear accelerator (linac) and the linear induction accelerator have been considered as injectors in a driver system for heavy ion fusion (HIF). In order to relax beam defocusing by space charge effect in the low-energy region, the accelerating beams that were merged and had their beam currents increased by the funnel tree system are injected into storage rings. A multi-beam linac that accelerates multiple beams in an accelerator cavity has the advantages of cost reduction and downsizing of the system. We modeled the multi-beam Interdigital-H type radio frequency quadruple (IH-RFQ) cavities with the different beam numbers and evaluated the electromagnetic characteristics by simulation. As a result, the reasonable ranges of their configuration were indicated for a practical use.

  18. Electrolytes in a nanometer slab-confinement: ion-specific structure and solvation forces.

    PubMed

    Kalcher, Immanuel; Schulz, Julius C F; Dzubiella, Joachim

    2010-10-28

    We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

  19. In situ tracking the reversible spinel-rocksalt structural transformation between Mn3O4 and MnO.

    PubMed

    San, Xingyuan; Zhang, Bo; Wang, Jing; Wu, Bo; Ma, Xiuliang

    2017-01-01

    Electron beam irradiation is well known to induce damage in materials. The structural transformation involved in the damage is usually believed to be an irreversible solid state chemical reaction. Here we use in situ transmission electron microscopy (TEM) combined electron-energy loss spectroscopy (EELS) technique in an aberration-corrected TEM to track the structural transformation in spinel Mn3O4 induced by electron beam irradiation. It is clarified that spinel Mn3O4 is transformed to rocksalt structured MnO by irradiation and the reversed recovering transition from rocksalt MnO to spinel Mn3O4 can occur by aging in the gentle electron beam circumstance. The mechanisms including the role of O desorption/adsorption and the displacement of Mn and O involved in the reversible transformation processes are discussed. The work presents an implication that electron beam can modify the structure at atomic dimension yielding diverse assemblies of surfaces, interfaces and colorful properties.

  20. Crystal structures of Bacillus alkaline phytase in complex with divalent metal ions and inositol hexasulfate.

    PubMed

    Zeng, Yi-Fang; Ko, Tzu-Ping; Lai, Hui-Lin; Cheng, Ya-Shan; Wu, Tzu-Hui; Ma, Yanhe; Chen, Chun-Chi; Yang, Chii-Shen; Cheng, Kuo-Joan; Huang, Chun-Hsiang; Guo, Rey-Ting; Liu, Je-Ruei

    2011-06-03

    Alkaline phytases from Bacillus species, which hydrolyze phytate to less phosphorylated myo-inositols and inorganic phosphate, have great potential as additives to animal feed. The thermostability and neutral optimum pH of Bacillus phytase are attributed largely to the presence of calcium ions. Nonetheless, no report has demonstrated directly how the metal ions coordinate phytase and its substrate to facilitate the catalytic reaction. In this study, the interactions between a phytate analog (myo-inositol hexasulfate) and divalent metal ions in Bacillus subtilis phytase were revealed by the crystal structure at 1.25 Å resolution. We found all, except the first, sulfates on the substrate analog have direct or indirect interactions with amino acid residues in the enzyme active site. The structures also unraveled two active site-associated metal ions that were not explored in earlier studies. Significantly, one metal ion could be crucial to substrate binding. In addition, binding of the fourth sulfate of the substrate analog to the active site appears to be stronger than that of the others. These results indicate that alkaline phytase starts by cleaving the fourth phosphate, instead of the third or the sixth that were proposed earlier. Our high-resolution, structural representation of Bacillus phytase in complex with a substrate analog and divalent metal ions provides new insight into the catalytic mechanism of alkaline phytases in general.

  1. The structures and stabilities of helium cluster ions

    NASA Astrophysics Data System (ADS)

    Knowles, Peter J.; Murrell, John N.

    Previously published 2-body and 3-body terms for an n-valued representation of the potential functions of Hen+ have been used to examine the structures of larger clusters. For n = 3-8 the most stable structure has a linear He3+ core surrounded by weakly bound, nearly neutral atoms, with up to four lying in an equatorial plane. Such structures persist as metastable species up to n = 12. For n > 8 the most stable structure consists of a He2+ core with up to nine atoms closely attached. The first excited state is predicted to have a vertical excitation energy of between 5·5 eV and 5·9 eV, changing little with n. This is in broad agreement with experimental observations.

  2. A Railroad Track Structural Analysis Method for Work Planning: Development and Example Application

    DTIC Science & Technology

    1990-10-01

    situations or those that allow for easy visualization and comparison. The reference frack system represents common track construction at an Army...correct response to the query is Y [Enter]. Note that the default to this question is always the affirmative. Only an N will cause the program to bypass...would care to try some new values, type Y [Enter]. Again, the default is affirmative. Typing N will cause the program to end. When entering a new set

  3. Erbium ion implantation into diamond - measurement and modelling of the crystal structure.

    PubMed

    Cajzl, Jakub; Nekvindová, Pavla; Macková, Anna; Malinský, Petr; Sedmidubský, David; Hušák, Michal; Remeš, Zdeněk; Varga, Marián; Kromka, Alexander; Böttger, Roman; Oswald, Jiří

    2017-02-22

    Diamond is proposed as an extraordinary material usable in interdisciplinary fields, especially in optics and photonics. In this contribution we focus on the doping of diamond with erbium as an optically active centre. In the theoretical part of the study based on DFT simulations we have developed two Er-doped diamond structural models with 0 to 4 carbon vacancies in the vicinity of the Er atom and performed geometry optimizations by the calculation of cohesive energies and defect formation energies. The theoretical results showed an excellent agreement between the calculated and experimental cohesive energies for the parent diamond. The highest values of cohesive energies and the lowest values of defect formation energies were obtained for models with erbium in the substitutional carbon position with 1 or 3 vacancies in the vicinity of the erbium atom. From the geometry optimization the structural model with 1 vacancy had an octahedral symmetry whereas the model with 3 vacancies had a coordination of 10 forming a trigonal structure with a hexagonal ring. In the experimental part, erbium doped diamond crystal samples were prepared by ion implantation of Er(+) ions using ion implantation fluences ranging from 1 × 10(14) ions per cm(2) to 5 × 10(15) ions per cm(2). The experimental results revealed a high degree of diamond structural damage after the ion implantation process reaching up to 69% of disordered atoms in the samples. The prepared Er-doped diamond samples annealed at the temperatures of 400, 600 and 800 °C in a vacuum revealed clear luminescence, where the 〈110〉 cut sample has approximately 6-7 times higher luminescence intensity than the 〈001〉 cut sample with the same ion implantation fluence. The reported results are the first demonstration of the Er luminescence in the single crystal diamond structure for the near-infrared spectral region.

  4. Assigning structures to gas-phase peptide cations and cation-radicals. An infrared multiphoton dissociation, ion mobility, electron transfer, and computational study of a histidine peptide ion.

    PubMed

    Moss, Christopher L; Chamot-Rooke, Julia; Nicol, Edith; Brown, Jeffery; Campuzano, Iain; Richardson, Keith; Williams, Jonathan P; Bush, Matthew F; Bythell, Benjamin; Paizs, Bela; Turecek, Frantisek

    2012-03-15

    Infrared multiphoton dissociation (IRMPD) spectroscopy, using a free-electron laser, and ion mobility measurements, using both drift-cell and traveling-wave instruments, were used to investigate the structure of gas-phase peptide (AAHAL + 2H)(2+) ions produced by electrospray ionization. The experimental data from the IRMPD spectra and collisional cross section (Ω) measurements were consistent with the respective infrared spectra and Ω calculated for the lowest-energy peptide ion conformer obtained by extensive molecular dynamics searches and combined density functional theory and ab initio geometry optimizations and energy calculations. Traveling-wave ion mobility measurements were employed to obtain the Ω of charge-reduced peptide cation-radicals, (AAHAL + 2H)(+●), and the c(3), c(4), z(3), and z(4) fragments from electron-transfer dissociation (ETD) of (AAHAL + 2H)(2+). The experimental Ω for the ETD charge-reduced and fragment ions were consistent with the values calculated for fully optimized ion structures and indicated that the ions retained specific hydrogen bonding motifs from the precursor ion. In particular, the Ω for the doubly protonated ions and charge-reduced cation-radicals were nearly identical, indicating negligible unfolding and small secondary structure changes upon electron transfer. The experimental Ω for the (AAHAL + 2H)(+●) cation-radicals were compatible with both zwitterionic and histidine radical structures formed by electron attachment to different sites in the precursor ion, but did not allow their distinction. The best agreement with the experimental Ω was found for ion structures fully optimized with M06-2X/6-31+G(d,p) and using both projection approximation and trajectory methods to calculate the theoretical Ω values.

  5. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    DOE PAGES

    Hofmann, Felix; Robinson, Ian K.; Tarleton, Edmund; ...

    2017-04-06

    The ability of Focused Ion Beam (FIB) techniques to cut solid matter at the nano-scale revolutionized the study of material structure across the life-, earth- and material sciences. But a detailed understanding of the damage caused by the ion beam and its effect on material properties remains elusive. We examine this damage in 3D using coherent X-ray diffraction to measure the full lattice strain tensor in FIB-milled gold nano-crystals. We also found that even very low ion doses, previously thought to be negligible, cause substantial lattice distortions. At higher doses, extended self-organized defect structures appear. Combined with detailed numerical calculations,more » these observations allow fundamental insight into the nature of the damage created and the structural instabilities that lead to a surprisingly inhomogeneous morphology.« less

  6. Crystal-chemical role of malonate ions in the structure of coordination polymers

    NASA Astrophysics Data System (ADS)

    Serezhkin, V. N.; Medvedkov, Ya. A.; Serezhkina, L. B.; Pushkin, D. V.

    2015-06-01

    In the crystal structures of the malonate-containing compounds of d- or f-metals, the C3H2O{4/2-} anions were found to exhibit 17 topologically different types of coordination to the metal atoms A, playing the role of mono-, bi-, tri-, or tetradentate ligands and forming one to seven O-A bonds. The C-C-C bond angle in the malonate ions changed from 103° to 126° and depended linearly on the dihedral angle (φCOO) between the planes of the two carboxyl groups of the anion. At φCOO < 60°, the malonate ions in the crystal structures always form six-membered metallocycles with d- or f-metal atoms, while at φCOO > 67°, they can form only four-membered metallocycles. The factors that influence the conformation of malonate ions in the structures of coordination polymers were discussed.

  7. Structure of a CLC chloride ion channel by cryo-electron microscopy.

    PubMed

    Park, Eunyong; Campbell, Ernest B; MacKinnon, Roderick

    2017-01-26

    CLC proteins transport chloride (Cl(-)) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl(-) ions passively, whereas others are secondary active transporters that exchange two Cl(-) ions for one H(+). The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl(-) transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl(-) passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl(-)/H(+) transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl(-) down its electrochemical gradient.

  8. FTIR spectroscopy structural analysis of the interaction between Lactobacillus kefir S-layers and metal ions

    NASA Astrophysics Data System (ADS)

    Gerbino, E.; Mobili, P.; Tymczyszyn, E.; Fausto, R.; Gómez-Zavaglia, A.

    2011-02-01

    FTIR spectroscopy was used to structurally characterize the interaction of S-layer proteins extracted from two strains of Lactobacillus kefir (the aggregating CIDCA 8348 and the non-aggregating JCM 5818) with metal ions (Cd +2, Zn +2, Pb +2 and Ni +2). The infrared spectra indicate that the metal/protein interaction occurs mainly through the carboxylate groups of the side chains of Asp and Glut residues, with some contribution of the NH groups belonging to the peptide backbone. The frequency separation between the νCOO - anti-symmetric and symmetric stretching vibrations in the spectra of the S-layers in presence of the metal ions was found to be ca. 190 cm -1 for S-layer CIDCA 8348 and ca. 170 cm -1 for JCM 5818, denoting an unidentate coordination in both cases. Changes in the secondary structures of the S-layers induced by the interaction with the metal ions were also noticed: a general trend to increase the amount of β-sheet structures and to reduce the amount of α-helices was observed. These changes allow the proteins to adjust their structure to the presence of the metal ions at minimum energy expense, and accordingly, these adjustments were found to be more important for the bigger ions.

  9. Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

    PubMed Central

    D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

    2015-01-01

    Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26259654

  10. Hydrodynamic theory for ion structure and stopping power in quantum plasmas.

    PubMed

    Shukla, P K; Akbari-Moghanjoughi, M

    2013-04-01

    We present a theory for the dynamical ion structure factor (DISF) and ion stopping power in an unmagnetized collisional quantum plasma with degenerate electron fluids and nondegenerate strongly correlated ion fluids. Our theory is based on the fluctuation dissipation theorem and the quantum plasma dielectric constant that is deduced from a linearized viscoelastic quantum hydrodynamical (LVQHD) model. The latter incorporates the essential physics of quantum forces, which are associated with the quantum statistical pressure, electron-exchange, and electron-correlation effects, the quantum electron recoil effect caused by the dispersion of overlapping electron wave functions that control the dynamics of degenerate electron fluids, and the viscoelastic properties of strongly correlated ion fluids. Both degenerate electrons and nondegenerate strongly correlated ions are coupled with each other via the space charge electric force. Thus, our LVQHD theory is valid for a collisional quantum plasma at atomic scales with a wide range of the ion coupling parameter, the plasma composition, and plasma number densities that are relevant for compressed plasmas in laboratories (inertial confinement fusion schemes) and in astrophysical environments (e.g., warm dense matter and the cores of white dwarf stars). It is found that quantum electron effects and viscoelastic properties of strongly correlated ions significantly affect the features of the DISF and the ion stopping power (ISP). Unlike previous theories, which have studied ion correlations in terms of the ion coupling parameter, by neglecting the essential physics of collective effects that are competing among each other, we have here developed a method to evaluate the dependence of the plasma static and dynamical features in terms of individual parameters, like the Wigner-Seitz radius, the ion atomic number, and the ion temperature. It is found that due to the complex nature of charge screening in quantum plasmas, the ion

  11. Neutral Exosphere Densities and Structures at Titan Inferred from Pickup Ions Observed by CAPS

    NASA Astrophysics Data System (ADS)

    Hartle, R. E.; Sittler, E. C.; Neubauer, F. M.; Johnson, R. E.; Crary, F.; McComas, D. J.; Young, D. T.; Coates, A. J.; Simpson, D. J.; Bolton, S.; Reisenfeld, D.; Szego, K.; Berthelier, J.

    2005-12-01

    Measurements of pickup ions, born from neutral exospheres imbedded in moving plasmas, can be used to determine the composition and structure of the parent neutral exosphere constituents [1]. Pickup ions have been observed in Saturn's rotating magnetosphere near Titan by the Cassini Plasma Spectrometer (CAPS) instrument during the Cassini orbiter's recent flybys of the moon. Pickup ions observed by CAPS include H+, H2+, N+/CH2+, CH4+, and N2+. These ions slow down Saturn's magnetospheric plasma beyond Titan's ionosphere through mass loading. Because of its relatively high mass and high concentration, CH4+ is the dominant mass loading ion. The other ions make negligible contributions to the mass loading process except for N2+ just above the ionopause, where its concentration becomes important. The phase space densities of pickup ions are sensitive functions of the spatial variations of the parent exosphere gasses of the pickup ions [2]. Accounting for such variations, model phase space densities [2], derived from the Vlasov equation, are used in an algorithm to obtain ion density and velocity moments from CAPS measurements. The model implicitly maps an ions trajectory from its observation point to its source point. The analysis shows that because the gyroradius of CH4+ is much greater than the scale height of the source gas, CH4, the ion fluxes are beamlike with velocities distributed over a narrow range. The observed pickup ion velocities are found to be in ring distributions, with the light ion H+ occupying all of its allowed velocities and CH4+ only a small portion of its ring velocities. Applying the algorithm, exosphere densities are inferred. Using CAPS time-of-flight data and empirical cracking patterns, we show that the 14 amu ion is more likely N+. We compare ratios of the inferred N and CH4 exosphere densities with existing exosphere models. 1. Hartle, R. E., K. W. Ogilvie and C. S. Wu, Planet Space Sci., 21, 2181, 1973. 2. Hartle, R. E. and E. C. Sittler

  12. Hydrodynamic theory for ion structure and stopping power in quantum plasmas

    NASA Astrophysics Data System (ADS)

    Shukla, P. K.; Akbari-Moghanjoughi, M.

    2013-04-01

    We present a theory for the dynamical ion structure factor (DISF) and ion stopping power in an unmagnetized collisional quantum plasma with degenerate electron fluids and nondegenerate strongly correlated ion fluids. Our theory is based on the fluctuation dissipation theorem and the quantum plasma dielectric constant that is deduced from a linearized viscoelastic quantum hydrodynamical (LVQHD) model. The latter incorporates the essential physics of quantum forces, which are associated with the quantum statistical pressure, electron-exchange, and electron-correlation effects, the quantum electron recoil effect caused by the dispersion of overlapping electron wave functions that control the dynamics of degenerate electron fluids, and the viscoelastic properties of strongly correlated ion fluids. Both degenerate electrons and nondegenerate strongly correlated ions are coupled with each other via the space charge electric force. Thus, our LVQHD theory is valid for a collisional quantum plasma at atomic scales with a wide range of the ion coupling parameter, the plasma composition, and plasma number densities that are relevant for compressed plasmas in laboratories (inertial confinement fusion schemes) and in astrophysical environments (e.g., warm dense matter and the cores of white dwarf stars). It is found that quantum electron effects and viscoelastic properties of strongly correlated ions significantly affect the features of the DISF and the ion stopping power (ISP). Unlike previous theories, which have studied ion correlations in terms of the ion coupling parameter, by neglecting the essential physics of collective effects that are competing among each other, we have here developed a method to evaluate the dependence of the plasma static and dynamical features in terms of individual parameters, like the Wigner-Seitz radius, the ion atomic number, and the ion temperature. It is found that due to the complex nature of charge screening in quantum plasmas, the ion

  13. Model of evolution of surface grain structure under ion bombardment

    SciTech Connect

    Knyazeva, Anna G.; Kryukova, Olga N.

    2014-11-14

    Diffusion and chemical reactions in multicomponent systems play an important role in numerous technology applications. For example, surface treatment of materials and coatings by particle beam leads to chemical composition and grain structure change. To investigate the thermal-diffusion and chemical processes affecting the evolution of surface structure, the mathematical modeling is efficient addition to experiment. In this paper two-dimensional model is discussed to describe the evolution of titanium nitride coating on the iron substrate under implantation of boron and carbon. The equation for diffusion fluxes and reaction rate are obtained using Gibbs energy expansion into series with respect to concentration and their gradients.

  14. Structured Tracking for Safety, Security, and Privacy: Algorithms for Fusing Noisy Estimates from Sensor, Robot, and Camera Networks

    DTIC Science & Technology

    2009-07-23

    robotic fly [181] to a location within a space for covert surveillance. Using the concepts of Structured Tracking , we place beacons in the space to...at the RSSI at multiple frequencies, and have a calibrated map of what the RSSI should be on each frequency at many locations in the space . Thus, they...prism in world- space and a specific pan, tilt, and zoom for the camera that maps to this location . 6.7 Simulation Results We implemented a simulator to

  15. Swift heavy ion-induced recrysallization of silicon-on-insulator (SOI) structures

    NASA Astrophysics Data System (ADS)

    Virdi, G. S.; Pathak, B. C.; Avasthi, D. K.; Kanjilal, D.

    2002-02-01

    Buried Si 3N 4-Si interfaces and overlayer in silicon-on-insulator (SOI) structures were improved by irradiation with 100 MeV 107Ag after the synthesis of buried silicon nitride layers by high dose nitrogen ion-implantation. Auger electron spectroscopy (AES) depth profile analysis illustrates that the MeV heavy ions irradiation in the SOI structure, modifies the distribution of nitrogen that results in better stoichiometry of the buried silicon nitride layers and abrupt Si 3N 4-Si interfaces. Electron spin resonance (ESR) technique shows the improvement in the crystalline structure of the Si over layer. Current-voltage and high frequency capacitance-voltage ( C- V) characteristics were studied, and electrical breakdown measurements were performed on metal nitride silicon (MNS) structures fabricated after removing the Si over layer in the SOI structure. In the ion-beam irradiated SOI specimens, buried silicon nitride layer show a high breakdown field strength of 4.5-6.5 MV/cm as compared to that of 3.0-3.9 MV/cm in the unirradiated one. The C- V analysis of the MNS capacitors reveals that the buried Si 3N 4-Si substrate interface exhibits a better quality with reduced fixed insulator charge and interface state densities after the ion-beam irradiation. Mid-gap interface state density at the buried Si 3N 4-Si substrate interface was as low as 1.0×10 11 cm-2 V-2 after the ion-beam irradiation, which is comparable to that of silicon nitride films deposited on silicon (Si) by the conventional low pressure chemical vapor deposition technique. The role of MeV ion-beam irradiation in improving the properties of SOI structures has been discussed on the basis of various models.

  16. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  17. Gramicidins A, B, and C form structurally equivalent ion channels.

    PubMed Central

    Sawyer, D B; Williams, L P; Whaley, W L; Koeppe, R E; Andersen, O S

    1990-01-01

    The membrane structure of the naturally occurring gramicidins A, B, and C was investigated using circular dichroism (CD) spectroscopy and single-channel recording techniques. All three gramicidins form channels with fairly similar properties (Bamberg, E., K. Noda, E. Gross, and P. Läuger. 1976. Biochim. Biophys. Acta. 419:223-228.). When incorporated into lysophosphatidylcholine micelles, however, the CD spectrum of gramicidin B is different from that of gramicidin A or C (cf. Prasad, K. U., T. L. Trapane, D. Busath, G. Szabo, and D. W. Urry. 1983. Int. J. Pept. Protein Res. 22:341-347.). The structural identity of the channels formed by gramicidin B has, therefore, been uncertain. We find that when gramicidins A and B are incorporated into dipalmitoylphosphatidylcholine vesicles, their CD spectra are fairly similar, suggesting that the two channel structures could be similar. In planar bilayers, gramicidins A, B, and C all form hybrid channels with each other. The properties of the hybrid channels are intermediate to those of the symmetric channels, and the appearance rates of the hybrid channels (relative to the symmetric channels) corresponds to what would be predicted if all three gramicidin molecules were to form structurally equivalent channels. These results allow us to interpret the different behavior of channels formed by the three gramicidins solely on the basis of the amino acid substitution at position 11. PMID:1705449

  18. Computational multiobjective topology optimization of silicon anode structures for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Mitchell, Sarah L.; Ortiz, Michael

    2016-09-01

    This study utilizes computational topology optimization methods for the systematic design of optimal multifunctional silicon anode structures for lithium-ion batteries. In order to develop next generation high performance lithium-ion batteries, key design challenges relating to the silicon anode structure must be addressed, namely the lithiation-induced mechanical degradation and the low intrinsic electrical conductivity of silicon. As such this work considers two design objectives, the first being minimum compliance under design dependent volume expansion, and the second maximum electrical conduction through the structure, both of which are subject to a constraint on material volume. Density-based topology optimization methods are employed in conjunction with regularization techniques, a continuation scheme, and mathematical programming methods. The objectives are first considered individually, during which the influence of the minimum structural feature size and prescribed volume fraction are investigated. The methodology is subsequently extended to a bi-objective formulation to simultaneously address both the structural and conduction design criteria. The weighted sum method is used to derive the Pareto fronts, which demonstrate a clear trade-off between the competing design objectives. A rigid frame structure was found to be an excellent compromise between the structural and conduction design criteria, providing both the required structural rigidity and direct conduction pathways. The developments and results presented in this work provide a foundation for the informed design and development of silicon anode structures for high performance lithium-ion batteries.

  19. Label-free fluorescent aptasensor for potassium ion using structure-switching aptamers and berberine

    NASA Astrophysics Data System (ADS)

    Guo, Yanqing; Chen, Yanxia; Wei, Yanli; Li, Huanhuan; Dong, Chuan

    2015-02-01

    A simple, rapid and label-free fluorescent aptasensor was fabricated for the detection of potassium ion (K+ ion) in aqueous solution using K+ ion-stabilized single stranded DNA (ssDNA) with G-rich sequence as the recognition element and a fluorescent dye, berberine, as the fluorescence probe. In the presence of K+ ion, the G-rich ssDNA is promoted to form the aptamer-target complex with a G-quadruplex conformation, and berberine binding to the G-quadruplex structure results in the enhancement of its fluorescence. The fluorescence intensity of the sensing system displayed a calibration response for K+ ion in the range of 0-1600 μM with a detection limit of 31 nM (S/N = 3) and a relative standard deviation (RSD) of 0.45%. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K+ ion in blood serum samples with the recovery range of 81.7-105.3%. The assay for detection of potassium ion is easy, economical, robust, and stable in rough conditions.

  20. Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    2017-02-01

    We use all atom molecular dynamics simulations to investigate the influence of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6) ionic liquid on the structure and transport properties of poly(ethylene oxide) (PEO) polymer electrolytes doped with LiPF6 salt. We observe enhanced diffusivities of the Li+, PF6-, and BMIM+ ions with increasing loading of the ionic liquid. Interplay between the different ion-ion and ion-polymer interactions is seen to lead to a destabilization of the Li-PF6 coordination and increase in the strength of association between the Li+ cations and the polymer backbone. As a consequence, the polymer segmental relaxation times are shown to be only moderately affected by the addition of ionic liquids. The ionic-liquid induced changes in the mobilities of Li+ ions are seen to be correlated to polymer segmental relaxation times. However, the mobilities of BMIM+ ions are seen to be more strongly correlated to the BMIM-PF6 ion-pair relaxation times.

  1. A structure zone diagram including plasma based deposition and ion etching

    SciTech Connect

    Anders, Andre

    2009-10-14

    An extended structure zone diagram is proposed that includes energetic deposition, characterized by a large flux of ions typical for deposition by filtered cathodic arcs and high power impulse magnetron sputtering. The axes are comprised of a generalized homologous temperature, the normalized kinetic energy flux, and the net film thickness, which can be negative due to ion etching. It is stressed that the number of primary physical parameters affecting growth by far exceeds the number of available axes in such a diagram and therefore it can only provide an approximate and simplified illustration of the growth condition?structure relationships.

  2. Plasma immersion ion implantation for surface treatment of complex branched structures

    NASA Astrophysics Data System (ADS)

    Kashin, Oleg A.; Lotkov, Alexander I.; Borisov, Dmitry P.; Slabodchikov, Vladimir A.; Kuznetsov, Vladimir M.; Kudryashov, Andrey N.; Krukovsky, Konstantin V.

    2016-11-01

    The paper presents experimental results demonstrating the capabilities of plasma immersion ion implantation of silicon (Si) for surface treatment of complex branched structures such are self-expanding intravascular nickel-titanium (NiTi) stents. Using NiTi stents of diameter 4 and 8 mm, it is shown that plasma immersion ion implantation can provide rather homogeneous doping of their outer and inner surfaces with Si atoms. Also presented are research data on the processes that determine the thickness, composition, and structure of surface layers subjected to this type of treatment.

  3. Structured copolymers and their use as absorbents, gels and carriers of metal ions

    DOEpatents

    Hedstrand, D.M.; Helmer, B.J.; Tomalia, D.A.

    1996-10-01

    Dense star polymers or dendrimers having a highly branched interior structure capable of associating or chelating with metal ions are modified by capping with a hydrophobic group capable of providing a hydrophobic outer shell. The modified dendrimers are useful for dispersing metal ions in a non-aqueous polymer matrix. Also dense star polymers or dendrimers having a highly branched hydrophilic interior structure are modified by capping with a hydrophobic group capable of providing a hydrophobic outer shell, which modified polymers are useful as gels and surfactants.

  4. Structured copolymers and their use as absorbents, gels and carriers of metal ions

    DOEpatents

    Hedstrand, David M.; Helmer, Bradley J.; Tomalia, Donald A.

    1996-01-01

    Dense star polymers or dendrimers having a highly branched interior structure capable of associating or chelating with metal ions are modified by capping with a hydrophobic group capable of providing a hydrophobic outer shell. The modified dendrimers are useful for dispersing metal ions in a non-aqueous polymer matrix. Also dense star polymers or dendrimers having a highly branched hydrophilic interior structure are modified by capping with a hydrophobic group capable of providing a hydrophobic outer shell, which modified polymers are useful as gels and surfactants.

  5. The response of the pyrochlore structure-type to ion-beam irradiation

    NASA Astrophysics Data System (ADS)

    Lian, Jie

    Pyrochlore with the general formula of A3+2B4+2O7 (Fd3m; Z = 8) has been proposed as the candidate waste form for the immobilization of actinides, particularly plutonium from dismantled nuclear weapons. Because actinides decay by alpha-decay events, radiation effects on the waste form are a concern. The effects of radiation on different pyrochlore compositions, A2B2O7 (A = La ˜ Lu, and Y; B = Ti, Sn, and Zr), have been investigated by 50 KeV He+, 600 KeV Ar+, 1.0 MeV Kr+, and 1.5 MeV Xe+ ion irradiations. Titanate pyrochlores are generally sensitive to ion beam damage and can be amorphized at a low damage level (˜0.2 dpa). The critical amorphization temperature, Tc, increases from ˜480 to ˜1120 K with increasing A-site cation size. A dramatically increasing radiation "resistance" to ion beam induced-amorphization has been observed with increasing Zr-content in the Gd2Ti2-xZrxO7 system. The pure end-member, Gd2Zr2O7, cannot be amorphized, even at doses as high as ˜100 dpa. Although zirconate pyrochlores are generally considered to be radiation "resistant", ion beam-induced amorphization occurs for La2Zr2O7 at a dose of ˜5.5 dpa at room temperature. Stannate pyrochlores A2Sn 2O7 (A = La, Nd, Gd) are readily amorphized by ion beam damage at a relatively low dose (˜1 dpa) at room temperature; while no evidence of amorphization has been observed in A2Sn2O7 (A = Er, Y, Lu) irradiated with 1 MeV Kr+ ions at a dose of ˜6 dpa at 25 K. The factors that influence the response of different pyrochlore compositions to ion irradiation-induced amorphization are discussed in terms of cation radius ratio, defect formation energies, and the tendency of the pyrochlore structure-type to undergo an order-disorder transition to the defect-fluorite structure. The "resistance" of the pyrochlore structure to ion beam-induced amorphization is not only affected by the relative sizes of the A- and B-site cations, but also the cation electronic configurations. Pyrochlore compositions

  6. Enhancement of maximum attainable ion energy in the radiation pressure acceleration regime using a guiding structure

    SciTech Connect

    Bulanov, S. S.; Esarey, E.; Schroeder, C. B.; Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Pegoraro, F.; Leemans, W. P.

    2015-03-13

    Radiation Pressure Acceleration is a highly efficient mechanism of laser driven ion acceleration, with the laser energy almost totally transferrable to the ions in the relativistic regime. There is a fundamental limit on the maximum attainable ion energy, which is determined by the group velocity of the laser. In the case of a tightly focused laser pulses, which are utilized to get the highest intensity, another factor limiting the maximum ion energy comes into play, the transverse expansion of the target. Transverse expansion makes the target transparent for radiation, thus reducing the effectiveness of acceleration. Utilization of an external guiding structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.

  7. Enhancement of maximum attainable ion energy in the radiation pressure acceleration regime using a guiding structure

    DOE PAGES

    Bulanov, S. S.; Esarey, E.; Schroeder, C. B.; ...

    2015-03-13

    Radiation Pressure Acceleration is a highly efficient mechanism of laser driven ion acceleration, with the laser energy almost totally transferrable to the ions in the relativistic regime. There is a fundamental limit on the maximum attainable ion energy, which is determined by the group velocity of the laser. In the case of a tightly focused laser pulses, which are utilized to get the highest intensity, another factor limiting the maximum ion energy comes into play, the transverse expansion of the target. Transverse expansion makes the target transparent for radiation, thus reducing the effectiveness of acceleration. Utilization of an external guidingmore » structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.« less

  8. Tuning heat transport in trapped-ion chains across a structural phase transition

    NASA Astrophysics Data System (ADS)

    Ruiz, A.; Alonso, D.; Plenio, M. B.; del Campo, A.

    2014-06-01

    We analyze the heat transport in an ion chain that is confined in a strongly anisotropic Paul trap. To drive a heat current across the chain different pairs of counterpropagating laser beams are applied to the ions on the edges. The lasers behave as heat reservoirs operating at different temperatures, and a nonequilibrium heat flow can be sustained. The control of the spatial distribution of the ions in the chain by variation of the trapping frequencies makes ion chains an ideal testbed to study heat transport properties in finite open systems of low dimensionality with tunable nonlinearities. We explore heat transport across a structural phase transition between the linear and zigzag configurations, identifying the condition for optimal heat transport.

  9. Growth of surface structures correlated with structural and mechanical modifications of brass by laser-induced Si plasma ions implantation

    NASA Astrophysics Data System (ADS)

    Ahmad, Shahbaz; Bashir, Shazia; Rafique, M. Shahid; Yousaf, Daniel

    2017-04-01

    Laser-produced Si plasma is employed as an ion source for implantation on the brass substrate for its surface, structural, and mechanical modifications. Thomson parabola technique is employed for the measurement of energy and flux of Si ions using CR-39. In response to stepwise increase in number of laser pulses from 3000 to 12000, four brass substrates were implanted by laser-induced Si plasma ions of energy 290 keV at different fluxes ranging from 45 × 1012 to 75 × 1015 ions/cm2. SEM analysis reveals the formation of nano/micro-sized irregular shaped cavities and pores for the various ion fluxes for varying numbers of laser pulses from 3000 to 9000. At the maximum ion flux for 12,000 pulses, distinct and organized grains with hexagonal and irregular shaped morphology are revealed. X-ray diffractometer (XRD) analysis exhibits that a new phase of CuSi (311) is identified which confirms the implantation of Si ions in brass substrate. A significant decrease in mechanical properties of implanted brass, such as Yield Stress (YS), Ultimate Tensile Strength (UTS), and hardness, with increasing laser pulses from 3000 to 6000 is observed. However, with increasing laser pulses from 9000 to a maximum value of 12,000, an increase in mechanical properties like hardness, YS, and UTS is observed. The generation as well as annihilation of defects, recrystallization, and intermixing of Si precipitates with brass matrix is considered to be responsible for variations in surface, structural, and mechanical modifications of brass.

  10. An ALE formulation of embedded boundary methods for tracking boundary layers in turbulent fluid-structure interaction problems

    NASA Astrophysics Data System (ADS)

    Farhat, Charbel; Lakshminarayan, Vinod K.

    2014-04-01

    Embedded Boundary Methods (EBMs) for Computational Fluid Dynamics (CFD) are usually constructed in the Eulerian set