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Sample records for diatomic molecular ions

  1. Studies on the full vibrational energy spectra for some electronic states of diatomic molecular ions XY+

    Institute of Scientific and Technical Information of China (English)

    LIU Yi-ding; SUN Wei-guo; REN Wei-yi

    2006-01-01

    The first accurate studies on the vibrational spectroscopic constants and the corresponding full vibrational energy spectra of some electronic states of diatomic molecular ions XY+ were performed using algebraic method(AM).The AM is applied on the X1Σ+ state of BeH+,the X2Σ+ state of CO+ , the X21-Π state of F2+ the A2Πu state of O2+ and theX2Σ+g Li2+.The results show that AM can generate accurate vibrational spectroscopic constants as well as accurate full vibrational energy spectra by using some accurate experimental vibrational energies,and that the AM vibrational energies are better than other theoretical data.

  2. Portable three-dimensional imaging for an explicit identification of the internal state of diatomic molecular ions

    Science.gov (United States)

    Andrianarijaona, V. M.; Alaime, C.; Fabre, B.; Vassantachart, A. K.; Jureta, J. J.; Urbain, X.

    2014-05-01

    A transportable experimental set-up was developed at the Université catholique de Louvain in Louvain-la-Neuve, Belgium to measure the internal energies of small diatomic molecular ions such as H2+.The technique, which scheme was first developed by D. P. de Bruijn and J. Los (Rev. Sci. Intstrum. 53, 1020, 1982) and included a resonant dissociative charge exchange with alkali atoms, consists in measuring the positions of the fragments and their flight time difference with two position sensitive detectors. The measured kinetic energy release is directly related to the original level of vibrational excitation of H2+.Details and applications will be presented. This research is supported by the Fund for Scientific Research - FNRS through IISN Grant No. 4.4504.10, and the National Science Foundation through Grant No. PHY-106887.

  3. Electronic states and wavefunctions of diatomic donor molecular ions in silicon: multi-valley envelope function theory.

    Science.gov (United States)

    Klymenko, M V; Remacle, F

    2014-02-12

    Using the Burt-Foreman envelope function theory and effective mass approximation, we develop a theoretical model for an arbitrary number of interacting donor atoms embedded in silicon which reproduces the electronic energy spectrum with high computational efficiency, taking into account the effective mass anisotropy and the valley-orbit coupling. We show that the variation of the relative magnitudes of the electronic coupling between the donor atoms with respect to the valley-orbit coupling as a function of the internuclear distance leads to different kinds of spatial interference patterns of the wavefunction. We also report on the impact of the orientation of the diatomic phosphorus donor molecular ion in the crystal lattice on the ionization energy and on the energy separation between the ground state and the lowest excited state.

  4. Molecular structure of diatomic lanthanide compounds

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The molecular constants of selected diatomic lanthanide compounds(LaH, LaO, LaF, EuH, EuO, EuF, EuS, GdO, GdF, GdH, YbH, YbO, YbF, YbS, LuH, LuO and LuF) have been calcu-lated by using relativistic small-core pseudopotentials and optimized(14s13p10d8f6g)/ [6s6p5d4f3g] valence basis sets. The results are in good agreement with available experimental data, with exception of YbO and LuF. The reasons for the discrepancies in case of YbO are due to a complicated mixing of configurations in the ground state, whereas in case of LuF the binding energy estimated by experimentalists appears to be too low.

  5. Molecular structure of diatomic lanthanide compounds

    Institute of Scientific and Technical Information of China (English)

    曹晓燕; 刘文剑; MichaelDolg

    2002-01-01

    The molecular constants of selected diatomic lanthanide compounds (LaH, LaO, LaF, EuH, EuO, EuF, EuS, GdO, GdF, GdH, YbH, YbO, YbF, YbS, LuH, LuO and LuF) have been calculated by using relativistic small-core pseudopotentials and optimized (14s13p10d8f6g)/ [6s6p5d4f3g] valence basis sets. The results are in good agreement with available experimental data, with exception of YbO and LuF. The reasons for the discrepancies in case of YbO are due to a complicated mixing of configurations in the ground state, whereas in case of LuF the binding energy estimated by experimentalists appears to be too low.

  6. Functionalized diatom silica microparticles for removal of mercury ions

    Directory of Open Access Journals (Sweden)

    Yang Yu, Jonas Addai-Mensah and Dusan Losic

    2012-01-01

    Full Text Available Diatom silica microparticles were chemically modified with self-assembled monolayers of 3-mercaptopropyl-trimethoxysilane (MPTMS, 3-aminopropyl-trimethoxysilane (APTES and n-(2-aminoethyl-3-aminopropyl-trimethoxysilane (AEAPTMS, and their application for the adsorption of mercury ions (Hg(II is demonstrated. Fourier transform infrared spectroscopy and x-ray photoelectron spectroscopy analyses revealed that the functional groups (–SH or –NH2 were successfully grafted onto the diatom silica surface. The kinetics and efficiency of Hg(II adsorption were markedly improved by the chemical functionalization of diatom microparticles. The relationship among the type of functional groups, pH and adsorption efficiency of mercury ions was established. The Hg(II adsorption reached equilibrium within 60 min with maximum adsorption capacities of 185.2, 131.7 and 169.5 mg g-1 for particles functionalized with MPTMS, APTES and AEAPTMS, respectively. The adsorption behavior followed a pseudo-second-order reaction model and Langmuirian isotherm. These results show that mercapto- or amino-functionalized diatom microparticles are promising natural, cost-effective and environmentally benign adsorbents suitable for the removal of mercury ions from aqueous solutions.

  7. Molecular Fossils as Time Indicators for the Evolution of Diatoms.

    Science.gov (United States)

    Rampen, S. W.; Schouten, S.; Muyzer, G.; Abbas, B.; Rowland, S. J.; Moldowan, M.; Sinninghe Damsté, J. S.

    2004-12-01

    Bacillariophyta (diatoms) are one of the most abundant divisions of phytoplankton, and contribute to almost 50% of the primary productivity of today's oceans. However, their ecological dominance is relatively young and little is known about the exact pace of their rapid evolution. DNA analyses on diatoms and the use of molecular clock calculations can help to reconstruct their evolution, but this molecular clock rate needs to be calibrated against the fossil record to determine the mutation rate. Until now, diatom silica skeletons have been used for reconstructing the evolution of diatoms, but their use is limited due to destruction by diagenesis. Molecular fossils may prove to be more useful for time reconstruction. To search for suitable compounds, we have analyzed both the lipid composition and 18S rRNA sequences of ca. 100 marine diatoms. This revealed that some specific phylogenetic clusters within the diatoms produce specific organic compounds, so-called diatom biomarkers. One group of diatom biomarkers are the C25 highly branched isoprenoid (HBI) alkenes (1,2). HBI biosynthesis evolved independently at least twice in the diatoms. The first group of HBI producers consists of the centric diatoms of the genus Rhizosolenia, the second group comprises pennate diatoms of the genera Haslea, Navicula and Pleurosigma. Based on the constructed phylogenetic tree it is likely that the HBI biosynthesis evolved first in the older group of centric diatoms (i.e. the Rhizosolenia genus). The fossil record was studied to determine the geological occurrence of C25 HBI alkenes, and this data set shows that HBI biosynthesis evolved ca. 91.5 My ago, so we can date the evolution of the genus Rizosolenia to ca. 91.5 My. With this information, we can now accurately predict the mutation rate of the 18S rDNA gene to 1% per 14.8 My for Rhizosolenia, which is substantially faster than the 1% per 18-26 My reported previously for diatoms in general. Another specific biomarker is 24

  8. The diatom molecular toolkit to handle nitrogen uptake.

    Science.gov (United States)

    Rogato, Alessandra; Amato, Alberto; Iudicone, Daniele; Chiurazzi, Maurizio; Ferrante, Maria Immacolata; d'Alcalà, Maurizio Ribera

    2015-12-01

    Nutrient concentrations in the oceans display significant temporal and spatial variability, which strongly affects growth, distribution and survival of phytoplankton. Nitrogen (N) in particular is often considered a limiting resource for prominent marine microalgae, such as diatoms. Diatoms possess a suite of N-related transporters and enzymes and utilize a variety of inorganic (e.g., nitrate, NO3(-); ammonium, NH4(+)) and organic (e.g., urea; amino acids) N sources for growth. However, the molecular mechanisms allowing diatoms to cope efficiently with N oscillations by controlling uptake capacities and signaling pathways involved in the perception of external and internal clues remain largely unknown. Data reported in the literature suggest that the regulation and the characteristic of the genes, and their products, involved in N metabolism are often diatom-specific, which correlates with the peculiar physiology of these organisms for what N utilization concerns. Our study reveals that diatoms host a larger suite of N transporters than one would expected for a unicellular organism, which may warrant flexible responses to variable conditions, possibly also correlated to the phases of life cycle of the cells. All this makes N transporters a crucial key to reveal the balance between proximate and ultimate factors in diatom life.

  9. Neural Network predictions of Diatomic and Triatomic Molecular Data

    Science.gov (United States)

    Blake Laing, W.

    1997-11-01

    The arrangement of molecules in periodic systems offers an enhanced comprehension of trends in molecular properties, a more efficient method of sorting and searching of molecular databases, and bases for the prediction of new data. Neural networks have the ability to "learn" existing data and to forecast a large amount of new data without a smoothing equation.(R. Hefferlin, B. Davis, W. B. Laing, "The Learning and Prediction of Triatomic Molecular Data with Neural Networks," International Arctic Seminar 1997, Murmansk, Russia)(J. Wohlers, W. B. Laing, R. Hefferlin, and B. Daivs, "Least-Squares and Neural-Network Forecasting from Citical Data: Diatomic Molecular Internuclear Separations and Triatomic Heats of Atomization and Ionization Potentials," Advances in Molecular Similarity: JIA book series, in press) This report will present periodic systems of molecules as well as neural network predictions for additional properties of diatomic and triatomic molecules.

  10. Stable Langmuir solitons in plasma with diatomic ions

    Directory of Open Access Journals (Sweden)

    M. Dvornikov

    2013-08-01

    Full Text Available We study stable axially and spherically symmetric spatial solitons in plasma with diatomic ions. The stability of a soliton against collapse is provided by the interaction of induced electric dipole moments of ions with the rapidly oscillating electric field of a plasmoid. We derive the new cubic-quintic nonlinear Schrödinger equation, which governs the soliton dynamics and numerically solve it. Then we discuss the possibility of implementation of such plasmoids in realistic atmospheric plasma. In particular, we suggest that spherically symmetric Langmuir solitons, described in the present work, can be excited at the formation stage of long-lived atmospheric plasma structures. The implication of our model for the interpretation of the results of experiments for the plasmoids generation is discussed.

  11. On the Born-Oppenheimer approximation of diatomic molecular resonances

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, André, E-mail: andre.martinez@unibo.it; Sordoni, Vania, E-mail: vania.sordoni@unibo.it [Dipartimento di Matematica, Università di Bologna, Piazza di Porta San Donato, 40127 Bologna (Italy)

    2015-10-15

    We give a new reduction of a general diatomic molecular Hamiltonian, without modifying it near the collision set of nuclei. The resulting effective Hamiltonian is the sum of a smooth semiclassical pseudodifferential operator (the semiclassical parameter being the inverse of the square-root of the nuclear mass) and a semibounded operator localised in the elliptic region corresponding to the nuclear collision set. We also study its behaviour on exponential weights and give several applications where molecular resonances appear and can be well located.

  12. Molecular basis of chromatic adaptation in pennate diatom Phaeodactylum tricornutum.

    Science.gov (United States)

    Herbstová, Miroslava; Bína, David; Koník, Peter; Gardian, Zdenko; Vácha, František; Litvín, Radek

    2015-01-01

    The remarkable adaptability of diatoms living in a highly variable environment assures their prominence among marine primary producers. The present study integrates biochemical, biophysical and genomic data to bring new insights into the molecular mechanism of chromatic adaptation of pennate diatoms in model species Phaeodactylum tricornutum, a marine eukaryote alga possessing the capability to shift its absorption up to ~700 nm as a consequence of incident light enhanced in the red component. Presence of these low energy spectral forms of Chl a is manifested by room temperature fluorescence emission maximum at 710 nm (F710). Here we report a successful isolation of the supramolecular protein complex emitting F710 and identify a member of the Fucoxanthin Chlorophyll a/c binding Protein family, Lhcf15, as its key building block. This red-shifted antenna complex of P. tricornutum appears to be functionally connected to photosystem II. Phylogenetic analyses do not support relation of Lhcf15 of P. tricornutum to other known red-shifted antenna proteins thus indicating a case of convergent evolutionary adaptation towards survival in shaded environments. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. An Investigation Into the Molecular and Isotopic Composition of Diatom Frustule-Bound Organic Matter: Method Development for New Proxies

    Science.gov (United States)

    Bridoux, M. C.; Ingalls, A. E.

    2009-12-01

    Diatoms are single cell phytoplankton that are ubiquitous in marine ecosystems and are responsible for up to 40% of the carbon fixed annually in the ocean. Their intricately nanopatterned siliceous frustules are formed under the control of template organic molecules, some of which are incorporated into the frustule during growth. Several diatom frustule-based paleoproxies have been developed to exploit these microfossils because they are from a known phytoplankton source that is relatively unaltered from diagenesis. Among these proxies, diatom frustule-bound organic matter (OM) is recognized as a potentially important material for use in paleoreconstructions of past productivity (13C/12C), nutrient utilization (15N/14N) as well as to determine the radiocarbon age of sedimentary frustules (Δ14C). Despite numerous advances, diatom frustule-bound OM remains poorly characterized. Here we focus on the chemical characterization of diatom frustule-bound OM with the goal of developing molecular and compound-specific isotope methods to better reconstruct the past environments of diatom rich regions such as the Southern Ocean and the North Pacific. To do this, we 1) chemically cleaned diatom frustules, 2) dissolve them in HF to release organic compounds embedded in the frustules and 3) unambiguously characterized this organic matter by ion pairing reversed phase liquid chromatography coupled to diode array, electrospray ionization - ion trap mass spectrometry (ESI/IT-MSn) and accurate mass quadrupole time of flight mass spectrometry (Q-TOF). These analyses reveal the presence of low molecular weight, UV light absorbing compounds called mycosporine-like amino acids (MAAs) and a series of long chain polyamines (LCPAs) consisting of N-methylated derivatives of polypropyleneimine units attached to putrescine. LCPAs are known to direct silicification, while MAAs are thought to provide sunscreen to many marine organisms. The presence of these specific biomarkers in sediment

  14. Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators

    Science.gov (United States)

    Sartori, E.; Brescaccin, L.; Serianni, G.

    2016-02-01

    Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production—detrimental for high current negative ion systems such as beam sources for fusion—are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient and energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.

  15. Comparative investigation of damage induced by diatomic and monoatomic ion implantation in silicon

    NARCIS (Netherlands)

    Lohner, T.; Toth, L.; Fried, M.; Khanh, N.Q.; Yang, Gen Qing; Lu, Lin Chen; Zou, Shichang; Hanekamp, L.J.; Silfhout, van A.; Gyulai, J.

    1994-01-01

    The damaging effect of mono- and diatomic phosphorus and arsenic ions implanted into silicon was investigated by spectroscopic ellipsometry (SE) and high-depth-resolution Rutherford backscattering and channeling techniques. A comparison was made between the two methods to check the capability of ell

  16. Molecular ion photofragment spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  17. Eigensolution techniques, their applications and the Fisher's information entropy of Tietz-Wei diatomic molecular potential

    CERN Document Server

    Falaye, B J; Ikhdair, S M; Hamzavi, M

    2014-01-01

    In this study, approximate analytical solution of Schr\\"odinger, Klein-Gordon and Dirac equations under the Tietz-Wei (TW) diatomic molecular potential are represented by using an approximation for the centrifugal term. We have applied three types of eigensolution techniques; the functional analysis approach (FAA), supersymmetry quantum mechanics (SUSYQM) and asymptotic iteration method (AIM) to solve Klein-Gordon Dirac and Schr\\"odinger equations, respectively. The energy eigenvalues and the corresponding eigenfunctions for these three wave equations are obtained and some numerical results and figures are reported. It has been shown that these techniques yielded exactly same results. some expectation values of the TW diatomic molecular potential within the framework of the Hellmann-Feynman theorem (HFT) have been presented. The probability distributions which characterize the quantum-mechanical states of TW diatomic molecular potential are analysed by means of complementary information measures of a probabil...

  18. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Science.gov (United States)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  19. Detection of silver nanoparticles inside marine diatom Thalassiosira pseudonana by electron microscopy and focused ion beam.

    Directory of Open Access Journals (Sweden)

    César Pascual García

    Full Text Available In the following article an electron/ion microscopy study will be presented which investigates the uptake of silver nanoparticles (AgNPs by the marine diatom Thalassiosira pseudonana, a primary producer aquatic species. This organism has a characteristic silica exoskeleton that may represent a barrier for the uptake of some chemical pollutants, including nanoparticles (NPs, but that presents a technical challenge when attempting to use electron-microscopy (EM methods to study NP uptake. Here we present a convenient method to detect the NPs interacting with the diatom cell. It is based on a fixation procedure involving critical point drying which, without prior slicing of the cell, allows its inspection using transmission electron microscopy. Employing a combination of electron and ion microscopy techniques to selectively cut the cell where the NPs were detected, we are able to demonstrate and visualize for the first time the presence of AgNPs inside the cell membrane.

  20. Rotational Laser Cooling of Vibrationally and Translationally Cold Molecular Ions

    DEFF Research Database (Denmark)

    Drewsen, Michael

    2011-01-01

    [7,8,9]. Furthermore, in order to learn more about the chemistry in interstellar clouds, astrochemists can benefit greatly from direct measurements on cold reactions in laboratories [9]. Working with MgH+ molecular ions in a linear Paul trap, we routinely cool their translational degree of freedom...... of a new technique for laser-induced rotational ground-state cooling of vibrationally and translationally cold MgH+ ions [10]. The scheme is based on excitation of a single rovibrational transition [11], and it should be generalizable to any diatomic polar molecular ion, given appropriate mid...

  1. Molecular fossils of diatoms. Applications in petroleum geochemistry and palaeoenvironmental studies

    Energy Technology Data Exchange (ETDEWEB)

    Rampen, S.W.

    2009-06-11

    Diatoms are one of the major groups of algae which originated relatively recently and evolved in the Late Jurassic/Cretaceous. This thesis presents the results of a comprehensive study of diatom lipids in cultures and in the environment and their applications in the age determination of petroleum and in palaeoenvironmental studies. Diatom DNA sequences were analyzed in order to relate the phylogenetic positions of diatoms to the lipid chemotaxonomy. Forty four different sterols were identified in diatoms, with 24-methylcholesta-5,24(28)-dien-3-beta-ol being most common. 24-Methylcholesta-5,22E-dien-3-beta-ol, previously described as a diatom biomarker, was only the fifth most common sterol and absent in some major diatom groups. All identified sterols have been reported in other algae, but within the diatoms, some sterols and sterol compositions seem to be specific for specific phylogenetic clusters. Sterol compositions confirmed the separate phylogenetic position of the genus Attheya, as also indicated by molecular phylogeny and microscopy. 23-Methyl and 23,24-dimethyl sterols, often associated with dinoflagellate algae, were present in a substantial number of diatoms, suggesting that diatoms may also be a major source. Their phylogenetic position suggests that these diatoms originated from a single common ancestor which evolved in the late Jurassic. In addition to 23-methyl and 23,24-dimethyl sterols, the unusual sterol gorgosterol was found in two diatom cultures of the genus Delphineis. 24-Norsterols were found in the diatom species Thalassiosira aff. antarctica and in dinoflagellate cultures. The evolutionary history of dinoflagellates and diatoms explains the stepwise increases of 24-norsterane concentrations, diagenetic products of 24-norsterols, in petroleum. Long-chain 1,14-diols and 12-hydroxy methyl alkanoates were detected in Proboscia diatoms and may be used as indicators for high-nutrient conditions and upwelling. Their distributions varied between

  2. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    Directory of Open Access Journals (Sweden)

    Lucia Cimarelli

    2015-05-01

    Full Text Available Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a and silicic acid transporter (SIT, as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  3. Energy of one-dimensional diatomic elastic granular gas: Theory and molecular dynamics Simulation

    CERN Document Server

    Khotimah, Siti Nurul; Widayani,; Waris, Abdul

    2011-01-01

    One-dimensional ideal diatomic gas is simulated through possible types of motion of a molecule. Energy of each type of its motion is calculated from theory and numerical method. Calculation of kinetic energy of an atom in translational-vibrational motion is not analytically simple, but it can be solved by numerical method of molecular dynamic simulation. This paper justifies that kinetic energy of a diatomic molecule can be determined by two different approaches. The first is the sum of kinetic energy of each atom and second is the sum of kinetic energy of translational motion and vibrational motion.

  4. Laboratory Rotational Spectroscopy of the Interstellar Diatomic Hydride Ion SH+ (X 3Σ-)

    Science.gov (United States)

    Halfen, DeWayne; Ziurys, Lucy M.

    2016-06-01

    Diatomic hydride are among the most common molecular species in the interstellar medium (ISM). The low molecular mass and thus moments of inertia cause their rotational spectra to lie principally in the submillimeter and far-infrared regions. Diatomic hydrides, both neutral (MH) and ionic (MH+) forms, are also basic building blocks of interstellar chemistry. In ionic form, they may be the “hidden” carriers of refractory elements in dense gas. They are therefore extremely good targets for space-borne and airborne platforms such as Herschel, SOFIA, and SAFIR. However, in order to detect these species in the ISM, their rotational spectra must first be measured in the laboratory. To date, there is very little high resolution data available for many hydride species, in particular the ionic form. Using submillimeter/THz direct absorption methods in the Ziurys laboratory, spectra of the interstellar diatomic hydride SH+ (X 3Σ-) have been recorded. Recent work has concerned measurement of all three fine structure components of the fundamental rotational transition N = 1 ← 0 in the range 345 - 683 GHz. SH+ was generated from H2S and argon in an AC discharge. The data have been analyzed, and spectroscopic constants for this species have been refined. SH+ is found in Photon Dominated Regions (PDRs) and X-ray Dominated Regions (XDRs) and is thought to trace energetic processes in the ISM. These current measurements confirm recent observations of this species at submillimeter/THz wavelengths with ALMA and other ground-based telescopes.

  5. An integrated analysis of molecular acclimation to high light in the marine diatom Phaeodactylum tricornutum.

    Directory of Open Access Journals (Sweden)

    Marianne Nymark

    Full Text Available Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to acclimate their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL, after which the cultures were transferred to high light (HL. Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0-0.5 h, an intermediate acclimation phase (3-12 h and a late acclimation phase (12-48 h. The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiance have been identified.

  6. Effect of diatomic molecular properties on binary laser pulse optimizations of quantum gate operations.

    Science.gov (United States)

    Zaari, Ryan R; Brown, Alex

    2011-07-28

    The importance of the ro-vibrational state energies on the ability to produce high fidelity binary shaped laser pulses for quantum logic gates is investigated. The single frequency 2-qubit ACNOT(1) and double frequency 2-qubit NOT(2) quantum gates are used as test cases to examine this behaviour. A range of diatomics is sampled. The laser pulses are optimized using a genetic algorithm for binary (two amplitude and two phase parameter) variation on a discretized frequency spectrum. The resulting trends in the fidelities were attributed to the intrinsic molecular properties and not the choice of method: a discretized frequency spectrum with genetic algorithm optimization. This is verified by using other common laser pulse optimization methods (including iterative optimal control theory), which result in the same qualitative trends in fidelity. The results differ from other studies that used vibrational state energies only. Moreover, appropriate choice of diatomic (relative ro-vibrational state arrangement) is critical for producing high fidelity optimized quantum logic gates. It is also suggested that global phase alignment imposes a significant restriction on obtaining high fidelity regions within the parameter search space. Overall, this indicates a complexity in the ability to provide appropriate binary laser pulse control of diatomics for molecular quantum computing.

  7. An integrated analysis of molecular acclimation to high light in the marine diatom Phaeodactylum tricornutum

    DEFF Research Database (Denmark)

    Nymark, Marianne; Valle, Kristin C; Brembu, Tore

    2009-01-01

    Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to acclimate their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate...... phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites...... occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show...

  8. Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.

    Science.gov (United States)

    Apothéloz-Perret-Gentil, Laure; Cordonier, Arielle; Straub, François; Iseli, Jennifer; Esling, Philippe; Pawlowski, Jan

    2017-03-14

    Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy-free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy-free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under-sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy-free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost-effective assessment of the biological quality of watercourses.

  9. Quantum logic with molecular ions

    CERN Document Server

    Wolf, Fabian; Heip, Jan C; Gebert, Florian; Shi, Chunyan; Schmidt, Piet O

    2015-01-01

    Laser spectroscopy of cold and trapped molecular ions is a powerful tool for fundamental physics, including the determination of fundamental constants, the laboratory test for their possible variation, and the search for a possible electric dipole moment of the electron. Optical clocks based on molecular ions sensitive to some of these effects are expected to achieve uncertainties approaching the $10^{-18}$ level. While the complexity of molecular structure facilitates these applications, the absence of cycling transitions poses a challenge for direct laser cooling, quantum state control, and detection. Previously employed state detection techniques based on photo-dissociation or chemical reactions are destructive and therefore inefficient. Here we experimentally demonstrate non-destructive state detection of a single trapped molecular ion through its strong Coulomb coupling to a well-controlled co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force(ODF) changes the internal state...

  10. Rotational Laser Cooling of Vibrationally and Translationally Cold Molecular Ions

    DEFF Research Database (Denmark)

    Drewsen, Michael

    2011-01-01

    by sympathetic cooling with Doppler laser cooled Mg+ ions. Giving the time for the molecules to equilibrate internally to the room temperature blackbody radiation, the vibrational degree of freedom will freeze out, leaving only the rotational degree of freedom to be cooled. We report here on the implementation...... of a new technique for laser-induced rotational ground-state cooling of vibrationally and translationally cold MgH+ ions [10]. The scheme is based on excitation of a single rovibrational transition [11], and it should be generalizable to any diatomic polar molecular ion, given appropriate mid......-infrared laser sources such as a quantum cascade laser are available. In recent experiments, a nearly 15-fold increase in the rotational ground-state population was obtained, with the resulting ground-state population of 36,7±1,2 %, equivalent to that of a thermal distribution at about 20 K. The obtained cooling...

  11. Molecular Response to Toxic Diatom-Derived Aldehydes in the Sea Urchin Paracentrotus lividus

    Directory of Open Access Journals (Sweden)

    Stefano Varrella

    2014-04-01

    Full Text Available Diatoms are dominant photosynthetic organisms in the world’s oceans and represent a major food source for zooplankton and benthic filter-feeders. However, their beneficial role in sustaining marine food webs has been challenged after the discovery that they produce secondary metabolites, such as polyunsaturated aldehydes (PUAs, which negatively affect the reproductive success of many invertebrates. Here, we report the effects of two common diatom PUAs, heptadienal and octadienal, which have never been tested before at the molecular level, using the sea urchin, Paracentrotus lividus, as a model organism. We show that both PUAs are able to induce teratogenesis (i.e., malformations, as already reported for decadienal, the better-studied PUA of this group. Moreover, post-recovery experiments show that embryos can recover after treatment with all three PUAs, indicating that negative effects depend both on PUA concentrations and the exposure time of the embryos to these metabolites. We also identify the time range during which PUAs exert the greatest effect on sea urchin embryogenesis. Finally, we report the expression levels of thirty one genes (having a key role in a broad range of functional responses, such as stress, development, differentiation, skeletogenesis and detoxification processes in order to identify the common targets affected by PUAs and their correlation with morphological abnormalities. This study opens new perspectives for understanding how marine organisms afford protection from environmental toxicants through an integrated network of genes.

  12. Molecular Response to Toxic Diatom-Derived Aldehydes in the Sea Urchin Paracentrotus lividus

    Science.gov (United States)

    Varrella, Stefano; Romano, Giovanna; Ianora, Adrianna; Bentley, Matt G.; Ruocco, Nadia; Costantini, Maria

    2014-01-01

    Diatoms are dominant photosynthetic organisms in the world’s oceans and represent a major food source for zooplankton and benthic filter-feeders. However, their beneficial role in sustaining marine food webs has been challenged after the discovery that they produce secondary metabolites, such as polyunsaturated aldehydes (PUAs), which negatively affect the reproductive success of many invertebrates. Here, we report the effects of two common diatom PUAs, heptadienal and octadienal, which have never been tested before at the molecular level, using the sea urchin, Paracentrotus lividus, as a model organism. We show that both PUAs are able to induce teratogenesis (i.e., malformations), as already reported for decadienal, the better-studied PUA of this group. Moreover, post-recovery experiments show that embryos can recover after treatment with all three PUAs, indicating that negative effects depend both on PUA concentrations and the exposure time of the embryos to these metabolites. We also identify the time range during which PUAs exert the greatest effect on sea urchin embryogenesis. Finally, we report the expression levels of thirty one genes (having a key role in a broad range of functional responses, such as stress, development, differentiation, skeletogenesis and detoxification processes) in order to identify the common targets affected by PUAs and their correlation with morphological abnormalities. This study opens new perspectives for understanding how marine organisms afford protection from environmental toxicants through an integrated network of genes. PMID:24714125

  13. Molecular fossils of diatoms : Applications in petroleum geochemistry and palaeoenvironmental studies

    NARCIS (Netherlands)

    Rampen, S.W.|info:eu-repo/dai/nl/330221574

    2009-01-01

    Diatoms are one of the major groups of algae which originated relatively recently and evolved in the Late Jurassic/Cretaceous. This thesis presents the results of a comprehensive study of diatom lipids in cultures and in the environment and their applications in the age determination of petroleum an

  14. Molecular fossils of diatoms: Applications in petroleum geochemistry and palaeoenvironmental studies

    NARCIS (Netherlands)

    Rampen, S.W.

    2009-01-01

    Diatoms are one of the major groups of algae which originated relatively recently and evolved in the Late Jurassic/Cretaceous. This thesis presents the results of a comprehensive study of diatom lipids in cultures and in the environment and their applications in the age determination of petroleum an

  15. Photodissociation of Trapped Rb2+: Implications for Simultaneous Trapping of Atoms and Molecular Ions

    Science.gov (United States)

    Jyothi, S.; Ray, Tridib; Dutta, Sourav; Allouche, A. R.; Vexiau, Romain; Dulieu, Olivier; Rangwala, S. A.

    2016-11-01

    The direct photodissociation of trapped 85Rb2+ (rubidium) molecular ions by the cooling light for the 85Rb magneto-optical trap (MOT) is studied, both experimentally and theoretically. Vibrationally excited Rb2+ ions are created by photoionization of Rb2 molecules formed photoassociatively in the Rb MOT and are trapped in a modified spherical Paul trap. The decay rate of the trapped Rb2+ ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is observed. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  16. Photodissociation of trapped Rb$^+_2$ : Implications for hybrid molecular ion-atom trapping

    CERN Document Server

    Jyothi, S; Dutta, Sourav; Allouche, A R; Vexiau, Romain; Dulieu, Olivier; Rangwala, S A

    2016-01-01

    We observe direct photodissociation of trapped $^{85}$Rb$_2^+$ molecular ions in the presence of cooling light for the $^{85}$Rb magneto optical trap (MOT). Vibrationally excited Rb$_{2}^{+}$ ions are created by photoionization of Rb$_{2}$ molecules formed photoassociatively in the rubidium (Rb) MOT and are trapped in a modified spherical Paul trap co-centric with the MOT. The decay rate of the trapped Rb$_{2}^{+}$ ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is established. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  17. Eigensolution techniques, their applications and Fisherʼs information entropy of the Tietz-Wei diatomic molecular model

    Science.gov (United States)

    Falaye, B. J.; Oyewumi, K. J.; Ikhdair, S. M.; Hamzavi, M.

    2014-11-01

    In this study, the approximate analytical solutions of Schrödinger, Klein-Gordon and Dirac equations under the Tietz-Wei (TW) diatomic molecular potential are represented by using an approximation for the centrifugal term. We have applied three types of eigensolution techniques: the functional analysis approach, supersymmetry quantum mechanics and the asymptotic iteration method to solve the Klein-Gordon, Dirac and Schrödinger equations, respectively. The energy eigenvalues and the corresponding eigenfunctions for these three wave equations are obtained, and some numerical results and figures are reported. It has been shown that these techniques yielded exactly the same results. some expectation values of the TW diatomic molecular potential within the framework of the Hellmann-Feynman theorem have been presented. The probability distributions that characterize the quantum mechanical states of TW diatomic molecular potential are analyzed by means of complementary information measures of a probability distribution called Fisher's information entropy. This distribution has been described in terms of Jacobi polynomials, whose characteristics are controlled by quantum numbers.

  18. Energy and angular distributions of electron emission from diatomic molecules by bare ion impact

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, A.; Mandal, C.R.; Purkait, M., E-mail: mpurkait_2007@rediffmail.com

    2015-06-15

    The three-Coulomb wave model has been used extensively to study the energy and angular distributions of double-differential cross sections (DDCS) of electron emissions from hydrogen and nitrogen molecules by bare ion impact at intermediate and high energies. In the present model, we have expressed the molecular triple differential cross section in terms of the corresponding atomic triple differential cross section multiplied by the occupation number and the average Rayleigh interference factor, which accounts for the two-center interference effect. Here we have used an active electron approximation of the molecule as a whole in the initial channel. To account for the effect of passive electrons, we have constructed a model potential that satisfies the initial conditions and the corresponding wavefunction has been calculated from the model Hamiltonian of the active electron in the target. In the final channel, we have used a hydrogenic model with an effective nuclear charge that is calculated from its binding energy. In this model, the correlated motion of the particles in the exit channel of the reaction is considered by an adequate product of three-Coulomb functions. The emitted electron, the incident projectile ion and the residual ion are considered to be in same plane. The obtained results are compared with other recent theoretical and experimental findings. There is an overall agreement of the calculations with the experimental data for electron emission cross sections.

  19. Cold molecular ions on a chip

    CERN Document Server

    Mokhberi, A

    2014-01-01

    We report the sympathetic cooling and Coulomb crystallization of molecular ions above the surface of an ion-trap chip. N$_2^+$ and CaH$^+$ ions were confined in a surface-electrode radiofrequency ion trap and cooled by the interaction with laser-cooled Ca$^{+}$ ions to secular translational temperatures in the millikelvin range. The configuration of trapping potentials generated by the surface electrodes enabled the formation of planar bicomponent Coulomb crystals and the spatial separation of the molecular from the atomic ions on the chip. The structural and thermal properties of the Coulomb crystals were characterized using molecular dynamics simulations. The present study extends chip-based trapping techniques to Coulomb-crystallized molecular ions with potential applications in mass spectrometry, cold chemistry, quantum information science and spectroscopy.

  20. Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis

    Directory of Open Access Journals (Sweden)

    Valentin Stonik

    2015-06-01

    Full Text Available Diatoms are abundant and important biological components of the marine environment that biosynthesize diverse natural products. These microalgae are rich in various lipids, carotenoids, sterols and isoprenoids, some of them containing toxins and other metabolites. Several groups of diatom natural products have attracted great interest due to their potential practical application as energy sources (biofuel, valuable food constituents, and prospective materials for nanotechnology. In addition, hydrocarbons, which are used in climate reconstruction, polyamines which participate in biomineralization, new apoptotic agents against tumor cells, attractants and deterrents that regulate the biochemical communications between marine species in seawaters have also been isolated from diatoms. However, chemical studies on these microalgae are complicated by difficulties, connected with obtaining their biomass, and the influence of nutrients and contaminators in their environment as well as by seasonal and climatic factors on the biosynthesis of the corresponding natural products. Overall, the number of chemically studied diatoms is lower than that of other algae, but further studies, particularly those connected with improvements in the isolation and structure elucidation technique as well as the genomics of diatoms, promise both to increase the number of studied species with isolated biologically active natural products and to provide a clearer perception of their biosynthesis.

  1. Molecular dynamical studies of the dissociation of a diatomic molecular crystal. II. Equilibrium kinetics

    Science.gov (United States)

    Trevino, S. F.; Tsai, D. H.

    1984-07-01

    The properties of a molecular dynamical model undergoing equilibrium chemical reactions are reported. It is shown that the kinetics of the modeled reaction is consistent with established thermodynamic considerations. Further, at constant pressure, the relation between the Arrhenius energy of reaction ΔE, the potential energy change upon dissociation Δɛ, and the work done due to the volume change PΔV, viz, -ΔE=-(Δɛ+PΔV), is satisfied.

  2. Molecular phylogeny of Amphora sensu lato (Bacillariophyta): an investigation into the monophyly and classification of the amphoroid diatoms.

    Science.gov (United States)

    Stepanek, Joshua G; Kociolek, J Patrick

    2014-03-01

    Amphora sensu lato encompasses a large group of raphid diatoms, diverse in both form and ecology. The defining feature of this group has been an extreme asymmetry of the valve mantle and girdle bands, bringing both faces of the cell onto a single plane. Although this 'amphoroid' structure has long been the diagnostic feature and thus considered 'conservative' for the group, many have argued that the diversity of forms presently assigned to Amphora likely does not represent a monophyletic group. With the exception of several taxonomic transfers and the recent elevation of Halamphora to the level of genus, much of Amphora classification has remained unchanged for over 100 years. This study presents a phylogenetic analysis of Amphora s.l. based on a concatenated molecular alignment including the nuclear marker SSU rDNA and the chloroplast markers rbcL and psbC. These results are discussed within the framework of the current classification system of Amphora and Halamphora and lay the groundwork for a taxonomic revision of the group based on monophyly. The results of this analysis demonstrate that the genus Amphora is polyphyletic and that lineages assigned to the genus are distributed widely across the raphid diatom tree of life. The feature of amphoroid symmetry appears to have evolved independently several times. We discuss the nature of conservative characters in the raphid diatoms and their usefulness as a guide to phylogenetic relationships.

  3. Molecular dynamical studies of the dissociation of a diatomic molecular crystal. I. Energy exchange in rapid exothermic reactions

    Science.gov (United States)

    Tsai, D. H.; Trevino, S. F.

    1983-08-01

    We discuss the results of a study of the exothermic dissociation of a model diatomic molecular crystal. Our main purpose is to investigate the dynamics of energy transport and energy sharing in this system during the dissociation process. The crystal was prepared in a metastable molecular form, in thermal equilibrium at a low initial temperature and pressure. When we heated the system to a higher temperature, at constant volume, we observed thermally initiated dissociations which progressed rapidly to completion. During the dissociation process, we found that the sharing of the potential energy released by the metastable molecules with the rest of the system, and the sharing of the kinetic energy of the dissociated fragments with the kinetic energy of the molecules in the translational degrees of freedom, were rather efficient. But the intra- and intermolecular exchange of the kinetic energy among the various degrees of freedom, viz., translation-rotation, translation-vibration, and rotation-vibration was inefficient. Dissociation would occur in one of the regions of high local kinetic energy density, after a molecule in that region had acquired sufficient vibrational energy to break apart, and when the ``caging'' effect was favorable to allow the molecule to dissociate. From such a reaction site, and there may be others, the reaction would spread to a neighboring site, and continue this way until all the molecules became dissociated. The induction time showed an approximately logarithmic dependence on the inverse of the temperature of the system after heating. But during the process of rapid dissociation, both the potential energy and the kinetic energy of the system underwent rapid changes, and thermal equilibrium was not reached until the end of the process.

  4. Molecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle- and energy-resolved photoelectron spectroscopy. I. Formalism

    Science.gov (United States)

    Park, Hongkun; Zare, Richard N.

    1996-03-01

    A theoretical formalism is developed for the quantum-state-specific photoelectron angular distributions (PADs) from the direct photoionization of a diatomic molecule in which both the ionizing state and the state of the ion follow Hund's case (b) coupling. The formalism is based on the molecular-orbital decomposition of the ionization continuum and therefore fully incorporates the molecular nature of the photoelectron-ion scattering within the independent electron approximation. The resulting expression for the quantum-state-specific PADs is dependent on two distinct types of dynamical quantities, one that pertains only to the ionization continuum and the other that depends both on the ionizing state and the ionization continuum. Specifically, the electronic dipole-moment matrix element rlλ exp(iηlλ) for the ejection of a photoelectron with orbital angular momentum quantum number l making a projection λ on the internuclear axis is expressed as ΣαλŪlαλλ exp (iπτ¯αλλ) Mαλλ, where Ūλ is the electronic transformation matrix, τ¯αλλ is the scattering phase shift associated with the αλth continuum molecular orbital, and Mαλλ is the real electronic dipole-moment matrix element that connects the ionizing orbital to the αλth continuum molecular orbital. Because Ūλ and τ¯αλλ depend only on the dynamics in the ionization continuum, this formalism allows maximal exploitation of the commonality between photoionization processes from different ionizing states. It also makes possible the direct experimental investigation of scattering matrices for the photoelectron-ion scattering and thus the dynamics in the ionization continuum by studying the quantum-state-specific PADs, as illustrated in the companion article on the photoionization of NO.

  5. Peltier Refrigerators for Molecular Ion Sources

    Science.gov (United States)

    Hershcovitch, Ady

    2008-11-01

    Molecular ion sources have been considered for various applications. In particular, there is considerable effort to develop decaborane and octadecaborane ion sources for the semiconductor industry. Since the invention of the transistor, the trend has been to miniaturize semiconductor devices. As semiconductors become smaller (and get miniaturized), ion energy needed for implantation decreases, since shallow implantation is desired. But, due to space charge (intra-ion repulsion) effects, forming and transporting ion beams becomes a rather difficult task. These problems associated with lower energy ion beams limit implanter ion currents, thus leading to low production rates. One way to tackle the space charge problem is to use singly charged molecular ions. A crucial aspect in generating large molecular ion beam currents is ion source temperature control. Peltier coolers, which have in the past successfully utilized in BaF2 and CSI gamma ray detectors, may be ideal for this application. Clogging prevention of molecular ion sources is also a hurdle, which was overcome with special slots. Both topics are to be presented.

  6. Infrared spectroscopy of weakly bound molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, Lisa I-Ching

    1988-11-01

    The infrared spectra of a series of hydrated hydronium cluster ions and of protonated ethane ion are presented. A tandem mass spectrometer is ideally suited to obtaining the spectra of such weakly bound molecular ions. Traditional absorption spectroscopy is not feasible in these situations, so the techniques described in this thesis make use of some consequence of photon absorption with higher sensitivity than simply attenuation of laser power. That consequence is dissociation. By first mass selecting the parent ion under study and then mass selecting the fragment ion formed from dissociation, the near unit detection efficiency of ion counting methods has been used to full advantage.

  7. Molecular ion sources for low energy semiconductor ion implantation (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Hershcovitch, A., E-mail: hershcovitch@bnl.gov [Brookhaven National Laboratory, Upton, New York 11973 (United States); Gushenets, V. I.; Bugaev, A. S.; Oks, E. M.; Vizir, A.; Yushkov, G. Yu. [High Current Electronics Institute, Siberian Branch of Russian Academy of Sciences, Tomsk 634055 (Russian Federation); Seleznev, D. N.; Kulevoy, T. V.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S. [Institute for Theoretical and Experimental Physics, Moscow 117218 (Russian Federation); Dugin, S.; Alexeyenko, O. [State Scientific Center of the Russian Federation State Research Institute for Chemistry and Technology of Organoelement Compounds, Moscow (Russian Federation)

    2016-02-15

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C{sub 4}H{sub 12}B{sub 10}O{sub 4}) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH{sub 3} = P{sub 4} + 6H{sub 2}; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P{sub 4}{sup +} ion beams were extracted. Results from devices and some additional concepts are described.

  8. Magnetic molecular materials with paramagnetic lanthanide ions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The diverse magnetic properties of lanthanide-based magnetic molecular materials are introduced in the following organization.First,the general aspects of magnetic molecular materials and electronic states of lanthanide ions are introduced.Then the structures and magnetic properties are described and analyzed for molecules with one lanthanide ion,4f-4f,4f-3d and 4f-p magnetic coupling interactions.In each section,magnetic coupling,magnetic ordering and magnetic relaxation phenomenon are briefly reviewed using some examples.Finally,some possibilities of developing magnetic molecular materials containing lanthanide ions are discussed in the outlook part.

  9. Design of optimal laser pulses to control molecular rovibrational excitation in a heteronuclear diatomic molecule

    Indian Academy of Sciences (India)

    Sitansh Sharma; Gabriel G Balint-Kurti; Harjinder Singh

    2012-01-01

    Optimal control theory in combination with time-dependent quantum dynamics is employed to design laser pulses which can perform selective vibrational and rotational excitations in a heteronuclear diatomic system. We have applied the conjugate gradient method for the constrained optimization of a suitably designed functional incorporating the desired objectives and constraints. Laser pulses designed for several excitation processes of the molecule were able to achieve predefined dynamical goals with almost 100% yield.

  10. Quantum State Control of Trapped Atomic and Molecular Ions

    Science.gov (United States)

    Seck, Christopher M.

    Full quantum control of a molecule would have a significant impact in molecular coherent control (alignment and orientation) and ultracold and quantum chemistry, quantum computing and simulation as well as hybrid quantum devices, and precision spectroscopy of importance to fundamental physics research. Precision spectroscopy of even simple diatomic molecules offers the possibility of uncovering physics beyond the standard model, specifically time variation of the proton-to-electron mass ratio, which is currently constrained by astronomical molecular observations at the 10-16 1/yr level and laboratory atomic measurements at the 10-17 1/yr level. To achieve this level of measurement and to avoid the complications of diatomic structure on traditional spectroscopy methods, molecular quantum logic spectroscopy (mQLS) will be the spectroscopy technique of choice. We discuss development of in-house external-cavity diode laser (ECDL) systems and improvements to the Libbrecht-Hall circuit, which is a well-known, low-noise current driver for narrow-linewidth diode lasers. However, as the current approaches the maximum set limit, the noise in the laser current increases dramatically. This behavior is documented and simple circuit modifications to alleviate this issue are explored. We cool trapped AlH+ molecules to their ground rotational-vibrational quantum state using an electronically-exciting broadband laser to simultaneously drive cooling resonances from many different rotational levels. We demonstrate rotational cooling on the 140(20) ms timescale from room temperature to 3.8 K, with the ground state population increasing from 3% to 95.4%. Since QLS does not require the high gate fidelities usually associated with quantum computation and quantum simulation, it is possible to make simplifying choices in ion species and quantum protocols at the expense of some fidelity. We demonstrate sideband cooling and motional state detection protocols for 138Ba+ of sufficient fidelity

  11. Photosynthetic and molecular responses of the marine diatom Thalassiosira pseudonana to triphenyltin exposure

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Andy Xianliang; Leung, Priscilla T.Y.; Leung, Kenneth M.Y., E-mail: kmyleung@hku.hk

    2014-09-15

    This study aimed to investigate the responses of the marine diatom Thalassiosira pseudonana upon waterborne exposure to triphenyltin chloride (TPTCl) through determining their photosynthetic response, growth performance, and expressions of genes and proteins. Based on the growth inhibition test, the 96-h IC{sub 50} (i.e., median inhibition concentration) was found to be 1.09 μg/L (95% confidence interval (CI): 0.89–1.34 μg/L). According to photosynthetic parameters, the 96-h EC{sub 50}s (i.e., median effect concentrations) were estimated at 1.54 μg/L (95% CI: 1.40–1.69 μg/L) and 1.51 μg/L (95% CI: 1.44–1.58 μg/L) for the maximum quantum yield of photosystem II (PSII) photochemistry (Φ{sub Po}) and the effective quantum yield of photochemical energy conversion in PSII (Φ{sub 2}), respectively. Non-photochemical quenching in the algae was increased at low concentrations of TPTCl (0.5–1.0 μg/L) but it decreased gradually when the TPTCl concentration further increased from 1.0 to 2.5 μg/L. Results of gene expressions showed that lipid metabolism related genes were not influenced by TPTCl at 0.5 or 1.0 μg/L, while silica shell formation genes were down-regulated at 0.5 μg/L. Photosynthesis related genes were up-regulated at 0.5 μg/L TPTCl but were down-regulated at 1.0 μg/L TPTCl. Proteomics analysis revealed that relatively less proteins could be detected after exposure to 1.0 μg/L TPTCl (only about 50–60 spots) compared with that observed in the 0.5 μg/L TPTCl treatment and two control groups (each with about 290–300 protein spots). At 0.5 μg/L TPTCl, five proteins were differentially expressed when compared with the seawater control and solvent control, and most of these proteins are involved in defence function to protect the biological systems from reactive oxygen species that generated by TPTCl. These proteins include oxygen-evolving enhancer protein 1 precursor, fucoxanthin chlorophyll a/c protein – LI818 clade, and mitochondrial

  12. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    Energy Technology Data Exchange (ETDEWEB)

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

  13. Fragmentation of metastable molecular ions of acetylanisoles

    Science.gov (United States)

    Sekiguchi, Osamu; Noguchi, Tsutomu; Ogino, Kazuo; Tajima, Susumu

    1994-04-01

    The spontaneous unimolecular dissociation reactions of the molecular ions of ortho-, meta- and para-acetylanisoles have been investigated by mass-analyzed ion kinetic energy spectrometry, high resolution mass spectrometry and deuterium labelling. Losses of CH3. from the molecular ions of all isomers occur exclusively from the acetyl group. The loss of CH3. for the o-isomer consists of two processes, i.e. one of them is a simple cleavage, and the other is a rearrangement. The latter is not observed for the m- and p-isomers. The loss of H2O from the molecular ion is also unique for the o-isomer, and the fragmentation mechanism is also explored.

  14. Carbon-based ion and molecular channels

    Science.gov (United States)

    Sint, Kyaw; Wang, Boyang; Kral, Petr

    2008-03-01

    We design ion and molecular channels based on layered carboneous materials, with chemically-functionalized pore entrances. Our molecular dynamics simulations demonstrate that these ultra-narrow pores, with diameters around 1 nm, are highly selective to the charges and sizes of the passing (Na^+ and Cl^-) ions and short alkanes. We demonstrate that the molecular flows through these pores can be easily controlled by electrical and mechanical means. These artificial pores could be integrated in fluidic nanodevices and lab-on-a-chip techniques with numerous potential applications. [1] Kyaw Sint, Boyang Wang and Petr Kral, submitted. [2] Boyang Wang and Petr Kral, JACS 128, 15984 (2006).

  15. Atomic hydrogen and diatomic titanium-monoxide molecular spectroscopy in laser-induced plasma

    Science.gov (United States)

    Parigger, Christian G.; Woods, Alexander C.

    2017-03-01

    This article gives a brief review of experimental studies of hydrogen Balmer series emission spectra. Ongoing research aims to evaluate early plasma evolution following optical breakdown in laboratory air. Of interest is as well laser ablation of metallic titanium and characterization of plasma evolution. Emission of titanium monoxide is discussed together with modeling of diatomic spectra to infer temperature. The behavior of titanium particles in plasma draws research interests ranging from the modeling of stellar atmospheres to the enhancement of thin film production via pulsed laser deposition.

  16. Chemical Dynamics of State-Selected Atomic and Diatomic Ions of Aerospace Relevance

    Science.gov (United States)

    2008-11-01

    modified the triple - quadrupole -double-octopole y<t&te Cy» LJMW • • Figure 1. Schematic diagram of the comprehensive VUV laser system, which...H. Xu, and C. Y. Ng, "The Study of State-Selected Ion-Molecule Reactions using the Pulsed-Field Ionization- Photoion Technique ", J. Chem. Phys...8217==0-4) + He collisions in the ET range of 0-3 eV have also been measured using the VUV-photoionization-guided-ion beam mass spectrometric technique

  17. Photoelectron momentum distributions of the hydrogen molecular ion driven by multicycle near-infrared laser pulses

    Science.gov (United States)

    Murakami, Mitsuko; Chu, Shih-I.

    2016-10-01

    The photoelectron momentum distributions (PMDs) of the hydrogen molecular ion H2+ driven by strong near-infrared laser pulses are studied based on the ab initio numerical solution of the time-dependent Schrödinger equation and the Volkov wave propagation. Both linear and circular polarization are considered, in accordance with the recent experiment by M. Odenweller et al. [Phys. Rev. A 89, 013424 (2014), 10.1103/PhysRevA.89.013424]. We will discuss the difference between the molecular (diatomic) and the atomic PMDs and the effect of molecular potential to the photoelectron energy. In particular, we demonstrate that the above-threshold ionization spectra of H2+ could upshift their energy when driven by a linearly polarized laser field parallel to the molecular axis.

  18. Mean excitation energies for molecular ions

    DEFF Research Database (Denmark)

    Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens;

    2017-01-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase...... with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state...... contributing to the mean excitation energy....

  19. Mean excitation energies for molecular ions

    Science.gov (United States)

    Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens; Sabin, John R.

    2017-03-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

  20. Mean excitation energies for molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Phillip W.K.; Sauer, Stephan P.A. [Department of Chemistry, University of Copenhagen, Copenhagen (Denmark); Oddershede, Jens [Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense (Denmark); Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, FL (United States); Sabin, John R., E-mail: sabin@qtp.ufl.edu [Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense (Denmark); Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, FL (United States)

    2017-03-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

  1. Collisions of antiprotons with hydrogen molecular ions

    DEFF Research Database (Denmark)

    Lühr, Armin Christian; Saenz, Alejandro

    2009-01-01

    Time-dependent close-coupling calculations of the ionization and excitation cross section for antiproton collisions with molecular hydrogen ions are performed in an impact energy range from 0.5 keV to 10 MeV. The Born-Oppenheimer and Franck-Condon approximations as well as the impact parameter...

  2. Molecular Characterization of CTR-type Copper Transporters in an Oceanic Diatom, Thalassiosira oceanica 1005

    Science.gov (United States)

    Kong, L.; Price, N. M.

    2016-02-01

    Copper is an essential micronutrient for phytoplankton growth because of its role as a redox cofactor in electron transfer proteins in photosynthesis and respiration, and a potentially limiting resource in parts of the open sea. Thalassiosira oceanica 1005 can grow at inorganic copper concentrations varying from 10 fmol/L to 10 nmol/L by regulating copper uptake across plasma membrane. Four putative CTR-type copper transporter genes (ToCTR1, ToCTR2, ToCTR3.1 and ToCTR3.2) were identified by BLASTP search against the T. oceanica genome. Predicted gene models were revised by assembled mRNA sequencing transcripts and updated gene models contained all conserved features of characterized CTR-type copper transporters. ToCTR3.1 and ToCTR3.2 may arise from one another by gene duplication as they shared a sequence similarity of 97.6% with a peptide insertion of 5 amino acids at N-terminus of ToCTR3.1. The expression of ToCTR1, ToCTR2 and ToCTR3.1/3.2 was upregulated in low copper concentrations, but only ToCTR3.1/3.2 showed a significant increase (2.5 fold) in copper-starved cells. Both ToCTR3.1 and ToCTR3.2 restored growth of a yeast double mutant, Saccharomyces cerevisiae ctr1Δctr3Δ, in copper deficient medium. GFP-fused ToCTR expression showed that some ToCTR3.1 localized to the plasma membrane but a large portion was retained in the endoplasmic reticulum. Inefficient targeting of ToCTR3.1 to the yeast outer membrane may explain poorer growth compared to the Saccharomyces native ScCTR1 transformant. Thus, diatom CTR genes encoding CTR-type copper transporters show high-affinity copper uptake and their regulation may enable diatoms to survive in ocean environments containing a wide range of copper concentrations.

  3. Arctic Diatoms

    DEFF Research Database (Denmark)

    Tammilehto, Anna

    are often dominated by diatoms. They are single-celled, eukaryotic algae, which play an essential role in ocean carbon and silica cycles. Many species of the diatom genus Pseudo-nitzschia Peragallo produce a neurotoxin, domoic acid (DA), which can be transferred to higher levels in food webs causing amnesic...... as vectors for DA to higher levels in the arctic marine food web, posing a possible risk also to humans. DA production in P. seriata was, for the first time, found to be induced by chemical cues from C. finmarchicus, C. hyperboreus and copepodite stages C3 and C4, suggesting that DA may be related to defense...... against grazing. This thesis also quantified population genetic composition and changes of the diatom Fragilariopsis cylindrus spring bloom using microsatellite markers. Diatom-dominated spring blooms in the Arctic are the key event of the year, providing the food web with fundamental pulses of organic...

  4. A hybridGaussian-discrete variable representation approach to molecular continuum processes II: application to photoionization of diatomic Li2+

    Energy Technology Data Exchange (ETDEWEB)

    Rescigno, Thomas N; Yip, Frank L.; McCurdy, C. William; Rescigno, Thomas N.

    2008-08-01

    We describe an approach for studying molecular photoionization with a hybrid basis that combines the functionality of analytic basis sets to represent electronic coordinates near the nuclei of a molecule with numerically-defined grid-based functions. We discuss the evaluation of the various classes of two-electron integrals that occur in a hybrid basis consisting of Gaussian type orbitals (GTOs) and discrete variable representation (DVR) functions. This combined basis is applied to calculate single photoionization cross sections for molecular Li_2+, which has a large equilibrium bond distance (R=5.86a_0). The highly non-spherical nature of Li_2+ molecules causes higher angular momentum components to contribute significantly to the cross section even at low photoelectron energies, resulting in angular distributions that appear to be f-wave dominated near the photoionization threshold. At higher energies, where the de Broglie wavelength of the photoelectron becomes comparable with the bond distance, interference effects appear in the photoionization cross section. These interference phenomena appear at much lower energies than would be expected for diatomic targets with shorter internuclear separations.

  5. Ion channels: molecular targets of neuroactive insecticides.

    Science.gov (United States)

    Raymond-Delpech, Valérie; Matsuda, Kazuhiko; Sattelle, Benedict M; Rauh, James J; Sattelle, David B

    2005-11-01

    Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p'-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); gamma-aminobutyric acid (GABA) receptors (cyclodienes, gamma-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.

  6. Dissociation mechanisms of photoexcited molecular ions

    CERN Document Server

    Inglis, L C

    2003-01-01

    Photoionisation of gas phase molecules, in the energy range 8 - 40 eV, and the subsequent dissociation mechanisms have been investigated using threshold photoelectron spectroscopy and ion time-of-flight mass spectrometry. The excitation source used was monochromatic radiation, delivered by station 3.2 at the Daresbury Laboratory Synchrotron Radiation Source. These two techniques have also been combined in threshold photoelectron-photoion coincidence experiments, in order to record coincidence time-of-flight mass spectra and thereby determine breakdown curves. Such curves display the ion fragmentation as a function of internal energy. In addition, computer modelling techniques have been employed to gain some understanding of the unimolecular dissociations of energy selected molecular ions by establishing theoretical breakdown graphs, appearance energies, fragmentation pathways and dissociation rates. Ab initio quantum chemistry calculations have been carried out, generating ionisation and appearance energies, ...

  7. Dissociative Recombination of Molecular Ions for Astrochemistry

    Science.gov (United States)

    Novotny, Oldrich; Becker, A.; Buhr, H.; Fleischmann, Andreas; Gamer, Lisa; Geppert, W.; Krantz, C.; Kreckel, H.; Schwalm, D.; Spruck, K.; Wolf, A.; Savin, Daniel Wolf

    2014-06-01

    Dissociative recombination (DR) of molecular ions is a key chemical process in the cold interstellar medium (ISM). DR affects the composition, charge state, and energy balance of such environments. Astrochemical models of the ISM require reliable total DR cross sections as well as knowledge of the chemical composition of the neutral DR products. We have systematically measured DR for many astrophysically relevant molecular ions utilizing the TSR storage ring at the Max-Planck-Institute for Nuclear Physics (MPIK) in Heidelberg, Germany. We used the merged ion-electron beam technique combined with an energy- and position-sensitive imaging detector and are able to study DR down to plasma temperatures as low as 10 K. The DR count rate is used to obtain an absolute merged beams DR rate coefficient from which we can derive a thermal rate coefficient needed for plasma models. Additionally we determine the masses of the DR products by measuring their kinetic energy in the laboratory reference frame. This allows us to assign particular DR fragmentation channels and to obtain their branching ratios. All this information is particularly important for understanding DR of heteronuclear polyatomic ions. We will present DR results for several ions recently investigated at TSR. A new Cryogenic Storage Ring (CSR) is currently being commissioned at MPIK. With the chamber cooled down to ~10 K and a base pressure better than 10-13 mbar, this setup will allow internal cooling of the stored ions down to their rotational ground states, thus opening a new era in DR experiments. New technological challenges arise due to the ultracold, ultra-high vacuum environment of the CSR and thus the detection techniques used at TSR cannot be easily transferred to CSR. We will present new approaches for DR fragment detection in cryogenic environment. This work is supported in part by NASA and the NSF.

  8. The Symmetry Properties of Linear Combination Coefficients for Molecular Orbitals of Diatomic Molecules

    Institute of Scientific and Technical Information of China (English)

    Metin Orbay; Telhat Ozdogan

    2003-01-01

    In this paper, the symmetry properties of linear combination coefficients for molecular orbitals of diatomicmolecules, using Slater type orbitals, are presented with the help of the symmetry operations in group theory. In order totest the presented symmetry properties, the linear combination coefficients of molecular orbitalsfor the ground electronicstate of pilot molecules F2 and CO are calculated using constructed computer programs for Hartree-Fock-Roothaanequation. It is seen that the obtained computing results satisfy the presented symmetry properties.

  9. The Wigner-Witmer diatomic eigenfunction

    CERN Document Server

    Hornkohl, James O; Parigger, Christian G

    2015-01-01

    Born and Oppenheimer reported an approximate separation of molecular eigenfunctions into electronic, vibrational, and rotational parts, but at the end of their paper showed that the two angles describing rotation of the nuclei in a diatomic molecule are exactly separable. A year later in a two-part work devoted strictly to diatomic molecules, Wigner and Witmer published (1) an exact diatomic eigenfunction and (2) the rules correlating the electronic state of a diatomic molecule to the orbital and spin momenta of the separated atoms. The second part of the Wigner-Witmer paper became famous for its correlation rules, but, oddly, the exact eigenfunction from which their rules were obtained received hardly any attention. Using three fundamental symmetries, we give a derivation of the Wigner-Witmer diatomic eigenfunction. Applications of our derivations are fundamental to predicting accurate diatomic molecular spectra that we compare with recorded spectra for diagnostic purposes, such as measurements of molecular ...

  10. Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    Science.gov (United States)

    2016-06-06

    ions affords many of the benefits of ultracold neutral molecules, while significantly reducing experimental complexity – e.g. large trap depths, long...affords many of the benefits of ultracold neutral molecules, while significantly reducing experimental complexity – e.g. large trap depths, long trap...cooling collisions. As shown in Fig . 2, which plots the results of a photodissociative thermometry measurement, the molecular ions have

  11. Controlling dynamics in diatomic systems

    Indian Academy of Sciences (India)

    Praveen Kumar; Harjinder Singh

    2007-09-01

    Controlling molecular energetics using laser pulses is exemplified for nuclear motion in two different diatomic systems. The problem of finding the optimized field for maximizing a desired quantum dynamical target is formulated using an iterative method. The method is applied for two diatomic systems, HF and OH. The power spectra of the fields and evolution of populations of different vibrational states during transitions are obtained.

  12. Modeling ion sensing in molecular electronics

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Caroline J.; Smeu, Manuel, E-mail: manuel.smeu@northwestern.edu; Ratner, Mark A., E-mail: ratner@northwestern.edu [Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (United States)

    2014-02-07

    We examine the ability of molecules to sense ions by measuring the change in molecular conductance in the presence of such charged species. The detection of protons (H{sup +}), alkali metal cations (M{sup +}), calcium ions (Ca{sup 2+}), and hydronium ions (H{sub 3}O{sup +}) is considered. Density functional theory (DFT) is used within the Keldysh non-equilibrium Green's function framework (NEGF) to model electron transport properties of quinolinedithiol (QDT, C{sub 9}H{sub 7}NS{sub 2}), bridging Al electrodes. The geometry of the transport region is relaxed with DFT. The transport properties of the device are modeled with NEGF-DFT to determine if this device can distinguish among the M{sup +} + QDT species containing monovalent cations, where M{sup +} = H{sup +}, Li{sup +}, Na{sup +}, or K{sup +}. Because of the asymmetry of QDT in between the two electrodes, both positive and negative biases are considered. The electron transmission function and conductance properties are simulated for electrode biases in the range from −0.5 V to 0.5 V at increments of 0.1 V. Scattering state analysis is used to determine the molecular orbitals that are the main contributors to the peaks in the transmission function near the Fermi level of the electrodes, and current-voltage relationships are obtained. The results show that QDT can be used as a proton detector by measuring transport through it and can conceivably act as a pH sensor in solutions. In addition, QDT may be able to distinguish among different monovalent species. This work suggests an approach to design modern molecular electronic conductance sensors with high sensitivity and specificity using well-established quantum chemistry.

  13. Trapped ion simulation of molecular spectrum

    Science.gov (United States)

    Shen, Yangchao; Lu, Yao; Zhang, Kuan; Zhang, Shuaining; Huh, Joonsuk; Kim, Kihwan

    2016-05-01

    Boson sampling had been suggested as a classically intractable and quantum mechanically manageable problem via computational complexity theory arguments. Recently, Huh and co-workers proposed theoretically a modified version of boson sampling, which is designed to simulate a molecular problem, as a practical application. Here, we report the experimental implementation of the theoretical proposal with a trapped ion system. As a first demonstration, we perform the quantum simulation of molecular vibronic profile of SO2, which incorporates squeezing, rotation and coherent displacements operations, and the collective projection measurement on phonon modes. This work was supported by the National Basic Research Program of China 11CBA00300, 2011CBA00301, National Natural Science Foundation of China 11374178, 11574002. Basic Science Research Program of Korea NRF-2015R1A6A3A04059773.

  14. Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology

    Directory of Open Access Journals (Sweden)

    Whittaker Kerry A

    2012-10-01

    Full Text Available Abstract Background Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspecific. Results Culture collection isolates of T. gravida and T. rotula diverged by 7.0 ± 0.3% at the ITS1 and by 0.8 ± 0.03% at the 28S. Within T. rotula, field and culture collection isolates were subdivided into three lineages that diverged by 0.6 ± 0.3% at the ITS1 and 0% at the 28S. The predicted ITS1 secondary structure revealed no compensatory base pair changes among lineages. Differences in genome size were observed among isolates, but were not correlated with ITS1 lineages. Maximum acclimated growth rates of isolates revealed genotype by environment effects, but these were also not correlated with ITS1 lineages. In contrast, intra-individual variation in the multi-copy ITS1 revealed no evidence of recombination amongst lineages, and molecular clock estimates indicated that lineages diverged 0.68 Mya. The three lineages exhibited different geographic distributions and, with one exception, each field sample was dominated by a single lineage. Conclusions The degree of inter- and intra-specific divergence between T. gravida and T. rotula suggests they should continue to be treated as separate species. The phylogenetic distinction of the three closely-related T. rotula lineages was unclear. On the one hand, the lineages showed no physiological differences, no consistent genome size differences and no significant changes in the ITS1 secondary structure, suggesting there are no barriers to interbreeding among lineages. In contrast, analysis of intra

  15. Physiological and molecular analysis of carbon source supplementation and pH stress-induced lipid accumulation in the marine diatom Phaeodactylum tricornutum.

    Science.gov (United States)

    Mus, Florence; Toussaint, Jean-Paul; Cooksey, Keith E; Fields, Matthew W; Gerlach, Robin; Peyton, Brent M; Carlson, Ross P

    2013-04-01

    A detailed physiological and molecular analysis of lipid accumulation under a suite of conditions including nitrogen limitation, alkaline pH stress, bicarbonate supplementation, and organic acid supplementation was performed on the marine diatom Phaeodactylum tricornutum. For all tested conditions, nitrogen limitation was a prerequisite for lipid accumulation and the other culturing strategies only enhanced accumulation highlighting the importance of compounded stresses on lipid metabolism. Volumetric lipid levels varied depending on condition; the observed rankings from highest to lowest were for inorganic carbon addition (15 mM bicarbonate), organic acid addition (15 carbon mM acetate), and alkaline pH stress (pH 9.0). For all lipid-accumulating cultures except acetate supplementation, a common series of physiological steps were observed. Upon extracellular nitrogen exhaustion, culture growth continued for approximately 1.5 cell doublings with decreases in specific protein and photosynthetic pigment content. As nitrogen limitation arrested cell growth, carbohydrate content decreased with a corresponding increase in lipid content. Addition of the organic carbon source acetate appeared to activate alternative metabolic pathways for lipid accumulation. Molecular level data on more than 50 central metabolism transcripts were measured using real-time PCR. Analysis of transcripts suggested the central metabolism pathways associated with bicarbonate transport, carbonic anhydrases, and C4 carbon fixations were important for lipid accumulation. Transcriptomic data also suggested that repurposing of phospholipids may play a role in lipid accumulation. This study provides a detailed physiological and molecular-level foundation for improved understanding of diatom nutrient cycling and contributes to a metabolic blueprint for controlling lipid accumulation in diatoms.

  16. Molecular and Photosynthetic Responses to Prolonged Darkness and Subsequent Acclimation to Re-Illumination in the Diatom Phaeodactylum tricornutum

    DEFF Research Database (Denmark)

    Nymark, Marianne; Valle, Kristi Collier; Hancke, Kasper

    2013-01-01

    and immediately utilize the available energy in photosynthesis and growth. We have investigated both the response to prolonged darkness and the re-acclimation to moderate intensity white irradiance (E = 100 µmol m−2 s−1) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global...

  17. Laboratory measurements and modeling of molecular photoabsorption in the ultraviolet for planetary atmospheres applications: diatomic sulfur and sulfur monoxide

    Science.gov (United States)

    Stark, Glenn

    2016-07-01

    Our research program comprises the measurement and modeling of ultraviolet molecular photoabsorption cross sections with the highest practical resolution. It supports efforts to interpret and model observations of planetary atmospheres. Measurement and modeling efforts on diatomic sulfur (S _{2}) and sulfur monoxide (SO) are in progress. S _{2}: Interpretations of atmospheric (Io, Jupiter, cometary comae) S _{2} absorption features are hindered by a complete lack of laboratory cross section data in the ultraviolet. We are working to quantify the photoabsorption spectrum of S _{2} from 240 to 300 nm based on laboratory measurements and theoretical calculations. We have constructed an experimental apparatus to produce a stable column of S _{2} vapor at a temperature of 800 K. High-resolution measurements of the absorption spectrum of the strong B - X system of S _{2} were completed using the NIST VUV-FTS at Gaithersburg, Maryland. These measurements are currently being incorporated into a coupled-channel model of the absorption spectrum of S _{2} to quantify the contributions from individual band features and to establish the mechanisms responsible for the strong predissociation signature of the B - X system. A successful coupled channels model can then be used to calculate the B - X absorption spectrum at any temperature. SO: There has been a long-standing need for high-resolution cross sections of sulfur monoxide radicals in the ultraviolet and vacuum ultraviolet regions, where the molecule strongly predissociates, for modeling the atmospheres of Io and Venus, and most recently for understanding sulfur isotope effects in the ancient (pre-O _{2}) atmosphere of Earth. We have produced a measurable column of SO in a continuous-flow DC discharge cell, using SO _{2} as a parent molecule. Photoabsorption measurements were recently recorded on the DESIRS beamline of the SOLEIL synchrotron, taking advantage of the high-resolution VUV-FTS on that beamline. A number of

  18. The electric quadrupole moment of molecular hydrogen ions and their potential for a molecular ion clock

    CERN Document Server

    Bakalov, Dimitar

    2013-01-01

    The systematic shifts of the transition frequencies in the molecular hydrogen ions are of relevance to ultra-high-resolution radio-frequency, microwave and optical spectroscopy of these systems, performed in ion traps. We develop the ab-initio description of the interaction of the electric quadrupole moment of this class of molecules with the static electric field gradients present in ion traps. In good approximation, it is described in terms of an effective perturbation hamiltonian. An approximate treatment is then performed in the Born-Oppenheimer approximation. We give an expression of the electric quadrupole coupling parameter valid for all hydrogen molecular ion species and evaluate it for a large number of states of H2+, HD+, and D2+. The systematic shifts can be evaluated as simple expectation values of the perturbation hamiltonian. Results on radio-frequency (M1), one-photon electric dipole (E1) and two-photon E1 transitions between hyperfine states in HD+ are reported. For two-photon E1 transitions b...

  19. Microwave quantum logic spectroscopy and control of molecular ions

    DEFF Research Database (Denmark)

    Shi, M.; F. Herskind, P.; Drewsen, M.;

    2013-01-01

    A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying AC Stark shifts, induced by far off-resonant, focused laser beams to achieve an effective coupling between the rotati......A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying AC Stark shifts, induced by far off-resonant, focused laser beams to achieve an effective coupling between...... the rotational state of a molecular ion and the electronic state of an atomic ion. In this setting, the atomic ion is used for read-out of the molecular ion state, in a manner analogous to quantum logic spectroscopy based on Raman transitions. In addition to high-precision spectroscopy, this setting allows...

  20. Molecular and Photosynthetic Responses to Prolonged Darkness and Subsequent Acclimation to Re-Illumination in the Diatom Phaeodactylum tricornutum

    DEFF Research Database (Denmark)

    Nymark, Marianne; Valle, Kristi Collier; Hancke, Kasper

    2013-01-01

    treatment of the cells led to 1) significantly decreased nuclear transcriptional activity, 2) distinct intracellular changes, 3) fixed ratios of the light-harvesting pigments despite a decrease in the total cell pigment pool, and 4) only a minor drop in photosynthetic efficiency (ΦPSII_max). Re......Photosynthetic diatoms that live suspended throughout the water column will constantly be swept up and down by vertical mixing. When returned to the photic zone after experiencing longer periods in darkness, mechanisms exist that enable the diatoms both to survive sudden light exposure...... transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance. The analyses resulted in several intriguing findings. Dark...

  1. Molecular and negative ion production by a standard electron cyclotron resonance ion source.

    Science.gov (United States)

    Rácz, R; Biri, S; Juhász, Z; Sulik, B; Pálinkás, J

    2012-02-01

    Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H(-), O(-), OH(-), O(2)(-), C(-), C(60)(-) negative ions and H(2)(+), H(3)(+), OH(+), H(2)O(+), H(3)O(+), O(2)(+) positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several μA and positive molecular ion beams in the mA range were successfully obtained.

  2. Adiabatic Cooling for Rovibrational Spectroscopy of Molecular Ions

    DEFF Research Database (Denmark)

    Fisher, Karin

    2017-01-01

    The field of cold molecular ions is a fast growing one, with applications in high resolution spectroscopy and metrology, the search for time variations of fundamental constants, cold chemistry and collisions, and quantum information processing, to name a few. The study of single molecular ions...... is attractive as it enables one to push the limits of spectroscopic accuracy. Non-destructive spectroscopic detection of molecular ions can be achieved by co-trapping with an easier to detect atomic ion. The ion chain has coupled motion, and transitions which change both the internal and motional states...... to the measured heating rates, almost perfectly fitting existing heating rate theory. Further, the same model successfully predicted the heating rates of the in-phase mode of a two-ion crystal, indicating that we can use it to predict the heating rates in experiments on molecule-atom chains. Adiabatic cooling...

  3. Production and sympathetic cooling of complex molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Chaobo

    2008-06-24

    This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO{sub 2}, Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the {sup 138}Ba{sup +} ions in the ({sup 2}P{sub 1/2}) excited state with gases such as O{sub 2}, CO{sub 2}, or N{sub 2}O, could be observed. If the initial {sup 138}Ba{sup +} ion ensemble is cold, the produced {sup 138}BaO{sup +} ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of {sup 138}BaO{sup +} ions with neutral CO to {sup 138}Ba{sup +} is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the

  4. Structural identification of long-chain polyamines associated with diatom biosilica in a Southern Ocean sediment core

    Science.gov (United States)

    Bridoux, Maxime C.; Ingalls, Anitra E.

    2010-07-01

    Long-chain polyamines (LCPAs) constitute a new family of natural organic compounds that have recently been isolated and characterized from the biosilicified cell walls of diatom cultures. To date, diatom-specific polyamines have not been investigated from the marine environment and their fate in the environment is entirely unknown. Here, we report a series of LCPAs in a diatom frustule-rich sediment core (TNO57-13 PC4), originating from the Atlantic sector of the Southern Ocean and spanning from the Holocene to the Last Glacial Maximum (LGM). Liquid chromatography with electrospray ionization mass spectrometry (LC-ESI-MS) revealed a complex mixture of linear polyamines with at least 28 individual molecular species. Ion trap mass fragmentation studies, combined with high resolution Time of Flight (TOF) mass spectrometry showed that the polyamine pool consisted of a series of N-methylated propylamine compounds attached to a putrescine moiety, with individual LCPAs varying in chain length and degree of methylation. The structural similarity between LCPAs extracted from the diatom-rich sediment core and those extracted from the frustules of cultured diatoms suggests that sedimentary LCPAs are derived from diatom frustules. We hypothesize that these intrinsically labile organic molecular fossils are protected from diagenesis by encapsulation within the frustule. These compounds constitute a new class of biomarkers that could potentially be indicators of diatom species distribution. Isotopic analysis of LCPAs could be used to improve age models for sediment cores that lack calcium carbonate and to improve current interpretations of diatom-based paleoproxies, including diatom-bound nitrogen isotopes.

  5. The electric quadrupole moment of molecular hydrogen ions and their potential for a molecular ion clock

    Science.gov (United States)

    Bakalov, D.; Schiller, S.

    2014-01-01

    The systematic shifts of the transition frequencies in the molecular hydrogen ions are of relevance to ultra-high-resolution radio-frequency, microwave and optical spectroscopy of these systems, performed in ion traps. We develop the ab initio description of the interaction of the electric quadrupole moment of this class of molecules with the static electric field gradients present in ion traps. In good approximation, it is described in terms of an effective perturbation Hamiltonian. An approximate treatment is then performed in the Born-Oppenheimer approximation. We give an expression of the electric quadrupole coupling parameter valid for all hydrogen molecular ion species and evaluate it for a large number of states of H{2/+}, HD+, and D{2/+}. The systematic shifts can be evaluated as simple expectation values of the perturbation Hamiltonian. Results on radio-frequency, one-photon electric dipole (E1), and two-photon E1 transitions between hyperfine states in HD+ are reported. For two-photon E1 transitions between rotationless states, the shifts vanish. For a large subset of rovibrational one-photon transitions, the absolute values of the quadrupole shifts range from 0.3 to 10 Hz for an electric field gradient of 108 V/m2. We point out an experimental procedure for determining the quadrupole shift which will allow reducing its contribution to the uncertainty of unperturbed rovibrational transition frequencies to the 1 × 10-15 fractional level and, for selected transitions, even below it. The combined contributions of black-body radiation, Zeeman, Stark and quadrupole effects are considered for a large set of transitions, and it is estimated that the total transition frequency uncertainty of selected transitions can be reduced below the 1 × 10-15 level.

  6. Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata.

    Science.gov (United States)

    Brandes, Josephin; Kuhajek, Jeanne M; Goodwin, Eric; Wood, Susanna A

    2016-10-01

    Didymosphenia geminata (Lyngbye) M. Schmidt is a stalked freshwater diatom that is expanding its range globally. In some rivers, D. geminata forms thick and expansive polysaccharide-dominated mats. Like other stalked diatoms, D. geminata cells attach to the substratum with a pad of adhesive extracellular polymeric substance. Research on D. geminata and other diatoms suggests that bacterial biofilm composition may contribute to successful attachment. The aim of this study was to investigate the composition and role of bacterial biofilm communities in D. geminata attachment and survival. Bacterial biofilms were collected at four sites in the main stem of a river (containing D. geminata) and in four tributaries (free of D. geminata). Samples were characterised using automated rRNA intergenic spacer analysis and high-throughput sequencing (HTS). Mat-associated bacteria were isolated and their effect on the early establishment of D. geminata cells assessed using co-culturing experiments. ARISA and HTS data showed differences in bacterial communities between samples with and without D. geminata at two of the four sites. Samples with D. geminata had a higher relative abundance of Sphingobacteria (p < 0.01) and variability in community composition was reduced. Analysis of the 76 bacteria isolated from the mat revealed 12 different strains representing 8 genera. Co-culturing of a Carnobacterium sp. with D. geminata reduced survival (p < 0.001) and attachment (p < 0.001) of D. geminata. Attachment was enhanced by Micrococcus sp. and Pseudomonas sp. (p < 0.001 and p < 0.01, respectively). These data provide evidence that bacteria play a role in the initial attachment and on-going survival of D. geminata, and may partly explain observed distribution patterns.

  7. Molecular and photosynthetic responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum.

    Directory of Open Access Journals (Sweden)

    Marianne Nymark

    Full Text Available Photosynthetic diatoms that live suspended throughout the water column will constantly be swept up and down by vertical mixing. When returned to the photic zone after experiencing longer periods in darkness, mechanisms exist that enable the diatoms both to survive sudden light exposure and immediately utilize the available energy in photosynthesis and growth. We have investigated both the response to prolonged darkness and the re-acclimation to moderate intensity white irradiance (E = 100 µmol m(-2 s(-1 in the diatom Phaeodactylum tricornutum, using an integrated approach involving global transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance. The analyses resulted in several intriguing findings. Dark treatment of the cells led to 1 significantly decreased nuclear transcriptional activity, 2 distinct intracellular changes, 3 fixed ratios of the light-harvesting pigments despite a decrease in the total cell pigment pool, and 4 only a minor drop in photosynthetic efficiency (Φ(PSII_max. Re-introduction of the cells to the initial light conditions revealed 5 distinct expression profiles for nuclear genes involved in photosynthesis and those involved in photoprotection, 6 rapid rise in photosynthetic parameters (α and rETR(max within 0.5 h of re-exposure to light despite a very modest de novo synthesis of photosynthetic compounds, and 7 increasingly efficient resonance energy transfer from fucoxanthin chlorophyll a/c-binding protein complexes to photosystem II reaction centers during the first 0.5 h, supporting the observations stated in 6. In summary, the results show that despite extensive transcriptional, metabolic and intracellular changes, the ability of cells to perform photosynthesis was kept intact during the length of the experiment. We

  8. Development of molecular closures for the reference interaction site model theory with application to square-well and Lennard-Jones homonuclear diatomics

    Science.gov (United States)

    Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo

    2016-10-01

    Inspired by significant improvements obtained for the performances of the polymer reference interaction site model (PRISM) theory of the fluid phase when coupled with ‘molecular closures’ (Schweizer and Yethiraj 1993 J. Chem. Phys. 98 9053), we exploit a matrix generalization of this concept, suitable for the more general RISM framework. We report a preliminary test of the formalism, as applied to prototype square-well homonuclear diatomics. As for the structure, comparison with Monte Carlo shows that molecular closures are slightly more predictive than their ‘atomic’ counterparts, and thermodynamic properties are equally accurate. We also devise an application of molecular closures to models interacting via continuous, soft-core potentials, by using well established prescriptions in liquid state perturbation theories. In the case of Lennard-Jones dimers, our scheme definitely improves over the atomic one, providing semi-quantitative structural results, and quite good estimates of internal energy, pressure and phase coexistence. Our finding paves the way to a systematic employment of molecular closures within the RISM framework to be applied to more complex systems, such as molecules constituted by several non-equivalent interaction sites.

  9. Development of molecular closures for the reference interaction site model theory with application to square-well and Lennard-Jones homonuclear diatomics.

    Science.gov (United States)

    Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo

    2016-10-19

    Inspired by significant improvements obtained for the performances of the polymer reference interaction site model (PRISM) theory of the fluid phase when coupled with 'molecular closures' (Schweizer and Yethiraj 1993 J. Chem. Phys. 98 9053), we exploit a matrix generalization of this concept, suitable for the more general RISM framework. We report a preliminary test of the formalism, as applied to prototype square-well homonuclear diatomics. As for the structure, comparison with Monte Carlo shows that molecular closures are slightly more predictive than their 'atomic' counterparts, and thermodynamic properties are equally accurate. We also devise an application of molecular closures to models interacting via continuous, soft-core potentials, by using well established prescriptions in liquid state perturbation theories. In the case of Lennard-Jones dimers, our scheme definitely improves over the atomic one, providing semi-quantitative structural results, and quite good estimates of internal energy, pressure and phase coexistence. Our finding paves the way to a systematic employment of molecular closures within the RISM framework to be applied to more complex systems, such as molecules constituted by several non-equivalent interaction sites.

  10. Understanding ion association states and molecular dynamics using infrared spectroscopy

    Science.gov (United States)

    Masser, Hanqing

    A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO

  11. Spectra of Cold Molecular Ions from Hot Helium Nanodroplets

    Science.gov (United States)

    Drabbels, Marcel

    2012-06-01

    The function of a molecule is intimately related to its structure. Accordingly, in the quest for a better understanding of molecular function, the development of spectroscopic methods to elucidate molecular structures increasingly takes central stage. The amount of detail that can be derived from spectra depends on the experimental conditions, most notably on the temperature of the sample and the intermolecular interactions a molecule experiences. Helium nanodroplets provide in this respect an almost ideal matrix [1, 2]. For neutral molecules, helium nanodroplet spectroscopy thus has led to important discoveries related to the structure of key molecular systems and has provided insight into the mechanisms underlying chemical reactions. Compared to the level of sophistication that has been reached for neutrals, the spectroscopic exploration of ions is still in its infancy. The use of helium droplets as a cryogenic matrix could potentially solve many of the technical challenges associated with recording high-resolution spectra of cold molecular ions. Here, we will present a method to record spectra of ion containing helium nanodroplets that finds its roots in the nonthermal cooling dynamics of excited molecular ions. In addition, spectra of several molecular ions will be present and the influence of the helium environment on these spectra will be discussed. [1] G. Scoles, and K. K. Lehmann, Science 287, 2429 (2000). [2] J. P. Toennies, and A. F. Vilesov, Angew. Chem. Int. Ed. 43, 2622 (2004).

  12. Dissociation curves of diatomic molecules: A DC-DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Eunji; Kim, Min-Cheol [Department of Chemistry and Institute of Nano-Bio Molecular Assemblies, Yonsei University, Seoul 120-749 (Korea, Republic of); Burke, Kieron [Department of Chemistry, University of California, Irvine, CA, 92697 (United States)

    2015-12-31

    We investigate dissociation of diatomic molecules using standard density functional theory (DFT) and density-corrected density functional theory (DC-DFT) compared with CCSD(T) results as reference. The results show the difference between the HOMO values of dissociated atomic species often can be used as an indicator whether DFT would predict the correct dissociation limit. DFT predicts incorrect dissociation limits and charge distribution in molecules or molecular ions when the fragments have large HOMO differences, while DC-DFT and CCSD(T) do not. The criteria for large HOMO difference is about 2 ∼ 4 eV.

  13. Molecular characterization of microbial mutations induced by ion beam irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ichida, Hiroyuki [Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271-8510 (Japan); Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198 (Japan)], E-mail: ichida@riken.jp; Matsuyama, Tomoki [Cellular Biochemistry Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama 351-0198 (Japan); Ryuto, Hiromichi [Accelerator Operation Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198 (Japan); Hayashi, Yoriko [Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198 (Japan); Fukunishi, Nobuhisa [Accelerator Operation Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198 (Japan); Abe, Tomoko [Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198 (Japan); Koba, Takato [Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271-8510 (Japan)

    2008-03-01

    A positive selection system for gene disruption using a sucrose-sensitive transgenic rhizobium was established and used for the molecular characterization of mutations induced by ion beam irradiations. Single nucleotide substitutions, insertions, and deletions were found to occur in the sucrose sensitivity gene, sacB, when the reporter line was irradiated with highly accelerated carbon and iron ion beams. In all of the insertion lines, fragments of essentially the same sequence and of approximately 1188 bp in size were identified in the sacB regions. In the deletion lines, iron ions showed a tendency to induce larger deletions than carbon ions, suggesting that higher LET beams cause larger deletions. We found also that ion beams, particularly 'heavier' ion beams, can produce single gene disruptions and may present an effective alternative to transgenic approaches.

  14. Low fragment polyatomic molecular ion source by using permanent magnets.

    Science.gov (United States)

    Takeuchi, Mitsuaki; Hayashi, Kyouhei; Imanaka, Kousuke; Ryuto, Hiromichi; Takaoka, Gikan H

    2014-02-01

    Electron-ionization-type polyatomic molecular ion source with low fragment was developed by using a pair of ring-shaped Sm-Co magnets. The magnets were placed forward and backward side of ionization part to confine electrons extracted from a thermionic cathode. Calculated electron trajectory of the developed ion source was 20 times longer than that of an ordinary outer filament configuration that has no magnetic confinement. Mass spectra of the molecular ions generated from n-tetradecane (C14H30) gas exhibited 4 times larger intensity than that of the ordinary configuration in a range of mass/charge from 93 to 210 u. This indicates that suppression of fragment ion was obtained by increase of low energy electrons resulted from the electron confinement.

  15. Towards the Precision Spectroscopy of a Single Molecular Ion

    Science.gov (United States)

    Lin, Yen-Wei

    This dissertation presents some development of the single molecular ion precision spectroscopy experiment including construction of the project, spectroscopy state readout, and production of ultracold molecules. Such molecular ion spectroscopy aims at testing fundamental physics such as probing the time variation of electron-proton mass ratio. The theories and characterization of ion traps are first discussed along with information regarding building the ion trapping systems. Then, routines in this project such as loading ions, Doppler laser cooling, excessive micromotion compensation, secular motion detection, and fluorescence imaging are deliberated. In the state readout experiment, the coherent motion of a single trapped barium ion resonantly driving by a radiation pressure is studied. By scattering of order only one hundred photons, the radiation pressure is able to seed a laser-cooled ion with a secular oscillation that is detectable by the Doppler velocimetry technique after proper motional amplification. This seeding method provides a mapping between the ion's internal configuration and its secular motion and can be used to read out the spectroscopy results from a single non-fluorescing ion with a partially-closed cycling transition. The work of ultracold molecule production is done with silicon monoxide ions, which has a strong vibration-conserved spontaneous decay branching. Therefore, by optically pumping the rotational cooling transitions in silicon monoxide ions with a broadband radiation, the population can be efficiently driven into the ground rotational state before falling into other manifolds. To avoid the rotational heating transition, the broadband source, derived from a femtosecond pulsed laser, is spectrally filtered using an ultrashort pulse shaper.

  16. Deposition of molecular probes in heavy ion tracks

    CERN Document Server

    Esser, M

    1999-01-01

    By using polarized fluorescence techniques the physical properties of heavy ion tracks such as the dielectric number, molecular alignment and track radius can be traced by molecular fluorescence probes. Foils of poly(ethylene terephthalate) (PET) were used as a matrix for the ion tracks wherein fluorescence probes such as aminostyryl-derivatives can be incorporated using a suitable solvent, e.g. N,N'-dimethylformamide (DMF) as transport medium. The high sensitivity of fluorescence methods allowed the comparison of the probe properties in ion tracks with the virgin material. From the fluorescence Stokes shift the dielectric constants could be calculated, describing the dielectric surroundings of the molecular probes. The lower dielectric constant in the tracks gives clear evidence that there is no higher accommodation of the highly polar solvent DMF in the tracks compared with the virgin material. Otherwise the dielectric constant in the tracks should be higher than in the virgin material. The orientation of t...

  17. Interferences in Photodetachment of a Negative Molecular Ion

    Institute of Scientific and Technical Information of China (English)

    Ahmad Afaq; DU Meng-Li

    2006-01-01

    The photodetachment of a negative molecular ion is studied theoretically using a two-center model. The detached electron wave function is obtained as a superposition of two coherent waves originating from each center. The photo-detached electron flux is evaluated on a screen placed at a large distance from the negative molecular ion. The electron flux on the screen displays strong interferences, the peak positions are related to the distance between the two centers in the negative molecular ion. We also obtained a simple analytical formula for the total photodetachment cross section. It approaches one and two times of the cross section for the one-center system in the high and low photon energy limits respectively.

  18. Microwave quantum logic spectroscopy and control of molecular ions

    DEFF Research Database (Denmark)

    Shi, M.; F. Herskind, P.; Drewsen, M.

    2013-01-01

    A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying AC Stark shifts, induced by far off-resonant, focused laser beams to achieve an effective coupling between the rotati......A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying AC Stark shifts, induced by far off-resonant, focused laser beams to achieve an effective coupling between...... for rotational ground state cooling, and can be considered as a candidate for the quantum information processing with polar molecular ions. All elements of our proposal can be realized with currently available technology....

  19. Formation of molecular ions by radiative association of cold trapped atoms and ions

    CERN Document Server

    Silva, Humberto Da; Aymar, Mireille; Dulieu, Olivier

    2015-01-01

    Radiative emission during cold collisions between trapped laser-cooled Rb atoms and alkaline-earth ions (Ca + , Sr + , Ba +) and Yb + are studied theoretically, using accurate effective-core-potential based quantum chemistry calculations of potential energy curves and transition dipole moments of the related molecular ions. Radiative association of molecular ions is predicted to occur for all systems with a cross section two to ten times larger than the radiative charge transfer one. Partial and total rate constants are also calculated and compared to available experiments. Narrow shape resonances are expected, which could be detectable at low temperature with an experimental resolution at the limit of the present standards. Vibrational distributions are also calculated, showing that the final molecular ions are not created in their ground state level.

  20. Influence of salt ions on binding to molecularly imprinted polymers.

    OpenAIRE

    Kempe, Henrik; Kempe, Maria

    2010-01-01

    Salt ions were found to have an influence on template binding to two model molecularly imprinted polymers (MIPs), targeted to penicillin G and propranolol, respectively, in water-acetonitrile mixtures. Water was detrimental to rebinding of penicillin G whereas propranolol bound in the entire water-acetonitrile range tested. In 100% aqueous solution, 3-M salt solutions augmented the binding of both templates. The effects followed the Hofmeister series with kosmotropic ions promoting the larges...

  1. Predicting Molecular Crowding Effects in Ion-RNA Interactions.

    Science.gov (United States)

    Yu, Tao; Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

    2016-09-01

    We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.

  2. Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

    Science.gov (United States)

    Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

    2015-08-20

    The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

  3. Nuclear spin-rotation interaction in the hydrogen molecular ion

    CERN Document Server

    Babb, J F

    1995-01-01

    The nuclear spin--rotation interaction in the hyperfine structure of the hydrogen molecular ion is investigated. The interaction constants are determined and are found to differ in sign and magnitude compared to another theory, but they are in agreement with some values derived from experiment.

  4. Behavior of molecules and molecular ions near a field emitter

    CERN Document Server

    Gault, Baptiste; Ashton, Michael V; Sinnott, Susan B; Chiaramonti, Ann N; Moody, Michael P; Schreiber, Daniel K

    2015-01-01

    The cold emission of particles from surfaces under intense electric fields is a process which underpins a variety of applications including atom probe tomography (APT), an analytical microscopy technique with near-atomic spatial resolution. Increasingly relying on fast laser pulsing to trigger the emission, APT experiments often incorporate the detection of molecular ions emitted from the specimen, in particular from covalently or ionically bonded materials. Notably, it has been proposed that neutral molecules can also be emitted during this process. However, this remains a contentious issue. To investigate the validity of this hypothesis, a careful review of the literature is combined with the development of new methods to treat experimental APT data, the modelling of ion trajectories, and the application of density-functional theory (DFT) simulations to derive molecular ion energetics. It is demonstrated that the direct thermal emission of neutral molecules is extremely unlikely. However, neutrals can still...

  5. Utilizing Ion-Mobility Data to Estimate Molecular Masses

    Science.gov (United States)

    Duong, Tuan; Kanik, Isik

    2008-01-01

    A method is being developed for utilizing readings of an ion-mobility spectrometer (IMS) to estimate molecular masses of ions that have passed through the spectrometer. The method involves the use of (1) some feature-based descriptors of structures of molecules of interest and (2) reduced ion mobilities calculated from IMS readings as inputs to (3) a neural network. This development is part of a larger effort to enable the use of IMSs as relatively inexpensive, robust, lightweight instruments to identify, via molecular masses, individual compounds or groups of compounds (especially organic compounds) that may be present in specific environments or samples. Potential applications include detection of organic molecules as signs of life on remote planets, modeling and detection of biochemicals of interest in the pharmaceutical and agricultural industries, and detection of chemical and biological hazards in industrial, homeland-security, and industrial settings.

  6. Interferences in Photodetachment of a Negative Molecular Ion Model

    Institute of Scientific and Technical Information of China (English)

    A. Afaq; DU Meng-Li

    2008-01-01

    By employing a two-center model, the total and differential cross sections in the photodetachment of "a negative molecular ion" are studied theoretically and obtained for the case of light polarization parallel to the molecular axis. We find that in contrast to the smooth behavior of the total cross section for perpendicular polarized light, the cross section for parallel polarized light shows an interesting oscillatory structure. The oscillations in the total cross section may provide a method to determine the distance between the two centers. We explain the oscillation in the total cross section as an interference effect using closed-orbit theory. We also calculated the detached-electron flux distributions on a screen placed at a large distance from the negative molecular ion. The distributions display multiple-ring-like interference patterns. Such interference patterns are similar to those in the photodetachment microscopy experiments.

  7. Calixarenes: Versatile molecules as molecular sensors for ion recognition study

    Indian Academy of Sciences (India)

    Subrata Patra; Debdeep Maity; Ravi Gunupuru; Pragati Agnihotri; Parimal Paul

    2012-11-01

    This article presents a brief account on designing of calixarene-based molecular sensor for recognition of various metal ions and anions and also different analytical techniques to monitor the recognition event. This review focuses only on calix[4]arene derivatives, in which mainly the lower rim is modified incorporating either crown moiety to make calix-crown hybrid ionophore to encapsulate metal ions or some fluoregenic inorganic and organic moieties to use it as signalling unit. In order to investigate effect of conformation of the calixarene unit and steric crowding on ion selectivity, designing of these molecules have been made using both the cone and 1,3-alternate conformations of the calixarene unit and also incorporating bulky tert-butyl group in few cases to impose controlled steric crowding. Among various ions, here focuses are mainly on biologically and commercially important alkali metal ion such as K+, toxic metal ions such as Hg2+, Pb2+, Cd2+, important transition metal ion such as Cu2+ and toxic anion like F−. The techniques used to monitor the recognition event and also to determine binding constants with strongly interacting ions are fluorescence, UV-vis and 1H NMR spectroscopy. Most of the ionophores reported in this review have been characterized crystallographically, however no structural information (except one case) are incorporated in this article, as it will occupy space without significant enhancement of chemistry part. Different factors such as size of the ionophore cavity, size of metal ion, coordination sites/donor atoms, steric crowding and solvents, which determine selectivity have been discussed. Response of ion recognition process to different analytical techniques is another interesting factor discussed in this article.

  8. State-selected ion-molecule reactions with Coulomb-crystallized molecular ions in traps

    CERN Document Server

    Tong, Xin; Reyes, Juvenal Yosa; Germann, Matthias; Meuwly, Markus; Willitsch, Stefan

    2012-01-01

    State-selected Coulomb-crystallized molecular ions were employed for the first time in ion-molecule reaction studies using the prototypical charge-transfer process $\\mathrm{N_2^++N_2\\rightarrow N_2+N_2^+}$ as an example. By preparing the reactant ions in a well-defined rovibrational state and localizing them in space by sympathetic cooling to millikelvin temperatures in an ion trap, state- and energy-controlled reaction experiments with sensitivities on the level of single ions were performed. The experimental results were interpreted with quasi-classical trajectory simulations on a six-dimensional potential-energy surface which provided detailed insight into translation-to-rotation energy transfer occurring during charge transfer between N$_2$ and N$_2^+$.

  9. Gas feeding molecular phosphorous ion source for semiconductor implanters

    Science.gov (United States)

    Gushenets, V. I.; Oks, E. M.; Bugaev, A. S.; Kulevoy, T. V.; Hershcovitch, A.

    2014-02-01

    Phosphorus is a much used dopant in semiconductor technology. Its vapors represent a rather stable tetratomic molecular compound and are produced from one of the most thermodynamically stable allotropic forms of phosphorus—red phosphorus. At vacuum heating temperatures ranging from 325 °C, red phosphorus evaporates solely as P4 molecules (P4/P2 ˜ 2 × 105, P4/P ˜ 1021). It is for this reason that red phosphorus is best suited as a source of polyatomic molecular ion beams. The paper reports on experimental research in the generation of polyatomic phosphorus ion beams with an alternative P vapor source for which a gaseous compound of phosphorus with hydrogen - phosphine - is used. The ion source is equipped with a specially designed dissociator in which phosphine heated to temperatures close to 700 °C decomposes into molecular hydrogen and phosphorus (P4) and then the reaction products are delivered through a vapor line to the discharge chamber. Experimental data are presented reflecting the influence of the discharge parameters and temperature of the dissociator heater on the mass-charge state of the ion beam.

  10. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  11. Precision Spectroscopy on Single Cold Trapped Molecular Nitrogen Ions

    Science.gov (United States)

    Hegi, Gregor; Najafian, Kaveh; Germann, Matthias; Sergachev, Ilia; Willitsch, Stefan

    2016-06-01

    The ability to precisely control and manipulate single cold trapped particles has enabled spectroscopic studies on narrow transitions of ions at unprecedented levels of precision. This has opened up a wide range of applications, from tests of fundamental physical concepts, e.g., possible time-variations of fundamental constants, to new and improved frequency standards. So far most of these experiments have concentrated on atomic ions. Recently, however, attention has also been focused on molecular species, and molecular nitrogen ions have been identified as promising candidates for testing a possible time-variation of the proton/electron mass ratio. Here, we report progress towards precision-spectroscopic studies on dipole-forbidden vibrational transitions in single trapped N2+ ions. Our approach relies on the state-selective generation of single N2+ ions, subsequent infrared excitation using high intensity, narrow-band quantum-cascade lasers and a quantum-logic scheme for non-destructive state readout. We also characterize processes limiting the state lifetimes in our experiment, which impair the measurement fidelity. P. O. Schmidt et. al., Science 309 (2005), 749. M. Kajita et. al., Phys. Rev. A 89 (2014), 032509 M. Germann , X. Tong, S. Willitsch, Nature Physics 10 (2014), 820. X. Tong, A. Winney, S. Willitsch, Phys. Rev. Lett. 105 (2010), 143001

  12. Molecular dynamics simulation of ion transport in a nanochannel

    Institute of Scientific and Technical Information of China (English)

    CHEN Min; CHEN YunFei; ZHONG Wu; YANG JueKuan

    2008-01-01

    A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented,and the process of ion transport in the nanochannel was simulated in this paper.The model consists of two water sinks at the two ends and a pump in the middle,which is different from a single pump model in previous MD simulations.Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the en-richment of counterions in the nanochannel.A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel,and the current in the pump region is mainly induced by the motion of counterions.In addition,the ion number in the pump region rapidly decreases as the external electric field is applied.In the equilibrated system,the electrically neutral character in the pump region is destroyed and this region displays a certain electrical char-acter,which depends on the surface charge.The ion distribution is greatly different from the results predicted by the continuum theory,e.g.a smaller peak value of Na+ concentration appears near the wall.The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density.The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model.The mechanism of some special ex-perimental phenomena in a nanochannel and the effect of the surface charge den-sity on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.

  13. Molecular dynamics simulation of ion transport in a nanochannel

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented, and the process of ion transport in the nanochannel was simulated in this paper. The model consists of two water sinks at the two ends and a pump in the middle, which is different from a single pump model in previous MD simulations. Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the enrichment of counterions in the nanochannel. A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel, and the current in the pump region is mainly induced by the motion of counterions. In addition, the ion number in the pump region rapidly decreases as the external electric field is applied. In the equilibrated system, the electrically neutral character in the pump region is destroyed and this region displays a certain electrical character, which depends on the surface charge. The ion distribution is greatly different from the results predicted by the continuum theory, e.g. a smaller peak value of Na+ concentration appears near the wall. The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density. The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model. The mechanism of some special experimental phenomena in a nanochannel and the effect of the surface charge density on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.

  14. Ion-Pair States in Triplet Molecular Hydrogen

    Science.gov (United States)

    Setzer, W.; Baker, B. C.; Ashman, S.; Morgan, T. J.

    2016-05-01

    An experimental search is underway to observe the long range triplet ionic states H+ H- of molecular hydrogen. Resonantly enhanced multi-photon ionization of the metastable c 3∏u- 2 pπ state is used access to the R(1)nd1 n = 21 Rydberg state that serves as an intermediate stepping stone state to probe the energy region above the ionization limit with a second tunable laser photon. The metastable state is prepared by electron capture of 6 keV H2+ions in potassium in a molecular beam. Formation of the H+ H- triplet configuration involves triplet excited states of the H- ion, especially the 2p23Pe state, the second bound state of H- predicted to exist with a lifetime long compared to typical auto ionization lifetimes but not yet observed experimentally. Details of the experiment and preliminary results to date will be presented at the conference.

  15. Photodetachment of a Negative Hydrogen Molecular Ion near an Interface

    Institute of Scientific and Technical Information of China (English)

    WANG Pe-Hua

    2007-01-01

    Photodetachment of a negative hydrogen molecular ion near an interface is studied by using the two-centre model and the closed orbit theory. The calculation results show that the photodetachment cross section is related to the distance between the two centres in the H-2 and different molecular ion-interface distances. The comparison between the cross section of H-2 near an interface with the section of H- shows that at the equilibrium distance of two centres and at low photon energy, the photodetachment cross section of H-2 is about twice the cross section of H-, which shows that the interference of the two nuclei is very strong; when the distance between the two centres is large, the section of H-2 is almost the same as the cross section of H- near one interface, which indicates that the interference effect of the two centres vanishes.

  16. Molecular ions of ionic liquids in the gas phase.

    Science.gov (United States)

    Gross, Jürgen H

    2008-09-01

    Ionic liquids form neutral ion pairs (CA) upon evaporation. The softness of the gas-phase ionization of field ionization has been used to generate "molecular ions," CA(+*), of ionic liquids, most probably by neutralization of the anion. In detail, 1-ethyl-3-methylimidazolium-thiocyanate, [C(6)H(11)N(2)](+) [SCN](-), 1-butyl-3-methylimidazolium-tricyanomethide, [C(8)H(15)N(2)](+) [C(4)N(3)](-), N-butyl-3-methylpyridinium-dicyanamide, [C(10)H(16)N](+) [C(2)N(3)](-), and 1-butyl-1-methylpyrrolidinium-bis[(trifluormethyl)sulfonyl]amide, [C(9)H(20)N](+) [C(2)F(6)NO(4)S(2)](-) were used. The assignment as CA(+*) ions, which has been confirmed by accurate mass measurements and misassignments due to thermal decomposition of the ionic liquids, has been ruled out by field desorption and electrospray ionization mass spectrometry of the residues.

  17. Sympathetic cooling of molecular ion motion to the ground state

    CERN Document Server

    Rugango, Rene; Dixon, Thomas H; Gray, John M; Khanyile, Ncamiso; Shu, Gang; Clark, Robert J; Brown, Kenneth R

    2014-01-01

    We demonstrate sympathetic sideband cooling of a $^{40}$CaH$^{+}$ molecular ion co-trapped with a $^{40}$Ca$^{+}$ atomic ion in a linear Paul trap. Both axial modes of the two-ion chain are simultaneously cooled to near the ground state of motion. The center of mass mode is cooled to an average quanta of harmonic motion $\\overline{n}_{\\mathrm{COM}} = 0.13 \\pm 0.03$, corresponding to a temperature of $12.47 \\pm 0.03 ~\\mu$K. The breathing mode is cooled to $\\overline{n}_{\\mathrm{BM}} = 0.05 \\pm 0.02$, corresponding to a temperature of $15.36 \\pm 0.01~\\mu$K.

  18. Electron collisions and internal excitation in stored molecular ion beams

    Energy Technology Data Exchange (ETDEWEB)

    Buhr, H.

    2006-07-26

    In storage ring experiments the role, which the initial internal excitation of a molecular ion can play in electron collisions, and the effect of these collisions on the internal excitation are investigated. Dissociative recombination (DR) and inelastic and super-elastic collisions are studied in the system of He{sup +}{sub 2}. The DR rate coefficient at low energies depends strongly on the initial vibrational excitation in this system. Therefore changes in the DR rate coefficient are a very sensitive probe for changes in the vibrational excitation in He{sup +}{sub 2}, which is used to investigate the effects of collisions with electrons and residual gas species. The low-energy DR of HD{sup +} is rich with resonances from the indirect DR process, when certain initial rotational levels in the molecular ion are coupled to levels in neutral Rydberg states lying below the ion state. Using new procedures for high-resolution electron-ion collision spectroscopy developed here, these resonances in the DR cross section can be measured with high energy sensitivity. This allows a detailed comparison with results of a MQDT calculation in an effort to assign some or all of the resonances to certain intermediate Rydberg levels. (orig.)

  19. Influence of salt ions on binding to molecularly imprinted polymers.

    Science.gov (United States)

    Kempe, Henrik; Kempe, Maria

    2010-02-01

    Salt ions were found to have an influence on template binding to two model molecularly imprinted polymers (MIPs), targeted to penicillin G and propranolol, respectively, in water-acetonitrile mixtures. Water was detrimental to rebinding of penicillin G whereas propranolol bound in the entire water-acetonitrile range tested. In 100% aqueous solution, 3-M salt solutions augmented the binding of both templates. The effects followed the Hofmeister series with kosmotropic ions promoting the largest increase. Binding was mainly of a non-specific nature under these conditions. In acetonitrile containing low amounts of water, the specific binding to the MIPs increased with the addition of salts. Binding of penicillin G followed the Hofmeister series while an ion-exchange mechanism was observed for propranolol. The results suggest that hydration of kosmotropic ions reduces the water activity in water-poor media providing a stabilizing effect on water-sensitive MIP-template interactions. The effects were utilized to develop a procedure for molecularly imprinted solid-phase extraction (MISPE) of penicillin G from milk with a recovery of 87%.

  20. A controllable molecular sieve for Na+ and K+ ions.

    Science.gov (United States)

    Gong, Xiaojing; Li, Jichen; Xu, Ke; Wang, Jianfeng; Yang, Hui

    2010-02-17

    The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water.

  1. Diatom-Based Material Production Demonstration

    Science.gov (United States)

    2016-03-14

    diatom cell walls. ............................................................... 19! Fig. 12 Setup for sieving diatom cell walls on the left, metal ...of diatom biomass. .............. 15! Table 4 P1 and P2 step details for cleaning of diatom cell walls at the farm. .................. 19! Table 5...are the most silicified and have the most intricate structures . Diatom valves are used to identify diatoms based on their morphology. Diatom

  2. Seasonal variations in fouling diatom communities on the Yantai coast

    Science.gov (United States)

    Yang, Cuiyun; Wang, Jianhua; Yu, Yang; Liu, Sujing; Xia, Chuanhai

    2015-03-01

    Fouling diatoms are a main component of biofilm, and play an important role in marine biofouling formation. We investigated seasonal variations in fouling diatom communities that developed on glass slides immersed in seawater, on the Yantai coast, northern Yellow Sea, China, using microscopy and molecular techniques. Studies were conducted during 2012 and 2013 over 3, 7, 14, and 21 days in each season. The abundance of attached diatoms and extracellular polymeric substances increased with exposure time of the slides to seawater. The lowest diatom density appeared in winter and the highest species richness and diversity were found in summer and autumn. Seasonal variation was observed in the structure of fouling diatom communities. Pennate diatoms Cylindrotheca, Nitzschia, Navicula, Amphora, Gomphonema, and Licmophora were the main fouling groups. Cylindrotheca sp. dominated in the spring. Under laboratory culture conditions, we found that Cylindrotheca grew very fast, which might account for the highest density of this diatom in spring. The lower densities in summer and autumn might result from the emergence of fouling animals and environmental factors. The Cylindrotheca sp. was identified as Cylindrotheca closterium using18S rDNA sequencing. The colonization process of fouling diatoms and significant seasonal variation in this study depended on environmental and biological factors. Understanding the basis of fouling diatoms is essential and important for developing new antifouling techniques.

  3. Imaging ion and molecular transport at subcellular resolution by secondary ion mass spectrometry

    Science.gov (United States)

    Chandra, Subhash; Morrison, George H.

    1995-05-01

    The transport of K+, Na+, and Ca2+ were imaged in individual cells with a Cameca IMS-3f ion microscope. Strict cryogenic frozen freeze-dry sample preparations were employed. Ion redistribution artifacts in conventional chemical preparations are discussed. Cryogenically prepared freeze-fractured freeze-dried cultured cells allowed the three-dimensional ion microscopic imaging of elements. As smaller structures in calcium images can be resolved with the 0.5 [mu]m spatial resolution, correlative techniques are needed to confirm their identity. The potentials of reflected light microscopy, scanning electron microscopy and laser scanning confocal microscopy are discussed for microfeature recognition in freeze-fractured freeze-dried cells. The feasibility of using frozen freeze-dried cells for imaging molecular transport at subcellular resolution was tested. Ion microscopy successfully imaged the transport of the isotopically tagged (13C, 15N) amino acid, -arginine. The labeled amino acid was imaged at mass 28 with a Cs+ primary ion beam as the 28(13C15N)- species. After a 4 h exposure of LLC-PK1 kidney cells to 4 mM labeled arginine, the amino acid was localized throughout the cell with a preferential incorporation into the nucleus and nucleolus. An example is also shown of the ion microscopic imaging of sodium borocaptate, an experimental therapeutic drug for brain tumors, in cryogenically prepared frozen freeze-dried Swiss 3T3 cells.

  4. Understanding Molecular-Ion Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    Science.gov (United States)

    2014-02-03

    the center of the vacuum chamber, denoted by the blue arrow, is 40Ca magneto - optical trap (MOT) co- located with a linear quadrupole radio- frequency...ion trap (LQT) system. The 40Ca MOT laser beams (blue) are evidenced by scattered light from the optics . The necessary computer and laser controls...cold molecules ,” Nature 495, 490 (2012)]. Construction of the next generation MOTION trap : Using what was learned in the sympatehtic cooling

  5. Ionic fragmentation channels in electron collisions of small molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Hoffmann, Jens

    2009-01-28

    Dissociative Recombination (DR) is one of the most important loss processes of molecular ions in the interstellar medium (IM). Ion storage rings allow to investigate these processes under realistic conditions. At the Heidelberg test storage ring TSR a new detector system was installed within the present work in order to study the DR sub-process of ion pair formation (IPF). The new detector expands the existing electron target setup by the possibility to measure strongly deflected negative ionic fragments. At the TSR such measurements can be performed with a uniquely high energy resolution by independently merging two electron beams with the ion beam. In this work IPF of HD{sup +}, H{sub 3}{sup +} and HF{sup +} has been studied. In the case of HD{sup +} the result of the high resolution experiment shows quantum interferences. Analysis of the quantum oscillations leads to a new understanding of the reaction dynamics. For H{sub 3}{sup +} it was for the first time possible to distinguish different IPF channels and to detect quantum interferences in the data. Finally the IPF of HF{sup +} was investigated in an energy range, where in previous experiments no conclusive results could be obtained. (orig.)

  6. Molecular Mechanism of Ion-Ion and Ion-Substrate Coupling in the Na+-Dependent Leucine Transporter LeuT

    OpenAIRE

    Caplan, David A.; Subbotina, Julia O.; Noskov, Sergei Yu.

    2008-01-01

    Ion-coupled transport of neurotransmitter molecules by neurotransmitter:sodium symporters (NSS) play an important role in the regulation of neuronal signaling. One of the major events in the transport cycle is ion-substrate coupling and formation of the high-affinity occluded state with bound ions and substrate. Molecular mechanisms of ion-substrate coupling and the corresponding ion-substrate stoichiometry in NSS transporters has yet to be understood. The recent determination of a high-resol...

  7. Metal salts for molecular ion yield enhancement in organic secondary ion mass spectrometry: a critical assessment.

    Science.gov (United States)

    Delcorte, A; Bertrand, P

    2005-04-01

    In a search for molecular ion signal enhancement in organic SIMS, the efficiency of a series of organic and inorganic salts for molecular cationization has been tested using a panel of nonvolatile molecules with very different chemical characteristics (leucine enkephalin, Irganox 1010, tetraphenylnaphthalene, polystyrene). The compounds used for cationization include alkali bromide and group Ib metal salts (XBr with X = Li, Na, K; CF3CO2Ag; AgNO3; [CH3COCH=C(O-)CH3]2Cu; AuCl3). Alkali ions, very good for polar molecule cationization, prove to be of limited interest for nonpolar molecules such as polystyrene. Silver trifluoroacetate displays excellent results for all the considered molecules, except for leucine enkephalin (which might be due to the use of different solvents for the analyte and the salt). Instead, silver nitrate mixed with leucine enkephalin in an ethanol solution provides intense molecular signals. The influence of the respective concentrations of analyte and salt in solution, of the silver trifluoroacetate solution stability, and of the sample microstructure on the secondary ion intensities are also investigated. The results of other combinations of analyte and salts are reported. Finally, the use of salts is critically compared to other sample preparation procedures previously proposed for SIMS analysis of large organic molecules.

  8. Small Ion Channel Linking Molecular Simulations and Electrophysiology

    Science.gov (United States)

    Pohorille, Andrzej

    2017-01-01

    Ion channels are pore-forming protein assemblies that mediate the transport of small ions across cell membranes. Otherwise, membrane bilayers would be almost impermeable to ions incapable to traverse the low dielectric constant, hydrophobic membrane core. Ion channels are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses, cardiac functions, muscle contraction and apoptosis. On the other extreme of biological complexity, viral ion channels (viroporins) influence many stages of the virus infection cycle either through regulating virus replication, such as entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. Ion channels were crucial components of protocells. Their emergence facilitated adaptation of nascent life to different environmental conditions. The earliest ion channels must have been much simpler than most of their modern ancestors. Viral channels are among only a few naturally occurring models to study the structure, function and evolution of primordial channels. Experimental studies of these properties are difficult and often unreliable. In principle, computational methods, and molecular dynamics (MD) simulations in particular, can aid in providing information about both the structure and the function of ion channels. However, MD suffers from its own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. It is, therefore, essential to determine the reliability of MD simulations. We propose to do so on the basis of two criteria. One is channel stability on time scales that extend for several microseconds or longer. The other is the ability to reproduce the measured ionic conductance as a function of applied voltage. If both the stability and the calculated ionic conductance are satisfactory it will greatly increase our confidence that the structure and the function of a

  9. Rotational laser cooling of vibrationally and translationally cold molecular ions

    DEFF Research Database (Denmark)

    Staanum, Peter; Højbjerre, Klaus; Skyt, Peter Sandegaard

    2010-01-01

    -molecular reactions with coherent light fields 8, 9 , for quantum-state-selected bi-molecular reactions 10, 11, 12 and for astrochemistry 12 . Here, we demonstrate rotational ground-state cooling of vibrationally and translationally cold MgH+ ions, using a laser-cooling scheme based on excitation of a single...... rovibrational transition 13, 14 . A nearly 15-fold increase in the rotational ground-state population of the X  1Σ+ electronic ground-state potential has been obtained. The resulting ground-state population of 36.7±1.2% is equivalent to that of a thermal distribution at about 20 K. The obtained cooling results...

  10. Heteronuclear diatomics in diffuse and translucent clouds

    CERN Document Server

    Weselak, T

    2013-01-01

    Diffuse and translucent molecular clouds fill a vast majority of the interstellar space in the galactic disk being thus the most typical objects of the Interstellar Medium (ISM). Recent advances in observational techniques of modern optical and ultraviolet spectroscopy led to detection of many features of atomic and molecular origin in spectra of such clouds. Molecular spectra of heteronuclear diatomic molecules, ie. OH, OH+, CH CH+, CN, NH, CO play an important role in understanding chemistry and physical conditions in environments they do populate. A historical review of astronomical observations of interstellar molecules is presented. Recent results based on visual and ultraviolet observations of molecular features in spectra of reddened, early type OB-stars are presented and discussed. Appearance of vibrational-rotational spectra with observed transitions based on high-quality spectra, are also presented. Relations between column densities of heteronuclear diatomics (based on the recommended oscillator st...

  11. Application of atomic and molecular primary ions for TOF SIMS analysis of additive containing polymer surfaces

    Science.gov (United States)

    Stapel, D.; Benninghoven, A.

    2001-04-01

    The influence of primary ion mass and composition on secondary ion emission of the additive Irganox 1010 ( m=1176 u) in polyethylene was investigated. O +, Ar +, Xe +, O 2+, CO 2+, SF 5+, C 7H 7+, C 10H 8+, C 6F 6+, and C 10F 8+ with a total energy of 11 keV were used as primary ions under static secondary ion mass spectrometry (SIMS) conditions. Positive and negative molecular secondary ions characterizing the additive were determined and their yields were evaluated. For all characteristic secondary ions we found a strong yield enhancement with increasing mass for atomic primary ions and increasing number of constituents for molecular primary ions. This yield enhancement is saturated once the molecular primary ion is made of more than six heavy atoms. In addition this yield increase depends on the mass and structure of the considered secondary ion. We did not find any evidence for an influence of the chemical composition of the applied molecular primary ions on the secondary ion emission when static SIMS conditions were met. The improved imaging capabilities of molecular primary ions was demonstrated by comparing focused Ar + and SF 5+ primary ion beams when mapping characteristic secondary ion emission from a structured additive containing polypropylene surface.

  12. Molecular ions in the protostellar shock L1157-B1

    CERN Document Server

    Podio, L; Ceccarelli, C; Codella, C; Bachiller, R

    2014-01-01

    We perform a complete census of molecular ions with an abundance larger than 1e-10 in the protostellar shock L1157-B1 by means of an unbiased high-sensitivity survey obtained with the IRAM-30m and Herschel/HIFI. By means of an LVG radiative transfer code the gas physical conditions and fractional abundances of molecular ions are derived. The latter are compared with estimates of steady-state abundances in the cloud and their evolution in the shock calculated with the chemical model Astrochem. We detect emission from HCO+, H13CO+, N2H+, HCS+, and, for the first time in a shock, from HOCO+, and SO+. The bulk of the emission peaks at blueshifted velocity, ~ 0.5-3 km/s with respect to systemic, has a width of ~ 4-8 km/s, and is associated with the outflow cavities (T_kin ~ 20-70 K, n(H2) ~ 1e5 cm-3). Observed HCO+ and N2H+ abundances are in agreement with steady-state abundances in the cloud and with their evolution in the compressed and heated gas in the shock for cosmic rays ionization rate Z = 3e-16 s-1. HOCO+...

  13. Photodissociation spectroscopy of the dysprosium monochloride molecular ion

    CERN Document Server

    Dunning, Alexander; Showalter, Steven J; Puri, Prateek; Kotochigova, Svetlana; Hudson, Eric R

    2015-01-01

    We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl$^+$. The cross section for the photon energy range 35,500 cm$^{-1}$ to 47,500 cm$^{-1}$ is measured using an integrated ion trap and time-of-flight mass spectrometer, and we observe a broad, asymmetric profile that is peaked near 43,000 cm$^{-1}$. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl$^+$ is unprecedentedly complex due to the presence of multiple open electronic shells, including 4f$^{10}$ orbitals. The molecule has nine attractive potentials with ionically-bonded electrons and 99 repulsive potentials dissociating to a ground state Dy$^+$ ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between t...

  14. Photoionization and photofragmentation of the C60+ molecular ion

    Science.gov (United States)

    Baral, K. K.; Aryal, N. B.; Esteves-Macaluso, D. A.; Thomas, C. M.; Hellhund, J.; Lomsadze, R.; Kilcoyne, A. L. D.; Müller, A.; Schippers, S.; Phaneuf, R. A.

    2016-03-01

    Cross-section measurements are reported for single and double photoionization of C60+ ions in the photon energy range 18-150 eV accompanied by the loss of zero to seven pairs of carbon atoms, as well as for fragmentation without ionization resulting in loss of two to eight pairs of C atoms in the photon energy range 18-65 eV. Absolute measurements were performed by merging a beam of C60+ molecular ions with a beam of monochromatized synchrotron radiation. Product channels involving dissociation yielding smaller fullerene fragment ions account for nearly half of the total measured oscillator strength in this energy range. The sum of cross sections for the measured product channels is compared to a published calculation of the total photoabsorption cross section of neutral C60 based on time-dependent density-functional theory. This comparison and an accounting of oscillator strengths indicate that with the exception of C58+, the most important product channels resulting from photoabsorption were accounted for in the experiment. Threshold energies for the successive removal of carbon atom pairs accompanying photoionization are also determined from the measurements.

  15. The Central Carbon and Energy Metabolism of Marine Diatoms

    Directory of Open Access Journals (Sweden)

    Adriano Nunes-Nesi

    2013-05-01

    Full Text Available Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.

  16. Molecular level characterization of diatom-associated biopolymers that bind 234Th, 233Pa, 210Pb, and 7Be in seawater: A case study with Phaeodactylum tricornutum

    Science.gov (United States)

    Chuang, Chia-Ying; Santschi, Peter H.; Xu, Chen; Jiang, Yuelu; Ho, Yi-Fang; Quigg, Antonietta; Guo, Laodong; Hatcher, Patrick G.; Ayranov, Marin; Schumann, Dorothea

    2015-09-01

    In order to investigate the importance of biogenic silica associated biopolymers on the scavenging of radionuclides, the diatom Phaeodactylum tricornutum was incubated together with the radionuclides 234Th, 233Pa, 210Pb, and 7Be during their growth phase. Normalized affinity coefficients were determined for the radionuclides bound with different organic compound classes (i.e., proteins, total carbohydrates, uronic acids) in extracellular (nonattached and attached exopolymeric substances), intracellular (ethylene diamine tetraacetic acid and sodium dodecyl sulfate extractable), and frustule embedded biopolymeric fractions (BF). Results indicated that radionuclides were mostly concentrated in frustule BF. Among three measured organic components, Uronic acids showed the strongest affinities to all tested radionuclides. Confirmed by spectrophotometry and two-dimensional heteronuclear single quantum coherence-nuclear magnetic resonance analyses, the frustule BF were mainly composed of carboxyl-rich, aliphatic-phosphoproteins, which were likely responsible for the strong binding of many of the radionuclides. Results from this study provide evidence for selective absorption of radionuclides with different kinds of diatom-associated biopolymers acting in concert rather than as a single compound. This clearly indicates the importance of these diatom-related biopolymers, especially frustule biopolymers, in the scavenging and fractionation of radionuclides used as particle tracers in the ocean.

  17. The Microscopic World of Diatoms

    Science.gov (United States)

    Sultany, Molly; Bixby, Rebecca

    2016-01-01

    For students in biology, chemistry, or environmental science, diatoms offer excellent insight into watershed health and human impact on the environment. Diatoms are found globally in virtually every habitat that has sunlight and moisture, including polar seas, tropical streams, and on moist soils and mosses. Studying diatoms as biological…

  18. Hydrogen molecular ions for improved determination of fundamental constants

    CERN Document Server

    Karr, J -Ph; Koelemeij, Jeroen; Korobov, Vladimir

    2016-01-01

    The possible use of high-resolution rovibrational spectroscopy of the hydrogen molecular ions H + 2 and HD + for an independent determination of several fundamental constants is analyzed. While these molecules had been proposed for metrology of nuclear-to-electron mass ratios, we show that they are also sensitive to the radii of the proton and deuteron and to the Rydberg constant at the level of the current discrepancies colloquially known as the proton size puzzle. The required level of accuracy, in the 10 --12 range, can be reached both by experiments, using Doppler-free two-photon spectroscopy schemes, and by theoretical predictions. It is shown how the measurement of several well-chosen rovibrational transitions may shed new light on the proton-radius puzzle, provide an alternative accurate determination of the Rydberg constant, and yield new values of the proton-to-electron and deuteron-to-proton mass ratios with one order of magnitude higher precision.

  19. Molecular dynamics simulations of water within models of ion channels.

    Science.gov (United States)

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-04-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

  20. Polarizabilities and Other Properties of the td Muons Molecular Ion

    Science.gov (United States)

    Bhatia, A. K.; Drachman, Richard J.; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    Wavefunctions of Hylleraas type were used earlier to calculate energy levels of muonic systems. Recently, we found in the case of the molecular ions H2+, D2+ and HD+ that it was necessary to include high powers of the internuclear distance in the Hylleraas functions to localize the nuclear motion when treating the ions as three-body systems without invoking the Born-Oppenheimer approximation. We try the same approach in a muonic system, td(mu-). Improved convergence is obtained for J = 0 and 1 states for shorter expansions when we use this type of generalized Hylleraas function, but as the expansion length increases the high powers are no longer useful. We obtain good energy values for the two lowest J = 0 and J = 1 states and compare them with the best earlier calculations. Expectation values are obtained for various operators, the Fermi contact parameters, and the permanent quadrupole moment. The cusp conditions are also calculated. The polarizability of the ground state is then calculated using second-order perturbation theory with intermediate J = 1 pseudostates. It should be possible to measure the polarizability by observing Rydberg states of atoms with td(mu-) acting as the nucleus.

  1. Molecular dynamics simulation of graphene bombardment with Si ion

    Science.gov (United States)

    Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

    2014-03-01

    Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

  2. Fragmentation of molecular ions in slow electron collisions

    Energy Technology Data Exchange (ETDEWEB)

    Novotny, Steffen

    2008-06-25

    The fragmentation of positively charged hydrogen molecular ions by the capture of slow electrons, the so called dissociative recombination (DR), has been investigated in storage ring experiments at the TSR, Heidelberg, where an unique twin-electron-beam arrangement was combined with high resolution fragment imaging detection. Provided with well directed cold electrons the fragmentation kinematics were measured down to meV collision energies where pronounced rovibrational Feshbach resonances appear in the DR cross section. For thermally excited HD{sup +} the fragmentation angle and the kinetic energy release were studied at variable precisely controlled electron collision energies on a dense energy grid from 10 to 80 meV. The anisotropy described for the first time by Legendre polynomials higher 2{sup nd} order and the extracted rotational state contributions were found to vary on a likewise narrow energy scale as the rotationally averaged DR rate coefficient. Ro-vibrationally resolved DR experiments were performed on H{sub 2}{sup +} produced in distinct internal excitations by a novel ion source. Both the low-energy DR rate as well as the fragmentation dynamics at selected resonances were measured individually in the lowest two vibrational and first three excited rotational states. State-specific DR rates and angular dependences are reported. (orig.)

  3. Deterministic delivery of externally cold and precisely positioned single molecular ions

    CERN Document Server

    Leschhorn, G; Schaetz, T

    2011-01-01

    We present the preparation and deterministic delivery of a selectable number of externally cold molecular ions. A laser cooled ensemble of Mg^+ ions subsequently confined in several linear Paul traps inter-connected via a quadrupole guide serves as a cold bath for a single or up to a few hundred molecular ions. Sympathetic cooling embeds the molecular ions in the crystalline structure. MgH^+ ions, that serve as a model system for a large variety of other possible molecular ions, are cooled down close to the Doppler limit and are positioned with an accuracy of one micrometer. After the production process, severely compromising the vacuum conditions, the molecular ion is efficiently transfered into nearly background-free environment. The transfer of a molecular ion between different traps as well as the control of the molecular ions in the traps is demonstrated. Schemes, optimized for the transfer of a specific number of ions, are realized and their efficiencies are evaluated. This versatile source applicable f...

  4. Molecular and Morphological Investigations of the Stauros-bearing, Raphid Pennate Diatoms (Bacillariophyceae): Craspedostauros E.J. Cox, and Staurotropis T.B.B. Paddock, and their Relationship to the Rest of the Mastogloiales.

    Science.gov (United States)

    Ashworth, Matt P; Lobban, Christopher S; Witkowski, Andrzej; Theriot, Edward C; Sabir, Meeshal J; Baeshen, Mohammad N; Hajarah, Nahid H; Baeshen, Nabih A; Sabir, Jamal S; Jansen, Robert K

    2017-02-01

    Several lineages of raphe-bearing diatoms possess a "stauros," which is a transverse, usually thickened area free of pores across the center of the valve. It has been suggested that this structure has evolved several times across the raphid diatoms, but we have noticed similarities beyond the stauros between two marine genera-Craspedostauros and Staurotropis-in the structure of their pore occlusions. We have isolated, cultured and extracted DNA from several strains of both genera to infer the phylogenetic relationship between these taxa, as well as test the suggested relationship of Craspedostauros to Achnanthes and Mastogloia based on plastid morphology. DNA sequence data (nuclear-encoded rRNA SSU, plastid-encoded rbcL and psbC) suggest that, except for Mastogloia, these genera are closely-related, though not sister taxa. The DNA phylogeny also suggests that the Mastogloiales are not monophyletic, with clades containing Achnanthes and Craspedostauros sister to clades containing taxa in the Bacillariales. Using evidence from molecular and morphological data, we describe the following new taxa: Craspedostauros alyoubii and C. paradoxa from the Red Sea and Guam, respectively; Staurotropis khiyamii and S. americana from the Red Sea and the Gulf of Mexico, respectively; and Dreuhlago cuneata n. gen., n. sp. from Guam.

  5. A diatom gene regulating nitric-oxide signaling and susceptibility to diatom-derived aldehydes.

    Science.gov (United States)

    Vardi, Assaf; Bidle, Kay D; Kwityn, Clifford; Hirsh, Donald J; Thompson, Stephanie M; Callow, James A; Falkowski, Paul; Bowler, Chris

    2008-06-24

    Diatoms are unicellular phytoplankton accounting for approximately 40% of global marine primary productivity [1], yet the molecular mechanisms underlying their ecological success are largely unexplored. We use a functional-genomics approach in the marine diatom Phaeodactylum tricornutum to characterize a novel protein belonging to the widely conserved YqeH subfamily [2] of GTP-binding proteins thought to play a role in ribosome biogenesis [3], sporulation [4], and nitric oxide (NO) generation [5]. Transgenic diatoms overexpressing this gene, designated PtNOA, displayed higher NO production, reduced growth, impaired photosynthetic efficiency, and a reduced ability to adhere to surfaces. A fused YFP-PtNOA protein was plastid localized, distinguishing it from a mitochondria-localized plant ortholog. PtNOA was upregulated in response to the diatom-derived unsaturated aldehyde 2E,4E/Z-decadienal (DD), a molecule previously shown to regulate intercellular signaling, stress surveillance [6], and defense against grazers [7]. Overexpressing cell lines were hypersensitive to sublethal levels of this aldehyde, manifested by altered expression of superoxide dismutase and metacaspases, key components of stress and death pathways [8, 9]. NOA-like sequences were found in diverse oceanic regions, suggesting that a novel NO-based system operates in diatoms and may be widespread in phytoplankton, providing a biological context for NO in the upper ocean [10].

  6. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics.

    OpenAIRE

    Kerr, I. D.; Sankararamakrishnan, R; Smart, O.S.; Sansom, M S

    1994-01-01

    A parallel bundle of transmembrane (TM) alpha-helices surrounding a central pore is present in several classes of ion channel, including the nicotinic acetylcholine receptor (nAChR). We have modeled bundles of hydrophobic and of amphipathic helices using simulated annealing via restrained molecular dynamics. Bundles of Ala20 helices, with N = 4, 5, or 6 helices/bundle were generated. For all three N values the helices formed left-handed coiled coils, with pitches ranging from 160 A (N = 4) to...

  7. Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms.

    Science.gov (United States)

    Groussman, Ryan D; Parker, Micaela S; Armbrust, E Virginia

    2015-01-01

    Ferroproteins arose early in Earth's history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world's oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III) permease); iron storage (ferritin); iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6) and defense against reactive oxygen species (superoxide dismutases). Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of paralogs. This

  8. Photosynthetic Pigments in Diatoms

    OpenAIRE

    Paulina Kuczynska; Malgorzata Jemiola-Rzeminska; Kazimierz Strzalka

    2015-01-01

    Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvestin...

  9. Photosynthetic Pigments in Diatoms

    Directory of Open Access Journals (Sweden)

    Paulina Kuczynska

    2015-09-01

    Full Text Available Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

  10. Forbidden Vibrational Transitions in Cold Molecular Ions: Experimental Observation and Potential Applications.

    Science.gov (United States)

    Germann, Matthias; Tonga, Xin; Willitsch, Stefan

    2015-01-01

    A range of interesting fundamental scientific questions can be addressed by high-precision molecular spectroscopy. A promising way towards this goal is the measurement of dipole-forbidden vibrational transitions in molecular ions. We have recently reported the first such observation in a molecular ion. Here, we give an overview of our method and our results as well as an outlook on potential future applications.

  11. Superstatistical velocity distributions of cold trapped ions in molecular dynamics simulations

    CERN Document Server

    Rouse, I

    2015-01-01

    We present a realistic molecular-dynamics treatment of laser-cooled ions in radiofrequency ion traps which avoids previously made simplifications such as modeling laser cooling as a friction force and combining individual heating mechanisms into a single effective heating force. Based on this implementation, we show that infrequent energetic collisions of single ions with background gas molecules lead to pronounced heating of the entire ion ensemble and a time-varying secular ensemble temperature which manifests itself in a superstatistical time-averaged velocity distribution of the ions. The effect of this finding on the experimental determination of ion temperatures and rate constants for cold chemical reactions is discussed.

  12. Photovoltaic lithium-ion battery fabricated by molecular precursor method

    Science.gov (United States)

    Nagai, Hiroki; Suzuki, Tatsuya; Takahashi, Yoshihisa; Sato, Mitsunobu

    2016-06-01

    A novel thin-film lithium-ion battery (LIB) which can be charged by the light irradiation was fabricated by molecular precursor method. The unprecedented, translucent thin-film LIB, fabricated on a fluorine-doped tin oxide pre-coated glass substrate, was attained by using the active materials, titania for anode and LiCoO2 for cathode, respectively. The averaged potential at 2.04V was observed by applying a constant current of 0.2mA. Then, that at 1.82V was detected after 60s during the sequential self-discharge process. The charging voltage of the assembled battery was 1.38V with irradiation of 1-sun, the self-discharge voltage was 1.37V. Based on the calibration curve of the charging voltages over constant currents ranging from 0-1.0mA, the detected value can be theoretically reduced to the charging operation by applying a constant current of approximately 60μA. The charge and discharge of this device was stable voltage at least 30 cycles. The two-in-one device can simultaneously generate and store electricity from solar light, the renewable energy source, and may be applied in smart windows for distributed power system according to on-site demand.

  13. Competition Between Two Excitation-dissociation Channels for Molecular Ions

    Institute of Scientific and Technical Information of China (English)

    Li-kun Lai; Li-min Zhang; Mao-ping Yang; Dan-na Zhou

    2009-01-01

    When the molecular ions XYZ+ (XY2+) are excited simultaneously from an electronic state E0 into two higher electronic states Eα and Eβ with supervened dissociation or predisso-ciation, competition between the α and β excitation-dissociation channels occurs. A the-oretical model is provided to deal with the competition of the two excitation-dissociation channels with more than two kinds of ionic products for XYZ+ (XY2+). Supposing that the photo-excitation rates of two states Eα and Eβ are much less than their dissociation or prc-dissociation rates, a theoretical equation can be deduced to fit the measured data, which reflects the dependence of the product branching ratios on the intensity ratios of two excitation lasers. From the fitted parameters the excitation cross section ratios are obtained. In experiment, we studied the competition between two excitation-dissociation channels of CO2+. By measuring the dependence of the product branching ratio on the intensity ra-tio of two dissociation lasers and fitting the experiment data with the theoretical equation, excitation cross section ratios were deduced.

  14. Using diatom indices for water quality assessment in a subtropical river, China.

    Science.gov (United States)

    Tan, Xiang; Sheldon, Fran; Bunn, Stuart E; Zhang, Quanfa

    2013-06-01

    Diatoms have been regularly used as bioindicators to assess water quality of surface waters. However, diatom-based indices developed for a specific geographic region may not be appropriate elsewhere. We sampled benthic diatom assemblages in the upper Han River, a subtropical river in China, to evaluate applicability of 14 diatom-based indices used worldwide for water quality assessment. A total of 194 taxa from 31 genera were identified in the dry season and 139 taxa from 23 genera in the wet season. During the dry season, significant relationships were found for all but one of the diatom-based indices (Index Diatom Artois-Picardie) with one or more physical and chemical variables including nutrients and ion concentrations in river waters. The Biological Diatom Index (IBD) and diatom-based eutrophication/pollution index (EPI-D) were strongly related to trophic status and ionic content, while Watanabe's Index was related to organic pollution and conductivity. Yet, the diatom indices showed weak relationships with physical and chemical variables during the wet season. It suggests that diatom-based indices developed in Europe can be applied with confidence as bioindicators of water quality in subtropical rivers of China, at least during base-flow conditions.

  15. Molecular design of the microbial cell surface toward the recovery of metal ions.

    Science.gov (United States)

    Kuroda, Kouichi; Ueda, Mitsuyoshi

    2011-06-01

    The genetic engineering of microorganisms to adsorb metal ions is an attractive method to facilitate the environmental cleanup of metal pollution and to enrich the recovery of metal ions such as rare metal ions. For the recovery of metal ions by microorganisms, cell surface design is an effective strategy for the molecular breeding of bioadsorbents as an alternative to intracellular accumulation. The cell surface display of known metal-binding proteins/peptides and the molecular design of novel metal-binding proteins/peptides have been performed using a cell surface engineering approach. The adsorption of specific metal ions is the important challenge for the practical recovery of metal ions. In this paper, we discuss the recent progress in surface-engineered bioadsorbents for the recovery of metal ions. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  17. Collision induced fragmentation of fast molecular ions in solids and gases. [Review, wake effects, excited states

    Energy Technology Data Exchange (ETDEWEB)

    Gemmell, D S

    1979-01-01

    A brief review is given of recent high resolution measurements on fragments arising from the collision-induced dissociation of fast (MeV) molecular ions. For solid targets, strong wake effects are observed. For gaseous targets, excited electronic states of the projectile ions play an important role. Measurements of this type provide useful information on the charge states of fast ions traversing matter. The experimental techniques show promise as a unique method for determining the geometrical structures of the molecular-ion projectiles. 41 references.

  18. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  19. Behavior of the Position-Spread Tensor in Diatomic Systems.

    Science.gov (United States)

    Brea, Oriana; El Khatib, Muammar; Angeli, Celestino; Bendazzoli, Gian Luigi; Evangelisti, Stefano; Leininger, Thierry

    2013-12-10

    The behavior of the Position-Spread Tensor (Λ) in a series of light diatomic molecules (either neutral or negative ions) is investigated at a Full Configuration Interaction level. This tensor, which is the second moment cumulant of the total position operator, is invariant with respect to molecular translations, while its trace is also rotationally invariant. Moreover, the tensor is additive in the case of noninteracting subsystems and can be seen as an intrinsic property of a molecule. In the present work, it is shown that the longitudinal component of the tensor, Λ∥, which is small for internuclear distances close to the equilibrium, tends to grow if the bond is stretched. A maximum is reached in the region of the bond breaking, then Λ∥ decreases and converges toward the isolated-atom value. The degenerate transversal components, Λ⊥, on the other hand, usually have a monotonic growth toward the atomic value. The Position Spread is extremely sensitive to reorganization of the molecular wave function, and it becomes larger in the case of an increase of the electron mobility, as illustrated by the neutral-ionic avoided crossing in LiF. For these reasons, the Position Spread can be an extremely useful property that characterizes the nature of the wave function in a molecular system.

  20. Production of silver nanoparticles by the diatom Phaeodactylum tricornutum

    Science.gov (United States)

    Wishkerman, Asher; Arad (Malis), Shoshana

    2017-05-01

    Diatoms (Bacillariophyceae) are the most species-rich group of algae, they are single-celled characterized by a silicified cell wall called a frustule. Diatoms are diverse in shape with many distinct features like raphe and fultoportulae. The diatom cell wall morphology and its hierarchy structure make it a unique unicellular organism for nanotechnology research and applications. Diatom cells are a promising system for green synthesis of nanomaterials like metallic nanoparticles (NPs), nanostructured polymers and other nanomaterials. The production of NPs is achieved today by using methods like attrition or pyrolysis. The cost and the toxic substances often used in these common methods of NPs synthesis limit their applications. Therefore, NPs biosynthesis by diatom cultures, which can be done at ambient CO2 concentrations, temperature and pressure, offers a sustainable alternative solution. In this work, we examined the formation of silver NPs (AgNPs) by the diatom Phaeodactylum tricornutum cultivated at 25°C for a period of 8 days. Using this approach, diatom cultures were either grown throughout the duration of the experiment in an artificial seawater (ASW)-f/2 medium enriched with 1 ppm Ag+ or grown in an ASW-f/2 medium where similar silver ion concentrations were added on experimental day 4. We found that 1 ppm Ag+ reduces the P. tricornutum growth by up to 50% as compared with the control. Moreover, scanning electron microscopy (SEM) in combination with Energy-Dispersive X-ray (EDX) showed the presence of AgNPs nanoparticles with different sizes and chemical composition associated with the diatom frustules and extracellular polymeric substances.

  1. Molecular dynamic simulation of secondaryion ion emission from an Al sample bombarded with MeV heavy ions

    Institute of Scientific and Technical Information of China (English)

    薛建明; 今西信嗣

    2002-01-01

    Sputtering yields and kinetic energy distributions (KED) of Al atomic ions ejected from a pure aluminium sampleunder MeV silicon ion bombardment were simulated with the molecular dynamic method. Since the electronic energyloss Se is much higher than the nuclear energy loss Sn when the incident ion energy is as high as several MeV, the Seeffect was also taken into consideration in the simulation. It was found that the simulated sputtering yield fits well withthe experimental data and the electronic energy loss has a slight effect at incident ion energies higher than 4 MeV. Thesimulated secondary ion KED spectrum is a little lower in the peak energy and narrower in the peak width than thatin the experiment.

  2. Formation and fragmentation of quadruply charged molecular ions by intense femtosecond laser pulses.

    Science.gov (United States)

    Yatsuhashi, Tomoyuki; Nakashima, Nobuaki

    2010-07-22

    We investigated the formation and fragmentation of multiply charged molecular ions of several aromatic molecules by intense nonresonant femtosecond laser pulses of 1.4 mum with a 130 fs pulse duration (up to 2 x 10(14) W cm(-2)). Quadruply charged states were produced for 2,3-benzofluorene and triphenylene molecular ion in large abundance, whereas naphthalene and 1,1'-binaphthyl resulted only in up to triply charged molecular ions. The laser wavelength was nonresonant with regard to the electronic transitions of the neutral molecules, and the degree of fragmentation was strongly correlated with the absorption of the singly charged cation radical. Little fragmentation was observed for naphthalene (off-resonant with cation), whereas heavy fragmentation was observed in the case of 1,1'-binaphthyl (resonant with cation). The degree of H(2) (2H) and 2H(2) (4H) elimination from molecular ions increased as the charge states increased in all the molecules examined. A striking difference was found between triply and quadruply charged 2,3-benzofluorene: significant suppression of molecular ions with loss of odd number of hydrogen was observed in the quadruply charged ions. The Coulomb explosion of protons in the quadruply charged state and succeeding fragmentation resulted in the formation of triply charged molecular ions with an odd number of hydrogens. The hydrogen elimination mechanism in the highly charged state is discussed.

  3. Diatomic gasdynamic lasers.

    Science.gov (United States)

    Mckenzie, R. L.

    1972-01-01

    Predictions from a numerical model of the vibrational relaxation of anharmonic diatomic oscillators in supersonic expansions are used to show the extent to which the small anharmonicity of gases like CO can cause significant overpopulations of upper vibrational states. When mixtures of CO and N2 are considered, radiative gain on many of the vibration-rotation transitions of CO is predicted. Experiments are described that qualitatively verify the predictions by demonstrating laser oscillation in CO-N2 expansions. The resulting CO-N2 gasdynamic laser displays performance characteristics that equal or exceed those of similar CO2 lasers.

  4. Planktonic diatoms of Lake Ontario

    Science.gov (United States)

    Reinwand, Jerry F.

    1969-01-01

    The major species of diatoms in surface collections from Lake Ontario in September 1964 were Asterionella formosa, Fragilaria crotonensis, and Tabellaris fenestrata. Dominant species in the deep-water samples were Stephanodiscus astraea, S. astraea var. mintula, and F. crotonensis. The diatom flora in surface collections varied among several stations in the eastern end of the lake.

  5. Developing diatoms for value-added products: challenges and opportunities.

    Science.gov (United States)

    Fu, Weiqi; Wichuk, Kristine; Brynjólfsson, Sigurður

    2015-12-25

    As a major primary producer in marine environments, diatoms have been considered as promising feedstocks for their applications in functional foods, bioactive pharmaceuticals, and cosmetics. This review focuses on the biotechnology potential of diatoms for value-added products like carotenoids. The impact of abiotic environmental stresses, such as intensity and quality of incident light, nutrient deficiency and silicon depletion, on diatoms has been examined to determine key factors that affect the growth performance and the accumulation of valuable compounds. Previous studies suggested that adaptive evolution could be an efficient method to improve the diatom productivity of valuable compounds. Light emitting diode (LED)-based photobioreactors were introduced and proposed as a promising new technology for producing quality products from diatoms. Currently available molecular biology tools were also summarized and discussed in relation to their application in the production of carotenoids and other valuable products. Taken together, systems biology and synthetic biology approaches have the potential to address the challenges faced while working toward the industrial application of diatoms.

  6. Marine Polysaccharide Networks and Diatoms at the Nanometric Scale

    Directory of Open Access Journals (Sweden)

    Tea Mišić Radić

    2013-10-01

    Full Text Available Despite many advances in research on photosynthetic carbon fixation in marine diatoms, the biophysical and biochemical mechanisms of extracellular polysaccharide production remain significant challenges to be resolved at the molecular scale in order to proceed toward an understanding of their functions at the cellular level, as well as their interactions and fate in the ocean. This review covers studies of diatom extracellular polysaccharides using atomic force microscopy (AFM imaging and the quantification of physical forces. Following a brief summary of the basic principle of the AFM experiment and the first AFM studies of diatom extracellular polymeric substance (EPS, we focus on the detection of supramolecular structures in polysaccharide systems produced by marine diatoms. Extracellular polysaccharide fibrils, attached to the diatom cell wall or released into the surrounding seawater, form distinct supramolecular assemblies best described as gel networks. AFM makes characterization of the diatom polysaccharide networks at the micro and nanometric scales and a clear distinction between the self-assembly and self-organization of these complex systems in marine environments possible.

  7. Trapping molecular ions formed via photo-associative ionization of ultracold atoms

    CERN Document Server

    Sullivan, Scott T; Kotochigova, Svetlana; Chen, Kuang; Schowalter, Steven J; Hudson, Eric R

    2011-01-01

    The formation of $^{40}$Ca$_2^+$ molecular ions is observed in a hybrid $^{40}$Ca magneto-optical and ion trap system. The molecular ion formation process is determined to be two-photon photo-associative ionization of ultracold $^{40}$Ca atoms. A lower bound for the two-body, two-photon rate constant is found to be $\\bar{\\beta} \\geq 2 \\pm 1 \\times 10^{-15}$ cm$^{3}$ Hz. $\\textit{Ab initio}$ molecular potential curves are calculated for the neutral Ca$_2$ and ionic Ca$_2^+$ molecules and used in a model that identifies the photo-associative ionization pathway. As this technique does not require a separate photo-association laser, it could find use as a simple, robust method for producing ultracold, state-selected molecular ions.

  8. Trapping molecular ions formed via photo-associative ionization of ultracold atoms.

    Science.gov (United States)

    Sullivan, Scott T; Rellergert, Wade G; Kotochigova, Svetlana; Chen, Kuang; Schowalter, Steven J; Hudson, Eric R

    2011-11-14

    The formation of (40)Ca(2)(+) molecular ions is observed in a hybrid (40)Ca magneto-optical and ion trap system. The molecular ion formation process is determined to be photo-associative ionization of ultracold (40)Ca atoms. A lower bound for the two-body rate constant is found to be beta ≥ 2 ± 1 × 10(-15) cm(3) Hz. Ab initio molecular potential curves are calculated for the neutral Ca(2) and ionic Ca(2)(+) molecules and used in a model that identifies the photo-associative ionization pathway. As this technique does not require a separate photo-association laser, it could find use as a simple, robust method for producing ultracold molecular ions.

  9. A SELDI-TOF approach to ecotoxicology: comparative profiling of low molecular weight proteins from a marine diatom exposed to CdSe/ZnS quantum dots.

    Science.gov (United States)

    Scebba, Francesca; Tognotti, Danika; Presciuttini, Gianluca; Gabellieri, Edi; Cioni, Patrizia; Angeloni, Debora; Basso, Barbara; Morelli, Elisabetta

    2016-01-01

    Quantum dots (QDs), namely semiconductor nanocrystals, due to their particular optical and electronic properties, have growing applications in device technology, biotechnology and biomedical fields. Nevertheless, the possible threat to human health and the environment have attracted increasing attention as the production and applications of QDs increases rapidly while standard evaluation of safety lags. In the present study we performed proteomic analyses, by means of 2D gel electrophoresis and Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometry (SELDI-TOF-MS). We aimed to identify potential biomarkers of exposure to CdSe/ZnS quantum dots. The marine diatom Phaeodactylum tricornutum exposed to 2.5nM QDs was used as a model system. Both 2DE and SELDI showed the presence of differentially expressed proteins. By Principal Component Analysis (PCA) we were able to show that the differentially expressed proteins can discriminate between exposed and not exposed cells. Furthermore, a protein profile specific for exposed cells was obtained by SELDI analysis. To our knowledge, this is the first example of the application of SELDI technology to the analysis of microorganisms used as biological sentinel model of marine environmental pollution.

  10. metal ion sequestration: an exciting dimension for molecularly ...

    African Journals Online (AJOL)

    The use of a tight binding macrocyclic ligand to complex a metal ion so that this serves as receptee on ... nickel(lI) ion whose chemistry is a reasonable substitute for many of the common environmentally .... certain soil bacteria secrete powerful.

  11. Radii broadening due to molecular collision in focused ion beams

    Science.gov (United States)

    Komuro, Masanori

    1988-01-01

    Point exposures of poly(methyl methacrylate) resist are carried out with focused ion beams of Si++ and Au++ from a liquid AuSi ion source in order to obtain a current density distribution in the probe. All the distributions are composed of a main Gaussian distribution and a long tail dependent on r-3.3 (r means radial distance). The magnitude of this tail increases with the increase in ambient pressure of the ion-drifting space. When the probe is steered at the corner of deflection field, two types of clear ghost patterns appear: (1) circular patterns and (2) lines trailing from the main spot toward the deflection center. It is revealed that they are produced by exposures to ions or energetic neutrals generated with charge transfer collision of the primary ions with residual gas molecules. It is shown that the long tail in the current density distribution is also due to scattering with the residual gas molecules.

  12. Molecular Layer Deposition for Surface Modification of Lithium-Ion Battery Electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Ban, Chunmei [Center of Chemistry and Nanoscience, National Renewable Energy Laboratory, Golden CO 80401 USA; George, Steven M. [Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder CO 80309 USA; Department of Mechanical Engineering, University of Colorado at Boulder, Boulder CO 80309 USA

    2016-10-21

    Inspired by recent successes in applying molecular layer deposition (MLD) to stabilize lithium-ion (Li-ion) electrodes, this review presents the MLD process and its outstanding attributes for electrochemical applications. The review discusses various MLD materials and their implementation in Li-ion electrodes. The rationale behind these emerging uses of MLD is examined to motivate future efforts on the fundamental understanding of interphase chemistry and the development of new materials for enhanced electrochemical performance.

  13. Processing and characterization of diatom nanoparticles and microparticles as potential source of silicon for bone tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Le, Thi Duy Hanh [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Bonani, Walter [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy); Speranza, Giorgio [Center for Materials and Microsystems, PAM-SE, Fondazione Bruno Kessler, Trento (Italy); Sglavo, Vincenzo; Ceccato, Riccardo [Department of Industrial Engineering, University of Trento, Trento (Italy); Maniglio, Devid; Motta, Antonella [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy); Migliaresi, Claudio, E-mail: claudio.migliaresi@unitn.it [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy)

    2016-02-01

    Silicon plays an important role in bone formation and maintenance, improving osteoblast cell function and inducing mineralization. Often, bone deformation and long bone abnormalities have been associated with silica/silicon deficiency. Diatomite, a natural deposit of diatom skeleton, is a cheap and abundant source of biogenic silica. The aim of the present study is to validate the potential of diatom particles derived from diatom skeletons as silicon-donor materials for bone tissue engineering applications. Raw diatomite (RD) and calcined diatomite (CD) powders were purified by acid treatments, and diatom microparticles (MPs) and nanoparticles (NPs) were produced by fragmentation of purified diatoms under alkaline conditions. The influence of processing on the surface chemical composition of purified diatomites was evaluated by X-ray photoelectron spectroscopy (XPS). Diatoms NPs were also characterized in terms of morphology and size distribution by transmission electron microscopy (TEM) and Dynamic light scattering (DLS), while diatom MPs morphology was analyzed by scanning electron microscopy (SEM). Surface area and microporosity of the diatom particles were evaluated by nitrogen physisorption methods. Release of silicon ions from diatom-derived particles was demonstrated using inductively coupled plasma optical emission spectrometry (ICP/OES); furthermore, silicon release kinetic was found to be influenced by diatomite purification method and particle size. Diatom-derived microparticles (MPs) and nanoparticles (NPs) showed limited or no cytotoxic effect in vitro depending on the administration conditions. - Highlights: • Diatomite is a natural source of silica and has a potential as silicon-donor for bone regenerative applications. • Diatom particles derived from purified diatom skeletons were prepared by fragmentation under extreme alkaline condition. • Dissolution of diatom particles derived from diatom skeletons in DI water depend on purification method

  14. Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study

    CERN Document Server

    Huang, Kai; Ma, C Derek; Abbott, Nicholas L; Szlufarska, Izabela

    2016-01-01

    Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using beta-peptide-inspired nano-rods, we investigate the effects of both free ions (dissolved salts) and proximally immobilized ions on hydrophobic interactions. We find that the free ion effect is correlated with the water density fluctuation near a non-polar molecular surface, showing that such fluctuation can be an indicator of hydrophobic interactions in the case of solution additives. In the case of immobilized ion, our results demonstrate that hydrophobic interactions can be switched on and off by choosing different spatial arrangements of proximal ions on a nano-rod. For globally amphiphilic nano-rods, we find that the magnitude of the interaction can be further tuned using proximal ions with varying ionic sizes. In general, univalent proximal anions are found to weaken hydrophobic interactions. This is in contras...

  15. Studies on Molecular and Ion Transport in Silicalite Membranes and Applications as Ion Separator for Redox Flow Battery

    Science.gov (United States)

    Yang, Ruidong

    Microporous zeolite membranes have been widely studied for molecular separations based on size exclusion or preferential adsorption-diffusion mechanisms. The MFI-type zeolite membranes were also demonstrated for brine water desalination by molecular sieving effect. In this research, the pure silica MFI-type zeolite (i.e. silicalite) membrane has been for the first time demonstrated for selective permeation of hydrated proton (i.e. H3O+) in acidic electrolyte solutions. The silicalite membrane allows for permeation of H 3O+ ions, but is inaccessible to the large hydrated multivalent vanadium ions due to steric effect. The silicalite membrane has been further demonstrated as an effective ion separator in the all-vanadium redox flow battery (RFB).The silicalite is nonionic and its proton conductivity relies on the electric field-driven H3O+ transport through the sub nanometer-sized pores under the RFB operation conditions. The silicalite membrane displayed a significantly reduced self-discharge rate because of its high proton-to-vanadium ion transport selectivity. However, the nonionic nature of the silicalite membrane and very small diffusion channel size render low proton conductivity and is therefore inefficient as ion exchange membranes (IEMs) for practical applications. The proton transport efficiency may be improved by reducing the membrane thickness. However, the zeolite thin films are extremely fragile and must be supported on mechanically strong and rigid porous substrates. In this work, silicalite-Nafion composite membranes were synthesized to achieve a colloidal silicalite skin on the Nafion thin film base. The "colloidal zeolite-ionic polymer" layered composite membrane combines the advantages of high proton-selectivity of the zeolite layer and the mechanical flexibility and low proton transport resistance of the ionic polymer membrane. The composite membrane exhibited higher proton/vanadium ion separation selectivity and lower electrical resistance than

  16. Influence of primary ion bombardment conditions on the emission of molecular secondary ions

    Energy Technology Data Exchange (ETDEWEB)

    Kersting, R.; Hagenhoff, B.; Kollmer, F.; Moellers, R.; Niehuis, E

    2004-06-15

    In order to further our understanding of the secondary ion emission behavior from organic surfaces, we have performed a systematic study on the influence of the primary ion parameters. As model sample Irganox 1010 on low density polyethylene (LDPE) was used. Both monoatomic (Ga, Cs, Au) and polyatomic (Au{sub 2}, Au{sub 3}, SF{sub 5}, C{sub 60}) primary ions were used. Additionally, the primary ion energy was varied. The data were evaluated by calculating secondary ion yields, disappearance cross sections and ion formation efficiencies (yield/damage cross section). The results show that heavier monoatomic ions are more efficient than lighter ones and that polyatomic primary ions are more efficient than monoatomic ones. Highest efficiency values are found for C{sub 60} bombardment at 20 keV. Compared to Ga bombardment the efficiency gain in this case is more than 2000-fold. Additionally it can be shown that the higher efficiency is correlated with a softer ionization, i.e. less fragmentation. The results suggest a much more homogeneous energy distribution in the sample surface by polyatomic primary ions compared to monoatomic ones.

  17. Influence of primary ion bombardment conditions on the emission of molecular secondary ions

    Science.gov (United States)

    Kersting, R.; Hagenhoff, B.; Kollmer, F.; Möllers, R.; Niehuis, E.

    2004-06-01

    In order to further our understanding of the secondary ion emission behavior from organic surfaces, we have performed a systematic study on the influence of the primary ion parameters. As model sample Irganox 1010 on low density polyethylene (LDPE) was used. Both monoatomic (Ga, Cs, Au) and polyatomic (Au 2, Au 3, SF 5, C 60) primary ions were used. Additionally, the primary ion energy was varied. The data were evaluated by calculating secondary ion yields, disappearance cross sections and ion formation efficiencies (yield/damage cross section). The results show that heavier monoatomic ions are more efficient than lighter ones and that polyatomic primary ions are more efficient than monoatomic ones. Highest efficiency values are found for C 60 bombardment at 20 keV. Compared to Ga bombardment the efficiency gain in this case is more than 2000-fold. Additionally it can be shown that the higher efficiency is correlated with a softer ionization, i.e. less fragmentation. The results suggest a much more homogeneous energy distribution in the sample surface by polyatomic primary ions compared to monoatomic ones.

  18. 1-Pyrenecarboxaldehyde thiosemicarbazone:A novel fluorescent molecular sensor towards mercury(Ⅱ)ion

    Institute of Scientific and Technical Information of China (English)

    Xue Mei Wang; Hua Yan; Xin Lu Feng; Yong Chen

    2010-01-01

    A novel and simple fluorescent molecular sensor,1-pyrenecarboxaldehyde thiosemicarbazone(Hpytsc),was synthesized.Its higher sensitivity and selectivity to mercury(Ⅱ)ion were studied through absorption and emission channels.The UV-vis spectra show that the increasing mercury(Ⅱ)ion concentrations result in the decreasing absorption intensity.The fluorescence monomer emission of Hpytsc is enhanced upon binding mercury(Ⅱ)ion,which should be due to the 1:1 complex formation between Hpytsc and metal ion.

  19. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  20. Determination of molecular-ion structures through the use of accelerated beams

    Science.gov (United States)

    Gemmell, D. S.

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the Coulomb-explosion technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, was termed a Coulomb explosion.

  1. Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation

    DEFF Research Database (Denmark)

    Ekroos, Kim; Ejsing, Christer S.; Bahr, Ute

    2003-01-01

    The molecular composition of phosphatidylcholines (PCs) in total lipid extracts was characterized by a combination of multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer and MS3 fragmentation on an ion trap mass spectrometer. Precursor ion spectra for 50 acyl...... spectrometer quantified the relative amount of their positional isomers, thus providing the most detailed and comprehensive characterization of the molecular composition of the pool of PCs at the low-picomole level. The method is vastly simplified, compared with conventional approaches, and does not require...... preliminary separation of lipid classes or of individual molecular species, enzymatic digestion, or chemical derivatization. The approach was validated by the comparative analysis of the molecular composition of PCs from human red blood cells. In the total lipid extract of Madin-Darby canine kidney II cells...

  2. Voltage-Sensitive Ion Channels Biophysics of Molecular Excitability

    CERN Document Server

    Leuchtag, H. Richard

    2008-01-01

    Voltage-sensitive ion channels are macromolecules embedded in the membranes of nerve and muscle fibers of animals. Because of their physiological functions, biochemical structures and electrical switching properties, they are at an intersection of biology, chemistry and physics. Despite decades of intensive research under the traditional approach of gated structural pores, the relation between the structure of these molecules and their function remains enigmatic. This book critically examines physically oriented approaches not covered in other ion-channel books. It looks at optical and thermal as well as electrical data, and at studies in the frequency domain as well as in the time domain. Rather than presenting the reader with only an option of mechanistic models at an inappropriate pseudo-macroscopic scale, it emphasizes concepts established in organic chemistry and condensed state physics. The book’s approach to the understanding of these unique structures breaks with the unproven view of ion channels as...

  3. A toy model for a diatomic molecule

    Science.gov (United States)

    Hecker Denschlag, Johannes

    2016-08-01

    We introduce a toy model for a diatomic molecule which is based on coupling electronic and nuclear spins to a rigid rotor. Despite its simplicity, the model can be used scientifically to analyze and understand complex molecular hyperfine spectra. In addition, the model has educational value as a number of fundamental symmetries and conservation laws of the molecule can be studied. Because of its simple structure, the model can be readily implemented as a computer program with comparatively short computing times on the order of a few seconds.

  4. Stuart R. Stidolph diatom atlas

    Science.gov (United States)

    Stidolph, S.R.; Sterrenburg, F.A.S.; Smith, K.E.L.; Kraberg, A.

    2012-01-01

    The "Stuart R. Stidolph Diatom Atlas" is a comprehensive volume of diatom taxa identified and micrographed by Stuart R. Stidoph during the 1980s and 1990s. The samples were collected from marine coasts of various geographic regions within tropical and subtropical climates. The plates included within this report have never been published and are being published by the USGS as an online reference so that others may have access to this incredible collection.

  5. Molecular modeling of mechanosensory ion channel structural and functional features.

    Science.gov (United States)

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  6. Molecular modeling of mechanosensory ion channel structural and functional features.

    Directory of Open Access Journals (Sweden)

    Renate Gessmann

    Full Text Available The DEG/ENaC (Degenerin/Epithelial Sodium Channel protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1. MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  7. Thermodynamics and kinetics of ion speciation in supercritical aqueous solutions: A molecular based study

    Energy Technology Data Exchange (ETDEWEB)

    Chialvo, A.A.; Cummings, P.T. [Tennessee Univ., Knoxville, TN (United States). Dept. of Chemical Engineering]|[Oak Ridge National Lab., TN (United States); Simonson, J.M.; Mesmer, R.E. [Oak Ridge National Lab., TN (United States)

    1997-05-01

    Molecular simulation of infinitely dilute NaCl aqueous solutions are performed to study the Na{sup +}/Cl{sup -} ion pairing in a polarizable and a nonpolarizable solvent at supercritical conditions. The Simple Point Charge, Pettitt-Rossky, and Fumi-Tosi models for the water-water, ion-water, and ion-ion interactions are used in determining the degree of dissociation, its temperature and density dependence, and the kinetics of the interconversion between ion-pair configurations in a nonpolarizable medium. To assess the effect of the solvent polarizability on the stability of the ion-pair configurations, we replace the Simple Point Charge by the Polarizable Point Charge water model and determine the anion-cation potential of mean force at T{sub r}=1.20 and {rho}{sub r}=1.5.

  8. Investigation of the silicon ion density during molecular beam epitaxy growth

    Science.gov (United States)

    Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.

    2002-05-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.

  9. Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

    National Research Council Canada - National Science Library

    Alipanah, Leila; Rohloff, Jens; Winge, Per; Bones, Atle M; Brembu, Tore

    2015-01-01

    .... In this study, we integrated physiological data with transcriptional and metabolite data to reveal molecular and metabolic modifications in N-deprived conditions in the marine diatom Phaeodactylum tricornutum...

  10. Towards a representative periphytic diatom sample

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available The need to acquire a representative periphytic diatom sample for river water quality monitoring has been recognised in the development of existing diatom indices, important in the development and employment of diatom monitoring tools for the Water Framework Directive. In this study, a nested design with replication is employed to investigate the magnitude of variation in diatom biomass, composition and Trophic Diatom Index at varying scales within a small chalk river. The study shows that the use of artificial substrates may not result in diatom communities that are typical of the surrounding natural substrates. Periphytic diatom biomass and composition varies between artificial and natural substrates, riffles and glides and between two stretches of the river channel. The study also highlights the existence of high variation in diatom frustule frequency and biovolume at the individual replicate scale which may have implications for the use of diatoms in routine monitoring.

  11. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    Science.gov (United States)

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  12. Processing and characterization of diatom nanoparticles and microparticles as potential source of silicon for bone tissue engineering.

    Science.gov (United States)

    Le, Thi Duy Hanh; Bonani, Walter; Speranza, Giorgio; Sglavo, Vincenzo; Ceccato, Riccardo; Maniglio, Devid; Motta, Antonella; Migliaresi, Claudio

    2016-02-01

    Silicon plays an important role in bone formation and maintenance, improving osteoblast cell function and inducing mineralization. Often, bone deformation and long bone abnormalities have been associated with silica/silicon deficiency. Diatomite, a natural deposit of diatom skeleton, is a cheap and abundant source of biogenic silica. The aim of the present study is to validate the potential of diatom particles derived from diatom skeletons as silicon-donor materials for bone tissue engineering applications. Raw diatomite (RD) and calcined diatomite (CD) powders were purified by acid treatments, and diatom microparticles (MPs) and nanoparticles (NPs) were produced by fragmentation of purified diatoms under alkaline conditions. The influence of processing on the surface chemical composition of purified diatomites was evaluated by X-ray photoelectron spectroscopy (XPS). Diatoms NPs were also characterized in terms of morphology and size distribution by transmission electron microscopy (TEM) and Dynamic light scattering (DLS), while diatom MPs morphology was analyzed by scanning electron microscopy (SEM). Surface area and microporosity of the diatom particles were evaluated by nitrogen physisorption methods. Release of silicon ions from diatom-derived particles was demonstrated using inductively coupled plasma optical emission spectrometry (ICP/OES); furthermore, silicon release kinetic was found to be influenced by diatomite purification method and particle size. Diatom-derived microparticles (MPs) and nanoparticles (NPs) showed limited or no cytotoxic effect in vitro depending on the administration conditions.

  13. Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS.

    Science.gov (United States)

    Körsgen, Martin; Tyler, Bonnie J; Pelster, Andreas; Lipinsky, Dieter; Dreisewerd, Klaus; Arlinghaus, Heinrich F

    2016-06-01

    Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix.

  14. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    Science.gov (United States)

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

  15. Absorption of infra-red radiation by atmospheric molecular cluster-ions

    OpenAIRE

    Aplin, K. L.; R. A. McPheat

    2005-01-01

    Protonated water clusters are a common species of atmospheric molecular cluster-ion, produced by cosmic rays throughout the troposphere and stratosphere. Under clear-sky conditions or periods of increased atmospheric ionisation, such as solar proton events, the IR absorption by atmospheric ions may affect climate through the radiative balance. Fourier Transform Infrared Spectrometry in a long path cell, of path length 545m, has been used to detect IR absorption by corona-generated positive mo...

  16. Controlling the electromagnetism of single ion by "molecular surgery"

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Controlling and modifying the magnetic property of a single molecule is the frontier for the development of molecular science. With the funding support from NSFC,Scientific Innovation Program of CAS as well as 973 from Ministry of Science and Technology of China, Prof.Jianguo Hou (Member of CAS) and Prof.

  17. Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes.

    Science.gov (United States)

    Ravin, Nikolai V; Galachyants, Yuri P; Mardanov, Andrey V; Beletsky, Alexey V; Petrova, Darya P; Sherbakova, Tatyana A; Zakharova, Yuliya R; Likhoshway, Yelena V; Skryabin, Konstantin G; Grachev, Mikhail A

    2010-06-01

    The first two mitochondrial genomes of marine diatoms were previously reported for the centric Thalassiosira pseudonana and the raphid pennate Phaeodactylum tricornutum. As part of a genomic project, we sequenced the complete mitochondrial genome of the freshwater araphid pennate diatom Synedra acus. This 46,657 bp mtDNA encodes 2 rRNAs, 24 tRNAs, and 33 proteins. The mtDNA of S. acus contains three group II introns, two inserted into the cox1 gene and containing ORFs, and one inserted into the rnl gene and lacking an ORF. The compact gene organization contrasts with the presence of a 4.9-kb-long intergenic region, which contains repeat sequences. Comparison of the three sequenced mtDNAs showed that these three genomes carry similar gene pools, but the positions of some genes are rearranged. Phylogenetic analysis performed with a fragment of the cox1 gene of diatoms and other heterokonts produced a tree that is similar to that derived from 18S RNA genes. The introns of mtDNA in the diatoms seem to be polyphyletic. This study demonstrates that pyrosequencing is an efficient method for complete sequencing of mitochondrial genomes from diatoms, and may soon give valuable information about the molecular phylogeny of this outstanding group of unicellular organisms.

  18. Evolutions of Molecular Oxygen Formation and Sodium Migration in Xe Ion Irradiated Borosilicate Glasses

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Liang; Zhang, Duofei F.; Lv, Peng; Zhang, Jiandong; Du, Xing; Yuan, Wei; Nan, Shuai; Zhu, Zihua; Wang, Tieshan

    2016-07-23

    The modifications of a commercial borosilicate glass induced by Xe ion irradiation have been studied by Raman spectroscopy and ToF-SIMS depth profiling. A decrease in the average Si–O–Si angle, an increase in the population of three-membered rings and an increase of the glass polymerization are evidenced. The molecular oxygen appears in the irradiated glasses after the irradiation fluence reaches approximately 1015 ions/cm2. The O2 concentration decreaseswith the depth of irradiated glass at the ion fluence of 2 × 1016 ions/cm2. A sodiumdepleted layer at the surface and a depleted zone at around the penetration depth of 5 MeV Xe ions are observed. The thickness of the sodium depleted layer increases with the irradiation fluence. Moreover, comparing with previous results after electron and Ar ion irradiation, it can be concluded that the nuclear energy deposition can partially inhibit the formation of molecular oxygen and increase the threshold value of electron energy deposition for the molecular oxygen formation.

  19. Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

    Science.gov (United States)

    Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E.; Yu, Xiaofei; Lao, David B.; Heldebrant, David J.; Nune, Satish K.; Cao, Bin; Bowden, Mark E.; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

    2016-12-01

    In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces.

  20. Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

    Science.gov (United States)

    Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E.; Yu, Xiaofei; Lao, David B.; Heldebrant, David J.; Nune, Satish K.; Cao, Bin; Bowden, Mark E.; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

    2016-09-01

    In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces.

  1. Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E.; Yu, Xiaofei; Lao, David B.; Heldebrant, David J.; Nune, Satish K.; Cao, Bin; Bowden, Mark E.; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

    2016-09-06

    In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid–liquid and liquid–vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable to use for in situ liquid SIMS to study solid–liquid and liquid–vacuum interfaces.

  2. Properties of the Excited States of Molecular Ions.

    Science.gov (United States)

    1981-04-13

    photafragmem spmuum for 0; obtained for seperatkon enrgy W =0 from 5770 to 5860 A. The noted tranisition wavelength@ are for the 0;(b, v1 =4-a. v" 411 had...rotational levels. We shall discuss this point in more detail In a following section. 8 B. Dissociation enrgies of he N levels 7 Before attempting to...NO, molecules, and should the mystem have turl Idth, sufficient (-0.5 oV) vibrational enrgy , the ,O will Wt Is 1.0 Tor 11,0, ions of mass 60 were

  3. Leading order relativistic corrections to the dipole polarizability of the hydrogen molecular ions

    CERN Document Server

    Aznabayev, D T; Zhaugasheva, S A; Korobov, V I

    2016-01-01

    The static dipole polarizability for the hydrogen molecular ions H$_2^+$, HD$^+$, and D$_2^+$ are calculated. These new data for polarizability takes into account the leading order relativistic corrections to the wave function of the three-body system resulted from the Breit-Pauli Hamiltonian of $m\\alpha^4$ order. Our study covers a wide range of rotational ($L=0-5$) and vibrational ($v=0-10$) states, which are of practical interest for precision spectroscopy of the hydrogen molecular ions.

  4. Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

    Science.gov (United States)

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; van der Maarel, Johan R. C.

    2008-03-01

    All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

  5. Synthesis and Anion Recognition of Novel Molecular Tweezer Receptors Based on Carbonyl Thiosemicarbazide for Fluoride Ions

    Institute of Scientific and Technical Information of China (English)

    WEI,Wei; ZHANG,You-Ming; WEI,Tai-Bao

    2008-01-01

    Three title compounds have been designed and synthesized in high yields as novel anion receptors, which show a higher selectivity for F- than other halide ions. The binding properties for fluoride ions of the receptors have been examined by UV-Vis and 1H NMR spectroscopy, indicating that a 1 : 1 stoichiometry complex is formed between the receptors and fluoride ions through hydrogen bonding interactions in DMSO solution. In addition, because these receptors have more binding points, they have better binding properties for anions than the molecular tweezer receptors based on thiourea we reported last time.

  6. Molecular dynamics simulations of ion irradiation of a surface under an electric field

    Energy Technology Data Exchange (ETDEWEB)

    Parviainen, S., E-mail: stefan.parviainen@iki.fi; Djurabekova, F.

    2014-11-15

    The presence of high electric fields may affect significantly the process of sputtering of metal surfaces by energetic ions, especially in the vicinity of rough surface features. The effect can be significant if the energy of ions is fairly low. Moreover, the nanosized rough surface features – invisible to a naked eye, both intrinsic ones due to technological processing of surfaces and those forming because of sputtering – may affect the topology of surface erosion under ion bombardment. In this work we study by means of concurrent electrodynamics–molecular dynamics the sputtering yield of Cu{sup +} ions hitting a flat Cu surface or a nanosized Cu protrusion as a function of both ion energy and electric field strength. The results show that the sputtering yield is significantly enhanced in the presence of an electric field in both cases.

  7. Investigation of the silicon ion density during molecular beam epitaxy growth

    CERN Document Server

    Eifler, G; Ashurov, K; Morozov, S

    2002-01-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...

  8. The role of ion electrophoresis in electroporation-mediated molecular delivery

    Science.gov (United States)

    Li, Jianbo; Lin, Hao

    2009-11-01

    Electroporation is a widely applied technique to deliver active molecules into the cellular compartment, to perform a variety of tasks such as gene therapy and directed stem cell differentiation. In this technique, an electric field transiently permeabilizes the cellular membrane to facilitate molecular exchange. While the permeabilization process is relatively well-understood, the transport mechanisms for molecular delivery are still under debate. In this work, the role of ion electrophoresis in electroporation-mediated molecular delivery is investigated using numerical simulations. The result indicates that ion electrophoresis is the dominant mode of transport in the delivery of small charged molecules. Furthermore, the achievable intracellular concentration is strongly influenced by the conductivity difference between the cytoplasm and the buffer, a phenomenon known as ``field-amplified sample stacking''. The result agrees well with the fluorescence measurement by Gabriel and Teissi'e (1999), and suggests a new possibility to simultaneously improve cell viability and efficiency in electroporation-mediated molecular delivery.

  9. Laser cooling, slowing and trapping of a diatomic molecule

    Science.gov (United States)

    Barry, John

    2015-05-01

    Roughly three decades ago, laser cooling and trapping succeeded in producing ultracold ions and atoms, sparking a revolution in atomic physics and subsequently becoming workhorse techniques within the field. These techniques require a ``cycling transition,'' where the particle of interest is repeatedly driven by a photon into an excited electronic state and quickly decays back to the initial ground state, allowing the process to repeat. Because photon absorption transfers momentum to the particle, application of force is possible. Adjusting the geometry and frequency of the applied photons allows creation of a damping (cooling) force. Further addition of a quadrupole magnetic field allows for a restoring (trapping) force. Prior to this thesis, straightforward extension of these methods to molecules was considered a practical impossibility; electronic decays in molecules tend to populate multiple rotational and vibrational states, preventing creation of a cycling transition. While a variety of ultracold molecular species is desirable to satisfy a range of applications, the only other production method is limited to species where the constituent atoms are themselves amenable to laser cooling. For other species, a different technique is required. Here we outline the methods and experiments in which laser cooling and trapping were first applied to molecules. By careful molecule choice, by using a cooling transition that exploits selection rules, and by counteracting dark states with a magnetic field, we create a cycling transition for the diatomic molecule strontium monofluoride (SrF). We show the power of this technique by demonstrating Doppler and sub-Doppler cooling in 1-D, radiation pressure slowing and stopping of a molecular beam, and finally a 3-D magneto-optical trap (MOT). Our MOT produces the coldest trapped sample of directly-cooled molecules to date, with a temperature of T ~ 2.5 mK. This method is viable for several classes of diatomic molecules with a

  10. Vibrational Distribution of Hydrogen Molecular Ions in High-Energy Ionization Processes

    Institute of Scientific and Technical Information of China (English)

    CHEN Shao-Hao; HE Chun-Long; CHEN Chao; LI Jia-Ming

    2005-01-01

    @@ A theoretical time-dependent wave-packet dynamics method is applied to calculate the distribution of vibrational states of hydrogen molecular ions produced in high-energy ionization processes of hydrogen molecules. The isotope effect is elucidated in agreement with the available experimental measurements. Our proposed method should be readily applied in other atomic and molecular processes considering great advances in electronic computation science and technology.

  11. The effect of antibiotics on diatom communities

    Digital Repository Service at National Institute of Oceanography (India)

    DeCosta, P.M.; Anil, A.C.

    Effect of antibiotics (penicillin (P), streptomycin (S) and chloramphenicol (C)) on benthic diatom communities was evaluated using a modified extinction–dilution method. The high antibiotic combinations (2PSC and PSC) reduced diatoms by 99...

  12. Diatom genomics: genetic acquisitions and mergers.

    Science.gov (United States)

    Nisbet, R Ellen R; Kilian, Oliver; McFadden, Geoffrey I

    2004-12-29

    Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.

  13. Molecular Structure of the Human CFTR Ion Channel.

    Science.gov (United States)

    Liu, Fangyu; Zhang, Zhe; Csanády, László; Gadsby, David C; Chen, Jue

    2017-03-23

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening. By analyzing the sigmoid time course of CFTR current activation, we propose that PKA phosphorylation of the R domain is enabled by its infrequent spontaneous disengagement, which also explains residual ATPase and gating activity of dephosphorylated CFTR. From comparison with MRP1, a feature distinguishing CFTR from all other ABC transporters is the helix-loop transition in transmembrane helix 8, which likely forms the structural basis for CFTR's channel function.

  14. Photochemistry and molecular ions in carbon-rich circumstellar envelopes

    Science.gov (United States)

    Glassgold, A. E.; Mamon, G. A.; Omont, A.; Lucas, R.

    1987-01-01

    An earlier theory of ionization of C-rich circumstellar envelopes based on the photochemical model is extended to include the temperature dependence of ion-molecule reactions with polar molecules, particularly HCN, and line self-shielding of CO dissociating radiation. The results are applied to the abundances of HCO(+) and HNC in C-rich circumstellar envelopes. With standard parameters for IRC + 10216, the model is found to be consistent with the new upper limit to the antenna temperature of the J = 1-0 line of HCO(+) obtained with the IRAM 30-m telescope. The photochemical model provides a natural explanation of the relatively large ratio of HCN to HNC observed for C-rich circumstellar envelopes, and good agreement is obtained for the H(C-13)N/HNC antenna temperature ratio measured for IRC + 10216.

  15. Molecular biology and biophysical properties of ion channel gating pores.

    Science.gov (United States)

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-11-01

    The voltage sensitive domain (VSD) is a pivotal structure of voltage-gated ion channels (VGICs) and plays an essential role in the generation of electrochemical signals by neurons, striated muscle cells, and endocrine cells. The VSD is not unique to VGICs. Recent studies have shown that a VSD regulates a phosphatase. Similarly, Hv1, a voltage-sensitive protein that lacks an apparent pore domain, is a self-contained voltage sensor that operates as an H⁺ channel. VSDs are formed by four transmembrane helices (S1-S4). The S4 helix is positively charged due to the presence of arginine and lysine residues. It is surrounded by two water crevices that extend into the membrane from both the extracellular and intracellular milieus. A hydrophobic septum disrupts communication between these water crevices thus preventing the permeation of ions. The septum is maintained by interactions between the charged residues of the S4 segment and the gating charge transfer center. Mutating the charged residue of the S4 segment allows the water crevices to communicate and generate gating pore or omega pore. Gating pore currents have been reported to underlie several neuronal and striated muscle channelopathies. Depending on which charged residue on the S4 segment is mutated, gating pores are permeant either at depolarized or hyperpolarized voltages. Gating pores are cation selective and seem to converge toward Eisenmann's first or second selectivity sequences. Most gating pores are blocked by guanidine derivatives as well as trivalent and quadrivalent cations. Gating pores can be used to study the movement of the voltage sensor and could serve as targets for novel small therapeutic molecules.

  16. Magneto-optical trapping of diatomic molecules

    CERN Document Server

    Hummon, Matthew T; Stuhl, Benjamin K; Collopy, Alejandra L; Xia, Yong; Ye, Jun

    2012-01-01

    The development of the magneto-optical trap revolutionized the fields of atomic and quantum physics by providing a simple method for the rapid production of ultracold, trapped atoms. A similar technique for producing a diverse set of dense, ultracold diatomic molecular species will likewise transform the study of strongly interacting quantum systems, precision measurement, and physical chemistry. We demonstrate one- and two-dimensional transverse laser cooling and magneto-optical trapping of the polar molecule yttrium (II) oxide (YO). Using a quasicycling optical transition we observe transverse Doppler cooling of a YO molecular beam to a temperature of 5 mK, limited by interaction time. With the addition of an oscillating magnetic quadrupole field we demonstrate a transverse magneto-optical trap and achieve temperatures of 2 mK.

  17. A molecular dynamics analysis of ion irradiation of ultrathin amorphous carbon films

    Science.gov (United States)

    Qi, J.; Komvopoulos, K.

    2016-09-01

    Molecular dynamics (MD) simulations provide insight into nanoscale problems where continuum description breaks down, such as the modeling of ultrathin films. Amorphous carbon (a-C) films are commonly used as protective overcoats in various contemporary technologies, including microelectromechanical systems, bio-implantable devices, optical lenses, and hard-disk drives. In all of these technologies, the protective a-C film must be continuous and very thin. For example, to achieve high storage densities (e.g., on the order of 1 Tb/in.2) in magnetic recording, the thickness of the a-C film used to protect the magnetic media and the recording head against mechanical wear and corrosion must be 2-3 nm. Inert ion irradiation is an effective post-deposition method for reducing the film thickness, while preserving the mechanical and chemical characteristics. In this study, MD simulations of Ar+ ion irradiated a-C films were performed to elucidate the effects of the ion incidence angle and ion kinetic energy on the film thickness and structure. The MD results reveal that the film etching rate exhibits a strong dependence on the ion kinetic energy and ion incidence angle, with a maximum etching rate corresponding to an ion incidence angle of ˜20°. It is also shown that Ar+ ion irradiation mainly affects the structure of the upper half of the ultrathin a-C film and that carbon atom hybridization is a strong function of the ion kinetic energy and ion incidence angle. The results of this study elucidate the effects of important ion irradiation parameters on the structure and thickness of ultrathin films and provide fundamental insight into the physics of dry etching.

  18. Molecular Dynamics of XFEL-Induced Photo-Dissociation, Revealed by Ion-Ion Coincidence Measurements

    Directory of Open Access Journals (Sweden)

    Edwin Kukk

    2017-05-01

    Full Text Available X-ray free electron lasers (XFELs providing ultrashort intense pulses of X-rays have proven to be excellent tools to investigate the dynamics of radiation-induced dissociation and charge redistribution in molecules and nanoparticles. Coincidence techniques, in particular multi-ion time-of-flight (TOF coincident experiments, can provide detailed information on the photoabsorption, charge generation, and Coulomb explosion events. Here we review several such recent experiments performed at the SPring-8 Angstrom Compact free electron LAser (SACLA facility in Japan, with iodomethane, diiodomethane, and 5-iodouracil as targets. We demonstrate how to utilize the momentum-resolving capabilities of the ion TOF spectrometers to resolve and filter the coincidence data and extract various information essential in understanding the time evolution of the processes induced by the XFEL pulses.

  19. Storage compound production by phototrophic diatoms

    NARCIS (Netherlands)

    Mooij, P.R.; Van Loosdrecht, M.C.M.; Kleerebezem, R.

    2015-01-01

    The invention is directed to a method for producing an enriched diatom culture, comprising subjecting a starting culture comprising one or more diatom species to selective pressure, thus giving a competitive advantage to storage compound producing species of diatoms, by subjecting said starting cult

  20. On calculations of dipole moments of HCl+ and DCl+ molecular ions

    CERN Document Server

    Gurin, V S

    2015-01-01

    Dipole moment functions of isotopomeric molecular ions, HCl+ and DCl+, are considered in the two coordinate systems, center of mass of nuclei and center of nuclear charges, both through simple analytical derivations and ab initio calculations of electronic structure at various interatomic separations. An origin of the different values for dipole moments of the isotopomers is discussed and demonstrated by the calculation data.

  1. External-field shifts in precision spectroscopy of hydrogen molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Bakalov, Dimitar, E-mail: dbakalov@inrne.bas.bg [INRNE, Bulgarian Academy of Sciences (Bulgaria); Korobov, Vladimir [Joint Institute for Nuclear Research (Russian Federation); Schiller, Stephan [Heinrich-Heine-Universitat Dusseldorf, Institut fur Experimentalphysik (Germany)

    2015-08-15

    The Effective Hamiltonian of the hydrogen molecular ions is a convenient tool for the evaluation of the shift of the energy levels of the ro-vibrational states and the frequencies of the transitions between them, due to external electric and magnetic fields. Using the Effective Hamiltonian, composite frequencies of suppressed susceptibility to external fields are constructed.

  2. Electron loss from multiply protonated lysozyme ions in high energy collisions with molecular oxygen

    DEFF Research Database (Denmark)

    Hvelplund, P; Nielsen, SB; Sørensen, M

    2001-01-01

    We report on the electron loss from multiply protonated lysozyme ions Lys-Hn(n)+ (n = 7 - 17) and the concomitant formation of Lys-Hn(n+1)+. in high-energy collisions with molecular oxygen (laboratory kinetic energy = 50 x n keV). The cross section for electron loss increases with the charge stat...

  3. Diatomic interaction potential theory applications

    CERN Document Server

    Goodisman, Jerry

    2013-01-01

    Diatomic Interaction Potential Theory, Volume 2: Applications discusses the variety of applicable theoretical material and approaches in the calculations for diatomic systems in their ground states. The volume covers the descriptions and illustrations of modern calculations. Chapter I discusses the calculation of the interaction potential for large and small values of the internuclear distance R (separated and united atom limits). Chapter II covers the methods used for intermediate values of R, which in principle means any values of R. The Hartree-Fock and configuration interaction schemes des

  4. Absorption of infra-red radiation by atmospheric molecular cluster-ions

    CERN Document Server

    Aplin, K L

    2005-01-01

    Protonated water clusters are a common species of atmospheric molecular cluster-ion, produced by cosmic rays throughout the troposphere and stratosphere. Under clear-sky conditions or periods of increased atmospheric ionisation, such as solar proton events, the IR absorption by atmospheric ions may affect climate through the radiative balance. Fourier Transform Infrared Spectrometry in a long path cell, of path length 545m, has been used to detect IR absorption by corona-generated positive molecular cluster-ions. The column concentration of ions in the laboratory spectroscopy experiment was estimated to be ~10^13 m-2; the column concentration of protonated atmospheric ions estimated using a simple model is ~10^14 m-2. Two regions of absorption, at 12.3 and 9.1 um are associated with enhanced ion concentrations. After filtering of the measured spectra to compensate for spurious signals from neutral water vapour and residual carbon dioxide, the strongest absorption region is at 9.5 to 8.8 um (1050 to 1140 cm-1)...

  5. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

    Energy Technology Data Exchange (ETDEWEB)

    Chakravorty, Dhruva K.; Wang Bing [University of Florida, Department of Chemistry and the Quantum Theory Project (United States); Lee, Chul Won [Chonnam National University, Department of Chemistry (Korea, Republic of); Guerra, Alfredo J.; Giedroc, David P., E-mail: giedroc@indiana.edu [Indiana University, Department of Chemistry (United States); Merz, Kenneth M., E-mail: kmerz1@gmail.com [University of Florida, Department of Chemistry and the Quantum Theory Project (United States)

    2013-06-15

    Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.

  6. Molecular desorption of stainless steel vacuum chambers irradiated with 42 MeV/u lead ions

    CERN Document Server

    Mahner, E; Laurent, Jean Michel; Madsen, N

    2003-01-01

    In preparation for the heavy ion program of the Large Hadron Collider at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring. These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow discharges, nonevaporable getter coating) are reported in terms of the molecular desorption yields for H/sub 2 /, CH/sub 4/, CO, Ar, and CO/sub 2/. (16 refs).

  7. Lifetimes and stabilities of familiar explosives molecular adduct complexes during ion mobility measurements

    Science.gov (United States)

    McKenzie, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-01-01

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailors the stability of the molecular adduct complex. TIMS flexibility to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments / low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with higher confidence levels. PMID:26153567

  8. Next Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

    Science.gov (United States)

    2016-07-01

    AWARD NUMBER: W81XWH- 14-1-0192 TITLE: Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer...DATES COVERED 4. TITLE AND SUBTITLE Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue

  9. Molecular dynamics study on ion diffusion in LiFePO4 olivine materials.

    Science.gov (United States)

    Zhang, Peixin; Wu, Yanpeng; Zhang, Dongyun; Xu, Qiming; Liu, Jianhong; Ren, Xiangzhong; Luo, Zhongkuan; Wang, Mingliang; Hong, Weiliang

    2008-06-19

    Molecular dynamics (MD) simulations have been employed to investigate the ionic diffusion and the structure of LiFePO 4 cathode material. The results correspond well with the published experimental observations. The simulation results indicated that the diffusion of lithium ions was thermally activated and more significant than those of other ions. Compared with other cathode materials, the shifts of ions were less significant in LiFePO 4. This suggested that LiFePO 4 was more thermally stable. The snapshots of the positions of lithium atoms over a range of the steps provided a microscopic picture and the picture showed the lithium ions migrated through one-dimension channels.

  10. Molecular theories and simulation of ions and polar molecules in water

    CERN Document Server

    Hummer, G; García, A; Hummer, Gerhard; Pratt, Lawrence R.; Garcia, Angel E.

    1998-01-01

    Recent developments in molecular theories and simulation of ions and polar molecules in water are reviewed. The hydration of imidazole and imidazolium solutes is used to exemplify the theoretical issues. The treatment of long-ranged electrostatic interactions in simulations is discussed extensively. It is argued that the Ewald approach is an easy way to get correct hydration free energies in the thermodynamic limit from molecular calculations; and that molecular simulations with Ewald interactions and periodic boundary conditions can also be more efficient than many common alternatives. The Ewald treatment permits a conclusive extrapolation to infinite system size. The picture that emerges from testing of simple models is that the most prominent failings of the simplest theories are associated with solvent proton conformations that lead to non-gaussian fluctuations of electrostatic potentials. Thus, the most favorable cases for the second-order perturbation theories are monoatomic positive ions. For polar and...

  11. Secondary electron emission from Au by medium energy atomic and molecular ions

    CERN Document Server

    Itoh, A; Obata, F; Hamamoto, Y; Yogo, A

    2002-01-01

    Number distributions of secondary electrons emitted from a Au metal surface have been measured for atomic and molecular ions of H sup + , He sup + , C sup + , N sup + , O sup + , H sup + sub 2 , H sup + sub 3 , HeH sup + , CO sup + and O sup + sub 2 in the energy range 0.3-2.0 MeV. The emission statistics obtained are described fairly well by a Polya function. The Polya parameter b, determining the distribution shape, is found to decrease monotonously with increasing emission yield gamma, revealing a surprising relationship of b gamma approx 1 over the different projectile species and impact energies. This finding supports certainly the electron cascading model. Also we find a strong negative molecular effect for heavier molecular ions, showing a significant reduction of gamma compared to the estimated values using constituent atomic projectile data.

  12. Photodetachment of a Homo-Nuclear Linear Tetra-Atomic Negative Molecular Ion

    Institute of Scientific and Technical Information of China (English)

    A. Rahman; Iftikhar Ahmad; A. Afaq; H. J. Zhao

    2012-01-01

    The photodetachment of a homo-nuclear linear tetra-atomic negative molecular ion is studied theoretically for an arbitrary laser polarization.An expression for the total cross section is obtained by using an extended version of the two center model,where each center acts as a source of coherent photodetached-electron waves.Strong oscillations on observation plane,placed at a large distance from the ion,are observed.The amplitude of these oscillations is maximum when the laser polarization is parallel to the molecular axis.Furthermore,the amplitude decreases as the angle between the laser polarization and molecular axis increases and consequently vanishes when they are perpendicular to each other.It is also found that if the distance between the adjacent centers is very small or very large,then the ampplitude of oscillations is negligibly small.%The photodetachment of a homo-nuclear linear tetra-atomic negative molecular ion is studied theoretically for an arbitrary laser polarization. An expression for the total cross section is obtained by using an extended version of the two center model, where each center acts as a source of coherent photodetached-electron waves. Strong oscillations on observation plane, placed at a large distance from the ion, are observed. The amplitude of these oscillations is maximum when the laser polarization is parallel to the molecular axis. Furthermore, the amplitude decreases as the angle between the laser polarization and molecular axis increases and consequently vanishes when they are perpendicular to each other. It is also found that if the distance between the adjacent centers is very small or very large, then the amplitude of oscillations is negligibly small.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gwan, J.F.

    2007-01-19

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

  14. Molecular dynamics simulation analysis of ion irradiation effects on plasma-liquid interface

    Science.gov (United States)

    Minagawa, Yudai; Shirai, Naoki; Uchida, Satoshi; Tochikubo, Fumiyoshi

    2013-09-01

    Nonthermal atmospheric plasmas are used in a wide range of fields because the high-density plasma can be easily irradiated to various substances such as solid, liquid, biological object and so on. On the other hand, the mechanisms of physical and chemical phenomena at the plasma-liquid interface are not well understood yet. To investigate the effects of ion impact from plasma on water surface, we analyzed behavior of liquid water by classical molecular dynamics simulation. Simulation system consists of an irradiation particle in gas phase and 2000 water molecules in liquid phase. O+ ion with 10 eV or 100 eV was impinged on the water surface. Ion impact induced increasing water temperature and ejection of water molecules. The averaged number of evaporated water molecules by ion impact is 0.6 molecules at 10 eV and 7.0 molecules at 100 eV. The maximum ion penetration depth was 1.14 nm at 10 eV and 2.75 nm at 100 eV. Ion entering into water disturbs the stable hydrogen bonding configurations between water molecules and gives energy to water molecules. Some water molecules rotated and moved by ion interaction impact on other water molecules one after another. When the water molecule near the surface received strongly repulsive force, it released into gas phase. This work was supported financially in part by a Grant-in-Aid for Scientific Research on Innovation Areas (No21110007) from MEXT, Japan.

  15. IMF-induced escape of molecular ions from the Martian ionosphere

    Directory of Open Access Journals (Sweden)

    Y. Kubota

    2013-08-01

    Full Text Available Since Mars does not possess a significant global intrinsic magnetic field, the solar wind interacts directly with the Martian ionosphere and can induce ion escapes from it. Phobos-2 and recent Mars Express (MEX observations have shown that the escaping ions are O+ as well as molecular O2+ and CO2+. While O+ escape can be understood by the ion pick-up of non-thermal O corona extended around the planet, regarding the heavy molecular O2+ and CO2+, which are buried in the lower ionosphere, a novel escape mechanism needs to considered. Here we attack this problem by global magnetohydrodynamic (MHD simulations. First, we clarify the global structure of the streamlines that result from the interaction with the solar wind. Then, by focusing on the streamlines that dip into the low-altitude part of the dayside ionosphere, we investigate the escape path of the molecular ions. The effects of the interplanetary magnetic field (IMF on the molecular ion escape process are investigated by comparing the results with and without IMF. IMF has little effect on O+ escape via ion pick-up mediated by solar wind electron impact ionization of the O corona. O2+ and CO2+ are shoveled from the low-altitude regions of the dayside ionosphere by magnetic tension in the presence of IMF. These ions are pulled by the U-shaped field lines to the north and south poles, and at the terminator, they are concentrated in the noon–midnight meridian plane. These ions remain confined to the noon–midnight plane as they are transported to the nightside to form the tail ray. Then they escape along the streamlines open to the interplanetary space. Under a typical solar wind and IMF condition expected at Mars, O+, O2+ and CO2+ escape fluxes are 8.0 × 1023, 3.5 × 1023 and 5.0 × 1022 ion s−1, respectively, which are in good agreement with the MEX observations.

  16. An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations.

    Science.gov (United States)

    Law, Richard J; Munson, Keith; Sachs, George; Lightstone, Felice C

    2008-09-15

    Gastric H,K-ATPase is an electroneutral transmembrane pump that moves protons from the cytoplasm of the parietal cell into the gastric lumen in exchange for potassium ions. The mechanism of transport against the established electrochemical gradients includes intermediate conformations in which the transferred ions are trapped (occluded) within the membrane domain of the pump. The pump cycle involves switching between the E1 and E2P states. Molecular dynamics simulations on homology models of the E2P and E1 states were performed to investigate the mechanism of K(+) movement in this enzyme. We performed separate E2P simulations with one K(+) in the luminal channel, one K(+) ion in the occlusion site, two K(+) ions in the occlusion site, and targeted molecular dynamics from E2P to E1 with two K(+) ions in the occlusion site. The models were inserted into a lipid bilayer system and were stable over the time course of the simulations, and K(+) ions in the channel moved to a consistent location near the center of the membrane domain, thus defining the occlusion site. The backbone carbonyl oxygen from residues 337 through 342 on the nonhelical turn of M4, as well as side-chain oxygen from E343, E795, and E820, participated in the ion occlusion. A single water molecule was stably bound between the two K(+) ions in the occlusion site, providing an additional ligand and partial shielding the positive charges from one another. Targeted molecular dynamics was used to transform the protein from the E2P to the E1 state (two K(+) ions to the cytoplasm). This simulation identified the separation of the water column in the entry channel as the likely gating mechanism on the luminal side. A hydrated exit channel also formed on the cytoplasmic side of the occlusion site during this simulation. Hence, water molecules became available to hydrate the ions. The movement of the M1M2 transmembrane segments, and the displacement of residues Q159, E160, Q110, and T152 during the

  17. Biomimetic supercontainers for size-selective electrochemical sensing of molecular ions

    Science.gov (United States)

    Netzer, Nathan L.; Must, Indrek; Qiao, Yupu; Zhang, Shi-Li; Wang, Zhenqiang; Zhang, Zhen

    2017-01-01

    New ionophores are essential for advancing the art of selective ion sensing. Metal-organic supercontainers (MOSCs), a new family of biomimetic coordination capsules designed using sulfonylcalix[4]arenes as container precursors, are known for their tunable molecular recognition capabilities towards an array of guests. Herein, we demonstrate the use of MOSCs as a new class of size-selective ionophores dedicated to electrochemical sensing of molecular ions. Specifically, a MOSC molecule with its cavities matching the size of methylene blue (MB+), a versatile organic molecule used for bio-recognition, was incorporated into a polymeric mixed-matrix membrane and used as an ion-selective electrode. This MOSC-incorporated electrode showed a near-Nernstian potentiometric response to MB+ in the nano- to micro-molar range. The exceptional size-selectivity was also evident through contrast studies. To demonstrate the practical utility of our approach, a simulated wastewater experiment was conducted using water from the Fyris River (Sweden). It not only showed a near-Nernstian response to MB+ but also revealed a possible method for potentiometric titration of the redox indicator. Our study thus represents a new paradigm for the rational design of ionophores that can rapidly and precisely monitor molecular ions relevant to environmental, biomedical, and other related areas. PMID:28393841

  18. Luminescence properties of a nanoporous freshwater diatom.

    Science.gov (United States)

    Goswami, Bondita; Choudhury, Amarjyoti; Buragohain, Alak K

    2012-01-01

    Freshwater diatom frustules show special optical properties. In this paper we observed luminescence properties of the freshwater diatom Cyclotella meneghiniana. To confirm the morphological properties we present scanning electron microscopy (SEM) images. X-ray diffraction (XRD) studies were carried out to visualize the structural properties of the frustules, confirming that silica present in diatom frustules crystallizes in an α-quartz structure. Study of the optical properties of the silica frustules of diatoms using ultra-violet-visible (UV-vis) spectroscopy and photoluminescence spectroscopy confirmed that the diatom C. meneghiniana shows luminescence in the blue region of the electromagnetic spectrum when irradiated with UV light. This property of diatoms can be exploited to obtain many applications in day-to-day life. Also, using time-resolved photoluminescence spectroscopy (TRPL) it was confirmed that this species of diatom shows bi-exponential decay.

  19. Acceleration of cluster and molecular ions by TIARA 3 MV tandem accelerator

    CERN Document Server

    Saitoh, Y; Tajima, S

    2000-01-01

    We succeeded in accelerating molecular and cluster ions (B sub 2 sub - sub 4 , C sub 2 sub - sub 1 sub 0 , O sub 2 , Al sub 2 sub - sub 4 , Si sub 2 sub - sub 4 , Cu sub 2 sub - sub 3 , Au sub 2 sub - sub 3 , LiF, and AlO) to MeV energies with high-intensity beam currents by means of a 3 MV tandem accelerator in the TIARA facility. These cluster ions were generated by a cesium sputter-type negative ion source. We tested three types of carbon sputter cathodes in which graphite powder was compressed with different pressures. The pressure difference affected the generating ratio of clusters generated to single atom ions extracted from the source and it appeared that the high-density cathode was suitable. We also investigated the optimum gas pressure for charge exchange in the tandem high-voltage terminal. Clusters of larger size tend to require lower pressure than do smaller ones. In addition, we were able to obtain doubly charged AlO molecular ions. (authors)

  20. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies.

    Science.gov (United States)

    Gogoi, Prerana; Chandravanshi, Monika; Mandal, Suraj Kumar; Srivastava, Ambuj; Kanaujia, Shankar Prasad

    2016-07-01

    About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.

  1. Time slicing in 3D momentum imaging of the hydrogen molecular ion photo-fragmentation

    Science.gov (United States)

    Kaya, N.; Kaya, G.; Pham, F. V.; Strohaber, J.; Kolomenskii, A. A.; Schuessler, H. A.

    2017-02-01

    Photo-fragmentation of the hydrogen molecular ion was investigated with 800 nm, 50 fs laser pulses by employing a time slicing 3D imaging technique that enables the simultaneous measurement of all three momentum components which are linearly related with the pixel position and slicing time. This is done for each individual product particle arriving at the detector. This mode of detection allows us to directly measure the three-dimensional fragment momentum vector distribution without having to rely on mathematical reconstruction methods, which additionally require the investigated system to be cylindrically symmetric. We experimentally reconstruct the laser-induced photo-fragmentation of the hydrogen molecular ion. In previous experiments, neutral molecules were used as a target, but in this work, performed with molecular ions, the initial vibrational level populations are well-defined after electron bombardment, which facilitates the interpretation. We show that the employed time-slicing technique allows us to register the fragment momentum distribution that reflects the initial molecular states with greater detail, revealing features that were concealed in the full time-integrated distribution on the detector.

  2. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio

    2006-01-01

    We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment...... ions. Absolute quantification of identified species was linear within a concentration range of 10 nM-100 microM and was achieved by spiking into total lipid extracts a set of synthetic lipid standards with diheptadecanoyl (17:0/17:0) fatty acid moieties, representing six common classes...

  3. Ion Pair in Extreme Aqueous Environments, Molecular-Based and Electric Conductance Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chialvo, Ariel A [ORNL; Gruszkiewicz, Miroslaw {Mirek} S [ORNL; Simonson, J Michael {Mike} [ORNL; Palmer, Donald [ORNL; Cole, David R [ORNL

    2009-01-01

    We determine by molecular-based simulation the density profiles of the Na+!Cl! ion-pair association constant in steam environments along three supercritical isotherms to interrogate the behavior of ion speciation in dilute aqueous solutions at extreme conditions. Moreover, we describe a new ultra-sensitive flow-through electric conductance apparatus designed to bridge the gap between the currently lowest steam-density conditions at which we are experimentally able to attain electric conductance measurements and the theoretically-reachable zero-density limit. Finally, we highlight important modeling challenges encountered near the zero-density limit and discuss ways to overcome them.

  4. Cluster secondary ion mass spectrometry and the temperature dependence of molecular depth profiles.

    Science.gov (United States)

    Mao, Dan; Wucher, Andreas; Brenes, Daniel A; Lu, Caiyan; Winograd, Nicholas

    2012-05-01

    The quality of molecular depth profiles created by erosion of organic materials by cluster ion beams exhibits a strong dependence upon temperature. To elucidate the fundamental nature of this dependence, we employ the Irganox 3114/1010 organic delta-layer reference material as a model system. This delta-layer system is interrogated using a 40 keV C(60)(+) primary ion beam. Parameters associated with the depth profile such as depth resolution, uniformity of sputtering yield, and topography are evaluated between 90 and 300 K using a unique wedge-crater beveling strategy that allows these parameters to be determined as a function of erosion depth from atomic force microscope (AFM) measurements. The results show that the erosion rate calibration performed using the known Δ-layer depth in connection with the fluence needed to reach the peak of the corresponding secondary ion mass spectrometry (SIMS) signal response is misleading. Moreover, we show that the degradation of depth resolution is linked to a decrease of the average erosion rate and the buildup of surface topography in a thermally activated manner. This underlying process starts to influence the depth profile above a threshold temperature between 210 and 250 K for the system studied here. Below that threshold, the process is inhibited and steady-state conditions are reached with constant erosion rate, depth resolution, and molecular secondary ion signals from both the matrix and the Δ-layers. In particular, the results indicate that further reduction of the temperature below 90 K does not lead to further improvement of the depth profile. Above the threshold, the process becomes stronger at higher temperature, leading to an immediate decrease of the molecular secondary ion signals. This signal decay is most pronounced for the highest m/z ions but is less for the smaller m/z ions, indicating a shift toward small fragments by accumulation of chemical damage. The erosion rate decay and surface roughness buildup

  5. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses.

    Science.gov (United States)

    Schlathölter, Thomas; Reitsma, Geert; Egorov, Dmitrii; Gonzalez-Magaña, Olmo; Bari, Sadia; Boschman, Leon; Bodewits, Erwin; Schnorr, Kirsten; Schmid, Georg; Schröter, Claus Dieter; Moshammer, Robert; Hoekstra, Ronnie

    2016-08-26

    The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions and related ions, with yields increasing linearly with intensity. Ionization clearly triggers a localized molecular response that occurs before the excitation energy equilibrates. Consistent with this interpretation, the effect is almost unaffected by the charge state, as fragmentation of sixfold deprotonated ubiquitin leads to a very similar fragmentation pattern. Ubiquitin responds to EUV multiphoton ionization as an ensemble of small peptides.

  6. An efficient screening method for the isolation of heterotrophic bacteria influencing growth of diatoms under photoautotrophic conditions.

    Science.gov (United States)

    Zecher, Karsten; Jagmann, Nina; Seemann, Philipp; Philipp, Bodo

    2015-12-01

    Interactions between photoautotrophic diatoms and heterotrophic bacteria are important for the biogeochemical C-cycle in the oceans. Additionally, biofilms formed by diatoms and bacteria are the initiating step of biofouling processes, which causes high costs in shipping. Despite this ecological and economical importance, the knowledge about biochemical and molecular mechanisms underlying these interkingdom interactions is relatively small. For analyzing these mechanisms, laboratory model systems are required. In this study, an efficient screening method for isolating bacteria influencing photoautotrophic diatom growth was established. First, diatom cultures of Phaeodactylum tricornutum and Thalassiosira pseudonana were made axenic by applying β-lactam antibiotics. Second, a non-invasive method for measuring growth of multiple parallel diatom cultures by chlorophyll fluorescence was established. This method allowed semi-quantitative chlorophyll determination of cultures with up to 3 μg (chlorophyll) ml(-1). Axenic diatom cultures were then used for enriching bacteria and led to the isolation of 24 strains influencing growth of both diatom strains in various ways. For example, Rheinheimera sp. strain Tn16 inhibited growth of T. pseudonana, while it stimulated growth and cell aggregation of P. tricornutum. Thus, this screening method is appropriate for isolating heterotrophic bacteria showing different interactions with different diatom species ranging from synergistic to antagonistic. In consecutive applications, this method will be useful to screen for bacterial mutants with altered phenotypes regarding the influence on diatom growth.

  7. Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data.

    Science.gov (United States)

    Visco, Joana Amorim; Apothéloz-Perret-Gentil, Laure; Cordonier, Arielle; Esling, Philippe; Pillet, Loïc; Pawlowski, Jan

    2015-07-07

    Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

  8. Molecular modeling of the ion channel-like nanotube structure of amyloid β-peptide

    Institute of Scientific and Technical Information of China (English)

    JIAO Yong; YANG Pin

    2007-01-01

    The ion channel-like nanotube structure of the oligomers of amyloid β-peptide (Aβ) was first investigated by molecular modeling. The results reveal that the hydrogen bond net is one of the key factors to stabilize the structure. The hydrophobicity distribution mode of the side chains is in favor of the structure inserting into the bilayers and forming a hydrophilic pore. The lumen space is under the control of the negative potential, weaker but spreading continuously, to which the cation selectivity attributes; meanwhile, the alternate distribution of the stronger positive and negative potentials makes the electrostatic distribution of the structure framework balance, which is also one of the key factors stabilizing the structure. The results lay the theoretical foundation for illuminating the structure stability and the ion permeability, and give a clue to elucidating the molecular mechanism of Alzheimer's disease (AD) and designing novel drugs to prevent or reverse AD at the root.

  9. A novel protein refolding method integrating ion exchange chromatography with artificial molecular chaperone

    Institute of Scientific and Technical Information of China (English)

    Qin Ming Zhang; Chao Zhan Wang; Jiang Feng Liu; Li Li Wang

    2008-01-01

    Artificial molecular chaperone (AMC) and ion exchange chromatography (IEC) were integrated, thus a new refolding method,artificial molecular chaperone-ion exchange chromatography (AMC-IEC) was developed. Compared with AMC and IEC, theactivity recovery of lysozyme obtained by AMC-IEC was much higher in the investigated range of initial protein concentrations,and the results show that AMC-IEC is very efficient for protein refolding at high concentrations. When the initial concentration oflysozyme is 180 mg/mL, its activity recovery obtained by AMC-IEC is still as high as 76.6%, while the activity recoveries obtainedby AMC and IEC are 45.6% and 42.4%, respectively.2008 Chao Zhan Wang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  10. Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes

    Directory of Open Access Journals (Sweden)

    Evelyne Deplazes

    2017-02-01

    Full Text Available Disulfide-rich peptides isolated from the venom of arthropods and marine animals are a rich source of potent and selective modulators of ion channels. This makes these peptides valuable lead molecules for the development of new drugs to treat neurological disorders. Consequently, much effort goes into understanding their mechanism of action. This paper presents an overview of how molecular simulations have been used to study the interactions of disulfide-rich venom peptides with ion channels and membranes. The review is focused on the use of docking, molecular dynamics simulations, and free energy calculations to (i predict the structure of peptide-channel complexes; (ii calculate binding free energies including the effect of peptide modifications; and (iii study the membrane-binding properties of disulfide-rich venom peptides. The review concludes with a summary and outlook.

  11. Three-stage classical molecular dynamics model for simulation of heavy-ion fusion

    Directory of Open Access Journals (Sweden)

    Godre Subodh S.

    2015-01-01

    Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.

  12. Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

    Science.gov (United States)

    Shevkunov, S. V.

    2017-02-01

    The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

  13. Field-enhanced ion transport in solids: Reexamination with molecular dynamics simulations

    Science.gov (United States)

    Genreith-Schriever, A. R.; De Souza, R. A.

    2016-12-01

    Classical molecular-dynamics simulations were used to examine the effect of an electric field on the mobility of oxygen ions in the model crystalline oxide CeO2. Simulation cells containing oxygen vacancies were subjected at temperatures 1000 ≤T /K ≤1600 to electric field strengths 0.1 ≤E /MV cm-1≤40 to obtain the oxygen-ion mobility ui(E ,T ) . In addition, static nudged-elastic-band calculations were performed to obtain directly the forward/reverse barriers for oxygen-ion migration, Δ Hmigf /r . Qualitatively, ui behaves as expected: independent of E at low values of E and exponentially dependent on E at high values. The quantitative (standard) Mott-Gurney treatment, however, underestimates Δ Hmigf at high E and thus overestimates ui. A new, superior analytical expression for ui(E ,T ) is consequently derived.

  14. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  15. Towards using molecular ions as qubits: Femtosecond control of molecular fragmentation with multiple knobs

    Indian Academy of Sciences (India)

    Tapas Goswami; Dipak K Das; Debabrata Goswami

    2010-12-01

    Non-resonant molecular fragmentation of n-propyl benzene with femtosecond laser pulses is dependent on the phase and polarization characteristics of the laser. We find that the effect of the chirp and polarization of the femtosecond pulse when applied simultaneously is mutually independent of each other, which makes chirp and polarization as useful ‘logic’ implementing knobs.

  16. Nodal structure of the wave function for a two-dimensionalhydrogen molecular ion

    Institute of Scientific and Technical Information of China (English)

    段宜武; 周光辉; 鲍诚光; 袁建民

    1996-01-01

    Under the Born-Oppenheimer approximation, the exact solution of the Schrodinger equation for a two-dimensional hydrogen molecular ion is obtained through separation of variables. The inter-quantum numbers and the modes of internal motion are determined by analysing the nodal structure of the wavefunction. The eigenstates are classified and the classical periodic orbits corresponding to the modes of internal motion are found. two-center molecule, nodal structure, mode of internal motion.

  17. Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

    Science.gov (United States)

    Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew

    2011-01-01

    Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

  18. "Dinoflagellate Sterols" in marine diatoms.

    Science.gov (United States)

    Giner, José-Luis; Wikfors, Gary H

    2011-10-01

    Sterol compositions for three diatom species, recently shown to contain sterols with side chains typically found in dinoflagellates, were determined by HPLC and ¹H NMR spectroscopic analyses. The centric diatom Triceratium dubium (=Biddulphia sp., CCMP 147) contained the highest percentage of 23-methylated sterols (37.2% (24R)-23-methylergosta-5,22-dienol), whereas the pennate diatom Delphineis sp. (CCMP 1095) contained the cyclopropyl sterol gorgosterol, as well as the 27-norsterol occelasterol. The sterol composition of Ditylum brightwellii (CCMP 358) was the most complex, containing Δ⁰- and Δ⁷-sterols, in addition to the predominant Δ⁵-sterols. A pair of previously unknown sterols, stigmasta-5,24,28-trienol and stigmasta-24,28-dienol, were detected in D. brightwellii and their structures were determined by NMR spectroscopic analysis and by synthesis of the former sterol from saringosterol. Also detected in D. brightwellii was the previously unknown 23-methylcholesta-7,22-dienol. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Multi-ion detection and molecular switching behaviour of reversible dual fluorescent sensor

    Science.gov (United States)

    Basheer, Sabeel M.; Muralisankar, M.; Anjana, T. V.; Aneesrahman, K. N.; Sreekanth, Anandaram

    2017-07-01

    The selective chemosensing behaviour of imidazole bisthiocarbohydrazone (IBTC) towards F- and Cu2 + are studied via colorimetric, UV-Visible, fluorescence spectra studies, and binding constants were calculated. The 1H NMR titration study strongly support that the deprotonation of IBTC followed by the hydrogen bond formation via N1sbnd H1 and N2sbnd H2 protons with fluoride ion. The fluorescence inactive IBTC-Cu complex became fluorescence active in the presence of perchlorate (ClO4-) ion. The selective detection of perchlorate ion was also explained. The F- sensing mechanism of IBTC has been investigated by Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) methods. The theoretical outcomes well reproduce the experimental results. And it concluded the Nsbnd H protons, nearby the imine group was first captured by the added F- ion and then deprotonation happened followed by the formation of hydrogen bond. The IBTC found good reversibility character with the alternative addition of Ca2 + and F-. The multi-ion detection of IBTC was used to construct the NOR, OR and INHIBITION molecular logic gates.

  20. Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

    Science.gov (United States)

    Mogurampelly, Santosh; Ganesan, Venkat

    2015-03-01

    Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

  1. Rotation of cold molecular ions inside a Bose-Einstein condensate

    CERN Document Server

    Midya, Bikashkali; Schmidt, Richard; Lemeshko, Mikhail

    2016-01-01

    We use recently developed angulon theory [Phys. Rev. Lett. 114, 203001 (2015)] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on $\\textit {ab initio}$ potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the $\\textit {ab initio}$ potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.

  2. Lifetimes and stabilities of familiar explosive molecular adduct complexes during ion mobility measurements.

    Science.gov (United States)

    McKenzie-Coe, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-08-21

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailor the stability of the molecular adduct complex. The flexibility of TIMS to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments/low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with high confidence levels.

  3. Copper ion implanted aluminum nitride dilute magnetic semiconductors (DMS) prepared by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Shah, A., E-mail: attaullah77@yahoo.com [National Institute of Lasers and Optronics (NILOP), PO Nilore, Islamabad (Pakistan); DMME, Pakistan Institute of Engineering and Applied Science (PIEAS), PO Nilore, Islamabad (Pakistan); Ahmad, Jamil [DMME, Pakistan Institute of Engineering and Applied Science (PIEAS), PO Nilore, Islamabad (Pakistan); Ahmad, Ishaq [Experimental Physics Lab, National Center for Physics (NCP), Islamabad (Pakistan); Mehmood, Mazhar [DMME, Pakistan Institute of Engineering and Applied Science (PIEAS), PO Nilore, Islamabad (Pakistan); Mahmood, Arshad [National Institute of Lasers and Optronics (NILOP), PO Nilore, Islamabad (Pakistan); Rasheed, Muhammad Asim [DMME, Pakistan Institute of Engineering and Applied Science (PIEAS), PO Nilore, Islamabad (Pakistan)

    2014-10-30

    Highlights: • AlN:Cu dilute magnetic semiconductors were successfully prepared by molecular beam epitaxy followed by Cu{sup +} implantation. • Room temperature ferromagnetism was observed after annealing the samples at appropriate temperature. • XRD and Raman spectrometry excluded the possibility of formation of any secondary phases. • By doping intrinsically nonmagnetic dopants (Cu), it has been proved experimentally that their precipitates do not contribute to ferromagnetism. • The reason for ferromagnetism in Cu-doped AlN as observed was explained on the basis of p–d hybridization mechanism (Wu et al.). - Abstract: Diluted magnetic semiconductor (DMS) AlN:Cu films were fabricated by implanting Cu{sup +} ions into AlN thin films at various ion fluxes. AlN films were deposited on c-plane sapphire by molecular beam epitaxy followed by Cu{sup +} ion implantation. The structural and magnetic characterization of the samples was performed through Rutherford backscattering and channeling spectrometry (RBS/C), X-ray diffraction (XRD), Raman spectroscopy, vibrating sample magnetometer (VSM) and SQUID. Incorporation of copper into the AlN lattice was confirmed by RBS, while XRD revealed that no new phase was formed as a result of ion implantation. RBS also indicated formation of defects as a result of implantation process and the depth and degree of damage increased with an increase in ion fluence. Raman spectra showed only E{sub 2} (high) and A{sub 1} (LO) modes of wurtzite AlN crystal structure and confirmed that no secondary phases were formed. It was found that both Raman modes shift with Cu{sup +} fluences, indicating that Cu ion may go to interstitial or substitutional sites resulting in distortion or damage of lattice. Although as implanted samples showed no magnetization, annealing of the samples resulted in appearance of room temperature ferromagnetism. The saturation magnetization increased with both the annealing temperature as well as with ion

  4. Development of a molecularly imprinted polymer for pyridoxine using an ion-pair as template.

    Science.gov (United States)

    Alizadeh, Taher

    2008-08-01

    One of the main challenges in the molecularly imprinted polymers (MIP) field is the proper MIP design for water-soluble compounds because of appearance of serious drawbacks in polar solvents and insolubility of those compounds in non-polar solvents which are commonly used for MIP synthesis. In this work a novel and simple method for synthesis of molecularly imprinted polymers for a water-soluble compound was introduced. Pyridoxine was chosen as a target molecule and the ion-pair complex formed between pyridoxine ion (Py(+)) and dodecyl sulfate ion (DS(-)) was transferred into the chloroform via liquid-liquid extraction. Then polymerization was carried out in chloroform. The molecular mechanics and density functional theory were proposed to screen proper monomer. Binding energy, DeltaE, of a template and a monomer as a measure of their interaction was considered. Ion-pair [Py(+)-DS(-)] was supposed as a template molecule and acrylic acid, methacrylic acid, allyamine, vinylpridine and 2-hydroxy ethyl methacrylate were as tested monomers. The MIP synthesized using acrylic acid showed the highest selectivity to pyridoxine as predicted from the DeltaE calculation. The obtained MIP showed very high affinity against vitamin B6 in comparison to non-imprinted polymers (NIP). It was proved that the obtained MIP with introduced method was much better than that prepared in methanol as porogen. It was showed that the MIP prepared by this new method could be used as an adsorber for extraction and determination of pyridoxine in real and synthetic samples.

  5. Prospects for commercial production of diatoms

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jaw-Kai; Seibert, Michael

    2017-01-18

    In this review, a simple procedure that portends the open-pond growth of commercially viable diatoms is discussed. We examined a number of topics relevant to the production and harvesting of diatoms as well as topics concerning the production of bioproducts from diatoms. Among the former topics, we show that it is currently possible to continuously grow diatoms and control the presence of invasive species without chemical toxins at an average annual yield of 132 MT dry diatoms ha-1 over a period of almost 5 years, while maintaining the dominancy of the optimal diatom species on a seasonal basis. The dominant species varies during the year. The production of microalgae is essentially agriculture, but without the ability to control invasive species in the absence of herbicides and insecticides, pollution and production costs would be prohibitive. Among the latter topics are the discussions of whether it is better to produce lipids and then convert them to biofuels or maximize the production of diatom biomass and then convert it to biocrude products using, for example, hydrothermal processes. It is becoming increasingly evident that without massive public support, the commercial production of microalgal biofuels alone will remain elusive. While economically competitive production of biofuels from diatoms will be difficult, when priority is given to multiple high-value products, including wastewater treatment, and when biofuels are considered co-products in a systems approach to commercial production of diatoms, an economically competitive process will become more likely.

  6. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

    Science.gov (United States)

    Joung, In Suk; Cheatham, Thomas E

    2009-10-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.

  7. Molecular Ultrasound Imaging of Early Vascular Response in Prostate Tumors Irradiated with Carbon Ions

    Directory of Open Access Journals (Sweden)

    Moritz Palmowski

    2009-09-01

    Full Text Available Individualized treatments with combination of radiotherapy and targeted drugs require knowledge about the behavior of molecular targets after irradiation. Angiogenic marker expression has been studied after conventional radiotherapy, but little is known about marker response to charged particles. For the very first time, we used molecular ultrasound imaging to intraindividually track changes in angiogenic marker expression after carbon ion irradiation in experimental tumors. Expression of intercellular adhesion molecule-1 (ICAM-1 and of αvβ3-integrin in subcutaneous AT-1 prostate cancers in rats treated with carbon ions (16 Gy was studied using molecular ultrasound and immunohistochemistry. For this purpose, cyanoacrylate microbubbles were synthesized and linked to specific ligands. The accumulation of targeted microbubbles in tumors was quantified before and 36 hours after irradiation. In addition, tumor vascularization was analyzed using volumetric Doppler ultrasound. In tumors, the accumulation of targeted microbubbles was significantly higher than in nonspecific ones and could be inhibited competitively. Before irradiation, no difference in binding of αvβ3-integrin-specific or ICAM-1-specific microbubbles was observed in treated and untreated animals. After irradiation, however, treated animals showed a significantly higher binding of αvβ3-integrin-specific microbubbles and an enhanced binding of ICAM-1-specific microbubbles than untreated controls. In both groups, a decrease in vascularization occurred during tumor growth, but no significant difference was observed between irradiated and nonirradiated tumors. In conclusion, carbon ion irradiation upregulates ICAM-1 and αvβ3-integrin expression in tumor neovasculature. Molecular ultrasound can indicate the regulation of these markers and thus may help to identify the optimal drugs and time points in individualized therapy regimens.

  8. Structure, hydrolysis and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

    CERN Document Server

    Jiang, Zhen; Alexandrov, Vitaly

    2016-01-01

    A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries (RFB). Here, we employ Car-Parrinello molecular dynamics (CPMD) simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction and diffusion of aqueous V$^{2+}$, V$^{3+}$, VO$^{2+}$, and VO$_2^+$ ions at 300 K. The results indicate that the first hydration shell of both V$^{2+}$ and V$^{3+}$ contains six water molecules, while VO$^{2+}$ is coordinated to five and VO$_2^+$ to three water ligands. The first acidity constants (p$K_\\mathrm{a}$) estimated using metadynamics simulations are 2.47, 3.06 and 5.38 for aqueous V$^{3+}$, VO$_2^+$ and VO$^{2+}$, respectively, while V$^{2+}$ is predicted to be a fairly weak acid in aqueous solution with a p$K_\\mathrm{a}$ value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO$_2^+$ ion has a...

  9. Molecular terms, magnetic moments, and optical transitions of molecular ions C60mplus-or-minus

    Science.gov (United States)

    Nikolaev, A. V.; Michel, K. H.

    2002-09-01

    Starting from a multipole expansion of intramolecular Coulomb interactions, we present configuration interaction calculations of the molecular energy terms of the hole configurations (hu)+m, m=2-5, of C60m+ cations, of the electron configurations t1un, n=2-4, of the C60n- anions, and of the exciton configurations (hu+t1u)-, (hu+t1g)- of the neutral C60 molecule. The ground state of C602- is either 3T1g or 1Ag, depending on the energy separation between t1g and t1u levels. There are three close (approx0.03 eV) low lying spin triplets 3T1g, 3Gg, 3T2g for C602+, and three spin quartets 4T1u, 4Gu, 4T2u for C603+, which can be subjected to the Jahn-Teller effect. The number of low lying nearly degenerate states is largest for m=3 holes. We have calculated the magnetic moments of the hole and electron configurations and found that they are independent of molecular orientation with respect to an external magnetic field. The coupling of spin and orbital momenta differs from the atomic case. We analyze the electronic dipolar transitions (t1u)2[right arrow] t1ut1g and (t1u)3 [right arrow](t1u)2t1g for C602- and C603-. Three optical absorption lines (3T1g[right arrow] 3Hu, 3T1u, 3Au) are found for the ground level of C602- and only one line (4Au[right arrow]4T1g) for the ground state of C603-. We compare our results with the experimental data for C60n- in solutions and with earlier theoretical studies.

  10. Ion Transport and Structural Properties of Polymeric Electrolytes and Ionic Liquids from Molecular Dynamics Simulations

    Science.gov (United States)

    Borodin, Oleg

    2010-03-01

    Molecular dynamics simulations are well suited for exploring electrolyte structure and ion transport mechanisms on the nanometer length scale and the nanosecond time scales. In this presentation we will describe how MD simulations assist in answering fundamental questions about the lithium transport mechanisms in polymeric electrolytes and ionic liquids. In particular, in the first part of the presentation the extent of ion aggregation, the structure of ion aggregates and the lithium cation diffusion in binary polymeric electrolytes will be compared with that of single-ion conducting polymers. In the second part of the talk, the lithium transport in polymeric electrolytes will be compared with that of three ionic liquids ( [emim][FSI] doped with LiFSI , [pyr13][FSI] doped with LiFSI, [emim][BF4] doped with LiBF4). The relation between ionic liquid self-diffusion, conductivity and thermodynamic properties will be discussed in details. A number of correlations between heat of vaporization Hvap, cation-anion binding energy (E+/-), molar volume (Vm), self-diffusion coefficient (D) and ionic conductivity for 29 ionic liquids have been investigated using MD simulations. A significant correlation between D and Hvap has been found, while best correlation was found for -log((D Vm)) vs. Hvap+0.28E+/-. A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids.

  11. Novel sex cells and evidence for sex pheromones in diatoms.

    Science.gov (United States)

    Sato, Shinya; Beakes, Gordon; Idei, Masahiko; Nagumo, Tamotsu; Mann, David G

    2011-01-01

    Diatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs. Sexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy) and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'. The threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments are the first studies in which gametogenesis has been induced in diatoms by cell

  12. Novel sex cells and evidence for sex pheromones in diatoms.

    Directory of Open Access Journals (Sweden)

    Shinya Sato

    Full Text Available BACKGROUND: Diatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs. METHODS/PRINCIPAL FINDING: Sexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'. CONCLUSIONS/SIGNIFICANCE: The threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments

  13. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    Full Text Available Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III Hexamine ions or Mg(2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III Hexamine ions were found to bind stronger with the loop than Mg(2+ ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III Hexamine ions on CorA ions transportation.

  14. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  15. Efficient sympathetic motional ground-state cooling of a molecular ion

    CERN Document Server

    Wan, Yong; Wolf, Fabian; Schmidt, Piet O

    2015-01-01

    Cold molecular ions are promising candidates in various fields ranging from precision spectroscopy and test of fundamental physics to ultra-cold chemistry. Control of internal and external degrees of freedom is a prerequisite for many of these applications. Motional ground state cooling represents the starting point for quantum logic-assisted internal state preparation, detection, and spectroscopy protocols. Robust and fast cooling is crucial to maximize the fraction of time available for the actual experiment. We optimize the cooling rate of ground state cooling schemes for single $^{25}\\mathrm{Mg}^{+}$ ions and sympathetic ground state cooling of $^{24}\\mathrm{MgH}^{+}$. In particular, we show that robust cooling is achieved by combining pulsed Raman sideband cooling with continuous quench cooling. Furthermore, we experimentally demonstrate an efficient strategy for ground state cooling outside the Lamb-Dicke regime.

  16. Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.

    Science.gov (United States)

    Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo

    2006-12-29

    We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.

  17. The rotation of NO3− as a probe of molecular ion - water interactions

    Directory of Open Access Journals (Sweden)

    Ogden T.

    2013-03-01

    Full Text Available The hydration dynamics of aqueous nitrate, NO3−(aq, is studied by 2D-IR spectroscopy, UV-IR- and UV-UV transient absorption spectroscopy. The experimental results are compared to Car-Parinello molecular dynamics (MD simulations. The 2D-IR measurements and MD simulations of the non-degenerate asymmetric stretch vibrations of nitrate reveal an intermodal energy exchange occurring on a 0.2 ps time scale related to hydrogen bond fluctuations. The transient absorption measurements find that the nitrate ions rotate in 2 ps. The MD simulations indicate that the ion rotation is associated with the formation of new hydrogen bonds. The 2 ps rotation time thus indicates that the hydration shell of aqueous nitrate is rather labile.

  18. Evidence of anisotropic temperatures of molecular ions in the auroral ionosphere

    Energy Technology Data Exchange (ETDEWEB)

    Lathuillere, C.; Kofman, W. (CNRS-URA, St. Martin d' Heres (France)); Hubert, D. (CNRS-URA, Paris (France)); La Hoz, C. (Univ. of Tromsoe (Norway))

    1991-02-01

    Using incoherent scatter measurements obtained from Kiruna and Sodankyla EISCAT remote stations, and corresponding to different aspect angles, the authors show, for the first time, anisotropic temperatures of molecular ions. The electric field obtained for the 5 hours period of the 2nd February 1990 experiment presented here range from 20 to 50 mV/m. They show that the line of sight ion temperature deduced from Kiruna incoherent scatter spectra is larger than the one deduced from Sodankyla spectra which correspond to a smaller aspect angle. A statistical approach has been chosen to evaluate a {beta} parameter for Sodankyla measurements which describes the anisotropy. They found a value of 0.60 {plus minus} 0.02 which compares very well with values inferred from theoretical studies.

  19. Water rotational jump driven large amplitude molecular motions of nitrate ions in aqueous potassium nitrate solution

    CERN Document Server

    Banerjee, Puja; Bagchi, Biman

    2016-01-01

    Molecular dynamics simulations of aqueous potassium nitrate solution reveal a highly complex rotational dynamics of nitrate ions where, superimposed on the expected continuous Brownian motion, are large amplitude angular jumps that are coupled to and at least partly driven by similar large amplitude jump motions in water molecules which are associated with change in the hydrogen bonded water molecule. These jumps contribute significantly to rotational and translational motions of these ions. We explore the detailed mechanism of these correlated (or, coupled) jumps and introduce a new time correlation function to decompose the coupled orientational- jump dynamics of solvent and solute in the aqueous electrolytic solution. Time correlation function provides for the unequivocal determination of the time constant involved in orientational dynamics originating from making and breaking of hydrogen bonds. We discover two distinct mechanisms-both are coupled to density fluctuation but are of different types.

  20. Interaction of the model alkyltrimethylammonium ions with alkali halide salts: an explicit water molecular dynamics study

    Directory of Open Access Journals (Sweden)

    M. Druchok

    2013-01-01

    Full Text Available We present an explicit water molecular dynamics simulation of dilute solutions of model alkyltrimethylammonium surfactant ions (number of methylene groups in the tail is 3, 5, 8, 10, and 12 in mixture with NaF, NaCl, NaBr, and NaI salts, respectively. The SPC/E model is used to describe water molecules. Results of the simulation at 298 K are presented in form of the radial distribution functions between nitrogen and carbon atoms of CH2 groups on the alkyltrimethylammonium ion, and the counterion species in the solution. The running coordination numbers between carbon atoms of surfactants and counterions are also calculated. We show that I- counterion exhibits the highest, and F- the lowest affinity to "bind" to the model surfactants. The results are discussed in view of the available experimental and simulation data for this and similar solutions.

  1. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    Science.gov (United States)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-11-01

    The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion-water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion-water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water-water hydrogen bond interactions.

  2. A Time-Distinguished Analysis of the Harmonic Structure from a Model Molecular Ion

    Institute of Scientific and Technical Information of China (English)

    杨玉军; 陈高; 陈基根; 朱颀人

    2004-01-01

    We present high-order harmonic generation spectra resulted from a single-electron model molecular ion exposed to intense laser fields by numerically solving a one-dimensional time-dependent Schrodinger equation. There are three plateaus in the spectra and the maximal cutoff energy is Ip + 8.5Up, when the inter-nuclear distance R equals πα0/2. Here Ip is the ionization potential and Up = E02/(4ω2) is the ponderomotive potential with E0 and ω being the laser electric field amplitude and the central frequency. The harmonic structures are well interpreted by a modified three-step model in which the effects of the electron reflected by the non-parent ion are stressed.

  3. Molecular dynamics study of accelerated ion-induced shock waves in biological media

    CERN Document Server

    de Vera, Pablo; Currell, Fred J; Solov'yov, Andrey V

    2016-01-01

    We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which lies beyond the possibilities of the analytical model.

  4. Towards producing ultracold CaNa+ molecular ions in the ground electronic state

    Science.gov (United States)

    Gacesa, Marko; Montgomery, John A.; Michels, Harvey H.; Côté, Robin

    2015-05-01

    We present a theoretical analysis of optical pathways for the formation of cold Ca(1S)Na+(1S) molecular ions, based on accurate potential energy curves and transition dipole moments calculated using effective-core-potential methods of quantum chemistry. In the proposed approach, starting from a mixture of trapped laser-cooled Ca+ ions immersed into an ultracold gas of Na atoms, the (NaCa)+ are photoassociated in the excited E1Σ+ electronic state, followed by spontaneous radiative charge transfer and emission through an intermediate state. We find the optimal formation pathway and report radiative charge-exchange cross sections and vibrational distributions of participating electronic states. This work is partially supported by ARO.

  5. The ground state of the ${\\rm H}_3^+$ molecular ion: a physics behind

    CERN Document Server

    Turbiner, A V

    2012-01-01

    Five physics mechanisms of interaction leading to binding of the ${\\rm H}_3^+$ molecular ion are identified, realized in a form of variational trial functions and their respective total energies are calculated. Each of them provides subsequently the most accurate approximation for the Born-Oppenheimer (BO) ground state energy among (two-three-seven)-parametric trial functions being correspondingly, H$_2$-molecule plus proton (two variational parameters), H$_2^+$-ion plus H-atom (three variational parameters) and generalized Guillemin-Zener (seven variational parameters). These trial functions are chosen following a criterion of physical adequacy, they include the electronic correlation in the exponential form $\\sim\\exp{(\\gamma r_{12})}$, where $\\gamma$ is a variational parameter. Superpositions of two different mechanisms of binding are investigated and a particular one, which is a generalized Guillemin-Zener plus H$_2$-molecule plus proton (ten variational parameters), provides the total energy at the equili...

  6. Shifting nodal-plane suppressions in high-order harmonic spectra from diatomic molecules in orthogonally polarized driving fields

    CERN Document Server

    Das, T

    2016-01-01

    We analyze the imprint of nodal planes in high-order harmonic spectra from aligned diatomic molecules in intense laser fields whose components exhibit orthogonal polarizations. We show that the typical suppression in the spectra associated to nodal planes is distorted, and that this distortion can be employed to map the electron's angle of return to its parent ion. This investigation is performed semi-analytically at the single-molecule response and single-active orbital level, using the strong-field approximation and the steepest descent method. We show that the velocity form of the dipole operator is superior to the length form in providing information about this distortion. However, both forms introduce artifacts that are absent in the actual momentum-space wavefunction. Furthermore, elliptically polarized fields lead to larger distortions in comparison to two-color orthogonally polarized fields. These features are investigated in detail for $\\mathrm{O}_2$, whose highest occupied molecular orbital provides...

  7. Shifting nodal-plane suppressions in high-order-harmonic spectra from diatomic molecules in orthogonally polarized driving fields

    Science.gov (United States)

    Das, T.; Figueira de Morisson Faria, C.

    2016-08-01

    We analyze the imprint of nodal planes in high-order-harmonic spectra from aligned diatomic molecules in intense laser fields whose components exhibit orthogonal polarizations. We show that the typical suppression in the spectra associated to nodal planes is distorted, and that this distortion can be employed to map the electron's angle of return to its parent ion. This investigation is performed semianalytically at the single-molecule response and single-active orbital level, using the strong-field approximation and the steepest descent method. We show that the velocity form of the dipole operator is superior to the length form in providing information about this distortion. However, both forms introduce artifacts that are absent in the actual momentum-space wave function. Furthermore, elliptically polarized fields lead to larger distortions in comparison to two-color orthogonally polarized fields. These features are investigated in detail for O2, whose highest occupied molecular orbital provides two orthogonal nodal planes.

  8. Selective silicate-directed motility in diatoms

    DEFF Research Database (Denmark)

    Bondoc, Karen Grace V.; Heuschele, Jan; Gillard, Jeroen;

    2016-01-01

    Diatoms are highly abundant unicellular algae that often dominate pelagic as well as benthic primary production in the oceans and inland waters. Being strictly dependent on silica to build their biomineralized cell walls, marine diatoms precipitate 240 × 10(12) mol Si per year, which makes them t...

  9. Diatom Identification : a Double Challenge Called ADIAC

    NARCIS (Netherlands)

    Buf, Hans du; Bayer, Micha; Droop, Stephen; Head, Ritchie; Juggins, Steve; Fischer, Stefan; Bunke, Horst; Wilkinson, Michael; Roerdink, Jos; Pech-Pacheco, José; Cristóbal, Gabriel; Shahbazkia, Hamid; Ciobanu, Adrian

    1999-01-01

    This paper introduces the project ADIAC (Automatic Diatom Identification and Classification), which started in May 1998 and which is financed by the European MAST (Marine Science and Technology) programme. The main goal is to develop algorithms for an automatic identification of diatoms using image

  10. Dependence of the rate of LiF ion pairing on the description of molecular interaction

    Energy Technology Data Exchange (ETDEWEB)

    Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.; Jungwirth, Pavel; Mundy, Christopher J.

    2016-03-03

    We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response to ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored

  11. Mobility of O$_2^-$ ions in supercritical Ar: Experiment and Molecular Dynamics Simulations

    CERN Document Server

    Borghesani, A F

    2008-01-01

    A new analysis and new Molecular Dynamics (MD) simulations of the measurements of the mobility $\\mu_{i}$ of O$_{2}^{-} $ ions in dense supercritical Ar gas are reported. $\\mu_{i}$ shows a marked dependence on the distance from the critical temperature $T_{c}.$ A mobility defect appears as a function of the gas density and its maximum value occurs below the critical density. The locus of points of maximum mobility defect in the $P-T$ plane appears on the extrapolation of the coexistence curve into the single-phase region. MD simulations quantitatively reproduce the mobility defect near $T_{c}.$

  12. Molecular dynamics simulation of ion-beam-amorphization of Si, Ge and GaAs

    CERN Document Server

    Nord, J D; Keinonen, J

    2002-01-01

    We use molecular dynamics simulations to study ion-irradiation-induced amorphization in Si, Ge and GaAs using several different interatomic force models. We find that the coordination number is higher, and the average bond length longer, for the irradiated amorphous structures than for the molten ones in Si and Ge. For amorphous GaAs, we suggest that longer Ga-Ga bonds, also present in pure Ga, are produced during the irradiation. In Si the amorphization is found to proceed via growth of amorphous regions, and low energy recoils are found to induce athermal recrystallization during irradiation.

  13. Molecular dynamics studies of electron-ion temperature equilibration in the coupled-mode regime

    Science.gov (United States)

    Benedict, Lorin X.; Surh, Michael P.; Scullard, Christian R.; Stanton, Liam G.; Correa, Alfredo A.; Castor, John I.; Graziani, Frank R.; Collins, Lee A.; Kress, Joel D.; Cimarron Collaboration; T-1 Collaboration

    2016-10-01

    We use classical molecular dynamics (MD) to study electron-ion temperature equilibration in two-component plasmas in regimes in which the presence of coupled collective modes substantively impacts the equilibration rate. Guided by previous kinetic theory work in which predictions were made of both the regimes and the sizes of this effect, we examine hydrogen plasmas at a density of n =102 6 1/cm3, Ti =105 K, and 107 K Contract DE-AC52-07NA27344 and by Los Alamos National Laboratory under Contract DE-AC52-06NA25396.

  14. Fundamental Transitions and Ionization Energies of the Hydrogen Molecular Ions with Few ppt Uncertainty.

    Science.gov (United States)

    Korobov, Vladimir I; Hilico, L; Karr, J-Ph

    2017-06-09

    We calculate ionization energies and fundamental vibrational transitions for H_{2}^{+}, D_{2}^{+}, and HD^{+} molecular ions. The nonrelativistic quantum electrodynamics expansion for the energy in terms of the fine structure constant α is used. Previous calculations of orders mα^{6} and mα^{7} are improved by including second-order contributions due to the vibrational motion of nuclei. Furthermore, we evaluate the largest corrections at the order mα^{8}. That allows us to reduce the fractional uncertainty to the level of 7.6×10^{-12} for fundamental transitions and to 4.5×10^{-12} for the ionization energies.

  15. Young-type interference in collisions between hydrogen molecular ions and helium.

    Science.gov (United States)

    Schmidt, L Ph H; Schössler, S; Afaneh, F; Schöffler, M; Stiebing, K E; Schmidt-Böcking, H; Dörner, R

    2008-10-24

    The dissociative electron transfer from He into 10 keV H2+ was measured in a kinematically complete experiment by using the cold target recoil ion momentum spectroscopy imaging technique in combination with a highly resolving molecular fragment imaging technique. The electron transfer into the dissociative b(3)Sigma+_(u) state of H2 could be selected by kinematic conditions. We find a striking double slit interference pattern in the transverse momentum transfer which we can modify by selecting different internuclear distances. Compared to an optical double slit, interference minima and maxima are interchanged. The latter is the result of a phase shift in the electronic part of the wave function.

  16. Wave packet evolution approach to ionization of hydrogen molecular ion by fast electrons

    CERN Document Server

    Serov, V V; Joulakian, B B; Vinitsky, S I; Serov, Vladislav V.; Derbov, Vladimir L.; Joulakian, Boghos B.; Vinitsky, Sergue I.

    2000-01-01

    The multiply differential cross section of the ionization of hydrogen molecular ion by fast electron impact is calculated by a direct approach, which involves the reduction of the initial 6D Schr\\"{o}dinger equation to a 3D evolution problem followed by the modeling of the wave packet dynamics. This approach avoids the use of stationary Coulomb two-centre functions of the continuous spectrum of the ejected electron which demands cumbersome calculations. The results obtained, after verification of the procedure in the case atomic hydrogen, reveal interesting mechanisms in the case of small scattering angles.

  17. Molecular depth profiling with cluster secondary ion mass spectrometry and wedges.

    Science.gov (United States)

    Mao, Dan; Wucher, Andreas; Winograd, Nicholas

    2010-01-01

    Secondary ion mass spectrometry and atomic force microscopy are employed to characterize a wedge-shaped crater eroded by 40 keV C(60)(+) bombardment of a 395 nm thin film of Irganox 1010 doped with four delta layers of Irganox 3114. The wedge structure creates a laterally magnified cross section of the film. From an examination of the resulting surface, information about depth resolution, topography, and erosion rate can be obtained as a function of crater depth in a single experiment. This protocol provides a straightforward way to determine the parameters necessary to characterize molecular depth profiles and to obtain an accurate depth scale for erosion experiments.

  18. Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics.

    Directory of Open Access Journals (Sweden)

    Patrick Duchstein

    Full Text Available Molecular models of 5 nm sized ZnO/Zn(OH2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution.

  19. Molecular desorption of stainless steel vacuum chambers irradiated with 4.2  MeV/u lead ions

    Directory of Open Access Journals (Sweden)

    E. Mahner

    2003-01-01

    Full Text Available In preparation for the heavy ion program of the Large Hadron Collider at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring. These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2  MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow discharges, nonevaporable getter coating are reported in terms of the molecular desorption yields for H_{2}, CH_{4}, CO, Ar, and CO_{2}. Unexpected large values of molecular yields per incident ion up to 2×10^{4} molecules/ion have been observed. The reduction of the ion-induced desorption yield due to continuous bombardment with lead ions (beam cleaning has been investigated for five different stainless steel vacuum chambers. The implications of these results for the vacuum system of the future Low Energy Ion Ring and possible remedies to reduce the vacuum degradation are discussed.

  20. Molecular Dynamics Study of the Foam Stability of a Mixed Surfactant System with and without Calcium Ions

    Science.gov (United States)

    Yang, Xiaozhen; Yang, Wenhong; Institute of Chemistry, CAS Team

    2011-03-01

    Foam stability performance of a mixture surfactant system with and without calcium ions, including linear alkylbenzene sulfonate (LAS) and sodium dodecyl sulfate (SDS), has been studied by molecular dynamics. Microscopic interaction analysis reveals that the fraction of free calcium ions, Xf , in film system indicates the extent of the foam stabilities when Xf is in different calcium ion zones. In the system without ions, we found the variable of the surfactant tail mass out of water film, W , is indicator of foam stability. Performance of the mixture system predicted here was supported by experiments.

  1. Super-distant molecular hybridization of plant seeds by ion beam-mediated gene cluster

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The N beam-mediated distant molecular hybridization between Ginkgo biloba I and watermelon was studied. The results showed that the ester gene of Ginkgo biloba L was successfully expressed in two varieties of watermelon. 3-16 and SR2-14-2, in both of which the ester quantities were measured as 17.0756 μg/g and 45.9998 μg/g respectively. Meanwhile, superoxide dismutase (SOD) activity in leaves of the watennelon expressing ester gene was increased twofold as compared to that of the control, showing that ion beam could mediate distant and/or super-distant donor gene expression in the cells of a receptor. Furthermore, the molecular nechanism of distant hybridization was analyzed.

  2. Quadrupole transitions in the bound rotational-vibrational spectrum of the deuterium molecular ion

    CERN Document Server

    Pilón, Horacio Olivares

    2013-01-01

    After the study of the three body molecular system H$_2^+$ ({\\it J. Phys. B: At. Mol. Opt. Phys.} {\\bf 45} 065101), their isotope, the deuterium molecular ion D$_2^+$ is studied. The three-body Schr\\"odinger equation is solved using the Lagrange-mesh method in perimetric coordinates. Energies and wave functions for four vibrational states $v=0-3$ and bound or quasibound states for total orbital momenta from 0 to 56 are calculated. The 1986 fundamental constant $m_d=3670.483014\\,m_e$ is used. The obtained energies have an accuracy from about 13 digits for the lowest vibrational state to at least 9 digits for the third vibrational excited state. Quadrupole transition probabilities per time unit between those states over the whole rotational bands were calculated. Extensive results are presented with six significant figures.

  3. Molecular Structural Characterization and Quantitative Prediction of Reduced Ion Mobility Constants for Diversified Organic Compounds

    Institute of Scientific and Technical Information of China (English)

    HE Liu; LIANG Gui-Zhao; LI Zhi-Liang

    2008-01-01

    Based on two-dimensional topological structures, a novel molecular electronega- tivity interaction vector with hybridization (MEHIV) was developed to describe atomic hybri- dization state in different molecular environments. Five quantitative models by MEHIV cha- racterization and multiple linear regression modeling were successfully established to predict reduced ion mobility constants (K0) of alkanes, aromatic hydrocarbons, fatty alcohols, fatty aldehydes and ketones and carboxylic esters. The correlation coefficients Rcv by leave-one-out cross-validation are 0.792, 0.787, 0.949, 0.972 and 0.981, respectively, and the standard deviations SDcv are 0.067, 0.086, 0.064, 0.043 and 0.042, respectively. These results suggested that MEHIV is an excellent topological index descriptor with many advantages such as straightforward physicochemical meaning, high characterization competence, convenient expan- sibility and easy manipulation.

  4. Extraction of high quality DNA from bloodstains using diatoms.

    Science.gov (United States)

    Günther, S; Herold, J; Patzelt, D

    1995-01-01

    A simple method is described for the extraction of high quality DNA for PCR amplification. The DNA was extracted by using Chelex-100 ion exchange resin or a special cell lysis buffer containing proteinase K. For further purification the DNA was bound to silica in the presence of a chaotrophic agent. Hence it is possible to unlimitedly wash the bound DNA and inhibitory substances are removed. By using diatoms as a source of silicates, this method is very economical and can therefore be used as a routine method.

  5. Simulation of emission molecular spectra by a semi-automatic programme package: the case of C2 and CN diatomic molecules emitting during laser ablation of a graphite target in nitrogen environment.

    Science.gov (United States)

    Acquaviva, S

    2004-07-01

    Some emission spectra of diatomic molecules were calculated by a semi-automatic programme package in order to infer the rotational and vibrational temperatures in Boltzmann distribution by comparing them with the corresponding experimental ones. The calculation procedure was applied in the case of CN radical and C2 molecule whose optical emission spectra were recorded during pulsed excimer laser ablation of a graphite target in low-pressure nitrogen environment. Computed similar or dissimilar values of rotational and vibrational temperatures let to verify the existence or not of local thermodynamic equilibrium and to hypothesise the temporal range necessary to establish it in such experiments.

  6. Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells.

    Science.gov (United States)

    Sunda, Anurag Prakash; Venkatnathan, Arun

    2011-11-30

    Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.

  7. Isolation of Ion-Driven Conformations in Diphenylacetylene Molecular Switches Using Cryogenic Infrared Spectroscopy

    Science.gov (United States)

    Wolk, Arron B.; Garand, Etienne; Jones, Ian M.; Kamrath, Michael Z.; Hamilton, Rew; Johnson, Mark A.

    2012-06-01

    We report the infrared predissociation spectra of a family of ionic diphenylacetylene molecular switch complexes. The electrosprayed complexes were trapped and cooled in a cryogenic (10K) quadrupole ion trap and tagged with molecular deuterium. The infrared spectra of the vibrationally cold species reveal sharp transitions over a wide energy range (800 - 3800 cm-1), facilitating comparison to harmonic spectra. The evolution of the band pattern upon derivatization of the complexes exposes the signatures of the amide, urea, and carbonyl functionalities, enabling unambiguous identification of the non-covalent interactions that control the secondary structure of the molecule. Complexation with the tetramethylammonium cation reveals a conformation analogous to that of the neutral molecule, while halide ion attachment induces a conformational change similar to that observed earlier in solution. In several cases, both the donor and acceptor groups involved in the multidentate H-bonds are observed, providing a microscopic mechanical picture of the interactions at play. I. Jones, and A. Hamilton, Angew. Chem. Intl. Edit. 50, 4597 (2011).

  8. TaO$^+$, a Candidate Molecular Ion in Search of Physics Beyond the Standard Model

    CERN Document Server

    Fleig, Timo

    2016-01-01

    The TaO$^+$ molecular ion is proposed as a candidate system for detecting signatures of charge parity (${\\cal{CP}}$) violating physics beyond the standard model of elementary particles. The electron electric dipole moment (EDM) effective electric field $E_{\\text{eff}} = 20.2 \\left[\\frac{\\rm GV}{\\rm cm}\\right]$, the nucleon-electron scalar-pseudoscalar (ne-SPS) interaction constant $W_{S} = 17.7$ [kHz] and the nuclear magnetic quadrupole interaction constant $W_M = 0.45$ [$\\frac{10^{33} {\\text{Hz}}}{e\\, {\\text{cm}}^2}$] are found to be sizeable ${\\cal{P,T}}$-odd enhancements. The ratio of the leptonic and semi-leptonic enhancements differs strongly from the one for the ThO system which may provide improved limits on the electron EDM, $d_e$, and the SPS coupling constant, $C_S$. TaO$^+$ is found to have a ${^3\\Delta_1}$ electronic ground state like the previously proposed ThF$^+$ molecular ion, but an order of magnitude smaller parallel G-tensor component which makes it less vulnerable to systematic errors in e...

  9. Tuning Piezo ion channels to detect molecular-scale movements relevant for fine touch.

    Science.gov (United States)

    Poole, Kate; Herget, Regina; Lapatsina, Liudmila; Ngo, Ha-Duong; Lewin, Gary R

    2014-03-24

    In sensory neurons, mechanotransduction is sensitive, fast and requires mechanosensitive ion channels. Here we develop a new method to directly monitor mechanotransduction at defined regions of the cell-substrate interface. We show that molecular-scale (~13 nm) displacements are sufficient to gate mechanosensitive currents in mouse touch receptors. Using neurons from knockout mice, we show that displacement thresholds increase by one order of magnitude in the absence of stomatin-like protein 3 (STOML3). Piezo1 is the founding member of a class of mammalian stretch-activated ion channels, and we show that STOML3, but not other stomatin-domain proteins, brings the activation threshold for Piezo1 and Piezo2 currents down to ~10 nm. Structure-function experiments localize the Piezo modulatory activity of STOML3 to the stomatin domain, and higher-order scaffolds are a prerequisite for function. STOML3 is the first potent modulator of Piezo channels that tunes the sensitivity of mechanically gated channels to detect molecular-scale stimuli relevant for fine touch.

  10. Photocatalytic Oxidation of Hydrosulfide Ions by Molecular Oxygen Over Cadmium Sulfide Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Raevskaya, A. E., E-mail: photochem@e-mail.ru; Stroyuk, A.L., E-mail: photochem@e-mail.ru; Kuchmii, S.Ya. [National Academy of Sciences of Ukraine, L. V. Pysarzhevsky Institute of Physical Chemistry (Ukraine)], E-mail: photochem@e-mail.ru

    2004-06-15

    Photocatalytic activity of CdS nanoparticles in hydrosulfide-ions air oxidation was revealed and thoroughly investigated. HS{sup -} photooxidation in the presence of CdS nanoparticles results predominantly in the formation of SO{sub 3}{sup 2-} and SO{sub 4}{sup 2-} ions. Photocatalytic activity of ultrasmall CdS crystallites in HS{sup -} photooxidation is much more pronounced as compared to bulk CdS crystals due to high surface area of nanoparticles, their negligible light scattering, improved separation of photogenerated charge carriers etc. It was shown that hydrosulfide ions can be oxidized in two ways. The first is HS{sup -} oxidation by the CdS valence band holes. This process rate depends on the rate of comparatively slow reaction between molecular oxygen and CdS conduction band electrons. The second reaction route is the chain-radical HS{sup -} oxidation induced by photoexcited CdS nanoparticles and propagating in the bulk of a solution. In conditions favourable to chain-radical oxidation of HS{sup -}(i.e. at low light intensities and CdS concentration and high oxygen and Na{sub 2}S concentrations) quantum yields of the photoreaction reach 2.5.

  11. Cellular and molecular portrait of eleven human glioblastoma cell lines under photon and carbon ion irradiation.

    Science.gov (United States)

    Ferrandon, S; Magné, N; Battiston-Montagne, P; Hau-Desbat, N-H; Diaz, O; Beuve, M; Constanzo, J; Chargari, C; Poncet, D; Chautard, E; Ardail, D; Alphonse, G; Rodriguez-Lafrasse, C

    2015-04-28

    This study aimed to examine the cellular and molecular long-term responses of glioblastomas to radiotherapy and hadrontherapy in order to better understand the biological effects of carbon beams in cancer treatment. Eleven human glioblastoma cell lines, displaying gradual radiosensitivity, were irradiated with photons or carbon ions. Independently of p53 or O(6)-methylguanine-DNA methyltransferase(1) status, all cell lines responded to irradiation by a G2/M phase arrest followed by the appearance of mitotic catastrophe, which was concluded by a ceramide-dependent-apoptotic cell death. Statistical analysis demonstrated that: (i) the SF2(2) and the D10(3) values for photon are correlated with that obtained in response to carbon ions; (ii) regardless of the p53, MGMT status, and radiosensitivity, the release of ceramide is associated with the induction of late apoptosis; and (iii) the appearance of polyploid cells after photon irradiation could predict the Relative Biological Efficiency(4) to carbon ions. This large collection of data should increase our knowledge in glioblastoma radiobiology in order to better understand, and to later individualize, appropriate radiotherapy treatment for patients who are good candidates.

  12. Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

    Science.gov (United States)

    Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

    2016-09-01

    A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

  13. Iron oxide nanoparticle-micelles (ION-micelles for sensitive (molecular magnetic particle imaging and magnetic resonance imaging.

    Directory of Open Access Journals (Sweden)

    Lucas W E Starmans

    Full Text Available BACKGROUND: Iron oxide nanoparticles (IONs are a promising nanoplatform for contrast-enhanced MRI. Recently, magnetic particle imaging (MPI was introduced as a new imaging modality, which is able to directly visualize magnetic particles and could serve as a more sensitive and quantitative alternative to MRI. However, MPI requires magnetic particles with specific magnetic properties for optimal use. Current commercially available iron oxide formulations perform suboptimal in MPI, which is triggering research into optimized synthesis strategies. Most synthesis procedures aim at size control of iron oxide nanoparticles rather than control over the magnetic properties. In this study, we report on the synthesis, characterization and application of a novel ION platform for sensitive MPI and MRI. METHODS AND RESULTS: IONs were synthesized using a thermal-decomposition method and subsequently phase-transferred by encapsulation into lipidic micelles (ION-Micelles. Next, the material and magnetic properties of the ION-Micelles were analyzed. Most notably, vibrating sample magnetometry measurements showed that the effective magnetic core size of the IONs is 16 nm. In addition, magnetic particle spectrometry (MPS measurements were performed. MPS is essentially zero-dimensional MPI and therefore allows to probe the potential of iron oxide formulations for MPI. ION-Micelles induced up to 200 times higher signal in MPS measurements than commercially available iron oxide formulations (Endorem, Resovist and Sinerem and thus likely allow for significantly more sensitive MPI. In addition, the potential of the ION-Micelle platform for molecular MPI and MRI was showcased by MPS and MRI measurements of fibrin-binding peptide functionalized ION-Micelles (FibPep-ION-Micelles bound to blood clots. CONCLUSIONS: The presented data underlines the potential of the ION-Micelle nanoplatform for sensitive (molecular MPI and warrants further investigation of the FibPep-ION

  14. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    Energy Technology Data Exchange (ETDEWEB)

    Larriba, Carlos, E-mail: clarriba@umn.edu; Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  15. Complex dynamics in diatomic molecules. Part II: Quantum trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Yang, C.-D. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: cdyang@mail.ncku.edu.tw; Weng, H.-J. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: principlex@yahoo.com.tw

    2008-10-15

    The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum

  16. Physics with fast molecular-ion beams. Proceedings of workshop held at Argonne National Laboratory, August 20-21, 1979. [Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gemmell, D.S. (ed.)

    1979-01-01

    The Workshop on Physics with Fast Molecular-Ion Beams was held in the Physics Division, Argonne National Laboratory on August 20 and 21, 1979. The meeting brought together representatives from several groups studying the interactions of fast (MeV) molecular-ion beams with matter. By keeping the Workshop program sharply focussed on current work related to the interactions of fast molecular ions, it was made possible for the participants to engage in vigorous and detailed discussions concerning such specialized topics as molecular-ion dissociation and transmission, wake effects, ionic charge states, cluster stopping powers, beam-foil spectroscopy, electron-emissions studies with molecular-ion beams, and molecular-ion structure determinations.

  17. Heavy-ion beam induced effects in enriched gadolinium target films prepared by molecular plating

    Science.gov (United States)

    Mayorov, D. A.; Tereshatov, E. E.; Werke, T. A.; Frey, M. M.; Folden, C. M.

    2017-09-01

    A series of enriched gadolinium (Gd, Z = 64) targets was prepared using the molecular plating process for nuclear physics experiments at the Cyclotron Institute at Texas A&M University. After irradiation with 48Ca and 45Sc projectiles at center-of-target energies of Ecot = 3.8-4.7 MeV/u, the molecular films displayed visible discoloration. The morphology of the films was examined and compared to the intact target surface. The thin films underwent a heavy-ion beam-induced density change as identified by scanning electron microscopy and α-particle energy loss measurements. The films became thinner and more homogenous, with the transformation occurring early on in the irradiation. This transformation is best described as a crystalline-to-amorphous phase transition induced by atomic displacement and destruction of structural order of the original film. The chemical composition of the thin films was surveyed using energy dispersive spectroscopy and X-ray diffraction, with the results confirming the complex chemistry of the molecular films previously noted in other publications.

  18. Origin of CH+ in diffuse molecular clouds. Warm H2 and ion-neutral drift

    Science.gov (United States)

    Valdivia, Valeska; Godard, Benjamin; Hennebelle, Patrick; Gerin, Maryvonne; Lesaffre, Pierre; Le Bourlot, Jacques

    2017-04-01

    Context. Molecular clouds are known to be magnetised and to display a turbulent and complex structure where warm and cold phases are interwoven. The turbulent motions within molecular clouds transport molecules, and the presence of magnetic fields induces a relative velocity between neutrals and ions known as the ion-neutral drift (vd). These effects all together can influence the chemical evolution of the clouds. Aims: This paper assesses the roles of two physical phenomena which have previously been invoked to boost the production of CH+ under realistic physical conditions: the presence of warm H2 and the increased formation rate due to the ion-neutral drift. Methods: We performed ideal magnetohydrodynamical (MHD) simulations that include the heating and cooling of the multiphase interstellar medium (ISM), and where we treat dynamically the formation of the H2 molecule. In a post-processing step we compute the abundances of species at chemical equilibrium using a solver that we developed. The solver uses the physical conditions of the gas as input parameters, and can also prescribe the H2 fraction if needed. We validate our approach by showing that the H2 molecule generally has a much longer chemical evolution timescale compared to the other species. Results: We show that CH+ is efficiently formed at the edge of clumps, in regions where the H2 fraction is low (0.3-30%) but nevertheless higher than its equilibrium value, and where the gas temperature is high (≳ 300 K). We show that warm and out of equilibrium H2 increases the integrated column densities of CH+ by one order of magnitude up to values still 3-10 times lower than those observed in the diffuse ISM. We balance the Lorentz force with the ion-neutral drag to estimate the ion-drift velocities from our ideal MHD simulations. We find that the ion-neutral drift velocity distribution peaks around 0.04 km s-1, and that high drift velocities are too rare to have a significant statistical impact on the

  19. Magneto-optical trapping of a diatomic molecule

    Science.gov (United States)

    Barry, J. F.; McCarron, D. J.; Norrgard, E. B.; Steinecker, M. H.; Demille, D.

    2014-08-01

    Laser cooling and trapping are central to modern atomic physics. The most used technique in cold-atom physics is the magneto-optical trap (MOT), which combines laser cooling with a restoring force from radiation pressure. For a variety of atomic species, MOTs can capture and cool large numbers of particles to ultracold temperatures (less than ~1 millikelvin) this has enabled advances in areas that range from optical clocks to the study of ultracold collisions, while also serving as the ubiquitous starting point for further cooling into the regime of quantum degeneracy. Magneto-optical trapping of molecules could provide a similarly powerful starting point for the study and manipulation of ultracold molecular gases. The additional degrees of freedom associated with the vibration and rotation of molecules, particularly their permanent electric dipole moments, allow a broad array of applications not possible with ultracold atoms. Spurred by these ideas, a variety of methods has been developed to create ultracold molecules. Temperatures below 1 microkelvin have been demonstrated for diatomic molecules assembled from pre-cooled alkali atoms, but for the wider range of species amenable to direct cooling and trapping, only recently have temperatures below 100 millikelvin been achieved. The complex internal structure of molecules complicates magneto-optical trapping. However, ideas and methods necessary for creating a molecular MOT have been developed recently. Here we demonstrate three-dimensional magneto-optical trapping of a diatomic molecule, strontium monofluoride (SrF), at a temperature of approximately 2.5 millikelvin, the lowest yet achieved by direct cooling of a molecule. This method is a straightforward extension of atomic techniques and is expected to be viable for a significant number of diatomic species. With further development, we anticipate that this technique may be employed in any number of existing and proposed molecular experiments, in applications

  20. Photofragmentation spectroscopy of stored molecular ions at the dissociation limit; Photofragmentationsspektroskopie gespeicherter Molekuelionen an der Dissoziationsschwelle

    Energy Technology Data Exchange (ETDEWEB)

    Hechtfischer, U.

    2000-07-01

    Photofragmentation spectroscopy is a sensitive probe for nonadiabatic interactions in molecular dissociation, but for molecular ions detection and analysis of spectra are often hampered by the internal excitations of the ion beam. Therefore, near-threshold photofragmentation of CH{sup +} and OH{sup +} was studied in a heavy-ion storage ring where the ions rovibronically relax to room temperature within a few seconds. In the CH{sup +} spectrum, the Feshbach resonances between the fine-structure levels of the C{sup +} fragment were observed for the first time, the complex lineshapes indicating strong nonadiabatic couplings between the potentials. By a standard single-channel analysis, the spectrum was partially assigned and a more precise dissociation energy was deduced. The complete analysis was possible by multichannel close-coupling calculations only and yielded the vibrational defects of all coupled potentials. Furthermore, improved empirical potentials were constructed by an IPA approach, and conclusions on the reverse radiative association process in interstellar clouds were drawn. In OH{sup +}, numerous photofragmentation resonances were observed for both neutral and ionic oxygen fragments and assigned to the highest bound levels of the A{sup 3}II curve. In contrast to CH{sup +}, OH{sup +} hardly shows any multichannel behavior. (orig.) [German] Photofragmentationsspektroskopie ist eine empfindliche Sonde fuer nichtadiabatische Wechselwirkungen bei der Dissoziation von Molekuelen, aber bei Molekuelionen erschweren haeufig die internen Anregungen des Ionenstrahls Messung und Analyse der Spektren. Deshalb wurde hier die schwellennahe Photofragmentation von CH{sup +}- und OH{sup +}-Molekuelionen in einem Schwerionenspeicherring untersucht, wo die Ionen rovibronisch innerhalb von Sekunden Raumtemperatur annehmen. Im CH{sup +}-Spektrum wurden so erstmals die Feshbach-Resonanzen zwischen den Feinstrukturniveaus des C{sup +}-Fragments direkt beobachtet, deren

  1. The presence of pollutant hydrocarbons in estuarine epipelic diatom populations. II. Diatom slimes

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, S.; Eglinton, G.

    1979-01-01

    Diatom slime in sediment from the Severn intertidal estuary was analyzed for polycyclic aromatic hydrocarbons (PAH's) and aliphatic hydrocarbons, using computerized capillary gas chromatography/mass spectrometry. The distributions of these substances in diatoms were compared with those in the underlying sediment and in a sediment-free diatom population. Aliphatic hydrocarbon distribution in slime was about the same as that of separated diatoms and sediment, while PAH distribution in slime was about that of the sediment alone. These results suggest a loss of PAH's from the coalesced sediment in the slime, probably either by a photo-oxidative or catabolic process. 34 references, 2 tables.

  2. Experimental Investigation of Impact-Induced Molecular Desorption by 4.2 MeV/u Pb ions

    CERN Document Server

    Chanel, M; Laurent, Jean Michel; Madsen, N; Mahner, E

    2001-01-01

    In preparation for the heavy ion program of the LHC, accumulation and cooling test with lead ion beams have been performed in the LEAR storage ring. These tests have revealed that due to the unexpected, large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments are reported in terms of the molecular desorption yields for H2, CH4, CO and CO2. Unpexpected large values of molecular yields per incident ion up to 2x104 molecules/ion have been observed. The implications of these results for the vacuum system of the future ion accumulator ring (LEIR) and possi...

  3. Cadmium sensitivity, uptake, subcellular distribution and thiol induction in a marine diatom: exposure to cadmium.

    Science.gov (United States)

    Wang, Meng-Jiao; Wang, Wen-Xiong

    2011-01-25

    The aims of this study were to (1) evaluate the changes in the Cd tolerance of a marine diatom after exposure under different Cd concentrations for various durations and (2) to explore the potential subcellular and biochemical mechanisms underlying these changes. The 72-h toxicity, short-term Cd uptake, subcellular Cd distribution, as well as the synthesis of phytochelatins (PCs) were measured in a marine diatom Thalassiosira nordenskioeldii after exposure to a range of free Cd ion concentrations ([Cd(2+)], 0.01-84nM) for 1-15 days. Surprisingly, the diatoms did not acquire higher resistance to Cd after exposure; instead their sensitivity to Cd increased with a higher exposed [Cd(2+)] and a longer exposure period. The underlying mechanisms could be traced to the responses of Cd cellular accumulation and the intrinsic detoxification ability of the preconditioned diatoms. Generally, exposure to a higher [Cd(2+)] and for a longer period increased the Cd uptake rate, cellular accumulation, as well as the Cd concentration in metal-sensitive fraction (MSF) in these diatoms. In contrast, although PCs were induced by the environmental Cd stress (with PC(2) being the most affected), the increased intracellular Cd to PC-SH ratio implied that the PCs' detoxification ability had reduced after Cd exposure. All these responses resulted in an elevated Cd sensitivity as exposed [Cd(2+)] and duration increased. This study shows that the physiological/biochemical and kinetic responses of phytoplankton upon metal exposure deserve further investigation.

  4. Digitisation of the South African diatom collection

    CSIR Research Space (South Africa)

    Van der Molen, J

    2008-06-01

    Full Text Available This presentation gives the background of the Diatom collection as well as an overview of the collection content. The two phases of the digitisation process are described in detail...

  5. Amino Acid Biosynthesis Pathways in Diatoms

    Directory of Open Access Journals (Sweden)

    Mariusz A. Bromke

    2013-04-01

    Full Text Available Amino acids are not only building blocks for proteins but serve as precursors for the synthesis of many metabolites with multiple functions in growth and other biological processes of a living organism. The biosynthesis of amino acids is tightly connected with central carbon, nitrogen and sulfur metabolism. Recent publication of genome sequences for two diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum created an opportunity for extensive studies on the structure of these metabolic pathways. Based on sequence homology found in the analyzed diatomal genes, the biosynthesis of amino acids in diatoms seems to be similar to higher plants. However, one of the most striking differences between the pathways in plants and in diatomas is that the latter possess and utilize the urea cycle. It serves as an important anaplerotic pathway for carbon fixation into amino acids and other N-containing compounds, which are essential for diatom growth and contribute to their high productivity.

  6. Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report

    Energy Technology Data Exchange (ETDEWEB)

    Wasielewski, M.R.

    1997-01-01

    'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

  7. Molecular pharmacology of cell receptors for cardiac glycosides, opiates, ACTH and ion channel modulators

    Energy Technology Data Exchange (ETDEWEB)

    Hnatowich, M.R.

    1986-01-01

    The influence of light and oxygen on molecular interactions between the artificial food dye, erythrosine (ERY), and (/sup 3/H)ouabain ((/sup 3/H)OUA) binding sites on (Na/sup +/ + K/sup +/)-ATPase in rat brain and guinea pig heart was investigated. Putative endogenous digitalis-like factors (DLF's) were studied in four in vitro assays for cardiac glycosides. (/sup 3/H)Etorphine binding was characterized in rat brain homogenates, depleted of opioids, from animals acutely and chronically treated with morphine and naloxone, and either unstressed or cold-restraint-stressed. Binding sites for the ion channel modulators (/sup 3/H)verapamil ((/sup 3/H)VER) and (/sup 3/H) phencyclidine ((/sup 3/H)PCP) were characterized in rat brain.

  8. Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution

    KAUST Repository

    Yu, Weili

    2014-08-19

    A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Quadrupole transitions in the bound rotational-vibrational spectrum of the hydrogen molecular ion

    CERN Document Server

    Pilón, Horacio Olivares

    2013-01-01

    The three-body Schr\\"odinger equation of the H$_2^+$ hydrogen molecular ion with Coulomb potentials is solved in perimetric coordinates using the Lagrange-mesh method. The Lagrange-mesh method is an approximate variational calculation with variational accuracy and the simplicity of a calculation on a mesh. Energies and wave functions of up to four of the lowest vibrational bound or quasibound states for total orbital momenta from 0 to 40 are calculated. The obtained energies have an accuracy varying from about 13 digits for the lowest vibrational state to at least 9 digits for the third vibrational excited state. With the corresponding wave functions, a simple calculation using the associated Gauss quadrature provides accurate quadrupole transition probabilities per time unit between those states over the whole rotational bands. Extensive results are presented with six significant figures.

  10. Classical Dynamics of Harmonic Generation of the Hydrogen Molecular Ion Interacting with Ultrashort Intense Laser Pulses

    Institute of Scientific and Technical Information of China (English)

    LI Chao-Hong; DUAN Yi-Wu; Wing-Ki Liu; Jian-Min Yuan

    2001-01-01

    Within Born-Oppenheimer approximation, by using the classical trajectory theory, a description for the high order harmonic generation of the hydrogen molecular ion interacting with ultrashort laser pulses has been pre sented. The Coulomb singularities have been remedied by the regularization. The action-angle variables have been used to generate the initial inversion symmetry microcanonical distribution. Within a proper intensity range, a harmonic plateau with only odd harmonics appears. For a larger intensity, because of the existence of chaos, the harmonic spectra become noisier. For a large enough intensity, the ionization takes place and the harmonics disappear. So the chaos causes the noises, the ionization suppresses the harmonic generation, and the onset of the ionization follows the onset of chaos.

  11. Molecular dynamics study on low-energy sputtering of carbon material by Xe ion bombardment

    Science.gov (United States)

    Muramoto, T.; Hyakutake, T.

    2013-05-01

    The low-energy sputtering of carbon material under Xe ion bombardment is studied through the molecular dynamics (MD) simulation. For the normal incidence of Xe, the MD result of sputtering yield almost agrees with the experimental result by Williams et al. (AIAA-2004-3788). However, the experimental result shows a less incident angle dependence than the MD result because the experiment performed on a rough surface. It is found that the sputtered particles have memory of the projectile because the sputtered particles by the low-energy projectile undergo only a few collisions before the ejection. Low density of an amorphous carbon surface brings the decrease of the sputtering yield and the increase of high-energy sputtered atoms.

  12. Spatial scale and the diversity of benthic cyanobacteria and diatoms in a salina

    DEFF Research Database (Denmark)

    Nübel, U.; Garcia-Pichel, F.; Kühl, Michael

    1999-01-01

    We characterized the richness of benthic cyanobacteria and diatoms in a salina system using traditional and molecular biological methods. After determining the different morphotypes and 16S rRNA genes present in various localities within this hypersaline system, an analysis of the increase...

  13. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube

    Science.gov (United States)

    Liu, L.; Patey, G. N.

    2017-02-01

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l-1 and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  14. Broadband Velocity Modulation Spectroscopy of Molecular Ions for Use in the Jila Electron Edm Experiment

    Science.gov (United States)

    Gresh, Daniel N.; Cossel, Kevin C.; Cornell, Eric A.; Ye, Jun

    2013-06-01

    The JILA electron electric dipole moment (eEDM) experiment will use a low-lying, metastable ^3Δ_1 state in trapped molecular ions of HfF^+ or ThF^+. Prior to this work, the low-lying states of these molecules had been investigated by PFI-ZEKE spectroscopy. However, there were no detailed studies of the electronic structure. The recently developed technique of frequency comb velocity modulation spectroscopy (VMS) provides broad-bandwidth, high-resolution, ion-sensitive spectroscopy, allowing the acquisition of 150 cm^{-1} of continuous spectra in 30 minutes over 1500 simultaneous channels. By supplementing this technique with cw-laser VMS, we have investigated the electronic structure of HfF^+ in the frequency range of 9950 to 14600 cm^{-1}, accurately fitting and assigning 16 rovibronic transitions involving 8 different electronic states including the X^1Σ^+ and a^3Δ_1 states. In addition, an observed ^3Π_{0+} state with coupling to both the X and a states has been used in the actual eEDM experiment to coherently transfer population from the rovibronic ground state of HfF^+ to the eEDM science state. Furthermore, we report on current efforts of applying frequency comb VMS at 700 - 900 nm to the study of ThF^+, which has a lower energy ^3Δ_1 state and a greater effective electric field, and will provide increased sensitivity for a measurement of the eEDM. A. E. Leanhardt et. al., Journal of Molecular Spectroscopy 270, 1-25 (2011). B. J. Barker, I. O. Antonov, M. C. Heaven, K. A. Peterson, Journal of Chemical Physics 136, 104305 (2012). L. C. Sinclair, K. C. Cossel, T. Coffey, J. Ye, E. A. Cornell, Physical Review Letters 107, 093002 (2011). K.C. Cossel et. al., Chemical Physics Letters 546, 1-11 (2012).

  15. Determination of elemental compositions from mass peak profiles of the molecular ion (m) and the m + 1 and m + 2 ions.

    Science.gov (United States)

    Grange, A H; Donnelly, J R; Sovocool, G W; Brumley, W C

    1996-02-01

    The relative abundances of M + 1 and M + 2 ions help to identify the elemental composition of the molecular ion (M). But scan speed, sensitivity, and resolution limitations of mass spectrometers have impeded determination of these abundances. Mass peak profiling from selected ion recording data (MPPSIRD) provided faster sampling and enhanced sensitivity, which permitted use of higher resolution. M + 2 profiles having only a few percent of the ion abundance of M were monitored at 20 000 resolution. The relative abundances, exact masses, and shapes of M, M + 1, and M + 2 mass peak profiles were determined. By applying five criteria based on these quantities, elemental compositions were determined even for ions too large (up to 766 Da) to be uniquely assigned from their exact mass and accuracy limits alone. A profile generation model (PGM) was written to predict these resolution-dependent quantities by considering all M + 1 and M + 2 ions for each candidate composition. The model also provided assurance that no other compositions were possible. Characterization of the M + 1 and M + 2 profiles by MPPSIRD and the PGM greatly expanded the practical ability of high-resolution mass spectrometry to determine elemental compositions.

  16. Bound-free Spectra for Diatomic Molecules

    Science.gov (United States)

    Schwenke, David W.

    2012-01-01

    It is now recognized that prediction of radiative heating of entering space craft requires explicit treatment of the radiation field from the infrared (IR) to the vacuum ultra violet (VUV). While at low temperatures and longer wavelengths, molecular radiation is well described by bound-bound transitions, in the short wavelength, high temperature regime, bound-free transitions can play an important role. In this work we describe first principles calculations we have carried out for bound-bound and bound-free transitions in N2, O2, C2, CO, CN, NO, and N2+. Compared to bound ]bound transitions, bound-free transitions have several particularities that make them different to deal with. These include more complicated line shapes and a dependence of emission intensity on both bound state diatomic and atomic concentrations. These will be discussed in detail below. The general procedure we used was the same for all species. The first step is to generate potential energy curves, transition moments, and coupling matrix elements by carrying out ab initio electronic structure calculations. These calculations are expensive, and thus approximations need to be made in order to make the calculations tractable. The only practical method we have to carry out these calculations is the internally contracted multi-reference configuration interaction (icMRCI) method as implemented in the program suite Molpro. This is a widely used method for these kinds of calculations, and is capable of generating very accurate results. With this method, we must first of choose which electrons to correlate, the one-electron basis to use, and then how to generate the molecular orbitals.

  17. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  18. Analytical Formulas of Molecular Ion Abundances and N2H+ Ring in Protoplanetary Disks

    CERN Document Server

    Aikawa, Yuri; Nomura, Hideko; Qi, Chunhua

    2015-01-01

    We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of N$_2$H$^+$ ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N$_2$H$^+$ is abundant outside the CO snow line in spite of the similar sublimation temperatures of CO and N$_2$. Using the full gas-grain network model, we reproduced the N$_2$H$^+$ ring in a disk model with millimeter grains. The chemical conversion of CO and N$_2$ to less volatile species (sink effect hereinafter) is found to affect the N$_2$H$^+$ distribution. Since the efficiency of the sink depends on various parameters such as activation barriers of grain surface reactions, which are not well constrained, we also constructed the no-sink model; the total (gas and ice) CO and N$_2$ abundances are set constant, and their gaseous abundances are given by the balance between adsorption and desorption. Abundances of molecular ions in the no-sink model are calculated by analytical formulas, which a...

  19. Molecular Simulation of Hydrogen Storage in Ion-Exchanged X Zeolites

    Directory of Open Access Journals (Sweden)

    Xiaoming Du

    2014-01-01

    Full Text Available Grand Canonical Monte Carlo (GCMC method was employed to simulate the adsorption properties of molecular hydrogen on ion-exchanged X zeolites at 100–293 K and pressures up to 10 MPa in this paper. The effect of cation type, temperature, and pressure on hydrogen adsorption capacity, heat of adsorption, adsorption sites, and adsorption potential energy of ion-exchanged X zeolites was analyzed. The results indicate that the hydrogen adsorption capacity increases with the decrease in temperatures and the increase in pressures and decreases in the order of KX

  20. Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.

    Science.gov (United States)

    Ray, Andrew D; Hammond, Janet; Major, Hilary

    2010-01-01

    Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism.

  1. Ambient low temperature plasma etching of polymer films for secondary ion mass spectrometry molecular depth profiling.

    Science.gov (United States)

    Muramoto, Shin; Staymates, Matthew E; Brewer, Tim M; Gillen, Greg

    2012-12-18

    The feasibility of a low temperature plasma (LTP) probe as a way to prepare polymer bevel cross sections for secondary ion mass spectrometry (SIMS) applications was investigated. Poly(lactic acid) and poly(methyl methacrylate) films were etched using He LTP, and the resulting crater walls were depth profiled using time-of-flight secondary ion mass spectrometry (ToF-SIMS) to examine changes in chemistry over the depth of the film. ToF-SIMS results showed that while exposure to even 1 s of plasma resulted in integration of atmospheric nitrogen and contaminants to the newly exposed surface, the actual chemical modification to the polymer backbone was found to be chemistry-dependent. For PLA, sample modification was confined to the top 15 nm of the PLA surface regardless of plasma exposure dose, while measurable change was not seen for PMMA. The confinement of chemical modification to 15 nm or less of the top surface suggests that LTP can be used as a simple method to prepare cross sections or bevels of polymer thin films for subsequent analysis by surface-sensitive molecular depth profiling techniques such as SIMS, X-ray photoelectron spectroscopy (XPS), and other spatially resolved mass spectrometric techniques.

  2. A general potential for molecular dynamics of ion-sputtered surfaces

    CERN Document Server

    Akande, Raphael O

    2015-01-01

    Erosion of surface atoms of solid materials by ion bombardment (surface-sputtering) causes nano-ripples and quantum dots to self-organise on the surfaces. The self-organisation had been shown, in some sputtering experiments, to be influenced by unexpected contaminants (ions) from vacuum walls. Existing inter-atomic-interaction potentials of Molecular Dynamics (MD) simulations for studying this are unsuitable because they assume two-particle collisions at a time instead of many (including contaminants)-particle collisions (Wider-area Perturbations, (WP)). We designed this study to develop a suitable potential that incorporates WP of the MD. We developed the general potential to account for the possibility of WP due to contaminants (both foreign and local to the material) consequently shifting the eqiulibrium points of the MD the material. For instance, dynamics of Au and Fe were studied with O bombardments/contamination (oxygenated environments), and those of CSiGe were studied with W, Ti, and O. It was found ...

  3. Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

    Science.gov (United States)

    Moin, Syed Tarique; Hofer, Thomas S

    2014-12-21

    This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

  4. Molecular dynamics simulation of ion selectivity traits of nickel hexacyanoferrate thin films

    Institute of Scientific and Technical Information of China (English)

    HAO Xiao-gang; YU Qiu-ming; JIANG Shao-yi; D. T. SCHWARTZ

    2006-01-01

    The ion selectivity of nickel hexacyanoferrate thin film to alkali cations in ESIX (electrochemically switched ion exchange) processes was investigated using molecular dynamics(MD) techniques; water and cation (Na+ and Cs+) intercalation, configuration,and dynamics in reduced nickel hexacyanoferrate structures with different cation combinations were studied and compared with the experimental results. In the simulations, water was represented by an extended simple point-charge(SPC/E) model, and all other atomic interactions were represented by a universal force field(UFF). The potential energies of various cations combination (Cs+ and Na+) in reduced i-NiHCF and 1 mol/L Cs/NaCl mixed solution were obtained. In most cases, the total potential energy of the solid is reduced when water is intercalated into the various reduced NiHCF structures. Combining the solid and the solution simulation results, it is shown that the solid composition of 3Cs+/1Na+ is the stablest structure form (NaCs3Ni4[Fe(CN)6]3) over a range of solution compositions.

  5. Conversion of an atomic to a molecular argon ion and low pressure argon relaxation

    Science.gov (United States)

    M, N. Stankov; A, P. Jovanović; V, Lj Marković; S, N. Stamenković

    2016-01-01

    The dominant process in relaxation of DC glow discharge between two plane parallel electrodes in argon at pressure 200 Pa is analyzed by measuring the breakdown time delay and by analytical and numerical models. By using the approximate analytical model it is found that the relaxation in a range from 20 to 60 ms in afterglow is dominated by ions, produced by atomic-to-molecular conversion of Ar+ ions in the first several milliseconds after the cessation of the discharge. This conversion is confirmed by the presence of double-Gaussian distribution for the formative time delay, as well as conversion maxima in a set of memory curves measured in different conditions. Finally, the numerical one-dimensional (1D) model for determining the number densities of dominant particles in stationary DC glow discharge and two-dimensional (2D) model for the relaxation are used to confirm the previous assumptions and to determine the corresponding collision and transport coefficients of dominant species and processes. Project supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grant No. ON171025).

  6. Studies on dissociation energies of diatomic molecules using vibrational spectroscopic constants

    Institute of Scientific and Technical Information of China (English)

    HOU; Shilin(侯世林); SUN; Weiguo(孙卫国)

    2003-01-01

    New analytical expression and numerical approach are suggested to calculate dissociation energies De of diatomic molecular states using an extreme value method (EVM). Studies on some electronic states of OH, BH, N2, Br2, ClF and CO molecules show that the accuracy of the EVM dissociation energies depends on the number of correct vibrational constants used in the calculations. The convergence qualities of De are suggested to be an alternative physical criterion to measure the qualities of the various sets of vibrational constants from different literature for the same diatomic state.

  7. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Arnab; Tribedi, Lokesh C.; Misra, Deepankar, E-mail: dmisra@tifr.res.in [Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005 (India)

    2015-04-15

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

  8. Early stages of insulin fibrillogenesis examined with ion mobility mass spectrometry and molecular modelling.

    Science.gov (United States)

    Cole, Harriet; Porrini, Massimiliano; Morris, Ryan; Smith, Tom; Kalapothakis, Jason; Weidt, Stefan; Mackay, C Logan; MacPhee, Cait E; Barran, Perdita E

    2015-10-21

    A prevalent type of protein misfolding causes the formation of β-sheet-rich structures known as amyloid fibrils. Research into the mechanisms of fibril formation has implications for both disease prevention and nanoscale templating technologies. This investigation into the aggregation of insulin utilises ion mobility mass spectrometry coupled with molecular modelling to identify and characterise oligomers formed during the 'lag' phase that precedes fibril growth. High resolution mass spectrometry and collision induced dissociation is used to unequivocally assign species as m/z coincident multimers or confomers, providing a robust analytical approach that supports the use of molecular dynamics to atomistically resolve the observed oligomers. We show that insulin oligomerises to form species In where 2 ≤ n ≤ 12 and within this set of oligomers we delineate over 60 distinct conformations, the most dominant of which are compact species. Modelling trained with experimental data suggests that the dominant compact dimers are enriched in β-sheet secondary structure and dominated by hydrophobic interactions, and provides a linear relationship between Rg and collision cross section. This approach provides detailed insight to the early stages of assembly of this much studied amyloidogenic protein, and can be used to inform models of nucleation and growth.

  9. Molecular Dynamics Simulation of Na(+)-Cl(-) Ion-Pair in Water-Methanol Mixtures under Supercritical and Ambient Conditions.

    Science.gov (United States)

    Keshri, Sonanki; Sarkar, Atanu; Tembe, B L

    2015-12-17

    Constrained molecular dynamics simulations have been performed to investigate the structure and thermodynamics of Na(+)-Cl(-) ion-pair association in water-methanol mixtures under supercritical and ambient conditions in dilute solutions. From the computed potentials of mean force (PMFs) we find that contact ion pairs (CIPs) are more stable than all other associated states of the ion pairs in both ambient and supercritical conditions. Stabilities of CIPs increase with increase in the mole fraction of methanol. In supercritical conditions, major changes in PMFs occur as we go from x(methanol) = 0.00 to x(methanol) = 0.50. The stable solvent shared ion pair (SShIP) which occurs in x(methanol) = 0.00 and 0.25, vanishes when x(methanol) is 0.50 or greater. The stabilities of these ion pairs increase with increasing temperature. Local structures around the ions are studied using the radial distribution functions, density profiles, angular distribution functions, running coordination numbers and excess coordination numbers. Preferential solvation analysis shows that both Na(+) and Cl(-) ions are preferentially solvated by water. From the calculation of enthalpies and entropies, we find that Na(+)-Cl(-) ion-pair association in water-methanol binary mixtures is endothermic and driven by entropy both in ambient as well as under supercritical conditions.

  10.  Serial replacement of diatom endosymbiont in two freshwater dinoflagellates, Peridiniopsis spp., (Peridiniales, Dinophyceae)

    DEFF Research Database (Denmark)

    Takano, Y.; Hansen, Gert; Fujita, D.

    2008-01-01

    Two freshwater armoured dinoflagellates, Peridiniopsis cf. kevei from Japan and Peridiniopsis penardii from Japan and Italy, were examined by means of light, scanning and transmission electron microscopy. Morphological studies indicated that the two dinoflagellates had similar type of cellular...... structure and possessed an endosymbiotic diatom. The diatom endosymbiont, which contained a eukaryotic nucleus, chloroplasts and mitochondria, was separated from the dinoflagellate cytoplasm by a single unit membrane. The dinoflagellate cytoplasm contained a triple-membrane-bound eyespot, in addition...... to typical dinoflagellate organelles. Molecular phylogenetic analyses based on small subunit ribosomal RNA gene (SSU rDNA) revealed a close relationship between these two dinoflagellates. They formed a clade with other dinoflagellates possessing a diatom endosymbiont, suggesting a single origin of diatom...

  11. Molecular desorption of stainless steel vacuum chambers irradiated with 4.2 MeV/u lead ions

    CERN Document Server

    Mahner, E; Laurent, Jean Michel; Madsen, N

    2003-01-01

    In preparation for the heavy ion program of the Large Hadron Collider (LHC) at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring (LEAR). These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow-discharges, non-evaporable getter coating) are reported in terms of the molecular desorption yields for H2, CH4, CO, Ar and CO2. Unexpected large values of molecular yields per incident ion up to 2 104 molecules/ion have been observed. The red...

  12. Molecular characteristics of a fluorescent chemosensor for the recognition of ferric ion based on photoresponsive azobenzene derivative

    Science.gov (United States)

    Chi, Zhen; Ran, Xia; Shi, Lili; Lou, Jie; Kuang, Yanmin; Guo, Lijun

    2017-01-01

    Metal ion recognition is of great significance in biological and environmental detection. So far, there is very few research related to the ferric ion sensing based on photoresponsive azobenzene derivatives. In this work, we report a highly selective fluorescent "turn-off" sensor for Fe3 + ions and the molecular sensing characteristics based on an azobenzene derivative, N-(3,4,5-octanoxyphenyl)-N‧-4-[(4-hydroxyphenyl)azophenyl]1,3,4-oxadiazole (AOB-t8). The binding association constant was determined to be 6.07 × 103 M- 1 in ethanol and the stoichiometry ratio of 2:2 was obtained from Job's plot and MS spectra. The AOB-t8 might be likely to form the dimer structure through the chelation of ferric ion with the azobenzene moiety. Meanwhile, it was found that the photoisomerization property of AOB-t8 was regulated by the binding with Fe3 +. With the chelation of Fe3 +, the regulated molecular rigidity and the perturbed of electronic state and molecular geometry was suggested to be responsible for the accelerated isomerization of AOB-t8 to UV irradiation and the increased fluorescence lifetime of both trans- and cis-AOB-t8-Fe(III). Moreover, the reversible sensing of AOB-t8 was successfully observed by releasing the iron ion from AOB-t8-Fe(III) with the addition of citric acid.

  13. A tyrosine-rich cell surface protein in the diatom Amphora coffeaeformis identified through transcriptome analysis and genetic transformation.

    Directory of Open Access Journals (Sweden)

    Matthias T Buhmann

    Full Text Available Diatoms are single-celled eukaryotic microalgae that are ubiquitously found in almost all aquatic ecosystems, and are characterized by their intricately structured SiO2 (silica-based cell walls. Diatoms with a benthic life style are capable of attaching to any natural or man-made submerged surface, thus contributing substantially to both microbial biofilm communities and economic losses through biofouling. Surface attachment of diatoms is mediated by a carbohydrate- and protein- based glue, yet no protein involved in diatom underwater adhesion has been identified so far. In the present work, we have generated a normalized transcriptome database from the model adhesion diatom Amphora coffeaeformis. Using an unconventional bioinformatics analysis we have identified five proteins that exhibit unique amino acid sequences resembling the amino acid composition of the tyrosine-rich adhesion proteins from mussel footpads. Establishing the first method for the molecular genetic transformation of A. coffeaeformis has enabled investigations into the function of one of these proteins, AC3362, through expression as YFP fusion protein. Biochemical analysis and imaging by fluorescence microscopy revealed that AC3362 is not involved in adhesion, but rather plays a role in biosynthesis and/or structural stability of the cell wall. The methods established in the present study have paved the way for further molecular studies on the mechanisms of underwater adhesion and biological silica formation in the diatom A. coffeaeformis.

  14. Improvement in the assessment of direct and facilitated ion transfers by electrochemically induced redox transformations of common molecular probes

    DEFF Research Database (Denmark)

    Zhou, Min; Gan, Shiyu; Zhong, Lijie;

    2012-01-01

    A new strategy based on a thick organic film modified electrode allowed us, for the first time, to explore the voltammetric processes for a series of hydrophilic ions by electrochemically induced redox transformations of common molecular probes. During the limited time available for voltammetry, ...

  15. Mid-infrared continuous wave cavity ring down spectroscopy of molecular ions using an optical parametric oscillator

    NARCIS (Netherlands)

    Verbraak, H.; Ngai, A.K.Y.; Persijn, S.T.; Harren, F.J.M.; Linnartz, H.

    2007-01-01

    A sensitive infrared detection scheme is presented in which continuous wave cavity ring down spectroscopy is used to record rovibrational spectra of molecular ions in direct absorption through supersonically expanding planar plasma. A cw optical parametric oscillator is used as a light source and

  16. Static dipole polarizability for the 1s{sigma} electronic state of the H{sup +}{sub 2} molecular ion

    Energy Technology Data Exchange (ETDEWEB)

    Tsogbayar, Ts, E-mail: tsogbayar@ipt.ac.m [Institute of Physics and Technology, Mongolian Academy of Sciences, Peace Avenue 54B, 210651, Ulaanbaatar 51 (Mongolia)

    2009-08-28

    The static dipole polarizability for the 1s{sigma} electron state of the H{sup +}{sub 2} hydrogen molecular ion is calculated within the Born-Oppenheimer approximation. The variational expansion with randomly chosen exponents has been used for numerical studies. The results obtained for the dipole polarizability are accurate to nine digits.

  17. Biochemical Composition of Dissolved Organic Matter Released During Experimental Diatom Blooms

    Science.gov (United States)

    Mannino, Antonio; Harvey, H. Rodger

    2002-01-01

    An axenic culture of Skeletonema costatum was grown to late-log phase to examine the molecular weight distribution and the biochemical composition of high molecular weight dissolved organic matter released in the absence of actively growing bacteria. A second culture was grown in a 5 m(exp 3) mesocosm and placed in darkness for a period of 51 days to examine the impact of phytoplankton bloom dynamics and microbial decomposition on dissolved (DOM) and particulate organic matter (POM) composition. DOM was separated using tangential-flow ultrafiltration into three nominal size fractions: LDOM (less than 1 kDa DOM), HDOM (1-30 kDa) and VHDOM (30 kDa-0.2 micron) and characterized. Both axenic and mesocosm diatom blooms released 28-33% of net primary production as dissolved organic carbon (DOC). In the axenic culture, HDOM and LDOM each comprised about half of the diatom-released DOC with less than l% as VHDOM. Diatoms from both experiments released carbohydrate-rich high molecular weight DOM. Much of the axenic diatom-released high molecular weight DOC could be chemically characterized (61% of HDOM and 78% of VHDOM) with carbohydrates as the primary component (45% of HDOM and 55% of VHDOM). Substantial amounts of hydrolyzable amino acids (16% of HDOM and 22% of VHDOM) and small amounts of lipids (less than 1%) were also released. Proportions of recognizable biochemical components in DOM produced in the mesocosm bloom were lower compared to the axenic culture. The presence of bacterial fatty acids and peptidoglycan-derived D-amino acids within high molecular weight fractions from the mesocosm bloom revealed that bacteria contributed a variety of macromolecules to DOM during the growth and decay of the diatom bloom. Release of significant amounts of DOC by diatoms demonstrates that DOM excretion is an important component of phytoplankton primary production. Similarities in high molecular weight DOM composition in marine waters and diatom cultures highlight the importance

  18. Metal Ion Coordination Essential for Specific Molecular Interactions of Butea monosperma Lectin: ITC and MD Simulation Studies.

    Science.gov (United States)

    Abhilash, J; Haridas, M

    2015-05-01

    Crystal structure of Butea monosperma seed lectin (BML) was analyzed and the metal ion geometry identified. In order to understand the role of metal ions for the structural stability and ligand binding, studies of demetallized protein were carried out. Binding of different ligands like GalNAc, lactose, and galactose onto native and demetallized protein was studied by isothermal titration calorimetry as well as molecular simulation methods. Molecular dynamics was applied to the structure after removing the coordinates of metal ions, to identify the effect of demetallization in silico. Docking studies of different sugar molecules as well as the fungal α-amylase was carried out and compared the interactions in the native and apo states. It was found that metal ions are important for the ligand binding with increased affinity. However, their absence did not make any alteration to the secondary structure. Though the metal ions were not coordinated to the loops contacting the α-amylase, the absence of metal ions reduced the protein-protein binding strength due to long-range changes in irregular structures of the lectin.

  19. Electronic spectroscopy of diatomic VC.

    Science.gov (United States)

    Krechkivska, Olha; Morse, Michael D

    2013-12-19

    Resonant two-photon ionization spectroscopy has been applied to diatomic VC, providing the first optical spectrum of this molecule. The ground state is determined to be a (2)Δ3/2 state that arises from the 1σ(2)1π(4)2σ(2)1δ(1) configuration. The r0" ground-state bond length is 1.6167(3) Å. The manifold of excited vibronic states in the visible portion of the spectrum is quite dense, but two possible vibrational progressions have been identified. It is noted that VC joins CrC, NbC, and MoC as species in which the metal ns-based 3σ orbital is unoccupied, resulting in large dipole moments in the ground states of these molecules. In the corresponding 5d metal carbides, however, the 3σ orbital is occupied, leading to different ground electronic states of the 5d congeners, TaC and WC.

  20. Molecular Modeling of Acidic Treated PSTM-3T Polymer for Removal of Heavy Metal Ions by Experimental and Computational Studies

    Directory of Open Access Journals (Sweden)

    Natsagdorj Narantsogt

    2014-01-01

    Full Text Available The synthesized poly[N,N′-bis(3-silsesquioxanilpropyl-thiocarbamide] (PSTM-3T was used and the surface morphology and microstructure of it were analyzed by scanning electron microscopy with energy dispersive spectrometer (SEM/EDS. The molecular structure change of the PSTM-3T polymer of the PSTM-3T after treatment by acidic solution with different pHs was revealed using FT-IR experiments and ab initio calculations with density functional theory method. The sorption efficiency of the heavy metal ions depends on the molecular structure change of PSTM-3T after treatment of different pH aqueous solutions. After the treatment of acidic solution (pH = 2 of PSTM-3T, the polymer formed the tautomer state to increase the sorption efficiency for chromate ion. For the increment of pH value for acidic solution, the PSTM-3T polymer was dissociated to increase the sorption efficiency for copper ion.

  1. Diatom-Specific Oligosaccharide and Polysaccharide Structures Help to Unravel Biosynthetic Capabilities in Diatoms

    Directory of Open Access Journals (Sweden)

    Bruno Gügi

    2015-09-01

    Full Text Available Diatoms are marine organisms that represent one of the most important sources of biomass in the ocean, accounting for about 40% of marine primary production, and in the biosphere, contributing up to 20% of global CO2 fixation. There has been a recent surge in developing the use of diatoms as a source of bioactive compounds in the food and cosmetic industries. In addition, the potential of diatoms such as Phaeodactylum tricornutum as cell factories for the production of biopharmaceuticals is currently under evaluation. These biotechnological applications require a comprehensive understanding of the sugar biosynthesis pathways that operate in diatoms. Here, we review diatom glycan and polysaccharide structures, thus revealing their sugar biosynthesis capabilities.

  2. The hydrogen molecule and the H+2 molecular ion inside padded prolate spheroidal cavities with arbitrary nuclear positions

    Science.gov (United States)

    Colín-Rodríguez, R.; Díaz-García, C.; Cruz, S. A.

    2011-12-01

    A generalization of previous theoretical studies of molecular confinement based on the molecule-in-a-box model for the H+2 and H2 systems whereby the confining cavity is assumed to be prolate spheroidal in shape is presented. A finite height for the confining barrier potential is introduced and the independent variation of the nuclear positions from the cavity size and shape is allowed. Within this scheme, the non-separable Schrödinger problem for the confined H+2 and H2 molecules in their ground states is treated variationally. In both cases, an important dependence of the equilibrium bond length and total energy on the confining barrier height is observed for fixed cavity sizes and shapes. It is also shown that—given a barrier height—as the cavity size is reduced, the limit of stability of the confined molecule is attained for a critical size. The results of this work suggest the adequacy of the proposed method for more realistic studies of electronic and vibrational properties of confined one- and two-electron diatomics for proper comparison with experiment.

  3. Electron Interference in Molecular Circular Polarization Attosecond XUV Photoionization

    Directory of Open Access Journals (Sweden)

    Kai-Jun Yuan

    2015-01-01

    Full Text Available Two-center electron interference in molecular attosecond photoionization processes is investigated from numerical solutions of time-dependent Schrödinger equations. Both symmetric H\\(_2^+\\ and nonsymmetric HHe\\(^{2+}\\ one electron diatomic systems are ionized by intense attosecond circularly polarized XUV laser pulses. Photoionization of these molecular ions shows signature of interference with double peaks (minima in molecular attosecond photoelectron energy spectra (MAPES at critical angles \\(\\vartheta_c\\ between the molecular \\(\\textbf{R}\\ axis and the photoelectron momentum \\(\\textbf{p}\\. The interferences are shown to be a function of the symmetry of electronic states and the interference patterns are sensitive to the molecular orientation and pulse polarization. Such sensitivity offers possibility for imaging of molecular structure and orbitals.

  4. Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization.

    Science.gov (United States)

    Ran-Ressler, Rinat R; Lawrence, Peter; Brenna, J Thomas

    2012-01-01

    Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223-229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.

  5. Rotational state resolved photodissociation spectroscopy of translationally and vibrationally cold MgH+ ions: toward rotational cooling of molecular ions

    DEFF Research Database (Denmark)

    Højbjerre, Klaus; Hansen, Anders Kragh; Skyt, Peter Sandegaard

    2009-01-01

    and vibrationally cold MgH+ ions are presented, with and without the optical pumping laser being present. While rotational cooling is as yet not evident, first results showed evidence of a change in the rotational distribution in the presence of the optical pumping laser.......The first steps toward the implementation of a simple scheme for rotational cooling of MgH+ ions based on rotational state optical pumping is considered. The various aspects of such an experiment are described in detail, and the rotational state-selective dissociation spectra of translationally...

  6. Kinetic energy release of diatomic and linear triatomic molecules in intense femtosecond laser fields

    Institute of Scientific and Technical Information of China (English)

    Chen Jian-Xin; Ma Ri; Ren Hai-Zhen; Li Xia; Wu Cheng-Yin; Yang Hong; Gong Qi-Huang

    2004-01-01

    @@ The kinetic energy release of fragment ions produced by the interaction of femtosecond laser pulse radiation with diatomic and linear triatomic molecules N2, CO, CO2 and CS2 is investigated. In the case of linear polarization, angles at which the kinetic energy release of ions has the maximum value are different from the alignment of molecules though the kinetic energy release of fragment atomic ions depends on the angle between the laser polarization vector and the detection axis of the time-of-flight.

  7. Molecular dynamics simulation of polymerlike thin films irradiated by fast ions: A comparison between FENE and Lennard-Jones potentials

    Science.gov (United States)

    Lima, N. W.; Gutierres, L. I.; Gonzalez, R. I.; Müller, S.; Thomaz, R. S.; Bringa, E. M.; Papaléo, R. M.

    2016-11-01

    In this paper, the surface effects of individual heavy ions impacting thin polymerlike films were investigated, using molecular dynamics simulations with the finite extensible nonlinear elastic (FENE) potential to describe the molecular chains. The perturbation introduced by the ions in the lattice was modeled assuming that the initial excitation energy in the ion track is converted into an effective temperature, as in a thermal spike. The track was heated only within the film thickness h , leaving a nonexcited substrate below. The effect of decreasing thickness on cratering and sputtering was evaluated. The results were compared to experimental data of thin polymer films bombarded by MeV-GeV ions and to simulations performed with the Lennard-Jones potential. While several qualitative results observed in the experiments were also seen in the simulations, irrespective of the potential used, there are important differences observed on FENE films. Crater dimensions, rim volume, and sputtering yields are substantially reduced, and a threshold thickness for molecular ejection appears in FENE simulations. This is attributed to the additional restrictions on mass transport out of the excited track region imposed by interchain interactions (entanglements) and by the low mobility of the molten phase induced by the spike.

  8. Epiphytic diatoms along environmental gradients in Western European shallow lakes

    NARCIS (Netherlands)

    Blanco, S.; Cejudo-Figueiras, C.; Álvarez-Blanco, I.; Van Donk, E.; Gross, E.M.; Hansson, L-A.; Irvine, K.; Jeppesen, E.; Kairesalo, T.; Moss, B.; Nõges, T.; Bécares, E.

    2014-01-01

    European shallow lakes; epiphyton; Bacillariophyta; bioindication; eutrophication; total phosphorus Diatom-based assays have been successfully associated worldwide with the trophic status of lakes. Several studies have demonstrated a correlation between epiphytic diatoms and nutrient load in shallow

  9. Colonization of diatom aggregates by the dinoflagellate Noctiluca scintillans

    DEFF Research Database (Denmark)

    Tiselius, P.; Kiørboe, Thomas

    1998-01-01

    Abundance and vertical distribution of the dinoflagellate Noctiluca scintillans were studied during a diatom bloom in the Benguela current. Video observations showed the occurrence of abundant Chaetoceros spp. aggregates colonized by N. scintillans. The diatom aggregates were formed by regular...

  10. Diatoms: a fossil fuel of the future.

    Science.gov (United States)

    Levitan, Orly; Dinamarca, Jorge; Hochman, Gal; Falkowski, Paul G

    2014-03-01

    Long-term global climate change, caused by burning petroleum and other fossil fuels, has motivated an urgent need to develop renewable, carbon-neutral, economically viable alternatives to displace petroleum using existing infrastructure. Algal feedstocks are promising candidate replacements as a 'drop-in' fuel. Here, we focus on a specific algal taxon, diatoms, to become the fossil fuel of the future. We summarize past attempts to obtain suitable diatom strains, propose future directions for their genetic manipulation, and offer biotechnological pathways to improve yield. We calculate that the yields obtained by using diatoms as a production platform are theoretically sufficient to satisfy the total oil consumption of the US, using between 3 and 5% of its land area. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Biofilm diatom community structure: Influence of temporal and substratum variability

    Digital Repository Service at National Institute of Oceanography (India)

    Patil, J.S.; Anil, A.C.

    . delicatula and Amphora (TableIIa–d).ANOVAalsorevealedsignificantsub- stratum variations with respect to months (Table III). Diatomdistributionencounteredonthetestsubstrata Figure 4. Cluster dendrogram based on density of diatoms from the ambient water. a... suggested that pennate diatoms dominate the diatom fouling community irrespective of the nature of the sub- stratum and the exposure period. The dominance of pennate diatoms has also been reported in biofouling on test coupons exposed in the Arabian Sea...

  12. Aromaticity of Heterofullerenes C18BxNy (x+y=2) and Their Molecular Ions

    Institute of Scientific and Technical Information of China (English)

    Jia-li Chen; Ablikim Kerim

    2008-01-01

    The axomaticity of all possible substituted fullerene isomers of C18N2,C18N2,C18BN,and their molecular ions which originate from the C20 (Ih) cage were studied by the topological resonance energy (TRE) and the percentage topological resonance energy methods.The relationship between the aromaticity of C18BxNy isomers and the sites where the heteroatoms dope at the C20 (Ih) cage is discussed.Calculation results show that at the neutral and cationic states all the isomers axe predicted to be antiaromatic with negative TREs,but their polyvalent anions are predicted to be aromatic with positive TREs.The most stable isomer is formed by heteroatom doping at the 1,11-sites in C18N2,C18B2,and C18BN.Heterofullerenes are more aromatic than C20.The stability order in the neutral states is C18N2>C18BN>C18B2>C20.The stability order in closed-shell is C18B28->C206->C18BN6->C18N24-.This predicts theoretically that their polyvalent anions have high aromaticity.

  13. Importance of explicit salt ions for protein stability in molecular dynamics simulation.

    Science.gov (United States)

    Ibragimova, G T; Wade, R C

    1998-06-01

    The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.

  14. Three-body fragmentation of triatomic molecular ions in a strong laser field

    Science.gov (United States)

    Ablikim, U.; Zohrabi, M.; Jochim, Bethany; Berry, Ben; Carnes, K. D.; Ben-Itzhak, I.

    2014-05-01

    Coincidence three-dimensional momentum imaging measurements of three-body fragmentation of transient triply-charged CO2 molecules reveal competing fragmentation paths involving bending, symmetric and asymmetric stretching, as well as the more complex sequential breakup (i.e. one bond at a time). We have extended these studies using a CO2+molecular-ion-beam target, providing similar results for the breakup of the transient CO23+ --> O+ + C+ + O+. The detection of neutral fragments also enables kinematically complete measurements of the three-body breakup of the transient CO22+ . Our results, for CO2+in ultrashort (~26 fs) intense (1015 to 1016 W/cm2) laser pulses at 790 nm, suggest significant bending in the C+ + O+ + O+ channel as well as sequential breakup. In contrast, sequential breakup is suppressed in the O+ + C+ + O and O+ + C +O+ channels. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S.

  15. Custom-tailored adsorbers: A molecular dynamics study on optimal design of ion exchange chromatography material.

    Science.gov (United States)

    Lang, Katharina M H; Kittelmann, Jörg; Pilgram, Florian; Osberghaus, Anna; Hubbuch, Jürgen

    2015-09-25

    The performance of functionalized materials, e.g., ion exchange resins, depends on multiple resin characteristics, such as type of ligand, ligand density, the pore accessibility for a molecule, and backbone characteristics. Therefore, the screening and identification process for optimal resin characteristics for separation is very time and material consuming. Previous studies on the influence of resin characteristics have focused on an experimental approach and to a lesser extent on the mechanistic understanding of the adsorption mechanism. In this in silico study, a previously developed molecular dynamics (MD) tool is used, which simulates any given biomolecule on resins with varying ligand densities. We describe a set of simulations and experiments with four proteins and six resins varying in ligand density, and show that simulations and experiments correlate well in a wide range of ligand density. With this new approach simulations can be used as pre-experimental screening for optimal adsorber characteristics, reducing the actual number of screening experiments, which results in a faster and more knowledge-based development of custom-tailored adsorbers.

  16. Mapping of low molecular weight heparins using reversed phase ion pair liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Li, Daoyuan; Chi, Lequan; Jin, Lan; Xu, Xiaohui; Du, Xuzhao; Ji, Shengli; Chi, Lianli

    2014-01-01

    Low molecular weight heparins (LMWHs) are structurally complex, highly sulfated and negatively charged, linear carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. They are widely used as anticoagulant drugs possessing better bioavailability, longer half-life, and lower side effects than heparin. Comprehensive structure characterization of LMWHs is important for drug quality assurance, generic drug application, and new drug research and development. However, fully characterization of all oligosaccharide chains in LMWHs is not feasible for current available analytical technologies due to their structure complexity and heterogeneity. Fingerprinting profiling is an efficient way for LMWHs' characterization and comparison. In this work, we present a simple, sensitive, and powerful analytical approach for structural characterization of LMWHs. Two different LMWHs, enoxaparin and nadroparin, were analyzed using reversed phase ion pair electrospray ionization mass spectrometry (RPIP-ESI-MS). More than 200 components were identified, including major structures, minor structures, and process related impurities. This approach is robust for high resolution and complementary fingerprinting analysis of LMWHs.

  17. Investigation of electron localization in harmonic emission from asymmetric molecular ion

    Institute of Scientific and Technical Information of China (English)

    张彩萍; 苗向阳

    2015-01-01

    We theoretically investigate the electron localization around two nuclei in harmonic emission from asymmetric molec-ular ion. The results show that the ionization process of electron localized around one nucleus competes with its transfer process to the other nucleus. By increasing the initial vibrational level, more electrons localized around the nucleus D+tend to transfer to the nucleus He2+so that the ionizations of electrons localized around the nucleus He2+increase. In this case, the difference in harmonic efficiency between HeH2+and HeD2+decreases while the difference in harmonic spectral structure increases. The evident minimum can be observed in the harmonic spectrum of HeH2+ compared with that in the spectral structure of HeD2+, which is due to the strong interference of multiple recombination channels originating from two nuclei. Time-dependent nuclear probability density, electron-nuclear probability density, double-well model, and time-frequency maps are presented to explain the underlying mechanisms.

  18. Aromaticity of Heterofullerenes C18BxNy (x + y = 2) and Their Molecular Ions

    Science.gov (United States)

    Chen, Jia-li; Kerim, Ablikim

    2008-04-01

    The aromaticity of all possible substituted fullerene isomers of C18N2, C18B2, C18BN, and their molecular ions which originate from the C20 (Ih) cage were studied by the topological resonance energy (TRE) and the percentage topological resonance energy methods. The relationship between the aromaticity of C18BxNy isomers and the sites where the heteroatoms dope at the C20 (Ih) cage is discussed. Calculation results show that at the neutral and cationic states all the isomers are predicted to be antiaromatic with negative TREs, but their polyvalent anions are predicted to be aromatic with positive TREs. The most stable isomer is formed by heteroatom doping at the 1, 11-sites in C18N2, C18B2, and C18BN. Heterofullerenes are more aromatic than C20. The stability order in the neutral states is C18N2 > C18 BN > C18 B2 > C20. The stability order in closed-shell is C18B28- > C206- > C18BN6- > C18N24-. This predicts theoretically that their polyvalent anions have high aromaticity.

  19. In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Venkata Rama Ses; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R.; Wang, Chong M.

    2015-08-19

    Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

  20. Comparison of ion sites and diffusion paths in glasses obtained by molecular dynamics simulations and bond valence analysis

    OpenAIRE

    Muller, Christian; Zienicke, Egbert; Adams, Stefan; Habasaki, Junko; Maass, Philipp

    2006-01-01

    Based on molecular dynamics simulations of a lithium metasilicate glass we study the potential of bond valence sum calculations to identify sites and diffusion pathways of mobile Li ions in a glassy silicate network. We find that the bond valence method is not well suitable to locate the sites, but allows one to estimate the number of sites. Spatial regions of the glass determined as accessible for the Li ions by the bond valence method can capture up to 90% of the diffusion path. These regio...

  1. Cadmium-Containing Carbonic Anhydrase CDCA1 in Marine Diatom Thalassiosira weissflogii

    Directory of Open Access Journals (Sweden)

    Vincenzo Alterio

    2015-03-01

    Full Text Available The Carbon Concentration Mechanism (CCM allows phytoplakton species to accumulate the dissolved inorganic carbon (DIC necessary for an efficient photosynthesis even under carbon dioxide limitation. In this mechanism of primary importance for diatoms, a key role is played by carbonic anhydrase (CA enzymes which catalyze the reversible hydration of CO2, thus taking part in the acquisition of inorganic carbon for photosynthesis. A novel CA, named CDCA1, has been recently discovered in the marine diatom Thalassiosira weissflogii. CDCA1 is a cambialistic enzyme since it naturally uses Cd2+ as catalytic metal ion, but if necessary can spontaneously exchange Cd2+ to Zn2+. Here, the biochemical and structural features of CDCA1 enzyme will be presented together with its putative biotechnological applications for the detection of metal ions in seawaters.

  2. The relationship between molecular structure and ion adsorption on variable charge minerals

    NARCIS (Netherlands)

    Rietra, R.P.J.J.; Hiemstra, T.; Riemsdijk, van W.H.

    1999-01-01

    Ion adsorption modeling is influenced by the presumed binding structure of surface complexes. Ideally, surface complexes determined by modeling should correspond with those derived from spectroscopy, thereby assuring that the mechanistic description of ion binding scales from the nanoscopic molecula

  3. Treatise on the measurement of molecular masses with ion mobility spectrometry.

    Science.gov (United States)

    Valentine, Stephen J; Clemmer, David E

    2009-07-15

    The ability to separate isotopes by high-resolution ion mobility spectrometry techniques is considered as a direct means for determining mass at ambient pressures. Calculations of peak shapes from the transport equation show that it should be possible to separate isotopes for low-mass ions (ion mobility analyzers. The mass accuracy associated with this isotopic separation approach based on ion mobility separation is considered. Finally, we predict several isotopes that should be separable.

  4. The exotic molecular ion H{sub 4}{sup 3+} in a strong magnetic field; El ion molecular exotico H{sub 4}{sup 3+} en un campo magnetico intenso

    Energy Technology Data Exchange (ETDEWEB)

    Olivares P, H. [ICN-UNAM, A.P. 70-543, 04510 Mexico D.F. (Mexico)]. e-mail: horop@nucleares.unam.mx

    2006-07-01

    Using the variational method, a detailed study of the lowest m = 0, -1 electronic states of the exotic molecular ion H3+{sub 4} in a strong magnetic field, in the linear symmetric configuration parallel to the direction of the magnetic field is carried out. A extended study of the 1{sigma}g ground state (J.C. Lopez and A.Turbiner, Phys. Rev A 62, 022510, 2000) was performed obtaining that the potential energy curve displays a sufficiently deep minimum for finite internuclear distances, indicating the possible existence of the molecular ion H{sub 4}{sup 3+}, for magnetic fields of strength B > {approx} 3 x 10{sup 13} G. It is demonstrated that the excited state 1{pi}{sub u}, can exist for a magnetic field B = 4.414 x 10{sup 13} G corresponding to the limit of applicability of the non-relativistic theory. (Author)

  5. Effects of the oxylipin-producing diatom Skeletonema marinoi on gene expression levels of the calanoid copepod Calanus sinicus.

    Science.gov (United States)

    Lauritano, Chiara; Carotenuto, Ylenia; Vitiello, Valentina; Buttino, Isabella; Romano, Giovanna; Hwang, Jiang-Shiou; Ianora, Adrianna

    2015-12-01

    Diatoms are eukaryotic unicellular plants that constitute one of the major components of marine phytoplankton, comprising up to 40% of annual productivity at sea and representing 25% of global carbon-fixation. Diatoms have traditionally been considered a preferential food for zooplankton grazers such as copepods, but, in the last two decades, this beneficial role has been challenged after the discovery that many species of diatoms produce toxic metabolites, collectively termed oxylipins, that induce reproductive failure in zooplankton grazers. Diatoms are the dominant natural diet of Calanus sinicus, a cold-temperate calanoid copepod that supports secondary production of important fisheries in the shelf ecosystems of the Northwest Pacific Ocean, Yellow Sea, Sea of Japan and South China Sea. In this study, the effect of the oxylipin-producing diatom Skeletonema marinoi on C. sinicus has been evaluated by analyzing expression level changes of genes involved in defense and detoxification systems. Results show that C. sinicus is more resistant to a diet of this diatom species in terms of gene expression patterns, compared to the congeneric species Calanus helgolandicus which is an important constituent of the temperate waters of the Atlantic Ocean and northern Mediterranean Sea. These findings contribute to the better understanding of genetic and/or phenotypic flexibility of copepod species and their capabilities to cope with stress by identifying molecular markers (such as stress and detoxification genes) as biosensors for environmental perturbations (e.g. toxins and contaminants) affecting marine copepods.

  6. Diatoms respire nitrate to survive dark and anoxic conditions

    DEFF Research Database (Denmark)

    Kamp, Anja; de Beer, Dirk; Nitsch, Jana L.

    2011-01-01

    Diatoms survive in dark, anoxic sediment layers for months to decades. Our investigation reveals a correlation between the dark survival potential of marine diatoms and their ability to accumulate NO3− intracellularly. Axenic strains of benthic and pelagic diatoms that stored 11–274 mM NO3− in th...

  7. Diatoms respire nitrate to survive dark and anoxic conditions

    DEFF Research Database (Denmark)

    Kamp, Anja; de Beer, Dirk; Nitsch, Jana L.

    2011-01-01

    Diatoms survive in dark, anoxic sediment layers for months to decades. Our investigation reveals a correlation between the dark survival potential of marine diatoms and their ability to accumulate NO3− intracellularly. Axenic strains of benthic and pelagic diatoms that stored 11–274 mM NO3− in th...

  8. Fossil Diatoms in a New Carbonaceous Meteorite

    Science.gov (United States)

    Wickramasinghe, N. C.; Wallis, J.; Wallis, D. H.; Samaranayake, Anil

    2013-01-01

    We report the discovery for the first time of diatom frustules in a carbonaceous meteorite that fell in the North Central Province of Sri Lanka on 29 December 2012. Contamination is excluded by the circumstance that the elemental abundances within the structures match closely with those of the surrounding matrix. There is also evidence of structures morphologically similar to red rain cells that may have contributed to the episode of red rain that followed within days of the meteorite fall. The new data on "fossil" diatoms provide strong evidence to support the theory of cometary panspermia.

  9. Molecular dynamics investigation into the electric charge effect on the operation of ion-based carbon nanotube oscillators

    Science.gov (United States)

    Ansari, R.; Ajori, S.; Sadeghi, F.

    2015-10-01

    The fabrication of nanoscale oscillators working in the gigahertz (GHz) range and beyond has now become the focal center of interest to many researchers. Motivated by this issue, this paper proposes a new type of nano-oscillators with enhanced operating frequency in which both the inner core and outer shell are electrically charged. To this end, molecular dynamics (MD) simulations are performed to investigate the mechanical oscillatory behavior of ions, and in particular chloride ion, tunneling through electrically charged carbon nanotubes (CNTs). It is assumed that the electric charges with similar sign and magnitude are evenly distributed on two ends of nanotube. The interatomic interactions between carbon atoms and van der Waals (vdW) interactions between ion and nanotube are respectively modeled by Tersoff-Brenner and Lennard-Jones (LJ) potential functions, whereas the electrostatic interactions between ion and electric charges are modeled by Coulomb potential function. A comprehensive study is conducted to get an insight into the effects of different parameters such as sign and magnitude of electric charges, nanotube radius, nanotube length and initial conditions (initial separation distance and velocity) on the oscillatory behavior of chloride ion-charged CNT oscillators. It is shown that, the chloride ion frequency inside negatively charged CNTs is lower than that inside positively charged ones with the same magnitude of electric charge, while it is higher than that inside uncharged CNTs. It is further observed that, higher frequencies are generated at higher magnitudes of electric charges distributed on the nanotube.

  10. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    Energy Technology Data Exchange (ETDEWEB)

    Li, Huan [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Tang, Xiaobin, E-mail: tangxiaobin@nuaa.edu.cn [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Jiangsu Key Laboratory of Nuclear Energy Equipment Materials Engineering, Nanjing (China); Chen, Feida; Huang, Hai; Liu, Jian [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Chen, Da [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Jiangsu Key Laboratory of Nuclear Energy Equipment Materials Engineering, Nanjing (China)

    2016-07-01

    Highlights: • Various incident sites of CNTs are classified into three types for the first time. • Different ion energies and fluences are considered to study the radiation damage. • CNTs have ability to heal the radiation-induced damage at higher temperature. • Stability of a large-diameter tube excels in a slim one under the same conditions. - Abstract: The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  11. Above-Threshold Ionization and Laser-Induced Electron Diffraction in Diatomic Molecules

    CERN Document Server

    Suárez, N; Ciappina, M F; Wolter, B; Biegert, J; Lewenstein, M

    2016-01-01

    Strong field photoemission and electron recollision provide a viable route to extract electronic and nuclear dynamics from molecular targets with attosecond temporal resolution. However, since an {\\em ab-initio} treatment of even the simplest diatomic systems is beyond today's capabilities approximate qualitative descriptions are warranted. In this paper, we develop such a theoretical approach to model the photoelectrons resulting from intense laser-molecule interaction. We present a general theory for symmetric diatomic molecules in the single active electron approximation that, amongst other capabilities, allows adjusting both the internuclear separation and molecular potential in a direct and simple way. More importantly we derive an analytic approximate solution of the time dependent Schr\\"odinger equation (TDSE), based on a generalized strong field approximation (SFA) version. Using that approach we obtain expressions for electrons emitted transition amplitudes from two different molecular centres, and a...

  12. Dynamics of molecular superrotors in external magnetic field

    CERN Document Server

    Korobenko, Aleksey

    2015-01-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to the qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane in three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  13. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models.

    Science.gov (United States)

    Rebič, Matúš; Laaksonen, Aatto; Šponer, Jiří; Uličný, Jozef; Mocci, Francesca

    2016-08-04

    Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew

  14. Magneto-optical trapping of a diatomic molecule

    CERN Document Server

    Barry, J F; Norrgard, E B; Steinecker, M H; DeMille, D

    2014-01-01

    Laser cooling and trapping are central to modern atomic physics. The workhorse technique in cold-atom physics is the magneto-optical trap (MOT), which combines laser cooling with a restoring force from radiation pressure. For a variety of atomic species, MOTs can capture and cool large numbers of particles to ultracold temperatures (<1 mK); this has enabled the study of a wide range of phenomena from optical clocks to ultracold collisions whilst also serving as the ubiquitous starting point for further cooling into the regime of quantum degeneracy. Magneto-optical trapping of molecules could provide a similarly powerful starting point for the study and manipulation of ultracold molecular gases. Here, we demonstrate three-dimensional magneto-optical trapping of a diatomic molecule, strontium monofluoride (SrF), at a temperature of approximately 2.5 mK. This method is expected to be viable for a significant number of diatomic species. Such chemical diversity is desired for the wide array of existing and prop...

  15. MOL-D: A Collisional Database and Web Service within the Virtual Atomic and Molecular Data Center

    Indian Academy of Sciences (India)

    V. Vujčić; D. Jevremović; A. A. Mihajlov; Lj. M. Ignjatović; V. A. Srećković; M. S. Dimitrijević; M. Malović

    2015-12-01

    MOL-D database is a collection of cross-sections and rate coefficients for specific collisional processes and a web service within the Serbian Virtual Observatory (SerVO) and the Virtual Atomic and Molecular Data Center (VAMDC). This database contains photo-dissociation cross-sections for the individual ro-vibrational states of the diatomic molecular ions and rate coefficients for the atom-Rydberg atom chemiionization and inverse electron–ion–atom chemi-recombination processes. At the moment it contains data for photodissociation crosssections of hydrogen H+2 and helium H+2 molecular ions and the corresponding averaged thermal photodissociation cross-sections. The ro-vibrational energy states and the corresponding dipole matrix elements are provided as well. Hydrogen and helium molecular ion data are important for calculation of solar and stellar atmosphere models and for radiative transport, as well as for kinetics of other astrophysical and laboratory plasma (i.e. early Universe).

  16. Thermodynamic model for electron emission and negative- and positive-ion formation in keV molecular collisions

    CERN Document Server

    Juhász, Zoltán

    2016-01-01

    A statistical-type model is developed to describe the ion production and electron emission in collisions of (molecular) ions with atoms. The model is based on the Boltzmann population of the bound electronic energy levels of the quasi molecule formed in the collision and the discretized continuum. The discretization of the continuum is implemented by a free electron gas in a box model assuming an effective square potential of the quasi molecule. The temperature of the electron gas is calculated by taking into account a thermodynamically adiabatic process due to the change of the effective volume of the quasi molecule as the system evolves. The system may undergo a transition with a small probability from the discretized continuum to the states of the complementary continuum. It is assumed that these states are decoupled from the thermodynamic time development. The decoupled states overwhelmingly determine the yield of the asymptotically observed fragment ions. The main motivation of this work is to describe t...

  17. Effect of swift-ion irradiation on DNA molecules: A molecular dynamics study using the REAX force field

    Energy Technology Data Exchange (ETDEWEB)

    Bottländer, Dominik [Dept. of Mechanical, Aerospace, and Biomedical Engineering, Knoxville, TN 37996-2210 (United States); Mücksch, Christian [Physics Department and Research Center OPTIMAS, University Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern (Germany); Urbassek, Herbert M., E-mail: urbassek@rhrk.uni-kl.de [Physics Department and Research Center OPTIMAS, University Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern (Germany)

    2015-12-15

    Modern REAX potentials allow to use molecular dynamics simulation to study bond breaking and reformation in biomolecules. We use this technique to simulate the effects of a swift-ion track on a B-DNA fragment in water. We monitor the number of single- and double-strand breaks as a function of the deposited energy. In addition we compare the results of direct DNA heating with the effect of hydrolysis which we model by heating only the water environment.

  18. An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

    Science.gov (United States)

    Chakrabarti, Bornali; Bairagya, Hridoy R; Mallik, Payel; Mukhopadhyay, Bishnu P; Bera, Asim K

    2011-02-01

    Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

  19. Visualization and Interpretation of Attosecond Electron Dynamics in Laser-Driven Hydrogen Molecular Ion using Bohmian Trajectories

    CERN Document Server

    Takemoto, Norio

    2010-01-01

    We analyze the attosecond electron dynamics in hydrogen molecular ion driven by an external intense laser field using ab-initio numerical simulations of the corresponding time-dependent Schr{\\"{o}}dinger equation and Bohmian trajectories. To this end, we employ a one-dimensional model of the molecular ion in which the motion of the protons is frozen. The results of the Bohmian trajectory calculations do agree well with those of the ab-initio simulations and clearly visualize the electron transfer between the two protons in the field. In particular, the Bohmian trajectory calculations confirm the recently predicted attosecond transient localization of the electron at one of the protons and the related multiple bunches of the ionization current within a half cycle of the laser field. Further analysis based on the quantum trajectories shows that the electron dynamics in the molecular ion can be understood via the phase difference accumulated between the Coulomb wells at the two protons. Modeling of the dynamics ...

  20. Dynamic Chemistry-Based Sensing: A Molecular System for Detection of Saccharide, Formaldehyde, and the Silver Ion.

    Science.gov (United States)

    Chang, Xingmao; Wang, Zhaolong; Qi, Yanyu; Kang, Rui; Cui, Xinwen; Shang, Congdi; Liu, Kaiqiang; Fang, Yu

    2017-09-05

    Development of artificial complex molecular systems is of great importance in understanding complexity in natural processes and for achieving new functionalities. One of the strategies is to create them via optimized utilization of noncovalent interactions and dynamic covalent bonds. We report here on a new complex molecular system, which was constructed by integrating the multiple interactions containing a dynamic covalent interaction between 1,2-diol and boronic acid, a coordination interaction between the silver ion and pyridyl, and an easy accessible reaction between secondary amine and formaldehyde. By employing the three dynamic interactions, a pyrene (Py) labeled fluorophore, PPB, was designed and synthesized. The compound reacts with fructose (F), a monosaccharide, in aqueous phase and produces a fluorescent adduct, PPB-F, which can be further used as a sensing platform for formaldehyde (FA) and the silver ion. The respective dynamic interactions are accompanied with color changes due to the reversible switching between Py-monomer emission and excimer emission. The respective experimental detection limits (DLs) for the three analytes are much lower than 0.2 mM, 0.1 mM, and 2.5 μM, respectively. The presence of relevant compounds or ions shows little effect upon the sensing. No doubt, the results as presented show that the integration of supramolecular interactions including dynamic covalent bonds can be employed as a general strategy to develop new functional molecular systems or materials.

  1. Evaluation of European diatom trophic indices.

    NARCIS (Netherlands)

    Lototskaya, A.A.; Verdonschot, P.F.M.; Coste, M.; Vijver, van de B.

    2011-01-01

    Freshwater diatoms are considered to be reliable indicators of the trophic status of rivers and lakes. In the past 30 years, a number of indicator indices have been developed and used for the assessment of trophic conditions all over Europe. It is however still not clear whether the ecologic signatu

  2. Colloquium on diatom-copepod interactions

    DEFF Research Database (Denmark)

    Paffenhofer, G.A.; Ianora, A.; Miralto, A.;

    2005-01-01

    From 3 to 6 November 2002, a colloquium was convened at the Benthos Laboratory of the Stazione Zoologica Anton Dohrn on Ischia, Italy, with the goal of evaluating the present status of the effects of diatoms on their main consumers, planktonic copepods, and to develop future research strategies...

  3. Solvent controlled ion association in structured copolymers: Molecular dynamics simulations in dilute solutions

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

    2015-09-01

    Tailoring the nature of individual segments within ion containing block co-polymers is one critical design tool to achieve desired properties. The local structure including the size and distribution of the ionic blocks, as well as the long range correlations, are crucial for their transport ability. Here, we present molecular dynamics simulations on the effects of varying the concentrations of the ionizable groups on the conformations of pentablock ionomer that consist of a center block of ionic sulfonated styrene tethered to polyethylene and terminated by a bulky substituted styrene in dilute solutions. Sulfonation fractions f (0 ≤ f ≤ 0.55), spanning the range from ionomer to polyelectrolytes, were studied. Results for the equilibrium conformation of the chains in water and a 1:1 mixture of cyclohexane and heptane are compared to that in implicit poor solvents with dielectric constants ɛ = 1.0 and 77.73. In water, the pentablock collapses with the sulfonated groups on the outer surface. As f increases, the ionic, center block increasingly segregates from the hydrophobic regions. In the 1:1 mixture of cyclohexane and heptane, the flexible blocks swell, while the center ionic block collapses for f > 0. For f = 0, all blocks swell. In both implicit poor solvents, the pentablock collapses into a nearly spherical shape for all f. The sodium counterions disperse widely throughout the simulation cell for both water and ɛ = 77.73, whereas for ɛ = 1.0 and mixture of cyclohexane and heptane, the counterions largely condense onto the collapsed pentablock.

  4. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states

    Science.gov (United States)

    Coy, Stephen L.; Grimes, David D.; Zhou, Yan; Field, Robert W.; Wong, Bryan M.

    2016-12-01

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r4. We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF+ and HF showing the

  5. Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation.

    Science.gov (United States)

    Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Gao, Yi Qin; Zhuang, Wei

    2014-05-14

    We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significant deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.

  6. Vibrational and Electronic Energy Transfer and Dissociation of Diatomic Molecules by Electron Collisions

    Science.gov (United States)

    Huo, Winifred M.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    At high altitudes and velocities equal to or greater than the geosynchronous return velocity (10 kilometers per second), the shock layer of a hypersonic flight will be in thermochemical nonequilibrium and partially ionized. The amount of ionization is determined by the velocity. For a trans atmospheric flight of 10 kilometers per second and at an altitude of 80 kilometers, a maximum of 1% ionization is expected. At a velocity of 12 - 17 kilometer per second, such as a Mars return mission, up to 30% of the atoms and molecules in the flow field will be ionized. Under those circumstances, electrons play an important role in determining the internal states of atoms and molecules in the flow field and hence the amount of radiative heat load and the distance it takes for the flow field to re-establish equilibrium. Electron collisions provide an effective means of transferring energy even when the electron number density is as low as 1%. Because the mass of an electron is 12,760 times smaller than the reduced mass of N2, its average speed, and hence its average collision frequency, is more than 100 times larger. Even in the slightly ionized regime with only 1% electrons, the frequency of electron-molecule collisions is equal to or larger than that of molecule-molecule collisions, an important consideration in the low density part of the atmosphere. Three electron-molecule collision processes relevant to hypersonic flows will be considered: (1) vibrational excitation/de-excitation of a diatomic molecule by electron impact, (2) electronic excitation/de-excitation, and (3) dissociative recombination in electron-diatomic ion collisions. A review of available data, both theory and experiment, will be given. Particular attention will be paid to tailoring the molecular physics to the condition of hypersonic flows. For example, the high rotational temperatures in a hypersonic flow field means that most experimental data carried out under room temperatures are not applicable. Also

  7. Metal ion binding with dehydroannulenes - Plausible two-dimensional molecular sieves

    Indian Academy of Sciences (India)

    B Sateesh; Y Soujanya; G Narahari Sastry

    2007-09-01

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

  8. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states

    Science.gov (United States)

    Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.

  9. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    Science.gov (United States)

    Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

    2016-07-01

    The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  10. Detection and investigation of the molecular nature of low-molecular-mass copper ions in isolated rheumatoid knee-joint synovial fluid.

    Science.gov (United States)

    Naughton, D P; Knappitt, J; Fairburn, K; Gaffney, K; Blake, D R; Grootveld, M

    1995-03-20

    Low-molecular-mass copper(II) species have been detected and quantified in ultrafiltrates (n = 7) of rheumatoid synovial fluid (SF) by a highly-sensitive HPLC-based assay system with the ability to determine Cu(II) concentrations of ultrafiltrates resulted in complexation by histidine > alanine > formate > threonine > lactate > tyrosine > phenylalanine, their effectiveness in this context being in the given order. CD spectra of Cu(II)-treated samples of intact SF exhibited absorption bands typical of copper(II)-albumin complexes, in addition to a band attributable to a low-molecular-mass histidinate complex (lambda min 610 nm). Since both albumin and histidine are potent radical scavengers, these results indicate that any .OH radical generated from bound copper ions will be 'site-specifically' scavenged. Hence, low-molecular-mass copper complexes with the ability to promote the generation of .OH radical which can then escape from the metal ion co-ordination sphere (and in turn, cause damage to critical biomolecules) appear to be absent from inflammatory SF.

  11. Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

    Science.gov (United States)

    Anders, Christian; Urbassek, Herbert M.

    2017-01-01

    Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

  12. Density functional theory and RRKM calculations of decompositions of the metastable E-2,4-pentadienal molecular ions.

    Science.gov (United States)

    Solano Espinoza, Eduardo A; Vallejo Narváez, Wilmer E

    2010-07-01

    The potential energy profiles for the fragmentations that lead to [C(5)H(5)O](+) and [C(4)H(6)](+*) ions from the molecular ions [C(5)H(6)O](+*) of E-2,4-pentadienal were obtained from calculations at the UB3LYP/6-311G + + (3df,3pd)//UB3LYP/6-31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice-Ramsperger-Kassel-Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre-equilibrium and rate-controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C-H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E-2,4-pentadienal ions. The direct dissociation, however, can only become important in the high-energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2-hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion-neutral complex which, in turn, decomposes rapidly to the s-trans-1,3-butadiene ion [C(4)H(6)](+*). The predominating metastable channel is the second one, that is, a multi-step ring closure which starts with a rate-limiting cis-trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C(5)H(5)O](+). These results can be used to rationalize the CID mass spectrum of E-2,4-pentadienal in a low-energy regime.

  13. Tunneling Ionization of Diatomic Molecules

    DEFF Research Database (Denmark)

    Svensmark, Jens Søren Sieg

    2016-01-01

    barriers, an ability classical particles do not possess. Tunnelling is a fundamental quantum mechanical process, a process that is distinctly non-classical, so solving this tunnelling problem is not only relevant for molecular physics, but also for quantum theory in general. In this dissertation the theory...

  14. Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum.

    Science.gov (United States)

    Tanaka, Atsuko; De Martino, Alessandra; Amato, Alberto; Montsant, Anton; Mathieu, Benjamin; Rostaing, Philippe; Tirichine, Leila; Bowler, Chris

    2015-11-01

    The marine pennate diatom Phaeodactylum tricornutum has become a model for diatom biology, due to its ease of culture and accessibility to reverse genetics approaches. While several features underlying the molecular mechanisms of cell division have been described, morphological analyses are less advanced than they are in other diatoms. We therefore examined cell ultrastructure changes prior to and during cytokinesis. Following chloroplast division, cleavage furrows are formed at both longitudinal ends of the cell and are accompanied by significant vesicle transport. Although neither spindle nor microtubules were observed, the nucleus appeared to be split by the furrow after duplication of the Golgi apparatus. Finally, centripetal cytokinesis was completed by fusion of the furrows. Additionally, F-actin formed a ring structure and its diameter became smaller, accompanying the ingrowing furrows. To further analyse vesicular transport during cytokinesis, we generated transgenic cells expressing yellow fluorescent protein (YFP) fusions with putative diatom orthologs of small GTPase Sec4 and t-SNARE protein SyntaxinA. Time-lapse observations revealed that SyntaxinA-YFP localization expands from both cell tips toward the center, whereas Sec4-YFP was found in the Golgi and subsequently relocalizes to the future division plane. This work provides fundamental new information about cell replication processes in P. tricornutum.

  15. The relationship between the molecular structure and ion adsorption on goethite

    NARCIS (Netherlands)

    Rietra, R.P.J.J.

    2001-01-01

    Keywords:Ion adsorption modeling, goethite, iron oxide, CD-MUSIC, phosphate, arsenate, vanadate, molybdate, tungstate, sulfate, selenate.A study is presented on the adsorption of inorganic ions on goethite with emphasis on the adsorption of oxyanions. Experimental results for a range of oxyanions (P

  16. Rovibrational spectra of diatomic molecules in strong electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Ferez, R; Schmelcher, P [Departamento de Fisica Moderna and Instituto ' Carlos I' de Fisica Teorica y Computacional, Facultad de Ciencias, Universidad de Granada, E-18071 Granada (Spain); Theoretische Chemie, Physikalisch-Chemisches Institut, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Physikalisches Institut, Universitaet Heidelberg, Philosophenweg 12, D-69120 Heidelberg (Germany)

    2005-01-01

    We investigate the effects of a strong static electric field on the rovibrational spectra of diatomic heteronuclear molecules in a {sup 1}{sigma}{sup +} electronic ground state. Using a hybrid computational technique combining discretization and basis set methods the full rovibrational equation of motion is solved. As a prototype for our computations we take the carbon monoxide molecule. For experimentally accessible field strengths we observe that while low-lying states are not significantly affected by the field, for highly excited states strong orientation and hybridization are achieved. We propose an effective rotor Hamiltonian, including the main properties of each vibrational state, to describe the influence of the electric field on the rovibrational spectra of a molecular system with a small coupling between its rotational and vibrational motions. This effective rotor approach goes significantly beyond the rigid rotor approach and is able to describe the effect of the electric field for highly excited states.

  17. Cadmium sensitivity, uptake, subcellular distribution and thiol induction in a marine diatom: Exposure to cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Wang Mengjiao [State Key Laboratory in Marine Pollution, Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [State Key Laboratory in Marine Pollution, Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

    2011-01-25

    The aims of this study were to (1) evaluate the changes in the Cd tolerance of a marine diatom after exposure under different Cd concentrations for various durations and (2) to explore the potential subcellular and biochemical mechanisms underlying these changes. The 72-h toxicity, short-term Cd uptake, subcellular Cd distribution, as well as the synthesis of phytochelatins (PCs) were measured in a marine diatom Thalassiosira nordenskioeldii after exposure to a range of free Cd ion concentrations ([Cd{sup 2+}], 0.01-84 nM) for 1-15 days. Surprisingly, the diatoms did not acquire higher resistance to Cd after exposure; instead their sensitivity to Cd increased with a higher exposed [Cd{sup 2+}] and a longer exposure period. The underlying mechanisms could be traced to the responses of Cd cellular accumulation and the intrinsic detoxification ability of the preconditioned diatoms. Generally, exposure to a higher [Cd{sup 2+}] and for a longer period increased the Cd uptake rate, cellular accumulation, as well as the Cd concentration in metal-sensitive fraction (MSF) in these diatoms. In contrast, although PCs were induced by the environmental Cd stress (with PC{sub 2} being the most affected), the increased intracellular Cd to PC-SH ratio implied that the PCs' detoxification ability had reduced after Cd exposure. All these responses resulted in an elevated Cd sensitivity as exposed [Cd{sup 2+}] and duration increased. This study shows that the physiological/biochemical and kinetic responses of phytoplankton upon metal exposure deserve further investigation.

  18. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    Science.gov (United States)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  19. Relaxed geometries and dipole moments of positron complexes with diatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, CP 702, 30123-970, Belo Horizonte, MG (Brazil)

    2010-01-01

    Relaxed geometries and dipole moments of diatomic molecules interacting with a slow positron are reported as functions of the positron distance to the more electronegative atom. A molecular model for the complex that allows applications to large systems is used. The electron population on the positron is proposed as a weighting function to calculate the average quantities. Results show Self-Consistent-Field quality or better.

  20. Which-pass information in the double-slit experiment of diatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Ueda, Kiyoshi, E-mail: ueda@tagen.tohoku.ac.j [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan)

    2010-02-01

    Analogy between the double-slit experiment in quantum optics and the photoelectron emission from diatoms is discussed in the light of availabilities of which-pass information and quantum eraser. The availability of which-pass information and the degree of the predictability may be determined by the intrinsic molecular processes involved, whereas the erasing the which-pass information relies on the observation.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, Motoyuki; Gouaux, Eric (Oregon HSU)

    2012-10-24

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

  2. Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and Their Processes: Comparative Analysis of Sample Preparation

    Science.gov (United States)

    Tucker, Kevin R.; Li, Zhen; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-11-01

    Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (cell stabilization with glycerol and 4 % paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast.

  3. Quantum entanglement and the dissociation process of diatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Esquivel, Rodolfo O; Molina-Espiritu, Moyocoyani [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340-Mexico DF (Mexico); Flores-Gallegos, Nelson [Unidad Profesional Interdisciplinaria de IngenierIa, Campus Guanajuato del Instituto Politecnico Nacional, 36275-Guanajuato (Mexico); Plastino, A R; Angulo, Juan Carlos; Dehesa, Jesus S [Instituto Carlos I de Fisica Teorica y Computacional, and Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Antolin, Juan, E-mail: esquivel@xanum.uam.mx, E-mail: arplastino@ugr.es [Departamento de Fisica Aplicada, EUITIZ, Universidad de Zaragoza, 50018-Zaragoza (Spain)

    2011-09-14

    In this work, we investigate quantum entanglement-related aspects of the dissociation process of some selected, representative homo- and heteronuclear diatomic molecules. This study is based upon high-quality ab initio calculations of the (correlated) molecular wavefunctions involved in the dissociation processes. The values of the electronic entanglement characterizing the system in the limit cases corresponding to (i) the united-atom representation and (ii) the asymptotic region when atoms dissociate are discussed in detail. It is also shown that the behaviour of the electronic entanglement as a function of the reaction coordinate R exhibits remarkable correspondences with the phenomenological description of the physically meaningful regimes comprising the processes under study. In particular, the extrema of the total energies and the electronic entanglement are shown to be associated with the main physical changes experienced by the molecular spatial electronic density, such as charge depletion and accumulation or bond cleavage regions. These structural changes are characterized by several selected descriptors of the density, such as the Laplacian of the electronic molecular distributions (LAP), the molecular electrostatic potential (MEP) and the atomic electric potentials fitted to the MEP.

  4. Novel algorithm for simultaneous component detection and pseudo-molecular ion characterization in liquid chromatography–mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yufeng; Wang, Xiaoan; Wo, Siukwan [School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong (China); Ho, Hingman; Han, Quanbin [School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Hong Kong (China); Fan, Xiaohui [College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Zuo, Zhong, E-mail: joanzuo@cuhk.edu.hk [School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong (China)

    2015-01-01

    Highlights: • Novel stepwise component detection algorithm (SCDA) for LC–MS datasets. • New isotopic distribution and adduct-ion models for mass spectra. • Automatic component classification based on adduct-ion and isotopic distributions. - Abstract: Resolving components and determining their pseudo-molecular ions (PMIs) are crucial steps in identifying complex herbal mixtures by liquid chromatography–mass spectrometry. To tackle such labor-intensive steps, we present here a novel algorithm for simultaneous detection of components and their PMIs. Our method consists of three steps: (1) obtaining a simplified dataset containing only mono-isotopic masses by removal of background noise and isotopic cluster ions based on the isotopic distribution model derived from all the reported natural compounds in dictionary of natural products; (2) stepwise resolving and removing all features of the highest abundant component from current simplified dataset and calculating PMI of each component according to an adduct-ion model, in which all non-fragment ions in a mass spectrum are considered as PMI plus one or several neutral species; (3) visual classification of detected components by principal component analysis (PCA) to exclude possible non-natural compounds (such as pharmaceutical excipients). This algorithm has been successfully applied to a standard mixture and three herbal extract/preparations. It indicated that our algorithm could detect components’ features as a whole and report their PMI with an accuracy of more than 98%. Furthermore, components originated from excipients/contaminants could be easily separated from those natural components in the bi-plots of PCA.

  5. Theoretical Studies of the Electronic and Resonance Structure of Atomic and Molecular Negative Ions

    Science.gov (United States)

    1992-01-01

    rlg state of He2 was metastable relative to He2 [a3y- ] + e. More recently, by double charge exchange of He’ ions in lithium vapor, Kvale , et al. (Ref...928101 Iof the metastable He2 ion, and the more recent autodetachment experiments reported by Kvale , et al. (Ref. 26) for this system. Our results show...metastable. I More recently, by double charge exchange of He’ ions in lithium vapor, Kvale , et al. (Ref. 26) have examined the autodetachment spectrum

  6. Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy

    NARCIS (Netherlands)

    Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

    2015-01-01

    Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD

  7. Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy

    NARCIS (Netherlands)

    Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

    2015-01-01

    Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulat

  8. Bulk Sediment and Diatom Silica Carbon Isotope Composition from Coastal Marine Sediments off East Antarctica

    NARCIS (Netherlands)

    Berg, S.; Leng, M.J.; Kendrick, C.P.; Cremer, H.; Wagner, B.

    2013-01-01

    Organic carbon occluded in diatom silica is assumed to be protected from degradation in the sediment. δ13C from diatom carbon (δ13C(diatom)) therefore potentially provides a signal of conditions during diatom growth. However, there have been few studies based on δ13C(diatom). Numerous variables can

  9. Dissociation Energies of Diatomic Molecules

    Institute of Scientific and Technical Information of China (English)

    FAN Qun-Chao; SUN Wei-Guo

    2008-01-01

    Molecular dissociation energies of 10 electronic states of alkali molecules of KH, 7LID, 7LiH, 6LiH, NaK, NaLi and NaRb are studied using the highest three accurate vibrational energies of each electronic state, and an improved parameter-free analytical formula which is obtained starting from the LeRoy-Bernstein vibrational energy expression near the dissociation limit. The results show that as long as the highest three vibrational energies are accurate, the current analytical formula will give accurate theoretical dissociation energies Detheory, which are in excellent agreement with the experimental dissociation energies Dexpte.

  10. Measurement of atomic and molecular hydrogen in a tandem magnetic multicusp H sup minus ion source by VUV spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Young, A.T.; Stutzin, G.C.; Chen, P.; Kunkel, W.B.; Leung, K.N. (Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States))

    1992-04-01

    The populations of ground electronic state atomic hydrogen and ground electronic state, vibrationally--rotationally excited hydrogen molecule in a negative hydrogen ion source discharge have been measured using vacuum ultraviolet (VUV) laser absorption spectroscopy. These populations have been measured under a variety of discharge conditions in two different regions of a tandem chamber ion source. Preliminary results of the measurements in the driver region and filter region are given. It is observed that the atomic hydrogen density decreases as one goes from the driver to the filter region. This indicates that the surfaces directly adjacent to the filter region are net sinks for hydrogen atoms. In contrast, the molecular vibrational population distribution shows only a small difference between the two regions, indicating that these surfaces are not net sinks for the excited molecules.

  11. Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel

    DEFF Research Database (Denmark)

    Bjelkmar, Pär; Niemelä, Perttu S; Vattulainen, Ilpo;

    2009-01-01

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how...... transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements...... process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5-1 micros). Together with lipids binding in matching positions...

  12. Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana

    Directory of Open Access Journals (Sweden)

    Shrestha Roshan

    2012-09-01

    Full Text Available Abstract Background Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in the diatom Thalassiosira pseudonana using whole genome microarrays. Results Three known responses to silicon were examined, 1 silicified cell wall synthesis, 2 recovery from silicon starvation, and 3 co-regulation with silicon transporter (SIT genes. In terms of diatom cell wall formation, thus far only cell surface proteins and proteins tightly associated with silica have been characterized. Our analysis has identified new genes potentially involved in silica formation, and other genes potentially involved in signaling, trafficking, protein degradation, glycosylation and transport, which provides a larger-scale picture of the processes involved. During silicon starvation, an overrepresentation of transcription and translation related genes were up-regulated, indicating that T. pseudonana is poised to rapidly recover from silicon starvation and resume cell cycle progression upon silicon replenishment. This is in contrast to other types of limitation, and provides the first molecular data explaining the well-established environmental response of diatoms to grow as blooms and to out-compete other classes of microalgae for growth. Comparison of our data with a previous diatom cell cycle analysis indicates that assignment of the cell cycle specific stage of particular cyclins and cyclin dependent kinases should be re-evaluated. Finally, genes co-varying in expression with the SITs enabled identification of a new class of diatom-specific proteins containing a unique domain, and a putative silicon efflux protein. Conclusions Analysis of the T. pseudonana microarray data has provided a wealth of new genes to investigate previously uncharacterized cellular phenomenon related to silicon metabolism, silicon’s interaction with

  13. The physiological and ecological roles of volatile halogen production by marine diatoms

    Science.gov (United States)

    Hughes, Claire; Sun, Shuo

    2015-04-01

    Sea-to-air halogen flux is known to have a major impact on catalytic ozone cycling and aerosol formation in the troposphere. The biological production of volatile organic (e.g. bromoform, diiodomethane) and reactive inorganic halogens (e.g. molecular iodine) is believed to play an important role in mediating halogen emissions from the marine environment. Marine diatoms in particular are known to produce the organic and inorganic volatile halogens at high rates in pelagic waters and sea-ice systems. The climate-induced changes in diatom communities that have already been observed and are expected to occur throughout the world's oceans as warming progresses are likely to alter sea-to-air halogen flux. However, we currently have insufficient understanding of the physiological and ecological functions of volatile halogen production to develop modelling tools that can predict the nature and magnitude of the impact. The results of a series of laboratory studies aimed at establishing the physiological and ecological role of volatile halogen production in two marine polar diatoms (Thalassiosira antarctica and Porosira glacialis) will be described in this presentation. We will focus on our work investigating how the activity of the haloperoxidases, a group of enzymes known to be involved in halogenation reactions in marine organisms, is altered by environmental conditions. This will involve exploring the antioxidative defence role proposed for marine haloperoxidases by showing specifically how halogenating activity varies with photosynthetic rate and changes in the ambient light conditions in the two model marine diatoms. We will also present results from our experiments designed to investigate how volatile halogen production is impacted by and influences diatom-bacterial interactions. We will discuss how improved mechanistic understanding like this could pave the way for future volatile halogen-ecosystem model development.

  14. Nanoplasmonic photonic crystal diatoms and phytoliths

    Science.gov (United States)

    Andrews, Mark P.; Hajiaboli, Ahmadreza; Hiltz, Jonathan; Gonzalez, Timothy; Singh, Gursimranbir; Lennox, R. Bruce

    2011-03-01

    Evidence is emerging that silica-containing plant cells (phytoliths) and single cell micro-organisms (diatoms) exhibit optical properties reminiscent of photonic crystals. In the latter biosilicates, these properties appear to arise from light interactions with the intricate periodic patterns of micro- and nano-pores called foramina that are distributed over the frustule (outer silica shell). In this report, we show that Nitzschia Closterium pennate diatom frustules can be used to template arrays of nanoplasmonic particles to confer more complex physical properties, as shown by simulation and experiment. Selective templating of silver and gold nanoparticles in and around the array of pores was achieved by topochemical functionalization with nanoparticles deposited from solution, or by differential wetting/dewetting of evaporated gold films. The nanoplasmonic diatom frustules exhibit surface enhanced Raman scattering from chemisorbed 4-aminothiophenol. Thermally induced dewetting of gold films deposited on a frustule produces two classes of faceted gold nanoparticles. Larger particles of irregular shape are distributed with some degree of uniaxial anisotropy on the surface of the frustule. Smaller particles of more uniform size are deposited in a periodic manner in the frustule pores. It is thought that surface curvature and defects drive the hydrodynamic dewetting events that give rise to the different classes of nanoparticles. Finite difference time domain calculations on an idealized nanoplasmonic frustule suggest a complex electromagnetic field response due to coupling between localized surface plasmon modes of the nanoparticles in the foramina and an overlayer gold film.

  15. Ion association in concentrated NaCl brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Collings Matthew D

    2002-11-01

    Full Text Available Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m NaCl–water mixtures under ambient (25°C, 1 bar, hydrothermal (325°C, 1 kbar and deep crustal (625°C, 15 kbar conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757. With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClmn-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClmn-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.

  16. Detection of typhoid fever by diatom-based optical biosensor.

    Science.gov (United States)

    Selvaraj, Viji; Muthukumar, Anbazhagi; Nagamony, Ponpandian; Chinnuswamy, Viswanathan

    2017-06-02

    Surface-modified diatom substrates are employed for the development of immunocomplex-based optical biosensor for diagnosis of typhoid. Biosensor has been prepared by covalent immobilization of Salmonella typhi antibody onto the crosslinked diatom substrates via glutaraldehyde. Photoluminescent (PL) studies revealed good specificity and ability of conjugated diatom substrates to distinguish complementary (S. typhi) and non-complementary (Escherichia coli) antigens. The immunocomplexed biosensor showed detection limit of 10 pg. The excellent performance of biosensor is associated to its large surface-to-volume ratio, good photoluminescent property, and biocompatibility of diatom frustules, which enhances the antibody immobilization and facilitates the nucleophilic electron transfer between antibody and conjugated diatom surface. Hence, immunocomplexed diatom substrates are considered to be a suitable platform for the environmental monitoring of water-borne pathogen S. typhi.

  17. Molecular nature of mutations induced by high-LET irradiation with argon and carbon ions in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Tomonari; Kazama, Yusuke [Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Innovation Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Ohbu, Sumie; Shirakawa, Yuki; Liu Yang; Kambara, Tadashi; Fukunishi, Nobuhisa [Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Abe, Tomoko, E-mail: tomoabe@riken.jp [Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Innovation Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2012-07-01

    Linear energy transfer (LET) is an important parameter to be considered in heavy-ion mutagenesis. However, in plants, no quantitative data are available on the molecular nature of the mutations induced with high-LET radiation above 101-124 keV {mu}m{sup -1}. In this study, we irradiated dry seeds of Arabidopsis thaliana with Ar and C ions with an LET of 290 keV {mu}m{sup -1}. We analyzed the DNA alterations caused by the higher-LET radiation. Mutants were identified from the M{sub 2} pools. In total, 14 and 13 mutated genes, including bin2, egy1, gl1, gl2, hy1, hy3-5, ttg1, and var2, were identified in the plants derived from Ar- and C-ions irradiation, respectively. In the mutants from both irradiations, deletion was the most frequent type of mutation; 13 of the 14 mutated genes from the Ar ion-irradiated plants and 11 of the 13 mutated genes from the C ion-irradiated plants harbored deletions. Analysis of junction regions generated by the 2 types of irradiation suggested that alternative non-homologous end-joining was the predominant pathway of repair of break points. Among the deletions, the proportion of large deletions (>100 bp) was about 54% for Ar-ion irradiation and about 64% for C-ion irradiation. Both current results and previously reported data revealed that the proportions of the large deletions induced by 290-keV {mu}m{sup -1} radiations were higher than those of the large deletions induced by lower-LET radiations (6% for 22.5-30.0 keV {mu}m{sup -1} and 27% for 101-124 keV {mu}m{sup -1}). Therefore, the 290 keV {mu}m{sup -1} heavy-ion beams can effectively induce large deletions and will prove useful as novel mutagens for plant breeding and analysis of gene functions, particularly tandemly arrayed genes.

  18. Computational design of molecular tweezers and cranes with enhanced ion-pi interactions

    OpenAIRE

    Sanchez Lozano, Marta

    2014-01-01

    El objetivo principal de esta tesis ha sido diseño computacional de pinzas y grúas moleculares. Las pinzas y grúas moleculares son motores a escala molecular que permiten el ensamblaje de estructuras complejas, como circuitos eléctricos, manipulando moléculas individuales de forma ordenada. En esta tesis se llevó a cabo el diseño de nuevas pinzas y grúas moleculares con una gran especificidad hacia el sustrato y que posean un mecanismo sencillo de control externo de su operatividad. Un aspect...

  19. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    Science.gov (United States)

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

    2017-02-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  20. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

    Science.gov (United States)

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

    2017-05-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.

  1. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    Science.gov (United States)

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

    2017-05-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  2. Spin filtering effect in colorimetric chemosensor L-based molecular devices modulated with different transition metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Shi, F.V.; Lv, Y.Z. [School of Physics and Technology, University of Jinan, Jinan 250022 (China); Zhao, P., E-mail: ss_zhaop@ujn.edu.cn [School of Physics and Technology, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Jining 273155 (China)

    2017-05-15

    Based on the density functional theory in conjunction with the non-equilibrium Green's function formalism, we explore the effect of transition metal (Mn, Fe, Co, Ni) ions on the magnetic transport properties of a new synthesized colorimetric chemosensor L. The calculated results show that only Mn-L can present high-efficiency spin filtering effect, even at room temperature. The underlying mechanism is explained by the spin-resolved electron occupation number, transmission spectra, molecular projected self-consistent Hamiltonian orbitals and their spatial distribution.

  3. Molecular dynamics studies of electron-ion temperature equilibration in hydrogen plasmas within the coupled-mode regime

    Science.gov (United States)

    Benedict, Lorin X.; Surh, Michael P.; Stanton, Liam G.; Scullard, Christian R.; Correa, Alfredo A.; Castor, John I.; Graziani, Frank R.; Collins, Lee A.; Čertík, Ondřej; Kress, Joel D.; Murillo, Michael S.

    2017-04-01

    We use classical molecular dynamics (MD) to study electron-ion temperature equilibration in two-component plasmas in regimes for which the presence of coupled collective modes has been predicted to substantively reduce the equilibration rate. Guided by previous kinetic theory work, we examine hydrogen plasmas at a density of n =1026cm-3 , Ti=105K , and 107K theory including the QSPs. In particular, it is shown that the energy equilibration rates from MD are more similar to those of the theory when coupled modes are neglected. We suggest possible reasons for this surprising result and propose directions of further research along these lines.

  4. Molecular treatment of the ion-pair formation reaction in H(1s) + H(1s) collisions

    Energy Technology Data Exchange (ETDEWEB)

    Borondo, F.; Martin, F.; Yaez, M.

    1987-01-01

    All the available theoretical calculations of the cross section for the ion-pair formation reaction H(1s)+H(1s)..-->..H/sup +/H/sup -/(1s/sup 2/) have been performed using methods that are only valid at high collision energies. They get good agreement with the experiments for impact energies greater than 25 keV, but fail completely at smaller energies. In this work we report the cross section for this reaction at impact energies less than 10 keV, calculated in the framework of the impact-parameter approximation and using the molecular method with a common translation factor.

  5. Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Yuri, Yosuke, E-mail: yuri.yosuke@jaea.go.jp [Takasaki Advanced Radiation Research Institute, Japan Atomic Energy Agency, 1233 Watanuki-machi Takasaki, Gunma 370-1292 Japan (Japan)

    2015-06-29

    Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

  6. New experimental molecular stopping cross section data of Al{sub 2}O{sub 3}, for heavy ions

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Aliz, E-mail: Aliz.Simon@iaea.org [International Atomic Energy Agency, Division of Physical and Chemical Sciences, Vienna International Centre, P.O. Box 100, A-1400 Vienna (Austria); Institute of Nuclear Research of the Hungarian Academy of Sciences, (ATOMKI), P.O. Box 51, H-4001 Debrecen (Hungary); Pessoa Barradas, Nuno [Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Unversidade de Lisboa, Estrada Nacional 10 ao km 139, 7, 2695-066 Bobadela LRS (Portugal); Bergmaier, Andreas [Institut für Angewandte Physik und Messtechnik, Fakultät für Luft und Raumfahrttechnik, Werner-Heisenberg-Weg 39, D-85577 Neubiberg (Germany); Msimanga, Mandlenkosi [iThemba LABS Gauteng, Private Bag 11, WITS, 2050 Johannesburg (South Africa); Bogdanovic Radovic, Iva [Ruđer Bošković Institute, Bijenicka Cesta 54, P.O. Box 180, 10000 Zagreb (Croatia); Räisänen, Jyrki [Department of Physics, University of Helsinki, P.O. Box 43, FI-00014 University of Helsinki (Finland); Sajavaara, Timo [Department of Physics, University of Jyväskylä, Survontie 9, 40014 Jyväskylä (Finland)

    2014-08-01

    Molecular stopping cross section data of Al{sub 2}O{sub 3}, for heavy ions of {sup 12}C, {sup 16}O, {sup 28}Si, {sup 35}Cl, {sup 79}Br within the energy range of 0.01–1.0 MeV/nucleon were measured. Both direct transmission and bulk analysis methods were applied. Stopping cross sections were calculated both with the SRIM and MSTAR codes. Evaluation and intercomparison of the new data with the calculated and previously measured ones are reported in this paper.

  7. Diatom flora in subterranean ecosystems: a review

    Directory of Open Access Journals (Sweden)

    Elisa Falasco

    2014-09-01

    Full Text Available In scarcity of light and primary producers, subterranean ecosystems are generally extremely oligotrophic habitats, receiving poor supplies of degradable organic matter from the surface. Human direct impacts on cave ecosystems mainly derive from intensive tourism and recreational caving, causing important alterations to the whole subterranean environment. In particular, artificial lighting systems in show caves support the growth of autotrophic organisms (the so-called lampenflora, mainly composed of cyanobacteria, diatoms, chlorophytes, mosses and ferns producing exocellular polymeric substances (EPSs made of polysaccharides, proteins, lipids and nucleic acids. This anionic EPSs matrix mediates to the intercellular communications and participates to the chemical exchanges with the substratum, inducing the adsorption of cations and dissolved organic molecules from the cave formations (speleothems. Coupled with the metabolic activities of heterotrophic microorganisms colonising such layer (biofilm, this phenomenon may lead to the corrosion of the mineral surfaces. In this review, we investigate the formation of biofilms, especially of diatom-dominated ones, as a consequence of artificial lighting and its impacts on speleothems. Whenever light reaches the subterranean habitat (both artificially and naturally a relative high number of species of diatoms may indeed colonise it. Cave entrances, artificially illuminated walls and speleothems inside the cave are generally the preferred substrates. This review focuses on the diatom flora colonising subterranean habitats, summarizing the information contained in all the scientific papers published from 1900 up to date. In this review we provide a complete checklist of the diatom taxa recorded in subterranean habitats, including a total of 363 taxa, belonging to 82 genera. The most frequent and abundant species recorded in caves and other low light subterranean habitats are generally aerophilic and

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

    Directory of Open Access Journals (Sweden)

    Chunfeng Zhao

    2013-10-01

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

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

    Science.gov (United States)

    Zhao, Chunfeng; Noskov, Sergei Yu

    2013-10-01

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

  10. Rotational Coherence Encoded in an “Air-Laser” Spectrum of Nitrogen Molecular Ions in an Intense Laser Field

    Directory of Open Access Journals (Sweden)

    Haisu Zhang

    2013-10-01

    Full Text Available We investigate lasing action in aligned nitrogen molecular ions (N_{2}^{+} produced in an intense laser field. We find that, besides the population inversion between the B^{2}Σ_{u}^{+}-X^{2}Σ_{g}^{+} states, which is responsible for the observed simulated amplification of a seed pulse, a rotational wave packet in the ground vibrational state (v=0 of the excited electronic B^{2}Σ_{u}^{+} state has been created in N_{2}^{+}. The rotational coherence can faithfully encode its characteristics into the amplified seed pulses, enabling reconstruction of rotational wave packets of molecules in a single-shot detection manner from the frequency-resolved laser spectrum. Our results suggest that the air laser can potentially provide a promising tool for remote characterization of coherent molecular rotational wave packets.

  11. Anistropy of quasi-molecular x-rays from collisions of slow H-like S ions with Ar

    Energy Technology Data Exchange (ETDEWEB)

    Justiniano, E.; Hoffmann, R.; Schuch, R. (Heidelberg Univ. (Germany, F.R.). Physikalisches Inst.)

    1991-04-28

    Quasi-molecular (MO) radiation from single collisions of decelerated H-like sulphur ions onto Ar atoms were measured. Coincidences between the X-rays (detected at 90{sup o} and 20{sup o} with respect to the beam direction) and the scattered projectiles (resolved in both polar and aximuthal angles) allowed us to determine the impact-parameter-dependent angular distribution of the MO radiation in both polar and azimuthal angles. The data, as a function of the MO X-ray energy, show a characteristic structure for interference between transitions taking place in the incoming and outgoing parts of the collision. slight shifts are observed between the interference spectra obtained under emission angles of 20{sup o} and 90{sup o}. The effect of this anisotropy on the spectroscopy of the quasi-molecular 1s{sigma}-2p{pi} energy difference is discussed. (author).

  12. G-SIMS-FPM: Molecular structure at surfaces—a combined positive and negative secondary ion study

    Science.gov (United States)

    Gilmore, I. S.; Green, F. M.; Seah, M. P.

    2006-07-01

    G-SIMS is an easy to use method that considerably simplifies complex static SIMS spectra. The G-SIMS peaks relate directly to the parent molecular structure and so provide a library independent method for direct interpretation and identification. For larger molecules (>100 u) the mass alone may be insufficient to identify the molecule unambiguously. A development of G-SIMS, G-SIMS-fragmentation pathway mapping (FPM), solves this problem. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. In this study, we develop the inclusion of negative secondary ion fragmentation data to provide a more complete analysis. This approach is exampled with data for complex molecules of Irganox 1010 and folic acid.

  13. Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

    Science.gov (United States)

    Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

    2010-01-19

    Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

  14. The influence of land use on water quality and diatom community ...

    African Journals Online (AJOL)

    The influence of land use on water quality and diatom community structures ... associated with agricultural, urban and natural (reference) adjacent land use respectively. ... Five diatom response indices (Generic Diatom Index, Specific Pollution ...

  15. Diatoms of the microphytobenthic community: Population structure in a tropical intertidal sand flat

    Digital Repository Service at National Institute of Oceanography (India)

    Mitbavkar, S.; Anil, A.C

    , Pleurosigma and Thalassiothrix. Wind stimulated the resuspension of the sediment, along with pennate diatoms, down to 5 cm depth. Correlation of chlorophyll-a with diatom cell numbers, which has been generally used as an indicator of diatom abundance, revealed...

  16. Molecular modelling of a chemodosimeter for the selective detection of As(III) ion in water

    Indian Academy of Sciences (India)

    Sairam S Mallajosyula; Usha H; Ayan Datta; Swapan K Pati

    2008-11-01

    We have modelled for the first time a chemodosimeter for As(III) detection in water. The chemodosimeter modelled is a 1,3-dithiole-2-thione derivative with an anthracene unit which has been previously described as a chemodosimeter for Hg(II) detection. Quantum chemical calculations at the DFT level have been used to describe the binding energies and selectivity of the chemodosimeter. We find that the dosimeter action is intrinsically dependent on the thiophillic affinity and the coordination sphere of the metal ion. Binding studies for a series of metal ions: Pb(II), Cd(II), Hg(II), Ni(II) and As(III) followed by an analysis of the complete reaction pathway explains the high selectivity of the dosimeter towards As(III). The dosimeter efficiency is calculated as 66% for As(III)-ion.

  17. Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis

    Energy Technology Data Exchange (ETDEWEB)

    Khozhaenko, Elena [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Kovalev, Valeri; Podkorytova, Elena [A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Khotimchenko, Maksim, E-mail: maxkhot@yandex.ru [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation)

    2016-09-15

    Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. - Highlights: • Low molecular nanoscaled pectin was obtained using original hydrolysis method • Metal binding activity of pectin compounds was studied in a batch sorption system • Pectins exert highest metal binding activity at pH 6.0 • Metal binding isotherms of all pectins are best described by the Langmuir equation • Low molecular pectin from seagrasses is more effective than high-molecular pectins.

  18. Molecular alteration and carbonization of aspartic acid upon N{sup +} ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Cui, F.Z. E-mail: biomater@mail.tsinghua.edu.cncuifz@sun.ihep.ac.cn; Sun, S.Q.; Zhang, D.M.; Ma, Z.L.; Chen, G.Q

    2000-06-02

    Structural changes of aspartic acid (Asp) irradiated by nitrogen ions of 30 keV were studied using Fourier transform infrared (FTIR) spectroscopy. Significant decreases of the intensities of COO{sup -}, NH{sub 3}{sup +}, COOH and CH{sub 2} vibrations in the FTIR spectra, compared with those of unirradiated Asp, were observed for the sample irradiated at the fluence of 1x10{sup 16} ions/cm{sup 2}. The decrease rates of the intensities of COO{sup -}, NH{sub 3}{sup +}, COOH and CH{sub 2} vibrations with respect to the increasing irradiation fluences up to 4x10{sup 16} ions/cm{sup 2} were different. The results were attributable to the nonstoichiometrical desorption of corresponding volatile species such as H{sub 2}, NH{sub 3}{sup +} and CO{sub 2}. The radiolysis residue of Asp after irradiation at a high fluence of 1x10{sup 17} ions/cm{sup 2} was analyzed and fatty acid was detected.

  19. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses

    NARCIS (Netherlands)

    Schlathölter, Thomas; Reitsma, Geert; Egorov, Dmitrii; Gonzalez-Magaña, Olmo; Bari, Sadia; Boschman, Leon; Bodewits, Erwin; Schnorr, Kirsten; Schmid, Georg; Schröter, Claus Dieter; Moshammer, Robert; Hoekstra, Ronnie

    2016-01-01

    The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions

  20. Cellular and molecular effects for mutation induction in normal human cells irradiated with accelerated neon ions.

    Science.gov (United States)

    Suzuki, Masao; Tsuruoka, Chizuru; Kanai, Tatsuaki; Kato, Takeshi; Yatagai, Fumio; Watanabe, Masami

    2006-02-22

    We investigated the linear energy transfer (LET) dependence of mutation induction on the hypoxanthine-guanine phosphoribosyl transferase (HPRT) locus in normal human fibroblast-like cells irradiated with accelerated neon-ion beams. The cells were irradiated with neon-ion beams at various LETs ranging from 63 to 335 keV/microm. Neon-ion beams were accelerated by the Riken Ring Cyclotron at the Institute of Physical and Chemical Research in Japan. Mutation induction at the HPRT locus was detected to measure 6-thioguanine-resistant clones. The mutation spectrum of the deletion pattern of exons of mutants was analyzed using the multiplex polymerase chain reaction (PCR). The dose-response curves increased steeply up to 0.5 Gy and leveled off or decreased between 0.5 and 1.0 Gy, compared to the response to (137)Cs gamma-rays. The mutation frequency increased up to 105 keV/microm and then there was a downward trend with increasing LET values. The deletion pattern of exons was non-specific. About 75-100% of the mutants produced using LETs ranging from 63 to 335 keV/mum showed all or partial deletions of exons, while among gamma-ray-induced mutants 30% showed no deletions, 30% partial deletions and 40% complete deletions. These results suggested that the dose-response curves of neon-ion-induced mutations were dependent upon LET values, but the deletion pattern of DNA was not.

  1. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mabuchi, Takuya, E-mail: mabuchi@nanoint.ifs.tohoku.ac.jp [Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Tokumasu, Takashi [Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577 (Japan)

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  2. Molecular characterization of monoterpene ozonolysis products using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry

    Science.gov (United States)

    Kundu, S.; Fisseha, R.; Putman, A.; Rahn, T.; Mazzoleni, L. R.

    2010-12-01

    A detailed knowledge of the chemical composition of secondary organic aerosols (SOA) is required to better understand their roles in climate change, biogeochemical cycling and public health. The chemical composition of the SOA produced by the ozonolysis of limonene was investigated using electrospray ionization Fourier transform ion cyclotron resonance (ESI FT-ICR) mass spectrometry. SOA was generated in a 1.5 m3 teflon chamber with 500 ppb of limonene and 250 ppb of O3, without the presence of hydroxyl radical scavenger. We have identified approximately 1300-1500 molecular masses from negative-ion spectra in the range of 105 Putman et al., 2010). We will compare the chemical composition of limonene-SOA with that of α- and β-pinene-SOA. We will also discuss the MSn fragmentation behavior of major ions for the structural elucidation of the oligomers. Putman, A., J. Offenberg, R. Fisseha, T. Rahn, and L. R. Mazzoleni, Ultrahigh-resolution mass spectrometry of the complex secondary organic aerosol products from ozonolysis of α-pinene: Investigating oligomers, in preparation, 2010.

  3. Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels

    Science.gov (United States)

    Lau, Carus H. Y.; King, Glenn F.; Mobli, Mehdi

    2016-01-01

    Voltage-sensor domains (VSDs) are modular transmembrane domains of voltage-gated ion channels that respond to changes in membrane potential by undergoing conformational changes that are coupled to gating of the ion-conducting pore. Most spider-venom peptides function as gating modifiers by binding to the VSDs of voltage-gated channels and trapping them in a closed or open state. To understand the molecular basis underlying this mode of action, we used nuclear magnetic resonance to delineate the atomic details of the interaction between the VSD of the voltage-gated potassium channel KvAP and the spider-venom peptide VSTx1. Our data reveal that the toxin interacts with residues in an aqueous cleft formed between the extracellular S1-S2 and S3-S4 loops of the VSD whilst maintaining lipid interactions in the gaps formed between the S1-S4 and S2-S3 helices. The resulting network of interactions increases the energetic barrier to the conformational changes required for channel gating, and we propose that this is the mechanism by which gating modifier toxins inhibit voltage-gated ion channels. PMID:27677715

  4. Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels

    Science.gov (United States)

    Lau, Carus H. Y.; King, Glenn F.; Mobli, Mehdi

    2016-09-01

    Voltage-sensor domains (VSDs) are modular transmembrane domains of voltage-gated ion channels that respond to changes in membrane potential by undergoing conformational changes that are coupled to gating of the ion-conducting pore. Most spider-venom peptides function as gating modifiers by binding to the VSDs of voltage-gated channels and trapping them in a closed or open state. To understand the molecular basis underlying this mode of action, we used nuclear magnetic resonance to delineate the atomic details of the interaction between the VSD of the voltage-gated potassium channel KvAP and the spider-venom peptide VSTx1. Our data reveal that the toxin interacts with residues in an aqueous cleft formed between the extracellular S1-S2 and S3-S4 loops of the VSD whilst maintaining lipid interactions in the gaps formed between the S1-S4 and S2-S3 helices. The resulting network of interactions increases the energetic barrier to the conformational changes required for channel gating, and we propose that this is the mechanism by which gating modifier toxins inhibit voltage-gated ion channels.

  5. Thermodynamics of small alkali metal halide cluster ions: comparison of classical molecular simulations with experiment and quantum chemistry.

    Science.gov (United States)

    Vlcek, Lukas; Uhlik, Filip; Moucka, Filip; Nezbeda, Ivo; Chialvo, Ariel A

    2015-01-22

    We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali metal halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge nonpolarizable SPC/E, (ii) Drude point charge polarizable SWM4-DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ion hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas-phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.

  6. Shifted Tietz-Wei oscillator for simulating the atomic interaction in diatomic molecules

    CERN Document Server

    Falaye, Babatunde J; Hamzavi, Majid

    2015-01-01

    The shifted Tietz-Wei (sTW) oscillator is as good as traditional Morse potential in simulating the atomic interaction in diatomic molecules. By using the Pekeris-type approximation to deal with the centrifugal term, we obtain the bound-state solutions of the radial Schr\\"odinger equation with this typical molecular model via the exact quantization rule (EQR). The energy spectrum for a set of diatomic molecules ($NO \\left(a^4\\Pi_i\\right)$, $NO \\left(B^2\\Pi_r\\right)$, $NO \\left(L'^2\\phi\\right)$, $NO \\left(b^4\\Sigma^{-}\\right)$, $ICl\\left(X^1\\Sigma_g^{+}\\right)$, $ICl\\left(A^3\\Pi_1\\right)$ and $ICl\\left(A'^3\\Pi_2\\right)$ for arbitrary values of $n$ and $\\ell$ quantum numbers are obtained. For the sake of completeness, we study the corresponding wavefunctions using the formula method.

  7. Partition functions and equilibrium constants for diatomic molecules and atoms of astrophysical interest

    CERN Document Server

    Barklem, Paul S

    2016-01-01

    Partition functions and dissociation equilibrium constants are presented for 291 diatomic molecules for temperatures in the range from near absolute zero to 10000 K, thus providing data for many diatomic molecules of astrophysical interest at low temperature. The calculations are based on molecular spectroscopic data from the book of Huber and Herzberg with significant improvements from the literature, especially updated data for ground states of many of the most important molecules by Irikura. Dissociation energies are collated from compilations of experimental and theoretical values. Partition functions for 284 species of atoms for all elements from H to U are also presented based on data collected at NIST. The calculated data are expected to be useful for modelling a range of low density astrophysical environments, especially star-forming regions, protoplanetary disks, the interstellar medium, and planetary and cool stellar atmospheres. The input data, which will be made available electronically, also prov...

  8. Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues.

    Science.gov (United States)

    Breed, J; Kerr, I D; Molle, G; Duclohier, H; Sansom, M S

    1997-12-04

    Several analogues of the channel-forming peptaibol alamethicin have been demonstrated to exhibit faster switching between channel substates than does unmodified alamethicin. Molecular modelling studies are used to explore the possible molecular basis of these differences. Models of channels formed by alamethicin analogues were generated by restrained molecular dynamics in vacuo and refined by short molecular dynamics simulations with water molecules within and at either mouth of the channel. A decrease in backbone solvation was found to correlate with a decrease in open channel stability between alamethicin and an analogue in which all alpha-amino-isobutyric acid residues of alamethicin were replaced by leucine. A decrease in the extent of hydrogen-bonding at residue 7 correlates with lower open channel stabilities of analogues in which the glutamine at position 7 was replaced by smaller polar sidechains. These two observations indicate the importance of alamethicin/water H-bonds in stabilizing the open channel.

  9. From molecular clusters to nanoparticles: second-generation ion-mediated nucleation model

    Directory of Open Access Journals (Sweden)

    F. Yu

    2006-01-01

    Full Text Available Ions, which are generated in the atmosphere by galactic cosmic rays and other ionization sources, may play an important role in the formation of atmospheric aerosols. In the paper, a new second-generation ion-mediated nucleation (IMN model is presented. The new model explicitly treats the evaporation of neutral and charged clusters and it describes the evolution of the size spectra and composition of both charged and neutral clusters/particles ranging from small clusters of few molecules to large particles of several micrometers in diameter. Schemes used to calculate the evaporation coefficients for small neutral and charged clusters are consistent with the experimental data within the uncertainty range. The present IMN model, which is size-, composition-, and type-resolved, is a powerful tool for investigating the dominant mechanisms and key parameters controlling the formation and subsequent growth of nanoparticles in the atmosphere. This model can be used to analyze simultaneous measurements of the ion-mobility spectra and particle size distributions, which became available only recently. General features of the spectra for ions smaller than the critical size, size-dependent fractions of charged nanoparticles, and asymmetrical charging of freshly nucleated particles predicted by the new IMN model are consistent with recent measurements. Results obtained using the second generation IMN model, in which the most recent thermodynamic data for neutral and charged H2SO4-H2O clusters were used, suggest that ion-mediated nucleation of H2SO4-H2O can lead to a significant production of new particles in the lower atmosphere (including the boundary layer under favorable conditions. It has been shown that freshly nucleated particles of few nanometers in size can grow by the condensation of low volatile organic compounds to the size of cloud condensation nuclei. In such cases, the chemical composition of nucleated particles larger than ~10 nm is dominated

  10. Diatom community structure on in-service cruise ship hulls.

    Science.gov (United States)

    Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

    2014-10-01

    Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm.

  11. Longitudinal photoelectron momentum shifts induced by absorbing a single XUV photon in diatomic molecules

    CERN Document Server

    Lao, Di; He, Feng

    2015-01-01

    The photoelectron momentum shifts along the laser propagation are investigated by the time-dependent perturbation theory for diatomic molecules, such as H$_2^+$, N$_2$ and O$_2$. Such longitudinal momentum shifts characterize the photon momentum sharing in atoms and molecules, and oscillate with respect to photon energies, presenting the double-slit interference structure. The atomic and molecular contributions are disentangled analytically, which gives intuitive picture how the double-slit interference structure is formed. Calculation results show the longitudinal photoelectron momentum distribution depends on the internuclear distance, molecular orientation and photon energy. The current laser technology is ready to approve these theoretical predictions.

  12. On the potential for terrestrial diatom communities and diatom indices to identify anthropic disturbance in soils

    NARCIS (Netherlands)

    Antonelli, Marta; Wetzel, Carlos E.; Ector, Luc; Teuling, Ryan; Pfister, Laurent

    2017-01-01

    A large amount of studies focuses on aquatic diatoms’ ecology and their use in the assessment of water quality. Little is known about terrestrial diatoms’ ecological behaviour and sensitivity to environmental factors. We hypothesise that terrestrial diatom communities can serve as a proxy of anth

  13. On the potential for terrestrial diatom communities and diatom indices to identify anthropic disturbance in soils

    NARCIS (Netherlands)

    Antonelli, Marta; Wetzel, Carlos E.; Ector, Luc; Teuling, Ryan; Pfister, Laurent

    2017-01-01

    A large amount of studies focuses on aquatic diatoms’ ecology and their use in the assessment of water quality. Little is known about terrestrial diatoms’ ecological behaviour and sensitivity to environmental factors. We hypothesise that terrestrial diatom communities can serve as a proxy of

  14. Electrophoretic protein profiles of mid-sized copepod Calanoides patagoniensis steadily fed bloom-forming diatoms

    Directory of Open Access Journals (Sweden)

    Victor M Aguilera

    2015-09-01

    Full Text Available Recent field and experimental evidence collected in the southern upwelling region off Concepción (36°5'S, 73°3'W showed an abrupt reduction (<72 h in the egg production rates (EPR of copepods when they were fed steadily and solely with the local bloom-forming diatom Thalassiosira rotula. Because diatoms were biochemically similar to dinoflagellate Prorocentrum minimum, a diet which supported higher reproductive outcomes, the fecundity reduction observed in copepod females fed with the diatom may have obeyed to post-ingestive processes, giving rise to resources reallocation. This hypothesis was tested by comparing feeding (clearance and ingestion rates, reproduction (EPR and hatching success and the structure of protein profiles (i.e., number and intensity of electrophoretic bands of copepods (adults and eggs incubated during 96 h with the two food conditions. The structure of protein profiles included molecular sizes that were calculated from the relative mobility of protein standards against the logarithm of their molecular sizes. After assessing the experimental conditions, feeding decreased over time for those females fed with T. rotula, while reproduction was higher in females fed with P. minimum. Electrophoretic profiles resulted similar mostly at a banding region of 100 to 89-kDa, while they showed partial differences around the region of 56-kDa band, especially in those females fed and eggs produced with T. rotula. Due to reproductive volume was impacted while larvae viability, a physiological processes with specific and high nutritional requirements, was independent on food type; post-ingestive processes, such as expression of stress-related proteins deviating resources to metabolic processes others than reproduction, are discussed under framework of nutritional-toxic mechanisms mediating copepod-diatoms relationships in productive upwelling areas.

  15. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution

    Science.gov (United States)

    Zou, J.; Wu, C.; Robertson, W. D.; Zhigilei, L. V.; Miller, R. J. D.

    2016-11-01

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 107 V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 1010 V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  16. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution.

    Science.gov (United States)

    Zou, J; Wu, C; Robertson, W D; Zhigilei, L V; Miller, R J D

    2016-11-28

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10(7) V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 10(10) V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  17. Effect of ion structure on conductivity in lithium-doped ionic liquid electrolytes: A molecular dynamics study

    Science.gov (United States)

    Liu, Hongjun; Maginn, Edward

    2013-09-01

    Molecular dynamics simulations were performed to examine the role cation and anion structure have on the performance of ionic liquid (IL) electrolytes for lithium conduction over the temperature range of 320-450 K. Two model ionic liquids were studied: 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([bmim][Tf2N]) and 1-butyl-4-methylpyridinium pyrrolide ([bmpyr][pyl]) doped with Li[Tf2N] and Li[pyl], respectively. The results have demonstrated that the Li+ doped IL containing the planar [bmpyr] cation paired with the planar [pyl] anion significantly outperformed the [bmim][Tf2N] IL. The different coordination of Li+ with the [Tf2N]- or [pyl]- anions produces a remarkable change in IL structure with a concomitant effect on the transport of all ions. For the doped [bmim][Tf2N], each Li+ is coordinated by four oxygen atoms from [Tf2N]- anions. Formation of a rigid structure between Li+ and [Tf2N]- induces a decrease in the mobility of all ions. In contrast, for the doped [bmpyr][pyl], each Li+ is coordinated by two nitrogen atoms from [pyl]- anions. The original alternating structure cation|anion|cation in the neat [bmpyr][pyl] is replaced by another alternating structure cation|anion|Li+|anion|cation in the doped [bmpyr][pyl]. Increases of Li+ mole fraction in doped [bmpyr][pyl] affects the dynamics to a much lesser extent compared with [bmim][Tf2N] and leads to reduced diffusivities of cations and anions, but little change in the dynamics of Li+. More importantly, the calculations predict that the Li+ ion conductivity of doped [bmpyr][pyl] is comparable to that observed in organic liquid electrolytes and is about an order of magnitude higher than that of doped [bmim][Tf2N]. Such Li+ conductivity improvement suggests that this and related ILs may be promising candidates for use as electrolytes in lithium ion batteries and capacitors.

  18. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  19. Cellular and molecular studies of mutation induction by low energy heavy ions

    Institute of Scientific and Technical Information of China (English)

    TomKHei; DavidJChen; 等

    1997-01-01

    Mutation induction by low energy heavy ions was scored at the hypoxanthine guanine phosphoribosyl transferase(HGPRT) locus using both normal human fibroblasts and the human-hamster hybrid AL cells.In addition,the mutation yield at a non-essential chromosome was also examined by using the S1 marker gene locating on human chromosome 11 in AL cells,Mutagenicity induced by low energy heavy ions was dose and LET dependent.THe induced mutant fractions at the S1 locus were consistently higher than those for HGPRT.Using a mutation system that can detect multilocus changes,it can be shown by either Southern blotting or multiplex PCR techniques that radiation can induce chromosomal deletions in the millions of basepairs.

  20. Continuum molecular simulation of large conformational changes during ion-channel gating.

    Directory of Open Access Journals (Sweden)

    Ali Nekouzadeh

    Full Text Available A modeling framework was developed to simulate large and gradual conformational changes within a macromolecule (protein when its low amplitude high frequency vibrations are not concerned. Governing equations were derived as alternative to Langevin and Smoluchowski equations and used to simulate gating conformational changes of the Kv7.1 ion-channel over the time scale of its gating process (tens of milliseconds. The alternative equations predict the statistical properties of the motion trajectories with good accuracy and do not require the force field to be constant over the diffusion length, as assumed in Langevin equation. The open probability of the ion-channel was determined considering cooperativity of four subunits and solving their concerted transition to the open state analytically. The simulated open probabilities for a series of voltage clamp tests produced current traces that were similar to experimentally recorded currents.

  1. Molecular effect on equilibrium charge-state distributions. [of nitrogen ions injected through carbon foil

    Science.gov (United States)

    Wickholm, D.; Bickel, W. S.

    1976-01-01

    The paper describes an experiment consisting of the acceleration of N(+) and N2(+) ions to energies between 0.25 and 1.75 MeV and their injection through a thin carbon foil, whereupon they were charge-state analyzed with an electrostatic analyzer. A foil-covered electrically suppressed Faraday cup, connected to a stepping motor, moved in the plane of the dispersed beams. The Faraday cup current, which was proportional to the number of incident ions, was sent to a current digitizer and computer programmed as a multiscaler. The energy-dependent charge-state fractions, the mean charge and the distribution width were calculated. It was shown that for incident atoms, the charge state distribution appeared to be spread over more charge states, while for the incident molecules, there was a greater fraction of charge states near the mean charge.

  2. Interference patterns and extinction ratio of the diatom Coscinodiscus granii

    DEFF Research Database (Denmark)

    Maibohm, Christian; Friis, Søren Michael Mørk; Ellegaard, M.;

    2015-01-01

    We report experimental and theoretical verification of the nature and position of multiple interference points of visible light transmitted through the valve of the centric diatom species Coscinodiscus granii. Furthermore, by coupling the transmitted light into an optical fiber and moving the dia...... the diatom valve between constructive and destructive interference points, an extinction ratio of 20 dB is shown...

  3. Copepod reproduction is unaffected by diatom aldehydes or lipid composition

    DEFF Research Database (Denmark)

    Dutz, Jörg; Koski, Marja; Jonasdottir, Sigrun

    2008-01-01

    production of Temora longicornis were measured for six different diatom species as well as for a nondiatom control diet (Rhodomonas sp.). The experiments were accompanied by determinations of fatty acids, sterols, and polyunsaturated aldehydes (PUA) in the food. Although diatoms were generally ingested...

  4. Epiphytic Diatoms along Environmental Gradients in Western European Shallow Lakes

    NARCIS (Netherlands)

    Blanco, Saul; Cejudo-Figueiras, Cristina; Alvarez-Blanco, Irene; van Donk, Ellen; Gross, Elisabeth M.; Hansson, Lars-Anders; Irvine, Kenneth; Jeppesen, Erik; Kairesalo, Timo; Moss, Brian; Noges, Tiina; Becares, Eloy

    2014-01-01

    Diatom-based assays have been successfully associated worldwide with the tropic status of lakes. Several studies have demonstrated a correlation between epiphytic diatoms and nutrient load in shallow lakes and wetlands. We examine the relative importance of environmental factors in explaining the st

  5. Preparation and method of study of fossil diatoms

    Digital Repository Service at National Institute of Oceanography (India)

    Setty, M.G.A.P.

    to be exercised during the preparation of the samples A method for the preparation of strewn slides is then explained A detailed procedure for the study of diatom-strewn slides under the microscope, using the "England finder", is described, and a note on diatom...

  6. Contributions of the Diatom flora of South Africa

    CSIR Research Space (South Africa)

    Giffen, MH

    1966-01-01

    Full Text Available The diatom flora of the marine littoral of South African coatal river estuaries is very superficially known. In a previous contribution (Giffen 1963) the author dealt with the diatoms of the Eastern Cape Province estuaries namely the Gulu River...

  7. A contribution to the epipsammic diatom flora of Estonia

    NARCIS (Netherlands)

    Cremer, H.

    2006-01-01

    A study of the modern epipsammic diatom flora in Lake Karujärv, Saaremaa Island, Estonia revealed seventy-one taxa representing thirty-one genera. The identity of all taxa is documented with light micrographs. Most abundant taxa of the epipsammic diatom community were Achnanthidium minutissimum sens

  8. Arctic Diatoms - Diversity, Plankton Interactions and Poulation Dynamics

    DEFF Research Database (Denmark)

    Tammilehto, Anna

    are often dominated by diatoms. They are single-celled, eukaryotic algae, which play an essential role in ocean carbon and silica cycles. Many species of the diatom genus Pseudo-nitzschia Peragallo produce a neurotoxin, domoic acid (DA), which can be transferred to higher levels in food webs causing amnesic...

  9. The molecular structure of the isopoly complex ion, decavanadate (V10O286-)

    Science.gov (United States)

    Evans, H.T.

    1966-01-01

    The structure of the decavanadate ion V10O286- has been found by a determination of the crystal structure of K2Zn2V10O28?? 16H2O. The soluble, orange crystals are triclinic with space group P1 and have a unit cell with a = 10.778 A, b = 11.146 A, c = 8.774 A, ?? = 104?? 57???, ?? = 109?? 3???', and ?? = 65?? 0??? (Z = 1). The structure was solved from a three-dimensional Patterson map based on 5143 Weissenberg-film data. The full-matrix, least-squares refinement gave R = 0.094 and ?? for V-O bond lengths of 0.008 A. The unit cell contains one V10O286- unit, two Zn(H2O)62+ groups, two K+ ions, and four additional water molecules. The decavanadate ion is an isolated group of ten condensed VO6 octahedra, six in a rectangular 2 x 3 array sharing edges, and four more, two fitted in above and two below by sharing sloping edges. The structure, which is based on a sodium-chloride-like arrangement of V and O atoms, has a close relationship to other isopoly complex molybdates, niobates, and tantalates. Strong distortions in the VO6 octahedra are analogous to square-pyramid and other special coordination features known in other vanadate structures.

  10. Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules

    Science.gov (United States)

    Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

    2011-01-01

    A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.

  11. Increasing measurement sensitivity for the electron's electric dipole moment using trapped molecular ions

    Science.gov (United States)

    Zhou, Yan; Gresh, Daniel; Cairncross, William; Grau, Matt; Ng, Kia Boon; Ni, Yiqi; Cornell, Eric; Ye, Jun

    2016-05-01

    Based on our latest measurements of the electron's electric dipole moment (eEDM) using trapped HfF+ ions, after 100 hours of data collection, the statistical error still dominates in our overall uncertainty budget. Overcoming the bottleneck of limited statistical sensitivity can increase the precision of the eEDM measurement directly. Here, we present the progress of three ongoing experiments: (1) applying STImulated Raman Adiabatic Passage (STIRAP) with rotating linear polarization for increased coherent population transfer from the ground X1Σ+ state to the eEDM-sensitive 3Δ1 state; (2) implementing a new ion-counting detector toward shot-noise limited sensitivity with significant suppression technical noise; (3) exploring the possibility of using the ground 3Δ1 state of ThF+ ions to realize a larger effective electric field and a longer coherence time. These experiments provide a route towards an order of magnitude increase in statistical sensitivity in the second generation of measurements.

  12. Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime

    Science.gov (United States)

    Shrivastav, Vaibhav; Nahin, Minal; Hogan, Christopher J.; Larriba-Andaluz, Carlos

    2017-08-01

    A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N2, when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N2, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N2 (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results.

  13. Magneto-optical Trapping of a Diatomic Molecule

    Science.gov (United States)

    Demille, Dave

    2014-05-01

    The magneto-optical trap (MOT) is the workhorse technique for atomic physics in the ultracold regime, serving as the starting point in applications from optical clocks to quantum-degenerate gases. Although MOTs have been used with a wide array of atomic species, realization of a molecular MOT was long considered infeasible. In this talk we will describe the first magneto-optical trap for a molecule, strontium monofluoride (SrF). Our MOT produces the coldest trapped sample of directly-cooled molecules to date, with temperature T ~2.5 mK. The SrF MOT is loaded from a cryogenic buffer-gas beam slowed by laser radiation pressure. Images of laser-induced fluorescence allow us to characterize the trap's properties. Although magneto-optical trapping of diatomic molecules is in its infancy, our results indicate that access to the ultracold regime may be possible for several molecular species, with potential applications from quantum simulation to tests of fundamental symmetries to ultracold chemistry.

  14. Ab initio potential energy curves of the valence, Rydberg, and ion-pair states of iodine monochloride, ICl.

    Science.gov (United States)

    Kalemos, Apostolos; Prosmiti, Rita

    2014-09-14

    We present for the first time a coherent ab initio study of 39 states of valence, Rydberg, and ion-pair character of the diatomic interhalogen ICl species through large scale multireference variational methods including spin-orbit effects coupled with quantitative basis sets. Various avoided crossings are responsible for a non-adiabatic behaviour creating a wonderful vista for its theoretical description. Our molecular constants are compared with all available experimental data with the aim to assist experimentalists especially in the high energy regime of up to ~95,000 cm(-1).

  15. Levitation effect: role of symmetry and dependence of diffusivity on the bond length of homonuclear and heteronuclear diatomic species.

    Science.gov (United States)

    Sharma, Manju; Yashonath, S

    2011-04-07

    Molecular dynamics investigation of model diatomic species confined to the α-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O(2), the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

  16. Direct Imaging of Laser-driven Ultrafast Molecular Rotation.

    Science.gov (United States)

    Mizuse, Kenta; Fujimoto, Romu; Mizutani, Nobuo; Ohshima, Yasuhiro

    2017-02-04

    We present a method for visualizing laser-induced, ultrafast molecular rotational wave packet dynamics. We have developed a new 2-dimensional Coulomb explosion imaging setup in which a hitherto-impractical camera angle is realized. In our imaging technique, diatomic molecules are irradiated with a circularly polarized strong laser pulse. The ejected atomic ions are accelerated perpendicularly to the laser propagation. The ions lying in the laser polarization plane are selected through the use of a mechanical slit and imaged with a high-throughput, 2-dimensional detector installed parallel to the polarization plane. Because a circularly polarized (isotropic) Coulomb exploding pulse is used, the observed angular distribution of the ejected ions directly corresponds to the squared rotational wave function at the time of the pulse irradiation. To create a real-time movie of molecular rotation, the present imaging technique is combined with a femtosecond pump-probe optical setup in which the pump pulses create unidirectionally rotating molecular ensembles. Due to the high image throughput of our detection system, the pump-probe experimental condition can be easily optimized by monitoring a real-time snapshot. As a result, the quality of the observed movie is sufficiently high for visualizing the detailed wave nature of motion. We also note that the present technique can be implemented in existing standard ion imaging setups, offering a new camera angle or viewpoint for the molecular systems without the need for extensive modification.

  17. Regulated growth of diatom cells on self-assembled monolayers

    Directory of Open Access Journals (Sweden)

    Kobayashi Koichi

    2007-03-01

    Full Text Available Abstract We succeeded in regulating the growth of diatom cells on chemically modified glass surfaces. Glass surfaces were functionalized with -CF3, -CH3, -COOH, and -NH2 groups using the technique of self-assembled monolayers (SAM, and diatom cells were subsequently cultured on these surfaces. When the samples were rinsed after the adhesion of the diatom cells on the modified surfaces, the diatoms formed two dimensional arrays; this was not possible without the rinsing treatment. Furthermore, we examined the number of cells that grew and their motility by time-lapse imaging in order to clarify the interaction between the cells and SAMs. We hope that our results will be a basis for developing biodevices using living photosynthetic diatom cells.

  18. Isolation and biochemical characterization of underwater adhesives from diatoms.

    Science.gov (United States)

    Poulsen, Nicole; Kröger, Nils; Harrington, Matthew J; Brunner, Eike; Paasch, Silvia; Buhmann, Matthias T

    2014-01-01

    Many aquatic organisms are able to colonize surfaces through the secretion of underwater adhesives. Diatoms are unicellular algae that have the capability to colonize any natural and man-made submerged surfaces. There is great technological interest in both mimicking and preventing diatom adhesion, yet the biomolecules responsible have so far remained unidentified. A new method for the isolation of diatom adhesive material is described and its amino acid and carbohydrate composition determined. The adhesive materials from two model diatoms show differences in their amino acid and carbohydrate compositions, but also share characteristic features including a high content of uronic acids, the predominance of hydrophilic amino acid residues, and the presence of 3,4-dihydroxyproline, an extremely rare amino acid. Proteins containing dihydroxyphenylalanine, which mediate underwater adhesion of mussels, are absent. The data on the composition of diatom adhesives are consistent with an adhesion mechanism based on complex coacervation of polyelectrolyte-like biomolecules.

  19. Applications of Diatoms as Potential Microalgae in Nanobiotechnology

    Science.gov (United States)

    Jamali, Ali Akbar; Akbari, Fariba; Ghorakhlu, Mohamad Moradi; de la Guardia, Miguel; Yari Khosroushahi, Ahmad

    2012-01-01

    Introduction Diatoms are single cell eukaryotic microalgae, which present in nearly every water habitat make them ideal tools for a wide range of applications such as oil explora-tion, forensic examination, environmental indication, biosilica pattern generation, toxicity testing and eutrophication of aqueous ecosystems. Methods Essential information on diatoms were reviewed and discussed towards impacts of diatoms on biosynthesis and bioremediation. Results In this review, we present the recent progress in this century on the application of diatoms in waste degradation, synthesis of biomaterial, biomineraliza-tion, toxicity and toxic effects of mineral elements evaluations. Conclusion Diatoms can be considered as metal toxicity bioindicators and they can be applied for biomineralization, synthesis of biomaterials, and degradation of wastes. PMID:23678445

  20. Applications of Diatoms as Potential Microalgae in Nanobiotechnology

    Directory of Open Access Journals (Sweden)

    Ahmad Yari Khosroushahi

    2012-05-01

    Full Text Available Introduction: Diatoms are single cell eukaryotic microalgae, which present in nearly every water habitat make them ideal tools for a wide range of applications such as oil explora­tion, forensic examination, environmental indication, biosilica pattern generation, toxicity testing and eutrophication of aqueous ecosystems. Methods: Essential information on diatoms were reviewed and discussed towards impacts of diatoms on biosynthesis and bioremediation. Results: In this review, we present the recent progress in this century on the application of diatoms in waste degradation, synthesis of biomaterial, biomineraliza­tion, toxicity and toxic effects of mineral elements evaluations. Conclusion: Diatoms can be considered as metal toxicity bioindicators and they can be applied for biomineralization, synthesis of biomaterials, and degradation of wastes.