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At least 415 records · Page 23

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

Review, Tutorial↗

Tracking structural solvent reorganization and recombination dynamics following e – photoabstraction from aqueous I – with femtosecond x-ray spectroscopy and scattering

Here we present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I–(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L 1 -edge of the generated nascent iodine atoms (I 0 ) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I 0 :e–) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H 2 O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I–) to an expanded cavity around I 0 with a more random orientation of the H 2 O molecules in a broadened first solvation shell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ortho and parahydrogen in interstellar material

The ortho/para molecular hydrogen ratio in the interstellar medium is considered. It is shown that the ortho/para ratio will be 3:1 in practically all chemical reactions, even at relatively low temperatures. Two examples of exothermic processes that will result in the formation of a 3:1 ortho:para ratio, corresponding to a high-temperature equilibrium, are examined: H2 formation via three-body or surface recombination and catalytic recombination involving electrons and H(-) ions. Gas-phase scrambling ion reactions are also discussed, and it is suggested that virtually all the H2 equilibrated via scrambling reactions involving H(+) and H3(+) ions should exist as parahydrogen in the J ? 0 quantum state. Arguments are given that deuterium cannot interfere with the long scrambling chain that results in parahydrogen formation.

Reeves, R. R.↗

Experimental Study on Interactions Between H Atoms and Organic Haze

In Titan s atmosphere composed of N2 and CH4, irradiations of both solar ultraviolet light and charged particles induce active chemical reactions. In the processes of these reactions, a large amount of hydrogen (H) atoms are expected to be formed by dissociation of CH4 and other hydrocarbons [e.g., 1, 2]. Theoretical models suggest that these active H atoms need to be converted to stable hydrogen molecules (H2) efficiently to maintain unsaturated hydrocarbons and organic haze in Titan s atmosphere [e.g., 1]. Furthermore, molecular hydrogen is an important greenhouse effect gas in Titan s atmosphere, and small variation in its abundance strongly affects Titan s surface temperature [3]. Thus, the formation of H2 molecules from H atoms is a key reaction for both the atmospheric chemistry and the surface environment of Titan. Although several numerical calculations have been conducted to investigate the atmospheric chemistry of Titan with hypothesized recombination reactions of H atoms, such as catalytic scheme of C4H2 [e.g., 1, 2], it is still unclear what chemical reaction is responsible for the conversion of H atoms to H2 molecules in Titan s atmosphere.

Sekine, Y.↗

Finite-rate chemistry effects in a Mach 2 reacting flow

UV spontaneous vibrational Raman scattering and laser-induced predissociative fluorescence (LIPF) are combined and applied to a supersonic flame. For the first time, simultaneous measurements of temperature, major species (H2, O2, N2, H2O), and minor species (OH) concentrations are obtained with a 'single' excimer laser in a supersonic-lifted hydrogen-air diffusion flame. In the supersonic flame, a small amount of reaction occurs upstream of the lifted flame base, due to shock wave interactions and mixing with hot vitiated air. The strong turbulent mixing and high total enthalpy fluctuations lead to nonequilibrium values of temperature, and major and minor species concentrations. Combustion occurs farther downstream of the lifted region where slow three-body recombination reactions result in superequilibrium OH concentrations that depress the temperatures below their equilibrium values. Farther downstream, ambient air entrainment contaminates flame properties.

Cheng, T. S.↗

Simulation study of CO 2 laser-plasma interactions and self-modulated wakefield acceleration

3D numerical simulations of the interaction of a powerful CO 2 laser with hydrogen jets demonstrating the role of ionization on the characteristics of induced wakes are presented. Simulations using SPACE, a parallel relativistic Particle-in-Cell code, are performed in support of the plasma wakefield accelerator experiments being conducted at the Brookhaven National Laboratory (BNL) Accelerator Test Facility (ATF). A novelty of the SPACE code is its set of efficient atomic physics algorithms that compute ionization and recombination rates on the grid and transfer them to particles. The influence of ionization on the spectrum of pump laser has been studied for a range of gas densities.Simulations reproduce both Stokes and anti-Stokes shifts in the spectrum of pump laser, similar to those observed in experiments in the spectrum of probe. A good agreement has been achieved with the experiments on the effect of variation in gas density on Stokes/anti-Stokes intensity. In addition, self-injection and trapping of electrons into the self-modulated wakes has been observed and analyzed. Here, the experimentally validated code SPACE will be used for predictive simulations to guide future experiments at BNL ATF.

97 MATHEMATICS AND COMPUTING↗

A search for HCCN in molecular clouds

We have conducted a deep search for HCCN towards the dark cloud TMC-l and several GMC's via its N(J) = 1(2)-->0(1) transition. HCCN was not detected in any of these sources. Towards TMC-l, assuming optically thin emission, the total column density upper limit is NHCCN < or = 2 x 10(12) cm-2, which corresponds to a fractional abundance upper limit with respect to molecular hydrogen of fHCCN < or = 2 x 10(-10). We find the abundance ratio of HCN:HCCN:HCCCN in TMC-l to be l : <0.01 : 0.3, which suggests that carbon-chain growth by the addition of single carbon atoms may not be efficient under dark cloud conditions. The HCCN abundance limit also places constraints on the branching ratio for the products of the dissociative electron recombination H3C2N+ + e.

Non-NASA Center↗

Nanorod length-dependent photodriven H2 production in 1D CdS–Pt heterostructures

Colloidal quantum confined semiconductor-metal heterostructures are promising candidates for solar energy conversion because their light absorbing semiconductor and catalytic components can be independently tuned and optimized. Although the light-to-hydrogen efficiencies of such systems have shown interesting dependences on the morphologies of the semiconductor and metal domains, the mechanisms of such dependences are poorly understood. Here, we use Pt tipped 0D CdS quantum dots (with ∼4.6 nm diameter) and 1D CdS nanorods (of ∼13.8, 27.8, 66.6, and 88.9 nm average rod lengths) as a model system to study the distance-dependence of charge separation and charge recombination times and their impacts on photo-driven H2 production. The H2 generation quantum efficiency increases from 0.2% ± 0.0% in quantum dots to 28.9% ± 0.4% at a rod length of 28 nm and shows negligible changes at longer rod lengths. The half-life time of electron transfer from CdS to Pt increases monotonically with rod length, from 0.7 ± 0.1 in quantum dots to 170.2 ± 29.5 ps in the longest rods, corresponding to a slight decrease in electron transfer quantum efficiency from 92% to 81%. The amplitude-weighted average lifetime of charge recombination of the electron in Pt with the hole in CdS increases from 4.7 ± 0.4 µs in quantum dots to 149 ± 34 µs in 28 nm nanorods, and the lifetime does not increase further in longer rods, resembling the trend in the observed H2 generation quantum efficiency. Our result suggests that the competition of the charge recombination process with the hole removal by the sacrificial electron donor plays a dominant role in the observed nanorod length dependent overall light driven H2 generation quantum efficiency.

Chemistry↗

Ionization equilibrium in isolated H II regions

Theoretical ionization equilibrium models are combined with Copernicus ultraviolet observations to study a particular H II region absorption-line component in the spectra of Lambda Sco and Upsilon Sco. The Lambda Sco observations imply that the region is characterized by a hydrogen density of approximately 0.2/cu cm and an extent along the line of sight of approximately 16 pc. Three choices for the relative placement of Lambda Sco and Upsilon Sco are considered. Conclusions are that Lambda Sco is the primary source of ionization and that there is a separation of approximately 5 pc between the H II region and Lambda Sco. Observational data support an enhanced dielectronic recombination rate for S III. Comparison of the Upsilon Sco and Lambda Sco observations suggests that spatial variations of density may be present.

Eder, D. C.↗

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa↗

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa↗

Multispectral observations of the Jovian aurora

This paper presents and analyzes images of the Jovian aurora gathered by the Hubble Space Telescope Faint Object Camera (FOC) and the ROSAT Position Sensitive Proportional Counter (PSPC) to determine the function of energetic heavy ion precipitation in the inner magnetosphere and electron acceleration in the outer magnetosphere. Hubble data includes hydrogen auroral spectra and reduced images of Jupiter's north and south poles. One important result is that acceleration of electrons may be largely responsible for the discrete auroral emission features seen in the data set. ROSAT PSPC data presented includes a photon energy spectrum. A two line emission model is shown to produce the best fit to the data. The production of these emission lines occurs as a result of recombination lines that are produced from the slowing of the energetic ion beam as it enters the Jupiter upper atmosphere. It is noted that the observed energetic ion precipitation does not contain sufficient power to explain the observed ultraviolet aurora; it is therefore concluded that both electrons and ions play a role in the Jupiter auroral emissions, but that the bulk of the ultraviolet emissions comes from electron processes.

Source record↗

The origin of the far-infrared luminosity within the spiral galaxy M51

High angular resolution 170 micron and H-alpha maps have been recombined in order to elucidate the origin of the far-IR luminosity within the late-type spiral galaxy M51. New quantitative evidence is presented supporting a common origin for the far-IR and H-alpha luminosities is the striking correspondence, at all locations measured within M51, between the luminosity in the far IR and that expected from the O and B stars which are required to ionize the hydrogen gas. The warm 33 K dust temperature measured for M51 is similar to that measured for galactic and extragalactic star formation regions. It is concluded that O and B stars can easily generate both the far-IR luminosity and the warm dust temperature at all locations within M51. The dust mass required to radiate the IRAS 60 and 100 micron emission measured for M51 represents only a small percentage of the total dust content of M51. Constraints are placed on the mass and temperature of the cold dust.

Devereux, Nicholas A.↗

High-Density Amorphous Ice, the Frost on Interstellar Grains

Most water ice in the universe is in a form which does not occur naturally on Earth and of which only minimal amounts have been made in the laboratory. We have encountered this 'high-density amorphous ice' in electron diffraction experiments of low-temperature (T less than 30 K) vapor-deposited water and have subsequently modeled its structure using molecular dynamics simulations. The characteristic feature of high-density amorphous ice is the presence of 'interstitial' oxygen pair distances between 3 and 4 A. However, we find that the structure is best described as a collapsed lattice of the more familiar low-density amorphous form. These distortions are frozen in at temperatures below 38 K because, we propose, it requires the breaking of one hydrogen bond, on average, per molecule to relieve the strain and to restructure the lattice to that of low-density amorphous ice. Several features of astrophysical ice analogs studied in laboratory experiments are readily explained by the structural transition from high-density amorphous ice into low-density amorphous ice. Changes in the shape of the 3.07 gm water band, trapping efficiency of CO, CO loss, changes in the CO band structure, and the recombination of radicals induced by low-temperature UV photolysis all covary with structural changes that occur in the ice during this amorphous to amorphous transition. While the 3.07 micrometers ice band in various astronomical environments can be modeled with spectra of simple mixtures of amorphous and crystalline forms, the contribution of the high-density amorphous form nearly always dominates.

Jenniskens, P.↗

Near-circularly polarized isolated attosecond pulse generation from coherent superposition state by a circularly polarized laser field

We theoretically investigate high-order harmonic generation (HHG) from a coherent superposition state of hydrogen atom in a circularly polarized (CP) laser field. The results show that, driven by the CP field, HHG from the coherent superposition state is enhanced by 4 to 5 orders of magnitude compared to that from the ground state. The enhanced intensity is comparable to that of the ground state in a linearly polarized laser field. Based on the classical and quantum analyses, we demonstrate that HHG in the CP laser field mainly arises from the recombination of electrons ionized at non-zero initial positions. The enhancement of HHG from the coherent superposition state is due to the higher ionization rate and also the larger probability density of electrons located far from the nucleus of the involved excited state. The obtained harmonic spectra support the generation of intense isolated attosecond pulses (IAPs) with the ellipticity as high as 0.93. Moreover, we show that the generation of IAPs with large ellipticity is robust against the variation of the carrier envelope phase (CEP) of the laser field. Our results provide a new route toward generating near-CP IAPs, which will be beneficial for ultrafast detection of chiral-sensitive light-matter interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nonequilibrium boundary layer at a stagnation point for a hydrogen-helium stream over ablating graphite

The nonequilibrium axisymmetric stagnation point boundary layer over an ablating graphite surface is considered. The external stream is a high temperature mixture of hydrogen and helium. Variable thermodynamic and transport properties are assumed. Lennard-Jones potential model is used to calculate the transport coefficients of each species. Although the mixture rules for viscosity of the gas mixture are used, the weighting functions are more sophisticated than those commonly employed. For the conductivity of the mixture, generalized Wassiljewa coefficients are used. Seven species with 28 dissociation/recombination reactions are considered. Hansen's model for the dissociation rate constants is employed. The recombination rate constants are obtained by invoking detailed balance principles assisted by the JANAF thermodynamic data and the Hansen-Pearson thermodynamic data for C3.

Liu, T.-M.↗

Understanding the Surface Structure and Catalytic Activity of SnO x /Au(111) Inverse Catalysts for CO 2 and H 2 Activation

Carbon dioxide hydrogenation is a promising approach for the reduction of greenhouse gas pollution via the production of fuels and high-value chemicals utilizing C1 chemistry. In this process, the activation of nonpolar molecules, CO 2 and H 2 , at mild conditions is challenging. In this study, we report a well-defined inverse SnO x /Au(111) catalyst that shows the ability to activate both CO 2 and H 2 at room temperature. Scanning tunneling microscopy (STM) and ambient pressure X-ray photoemission spectroscopy (AP-XPS) are combined to understand the surface structure, growth mode, chemical state, and activity of SnO x /Au(111) surfaces. Nanostructures of SnO x at the sub-monolayer level were prepared by depositing Sn on Au(111) followed by O 2 oxidation. For the as-prepared SnO x /Au(111), two-dimensionally formed SnO x thin films on a Au(111) substrate were observed with STM of two different moieties, discernible based on their height: clusters (~0.4 Å) and nanoparticles (NPs, 1–2.5 Å), which are assigned to Sn–Au alloys and SnO x , respectively, in corroboration with XPS analysis. Furthermore, SnO x /Au(111) was annealed under UHV to test its thermal stability. Upon annealing at 400–600 K, a disappearance of SnO x NPs and reappearance of highly dispersed Sn clusters were clearly noticeable from the STM and XPS results, identifying the thermal decomposition of SnO x and subsequent formation of Sn–Au alloys on the surface due to the recombination of Sn clusters with Au. We investigated the reactivity of the SnO x /Au(111) surfaces toward CH 4 , CO 2 , and H 2 . The SnO x /Au(111) surfaces have excellent CO 2 and H 2 activation abilities even at room temperature with negligible reactivity for methane activation. Our AP-XPS results show that H 2 can be activated on the SnO x NPs by the reduction to Sn. For CO 2 , the activation and further dissociation are identified by a reoxidation of Sn with newly formed Sn–O bonds and the formation of surface carbon. Therefore, we propose that SnO x is a potential catalyst or additive to achieve CO 2 hydrogenation under mild conditions.

36 MATERIALS SCIENCE↗

The Role of Surface Hydroxyls in the Mobility of Carboxylates on Surfaces: Dynamics of Acetate on Anatase TiO 2 (101)

The dynamics of reactive intermediates are important in catalysis for understanding transient species, which can drive reactivity and the transport of species to reaction centers. In particular, the interplay between surface-bound carboxylic acids and carboxylates is important for numerous chemical transformations, including CO 2 hydrogenation and ketonization. Here, we investigate the dynamics of acetic acid on anatase TiO 2 (101) using scanning tunneling microscopy experiments and density functional theory calculations. We demonstrate the concomitant diffusion of bidentate acetate and a bridging hydroxyl and provide evidence for the transient formation of molecular monodentate acetic acid. The diffusion rate is strongly dependent on the position of hydroxyl and adjacent acetate(s). A facile three-step diffusion process is proposed consisting of acetate and hydroxyl recombination, acetic acid rotation, and acetic acid dissociation. Here this study clearly demonstrates that the dynamics of bidentate acetate could be important in forming monodentate species, which are proposed to drive selective ketonization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗