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Sample records for gas-phase protein structure

  1. Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

    Science.gov (United States)

    Schennach, Moritz; Breuker, Kathrin

    2015-07-01

    The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

  2. Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

    Science.gov (United States)

    Khakinejad, Mahdiar

    Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS

  3. A direct comparison of protein structure in the gas and solution phase: the Trp-cage

    DEFF Research Database (Denmark)

    Patriksson, Alexandra; Adams, Christopher M; Kjeldsen, Frank

    2007-01-01

    Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location...

  4. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F

    2016-01-01

    Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-milliseco......Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub......-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution...

  5. Determination of gas phase protein ion densities via ion mobility analysis with charge reduction.

    Science.gov (United States)

    Maisser, Anne; Premnath, Vinay; Ghosh, Abhimanyu; Nguyen, Tuan Anh; Attoui, Michel; Hogan, Christopher J

    2011-12-28

    We use a charge reduction electrospray (ESI) source and subsequent ion mobility analysis with a differential mobility analyzer (DMA, with detection via both a Faraday cage electrometer and a condensation particle counter) to infer the densities of single and multiprotein ions of cytochrome C, lysozyme, myoglobin, ovalbumin, and bovine serum albumin produced from non-denaturing (20 mM aqueous ammonium acetate) and denaturing (1 : 49.5 : 49.5, formic acid : methanol : water) ESI. Charge reduction is achieved through use of a Po-210 radioactive source, which generates roughly equal concentrations of positive and negative ions. Ions produced by the source collide with and reduce the charge on ESI generated drops, preventing Coulombic fissions, and unlike typical protein ESI, leading to gas-phase protein ions with +1 to +3 excess charges. Therefore, charge reduction serves to effectively mitigate any role that Coulombic stretching may play on the structure of the gas phase ions. Density inference is made via determination of the mobility diameter, and correspondingly the spherical equivalent protein volume. Through this approach it is found that for both non-denaturing and denaturing ESI-generated ions, gas-phase protein ions are relatively compact, with average densities of 0.97 g cm(-3) and 0.86 g cm(-3), respectively. Ions from non-denaturing ESI are found to be slightly more compact than predicted from the protein crystal structures, suggesting that low charge state protein ions in the gas phase are slightly denser than their solution conformations. While a slight difference is detected between the ions produced with non-denaturing and denaturing ESI, the denatured ions are found to be much more dense than those examined previously by drift tube mobility analysis, in which charge reduction was not employed. This indicates that Coulombic stretching is typically what leads to non-compact ions in the gas-phase, and suggests that for gas phase

  6. Biofilm structure and mass transfer in a gas phase trickle-bed biofilter.

    Science.gov (United States)

    Zhu, X; Suidan, M T; Alonso, C; Yu, T; Kim, B J; Kim, B R

    2001-01-01

    Mass transport phenomena occurring in the biofilms of gas phase trickle-bed biofilters are investigated in this study. The effect of biofilm structure on mass transfer mechanisms is examined using experimental observation from the operating of biofilters, microelectrode techniques and microscopic examination. Since the biofilms of biofilters used for waste gas treatment are not completely saturated with water, there is not a distinguishable liquid layer outside the biofilm. Results suggest that due to this characteristic, gas phase substrates (such as oxygen or volatile organic compounds) may not be limited by the aqueous phase because transport of the compound into the biofilm can occur directly through non-wetted areas. On the other hand, for substrates that are present only in the liquid phase, such as nitrate, the mass transfer limitation is more serious because of the limited liquid supply. Microscopic observations show that a layered structure with void spaces exists within the biofilm. Oxygen concentration distributions along the depth of the biofilms are examined using an oxygen microelectrode. Results indicate that there are some high dissolved oxygen zones inside the biofilm, which suggests the existence of passages for oxygen transfer into the deeper sections of the biofilm in a gas phase trickle-bed biofilter. Both the low gas-liquid mass transfer resistance and the resulting internal structure contribute to the high oxygen penetration within the biofilms in gas phase trickle-bed biofilters.

  7. The gas phase structure of α -pinene, a main biogenic volatile organic compound

    Science.gov (United States)

    Neeman, Elias M.; Avilés Moreno, Juan Ramón; Huet, Thérèse R.

    2017-12-01

    The gas phase structure of the bicyclic atmospheric aerosol precursor α-pinene was investigated employing a combination of quantum chemical calculation and Fourier transform microwave spectroscopy coupled to a supersonic jet expansion. The very weak rotational spectra of the parent species and all singly substituted 13C in natural abundance have been identified, from 2 to 20 GHz, and fitted to Watson's Hamiltonian model. The rotational constants were used together with geometrical parameters from density functional theory and ab initio calculations to determine the rs, r0, and rm(1 ) structures of the skeleton, without any structural assumption in the fit concerning the heavy atoms. The double C=C bond was found to belong to a quasiplanar skeleton structure containing 6 carbon atoms. Comparison with solid phase structure is reported. The significant differences of α-pinene in gas phase and other gas phase bicyclic monoterpene structures (β-pinene, nopinone, myrtenal, and bicyclo[3.1.1]heptane) are discussed.

  8. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

    Science.gov (United States)

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2014-12-02

    Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

  9. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.

    Science.gov (United States)

    Rand, Kasper D; Zehl, Martin; Jørgensen, Thomas J D

    2014-10-21

    acidic conditions where the amide hydrogen exchange rate is slowed by many orders of magnitude). The ability to localize the individual deuterated residues (the spatial resolution) is determined by the size (typically ∼7-15 residues) and the number of peptic peptides. These peptides provide a relatively coarse-grained picture of the protein dynamics. A fundamental understanding of the relationship between protein function/dysfunction and conformational dynamics requires in many cases higher resolution and ultimately single-residue resolution. In this Account, we summarize our efforts to achieve single-residue deuterium levels in proteins by electron-based or laser-induced gas-phase fragmentation methods. A crucial analytical requirement for this approach is that the pattern of deuterium labeling from solution is retained in the gas-phase fragment ions. It is therefore essential to control and minimize any occurrence of gas-phase randomization of the solution deuterium label (H/D scrambling) during the MS experiment. For this purpose, we have developed model peptide probes to accurately measure the onset and extent of H/D scrambling. Our analytical procedures to control the occurrence of H/D scrambling are detailed along with the physical parameters that induce it during MS analysis. In light of the growing use of gas-phase dissociation experiments to measure the HDX of proteins in order to obtain a detailed characterization and understanding of the dynamic conformations and interactions of proteins at the molecular level, we discuss the perspectives and challenges of future high-resolution HDX-MS methodology.

  10. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    Science.gov (United States)

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. © 2015 The Protein Society.

  11. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries.

    Science.gov (United States)

    Prentice, Boone M; McLuckey, Scott A

    2013-02-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.

  12. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures.

    Science.gov (United States)

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

    2018-06-01

    Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.

  13. Gas-phase spectroscopy of ferric heme-NO complexes

    DEFF Research Database (Denmark)

    Wyer, J.A.; Jørgensen, Anders; Pedersen, Bjarke

    2013-01-01

    and significantly blue-shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q-band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily...... maxima of heme and its complexes with amino acids and NO. Not so innocent: Weakly bound complexes between ferric heme and NO were synthesised in the gas phase, and their absorption measured from photodissociation yields. Opposite absorption trends in the Soret-band are seen upon NO addition to heme ions...

  14. Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers

    OpenAIRE

    Jurchen, John C.; Williams, Evan R.

    2003-01-01

    The origin of asymmetric charge and mass partitioning observed for gas-phase dissociation of multiply charged macromolecular complexes has been hotly debated. These experiments hold the potential to provide detailed information about the interactions between the macromolecules within the complex. Here, this unusual phenomenon of asymmetric charge partitioning is investigated for several protein homodimers. Asymmetric charge partitioning in these ions depends on a number of factors, including ...

  15. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  16. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  17. Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

    Science.gov (United States)

    Rocha-Rinza, Toms; Christiansen, Ove; Rajput, Jyoti; Gopalan, Aravind; Rahbek, Dennis B; Andersen, Lars H; Bochenkova, Anastasia V; Granovsky, Alexander A; Bravaya, Ksenia B; Nemukhin, Alexander V; Christiansen, Kasper Lincke; Nielsen, Mogens Brøndsted

    2009-08-27

    Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems.

  18. Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer.

    Directory of Open Access Journals (Sweden)

    Xiang Liu

    Full Text Available The crystal structures of two proteins, a putative pyrazinamidase/nicotinamidase from the dental pathogen Streptococcus mutans (SmPncA and the human caspase-6 (Casp6, were solved by de novo arsenic single-wavelength anomalous diffraction (As-SAD phasing method. Arsenic (As, an uncommonly used element in SAD phasing, was covalently introduced into proteins by cacodylic acid, the buffering agent in the crystallization reservoirs. In SmPncA, the only cysteine was bound to dimethylarsinoyl, which is a pentavalent arsenic group (As (V. This arsenic atom and a protein-bound zinc atom both generated anomalous signals. The predominant contribution, however, was from the As anomalous signals, which were sufficient to phase the SmPncA structure alone. In Casp6, four cysteines were found to bind cacodyl, a trivalent arsenic group (As (III, in the presence of the reducing agent, dithiothreitol (DTT, and arsenic atoms were the only anomalous scatterers for SAD phasing. Analyses and discussion of these two As-SAD phasing examples and comparison of As with other traditional heavy atoms that generate anomalous signals, together with a few arsenic-based de novo phasing cases reported previously strongly suggest that As is an ideal anomalous scatterer for SAD phasing in protein crystallography.

  19. Membrane proteins bind lipids selectively to modulate their structure and function.

    Science.gov (United States)

    Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M; Ulmschneider, Martin B; Degiacomi, Matteo T; Baldwin, Andrew J; Robinson, Carol V

    2014-06-05

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane

  20. Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

    Science.gov (United States)

    Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

    2011-09-07

    Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum.

  1. Routine phasing of coiled-coil protein crystal structures with AMPLE

    Directory of Open Access Journals (Sweden)

    Jens M. H. Thomas

    2015-03-01

    Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

  2. Two-Phase Gas-Liquid Flow Structure Characteristics under Periodic Cross Forces Action

    Directory of Open Access Journals (Sweden)

    V. V. Perevezentsev

    2015-01-01

    Full Text Available The article presents a study of two-phase gas-liquid flow under the action of periodic cross forces. The work objective is to obtain experimental data for further analysis and have structure characteristics of the two-phase flow movement. For research, to obtain data without disturbing effect on the flow were used optic PIV (Particle Image Visualization methods because of their noninvasiveness. The cross forces influence was provided by an experimental stand design to change the angular amplitudes and the periods of channel movement cycle with two-phase flow. In the range of volume gas rates was shown a water flow rate versus the inclination angle of immovable riser section and the characteristic angular amplitudes and periods of riser section inclination cycle under periodic cross forces. Data on distribution of average water velocity in twophase flow in abovementioned cases were also obtained. These data allowed us to draw a conclusion that a velocity distribution depends on the angular amplitude and on the period of the riser section roll cycle. This article belongs to publications, which study two-phase flows with no disturbing effect on them. Obtained data give an insight into understanding a pattern of twophase gas-liquid flow under the action of periodic cross forces and can be used to verify the mathematical models of the CFD thermo-hydraulic codes. In the future, the work development expects taking measurements with more frequent interval in the ranges of angular amplitudes and periods of the channel movement cycle and create a mathematical model to show the action of periodic cross forces on two-phase gas-liquid flow.

  3. Structure of the gas-liquid annular two-phase flow in a nozzle section

    International Nuclear Information System (INIS)

    Yoshida, Kenji; Kataoka, Isao; Ohmori, Syuichi; Mori, Michitsugu

    2006-01-01

    Experimental studies on the flow behavior of gas-liquid annular two-phase flow passing through a nozzle section were carried out. This study is concerned with the central steam jet injector for a next generation nuclear reactor. In the central steam jet injector, steam/water annular two-phase flow is formed at the mixing nozzle. To make an appropriate design and to establish the high-performance steam injector system, it is very important to accumulate the fundamental data of the thermo-hydro dynamic characteristics of annular flow passing through a nozzle section. On the other hand, the transient behavior of multiphase flow, in which the interactions between two-phases occur, is one of the most interesting scientific issues and has attracted research attention. In this study, the transient gas-phase turbulence modification in annular flow due to the gas-liquid phase interaction is experimentally investigated. The annular flow passing through a throat section is under the transient state due to the changing cross sectional area of the channel and resultantly the superficial velocities of both phases are changed compared with a fully developed flow in a straight pipe. The measurements for the gas-phase turbulence were precisely performed by using a constant temperature hot-wire anemometer, and made clear the turbulence structure such as velocity profiles, fluctuation velocity profiles. The behavior of the interfacial waves in the liquid film flow such as the ripple or disturbance waves was also observed. The measurements for the liquid film thickness by the electrode needle method were also performed to measure the base film thickness, mean film thickness, maximum film thickness and wave height of the ripple or the disturbance waves. (author)

  4. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum

    Science.gov (United States)

    Jhingree, Jacquelyn R.; Bellina, Bruno; Pacholarz, Kamila J.; Barran, Perdita E.

    2017-07-01

    Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge.

  5. Noncovalent Halogen Bonding as a Mechanism for Gas-Phase Clustering

    DEFF Research Database (Denmark)

    Wegeberg, Christina; Donald, William A.; McKenzie, Christine

    2017-01-01

    in the crystalline phases of PhIO2 and its derivatives serve as models for the structures of larger gas-phase clusters, and calculations on simple model gas-phase dimer and trimer clusters result in similar motifs. This is the first account of halogen bonding playing an extensive role in gas-phase associations....

  6. Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

    Science.gov (United States)

    Somogyi, Arpád

    2008-12-01

    The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

  7. Novel bacterial gas sensor proteins with transition metal-containing prosthetic groups as active sites.

    Science.gov (United States)

    Aono, Shigetoshi

    2012-04-01

    Gas molecules function as signaling molecules in many biological regulatory systems responsible for transcription, chemotaxis, and other complex physiological processes. Gas sensor proteins play a crucial role in regulating such biological systems in response to gas molecules. New sensor proteins that sense oxygen or nitric oxide have recently been found, and they have been characterized by X-ray crystallographic and/or spectroscopic analysis. It has become clear that the interaction between a prosthetic group and gas molecules triggers dynamic structural changes in the protein backbone when a gas sensor protein senses gas molecules. Gas sensor proteins employ novel mechanisms to trigger conformational changes in the presence of a gas. In gas sensor proteins that have iron-sulfur clusters as active sites, the iron-sulfur clusters undergo structural changes, which trigger a conformational change. Heme-based gas sensor proteins reconstruct hydrogen-bonding networks around the heme and heme-bound ligand. Gas sensor proteins have two functional states, on and off, which are active and inactive, respectively, for subsequent signal transduction in response to their physiological effector molecules. To fully understand the structure-function relationships of gas sensor proteins, it is vital to perform X-ray crystal structure analyses of full-length proteins in both the on and off states.

  8. Activation of methane by zinc: gas-phase synthesis, structure, and bonding of HZnCH3.

    Science.gov (United States)

    Flory, Michael A; Apponi, Aldo J; Zack, Lindsay N; Ziurys, Lucy M

    2010-12-08

    The methylzinc hydride molecule, HZnCH3, has been observed in the gas phase for the first time in the monomeric form using high-resolution spectroscopic techniques. The molecule was synthesized by two methods: the reaction of dimethylzinc with hydrogen gas and methane in an AC discharge and the reaction of zinc vapor produced in a Broida-type oven with methane in a DC discharge. HZnCH3 was identified on the basis of its pure rotational spectrum, which was recorded using millimeter/submillimeter direct-absorption and Fourier transform microwave techniques over the frequency ranges 332-516 GHz and 18-41 GHz, respectively. Multiple rotational transitions were measured for this molecule in seven isotopic variants. K-ladder structure was clearly present in all of the spectra, indicating a molecule with C3v symmetry and a (1)A1 ground electronic state. Extensive quadrupole hyperfine structure arising from the (67)Zn nucleus was observed for the H(67)ZnCH3 species, suggesting covalent bonding to the zinc atom. From the multiple isotopic substitutions, a precise structure for HZnCH3 has been determined. The influence of the axial hydrogen atom slightly distorts the methyl group but stabilizes the Zn-C bond. This study suggests that HZnCH3 can be formed through the oxidative addition of zinc to methane in the gas phase under certain conditions. HZnCH3 is the first metal-methane insertion complex to be structurally characterized.

  9. Studies of matrix diffusion in gas phase

    International Nuclear Information System (INIS)

    Hartikainen, K.; Timonen, J.; Vaeaetaeinen, K.; Pietarila, H.

    1994-03-01

    The diffusion of solutes from fractures into rock matrix is an important factor in the safety analysis of disposal of radioactive waste. Laboratory measurements are needed to complement field investigations for a reliable determination of the necessary transport parameters. Measurements of diffusion coefficients in tight rock samples are usually time consuming because the diffusion processes are slow. On the other hand it is well known that diffusion coefficients in the gas phase are roughly four orders of magnitude larger than those in the liquid phase. Therefore, for samples whose structures do not change much upon drying, it is possible to estimate the diffusion properties of the liquid phase when the properties of the gas phase are known. Advantages of the gas method are quick and easy measurements. In the measurements nitrogen was used as the carrier gas and helium as the tracer gas, and standard techniques have been used for helium detection. Techniques have been developed for both channel flow and through-diffusion measurements. The breakthrough curves have been measured in every experiment and all measurements have been modelled by using appropriate analytical models. As a result matrix porosities and effective diffusion coefficients in the gas phase have been determined. (12 refs., 21 figs., 6 tabs.)

  10. Coexistence of Phases in a Protein Heterodimer

    Science.gov (United States)

    Krokhotin, Andrey; Liwo, Adam; Niemi, Antti J.; Scheraga, Harold A.

    2012-07-01

    A heterodimer consisting of two or more different kinds of proteins can display an enormous number of distinct molecular architectures. The conformational entropy is an essential ingredient in the Helmholtz free energy and, consequently, these heterodimers can have a very complex phase structure. Here, it is proposed that there is a state of proteins, in which the different components of a heterodimer exist in different phases. For this purpose, the structures in the protein data bank (PDB) have been analyzed, with radius of gyration as the order parameter. Two major classes of heterodimers with their protein components coexisting in different phases have been identified. An example is the PDB structure 3DXC. This is a transcriptionally active dimer. One of the components is an isoform of the intra-cellular domain of the Alzheimer-disease related amyloid precursor protein (AICD), and the other is a nuclear multidomain adaptor protein in the Fe65 family. It is concluded from the radius of gyration that neither of the two components in this dimer is in its own collapsed phase, corresponding to a biologically active protein. The UNRES energy function has been utilized to confirm that, if the two components are separated from each other, each of them collapses. The results presented in this work show that heterodimers whose protein components coexist in different phases, can have intriguing physical properties with potentially important biological consequences.

  11. Gas phase ion chemistry

    CERN Document Server

    Bowers, Michael T

    1979-01-01

    Gas Phase Ion Chemistry, Volume 2 covers the advances in gas phase ion chemistry. The book discusses the stabilities of positive ions from equilibrium gas-phase basicity measurements; the experimental methods used to determine molecular electron affinities, specifically photoelectron spectroscopy, photodetachment spectroscopy, charge transfer, and collisional ionization; and the gas-phase acidity scale. The text also describes the basis of the technique of chemical ionization mass spectrometry; the energetics and mechanisms of unimolecular reactions of positive ions; and the photodissociation

  12. Implications of protein polymorphism on protein phase behaviour

    NARCIS (Netherlands)

    Stegen, J.; Schoot, van der P.P.A.M.

    2015-01-01

    The phase behaviour of small globular proteins is often modeled by approximating them as spherical particles with fixed internal structure. However, changes in the local environment of a protein can lead to changes in its conformation rendering this approximation invalid. We present a simple

  13. Solid gas reaction phase diagram under high gas pressure

    International Nuclear Information System (INIS)

    Ishizaki, K.

    1992-01-01

    This paper reports that to evaluate which are the stable phases under high gas pressure conditions, a solid-gas reaction phase diagram under high gas pressure (HIP phase diagram) has been proposed by the author. The variables of the diagram are temperature, reactant gas partial pressure and total gas pressure. Up to the present time the diagrams have been constructed using isobaric conditions. In this work, the stable phases for a real HIP process were evaluated assuming an isochoric condition. To understand the effect of the total gas pressure on stability is of primary importance. Two possibilities were considered and evaluated, those are: the total gas pressure acts as an independent variable, or it only affects the fugacity values. The results of this work indicate that the total gas pressure acts as an independent variable, and in turn also affects the fugacity values

  14. Void fraction fluctuations in two-phase gas-liquid flow

    International Nuclear Information System (INIS)

    Ulbrich, R.

    1987-01-01

    Designs of the apparatus in which two-phase gas-liquid flow occurs are usually based on the mean value of parameters such as pressure drop and void fraction. The flow of two-phase mixtures generally presents a very complicated flow structure, both in terms of the unsteady formation on the interfacial area and in terms of the fluctuations of the velocity, pressure and other variables within the flow. When the gas void fraction is near 0 or 1 / bubble or dispersed flow regimes / then oscillations of void fraction are very small. The intermittent flow such as plug and slug/ froth is characterized by alternately flow portions of liquid and gas. It influences the change of void fractions in time. The results of experimental research of gas void fraction fluctuations in two-phase adiabatic gas-liquid flow in a vertical pipe are presented

  15. Gas Phase Nanoparticle Synthesis

    Science.gov (United States)

    Granqvist, Claes; Kish, Laszlo; Marlow, William

    This book deals with gas-phase nanoparticle synthesis and is intended for researchers and research students in nanomaterials science and engineering, condensed matter physics and chemistry, and aerosol science. Gas-phase nanoparticle synthesis is instrumental to nanotechnology - a field in current focus that raises hopes for environmentally benign, resource-lean manufacturing. Nanoparticles can be produced by many physical, chemical, and even biological routes. Gas-phase synthesis is particularly interesting since one can achieve accurate manufacturing control and hence industrial viability.

  16. Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex.

    Science.gov (United States)

    Hogan, Christopher J; Ruotolo, Brandon T; Robinson, Carol V; Fernandez de la Mora, Juan

    2011-04-07

    A parallel-plate differential mobility analyzer and a time-of-flight mass spectrometer (DMA-MS) are used in series to measure true mobility in dry atmospheric pressure air for mass-resolved electrosprayed GroEL tetradecamers (14-mers; ~800 kDa). Narrow mobility peaks are found (2.6-2.9% fwhm); hence, precise mobilities can be obtained for these ions without collisional activation, just following their generation by electrospray ionization. In contrast to previous studies, two conformers are found with mobilities (Z) differing by ~5% at charge state z ~ 79. By extrapolating to small z, a common mobility/charge ratio Z(0)/z = 0.0117 cm(2) V(-1) s(-1) is found for both conformers. When interpreted as if the GroEL ion surface were smooth and the gas molecule-protein collisions were perfectly elastic and specular, this mobility yields an experimental collision cross section, Ω, 11% smaller than in an earlier measurement, and close to the cross section, A(C,crystal), expected for the crystal structure (determined by a geometric approximation). However, the similarity between Ω and A(C,crystal) does not imply a coincidence between the native and gas-phase structures. The nonideal nature of protein-gas molecule collisions introduces a drag enhancement factor, ξ = 1.36, with which the true cross section A(C) is related to Ω via A(C) = Ω/ξ. Therefore, A(C) for GroEL 14-mer ions determined by DMA measurements is 0.69A(C,crystal). The factor 1.36 used here is based on the experimental Stokes-Millikan equation, as well as on prior and new numerical modeling accounting for multiple scattering events via exact hard-sphere scattering calculations. Therefore, we conclude that the gas-phase structure of the GroEL complex as electrosprayed is substantially more compact than the corresponding X-ray crystal structure.

  17. Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

    Science.gov (United States)

    Nakane, Takanori; Hanashima, Shinya; Suzuki, Mamoru; Saiki, Haruka; Hayashi, Taichi; Kakinouchi, Keisuke; Sugiyama, Shigeru; Kawatake, Satoshi; Matsuoka, Shigeru; Matsumori, Nobuaki; Nango, Eriko; Kobayashi, Jun; Shimamura, Tatsuro; Kimura, Kanako; Mori, Chihiro; Kunishima, Naoki; Sugahara, Michihiro; Takakyu, Yoko; Inoue, Shigeyuki; Masuda, Tetsuya; Hosaka, Toshiaki; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Inoue, Tsuyoshi; Nureki, Osamu; Iwata, So; Murata, Michio; Mizohata, Eiichi

    2016-01-01

    The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams. PMID:27799539

  18. Cold flame on Biofilm - Transport of Plasma Chemistry from Gas to Liquid Phase

    Science.gov (United States)

    Kong, Michael

    2014-10-01

    One of the most active and fastest growing fields in low-temperature plasma science today is biological effects of gas plasmas and their translation in many challenges of societal importance such as healthcare, environment, agriculture, and nanoscale fabrication and synthesis. Using medicine as an example, there are already three FDA-approved plasma-based surgical procedures for tissue ablation and blood coagulation and at least five phase-II clinical trials on plasma-assisted wound healing therapies. A key driver for realizing the immense application potential of near room-temperature ambient pressure gas plasmas, commonly known as cold atmospheric plasmas or CAP, is to build a sizeable interdisciplinary knowledge base with which to unravel, optimize, and indeed design how reactive plasma species interact with cells and their key components such as protein and DNA. Whilst a logical objective, it is a formidable challenge not least since existing knowledge of gas discharges is largely in the gas-phase and therefore not directly applicable to cell-containing matters that are covered by or embedded in liquid (e.g. biofluid). Here, we study plasma inactivation of biofilms, a jelly-like structure that bacteria use to protect themselves and a major source of antimicrobial resistance. As 60--90% of biofilm is made of water, we develop a holistic model incorporating physics and chemistry in the upstream CAP-generating region, a plasma-exit region as a buffer for as-phase transport, and a downstream liquid region bordering the gas buffer region. A special model is developed to account for rapid chemical reactions accompanied the transport of gas-phase plasma species through the gas-liquid interface and for liquid-phase chemical reactions. Numerical simulation is used to illustrate how key reactive oxygen species (ROS) are transported into the liquid, and this is supported with experimental data of both biofilm inactivation using plasmas and electron spin spectroscopy (ESR

  19. Evaporation and Condensation Flows of a Vapor-Gas Mixture from or onto the Condensed Phase with an Internal Structure

    National Research Council Canada - National Science Library

    Onishi, Yoshimoto; Yamada, Ken

    2005-01-01

    Transient motions of a vapor-gas mixture due to the evaporation and condensation processes from or onto the plane condensed phase, with a temperature field as its internal structure, have been studied...

  20. Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.

    Science.gov (United States)

    Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Tardivel, Benjamin; Dimicoli, Iliana; Mons, Michel

    2005-01-19

    Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

  1. Gas-phase infrared spectrum of the anionic GFP-chromophore

    NARCIS (Netherlands)

    Almasian, M.; Grzetic, J.; G. Berden,; Bakker, B.; Buma, W. J.; Oomens, J.

    2012-01-01

    The gas-phase IR spectrum of the anionic chromophore of the green fluorescent protein (p-hydroxy-benzylidene-2,3-dimethylimidazolidinone, HBDI) is recorded in the 800–1800 cm−1 frequency range using the free electron laser FELIX in combination with an electrospray ionization (ESI) Fourier

  2. Fundamental thermochemical properties of amino acids: gas-phase and aqueous acidities and gas-phase heats of formation.

    Science.gov (United States)

    Stover, Michele L; Jackson, Virgil E; Matus, Myrna H; Adams, Margaret A; Cassady, Carolyn J; Dixon, David A

    2012-03-08

    The gas-phase acidities of the 20 L-amino acids have been predicted at the composite G3(MP2) level. A broad range of structures of the neutral and anion were studied to determine the lowest energy conformer. Excellent agreement is found with the available experimental gas-phase deprotonation enthalpies, and the calculated values are within experimental error. We predict that tyrosine is deprotonated at the CO(2)H site. Cysteine is predicted to be deprotonated at the SH but the proton on the CO(2)H is shared with the S(-) site. Self-consistent reaction field (SCRF) calculations with the COSMO parametrization were used to predict the pK(a)'s of the non-zwitterion form in aqueous solution. The differences in the non-zwitterion pK(a) values were used to estimate the free energy difference between the zwitterion and nonzwitterion forms in solution. The heats of formation of the neutral compounds were calculated from atomization energies and isodesmic reactions to provide the first reliable set of these values in the gas phase. Further calculations were performed on five rare amino acids to predict their heats of formation, acidities, and pK(a) values.

  3. Statistical parameter characteristics of gas-phase fluctuations for gas-liquid intermittent flow

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, G.; Monji, H.; Takaguchi, M. [Univ. of Tsukuba (Japan)

    1995-09-01

    This study deals with theoretical analysis on the general behaviour of statistical parameters of gas-phase fluctuations and comparison of statistical parameter characteristics for the real void fraction fluctuations measured with those for the wave form modified the real fluctuations. In order to investigate the details of the relation between the behavior of the statistical parameters in real intermittent flow and analytical results obtained from information on the real flow, the distributions of statistical parameters for general fundamental wave form of gas-phase fluctuations are discussed in detail. By modifying the real gas-phase fluctuations to a trapezoidaly wave, the experimental results can be directly compared with the analytical results. The analytical results for intermittent flow show that the wave form parameter, and the total amplitude of void fraction fluctuations, affects strongly on the statistical parameter characteristics. The comparison with experiment using nitrogen gas-water intermittent flow suggests that the parameters of skewness and excess may be better as indicators of flow pattern. That is, the macroscopic nature of intermittent flow can be grasped by the skewness and the excess, and the detailed flow structure may be described by the mean and the standard deviation.

  4. Statistical parameter characteristics of gas-phase fluctuations for gas-liquid intermittent flow

    International Nuclear Information System (INIS)

    Matsui, G.; Monji, H.; Takaguchi, M.

    1995-01-01

    This study deals with theoretical analysis on the general behaviour of statistical parameters of gas-phase fluctuations and comparison of statistical parameter characteristics for the real void fraction fluctuations measured with those for the wave form modified the real fluctuations. In order to investigate the details of the relation between the behavior of the statistical parameters in real intermittent flow and analytical results obtained from information on the real flow, the distributions of statistical parameters for general fundamental wave form of gas-phase fluctuations are discussed in detail. By modifying the real gas-phase fluctuations to a trapezoidaly wave, the experimental results can be directly compared with the analytical results. The analytical results for intermittent flow show that the wave form parameter, and the total amplitude of void fraction fluctuations, affects strongly on the statistical parameter characteristics. The comparison with experiment using nitrogen gas-water intermittent flow suggests that the parameters of skewness and excess may be better as indicators of flow pattern. That is, the macroscopic nature of intermittent flow can be grasped by the skewness and the excess, and the detailed flow structure may be described by the mean and the standard deviation

  5. Evolution of the structure of a gas-liquid two-phase flow in a large vertical pipe

    International Nuclear Information System (INIS)

    Horst-Michael Prasser; Matthias Beyer; Helmar Carl; Sabine Gregor; Dirk Lucas; Peter Schuetz; Frank-Peter Weiss

    2005-01-01

    Full text of publication follows: Experimental results on the evolution of the radial gas fraction profiles, gas velocity profiles and bubble size distributions in a gas-liquid two-phase flow along a large vertical pipe of 194 mm inner diameter are presented. The tests were performed at the TOPFLOW facility in Rossendorf, where two wire-mesh sensors were used to measure sequences of two-dimensional distributions of local instantaneous gas fraction within the complete pipe cross-section with a lateral resolution of 3 mm and a sampling frequency of 2500 Hz. This data is the basis for a fast flow visualization and for the calculation of the mentioned profiles. The gas fraction profiles were obtained by averaging the sequences over time, velocities were measured by cross-correlation of the signals of the two sensors, which were located on a short (63 mm) distance behind each other. The high resolution of the mesh sensors allows to identify regions of connected measuring points in the data array, which are filled with the gas phase. This method was used to obtain the bubble size distributions. In the experiments, the superficial velocities ranged from 0.04 to 8 m/s for the gas phase and from 0.04 to 1.6 m/s for the liquid. In this way, the experiments cover the range from bubbly to churn turbulent flow regimes. The evolution of the flow structure was studied by varying the distance between the gas injection and the sensor position. This distance was changed by the help of a so-called variable gas injection set-up. It consists of 6 gas injection units, each of them equipped with three rings of orifices in the pipe wall for the gas injection. These rings are fed with the gas phase from ring chambers, which can be individually controlled by valves. The middle ring has orifices of 4 mm diameter, while the upper and the lower rings have nozzles of 1 mm diameter. In this way, 18 different inlet lengths and two different gas injection geometries can be chosen. The latter

  6. Comparison of electrical and optical characteristics in gas-phase and gas-liquid phase discharges

    Energy Technology Data Exchange (ETDEWEB)

    Qazi, H. I. A.; Li, He-Ping, E-mail: liheping@tsinghua.edu.cn; Zhang, Xiao-Fei; Bao, Cheng-Yu [Department of Engineering Physics, Tsinghua University, Beijing 100084 (China); Nie, Qiu-Yue [School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin, Heilongjiang Province 150001 (China)

    2015-12-15

    This paper presents an AC-excited argon discharge generated using a gas-liquid (two-phase) hybrid plasma reactor, which mainly consists of a powered needle electrode enclosed in a conical quartz tube and grounded deionized water electrode. The discharges in the gas-phase, as well as in the two-phase, exhibit two discharge modes, i.e., the low current glow-like diffuse mode and the high current streamer-like constrict mode, with a mode transition, which exhibits a negative resistance of the discharges. The optical emission spectral analysis shows that the stronger diffusion of the water vapor into the discharge region in the two-phase discharges boosts up the generation of OH (A–X) radicals, and consequently, leads to a higher rotational temperature in the water-phase plasma plume than that of the gas-phase discharges. Both the increase of the power input and the decrease of the argon flow rate result in the increase of the rotational temperature in the plasma plume of the water-phase discharge. The stable two-phase discharges with a long plasma plume in the water-phase under a low power input and gas flow rate may show a promising prospect for the degradation of organic pollutants, e.g., printing and dyeing wastewater, in the field of environmental protection.

  7. Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

    Science.gov (United States)

    Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

    2013-05-01

    Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still

  8. Photoresponse of the protonated Schiff-base retinal chromophore in the gas phase

    DEFF Research Database (Denmark)

    Toker, Jonathan; Rahbek, Dennis Bo; Kiefer, H V

    2013-01-01

    The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse. The sel......The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse...... modifications of the chromophore. We propose that isomerizations play an important role in the photoresponse of gas-phase retinal chromophores and guide internal conversion through conical intersections. The role of protein interactions is then to control the specificity of the photoisomerization in the primary...

  9. Gas-liquid phase coexistence in a tetrahedral patchy particle model

    International Nuclear Information System (INIS)

    Romano, Flavio; Tartaglia, Piero; Sciortino, Francesco

    2007-01-01

    We evaluate the location of the gas-liquid coexistence line and of the associated critical point for the primitive model for water (PMW), introduced by Kolafa and Nezbeda (1987 Mol. Phys. 61 161). Besides being a simple model for a molecular network forming liquid, the PMW is representative of patchy proteins and novel colloidal particles interacting with localized directional short-range attractions. We show that the gas-liquid phase separation is metastable, i.e. it takes place in the region of the phase diagram where the crystal phase is thermodynamically favoured, as in the case of particles interacting via short-range attractive spherical potentials. We do not observe crystallization close to the critical point. The region of gas-liquid instability of this patchy model is significantly reduced as compared to that from equivalent models of spherically interacting particles, confirming the possibility of observing kinetic arrest in a homogeneous sample driven by bonding as opposed to packing. (fast track communication)

  10. Flow-pattern identification and nonlinear dynamics of gas-liquid two-phase flow in complex networks.

    Science.gov (United States)

    Gao, Zhongke; Jin, Ningde

    2009-06-01

    The identification of flow pattern is a basic and important issue in multiphase systems. Because of the complexity of phase interaction in gas-liquid two-phase flow, it is difficult to discern its flow pattern objectively. In this paper, we make a systematic study on the vertical upward gas-liquid two-phase flow using complex network. Three unique network construction methods are proposed to build three types of networks, i.e., flow pattern complex network (FPCN), fluid dynamic complex network (FDCN), and fluid structure complex network (FSCN). Through detecting the community structure of FPCN by the community-detection algorithm based on K -mean clustering, useful and interesting results are found which can be used for identifying five vertical upward gas-liquid two-phase flow patterns. To investigate the dynamic characteristics of gas-liquid two-phase flow, we construct 50 FDCNs under different flow conditions, and find that the power-law exponent and the network information entropy, which are sensitive to the flow pattern transition, can both characterize the nonlinear dynamics of gas-liquid two-phase flow. Furthermore, we construct FSCN and demonstrate how network statistic can be used to reveal the fluid structure of gas-liquid two-phase flow. In this paper, from a different perspective, we not only introduce complex network theory to the study of gas-liquid two-phase flow but also indicate that complex network may be a powerful tool for exploring nonlinear time series in practice.

  11. Gas-Phase Reactivity of Microsolvated Anions

    DEFF Research Database (Denmark)

    Thomsen, Ditte Linde

    the gas-phase α-effect. The experimental studies are performed by means of the flowing after glow selected ion flow tube technique, and these are supplemented by electronic structure calculations. The α-nucleophile employed is the microsolvated hydrogen peroxide anion whose reactivity is compared......Gas-phase studies of ion-molecule reactions shed light on the intrinsic factors that govern reactivity; and even solvent effects can be examined in the gasphase environment by employing microsolvated ions. An area that has received considerable attention with regard to the interplay between...... to that of a series of microsolvated oxygen centered anions. The association of the nucleophiles with a single water or methanol molecule allows the α-effect to be observed in the SN2 reaction with methyl chloride; this effect was not apparent in the reactions of the unsolvated anions. The results suggest...

  12. Automated de novo phasing and model building of coiled-coil proteins.

    Science.gov (United States)

    Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

    2015-03-01

    Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

  13. Defect formation in fluoropolymer films at their condensation from a gas phase

    Science.gov (United States)

    Luchnikov, P. A.

    2018-01-01

    The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

  14. GAS PHASE ION CHEMISTRY OF COUMARINS: AB INITIO ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and ... Figure 1. Generic chemical structures of the coumarins in this study. ..... Part of this work was conducted using the resources of ...

  15. Radical Reactions in the Gas Phase: Recent Development and Application in Biomolecules

    Directory of Open Access Journals (Sweden)

    Yang Gao

    2014-01-01

    Full Text Available This review summarizes recent literature describing the use of gas phase radical reactions for structural characterization of complex biomolecules other than peptides. Specifically, chemical derivatization, in-source chemical reaction, and gas phase ion/ion reactions have been demonstrated as effective ways to generate radical precursor ions that yield structural informative fragments complementary to those from conventional collision-induced dissociation (CID. Radical driven dissociation has been applied to a variety of biomolecules including peptides, nucleic acids, carbohydrates, and phospholipids. The majority of the molecules discussed in this review see limited fragmentation from conventional CID, and the gas phase radical reactions open up completely new dissociation channels for these molecules and therefore yield high fidelity confirmation of the structures of the target molecules. Due to the extensively studied peptide fragmentation, this review focuses only on nonpeptide biomolecules such as nucleic acids, carbohydrates, and phospholipids.

  16. Characterizing the correlations between local phase fractions of gas-liquid two-phase flow with wire-mesh sensor.

    Science.gov (United States)

    Tan, C; Liu, W L; Dong, F

    2016-06-28

    Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas-liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas-liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue 'Supersensing through industrial process tomography'. © 2016 The Author(s).

  17. Isothermal phase equilibria for the (HFC-32 + HFC-134a) mixed-gas hydrate system

    International Nuclear Information System (INIS)

    Miyauchi, Hiroshi; Yasuda, Kenjiro; Matsumoto, Yuuki; Hashimoto, Shunsuke; Sugahara, Takeshi; Ohgaki, Kazunari

    2012-01-01

    Highlights: ► Structural phase transition results in the heterogeneous azeotropic-like behaviour. ► HFC-134a molecules, in spite of an s-II former, occupy the large cages of s-I. ► Negative azeotropic-like behaviour becomes more remarkable at higher temperatures. - Abstract: Isothermal phase equilibria (pressure-composition relations in hydrate, gas, and aqueous phases) in the {difluoromethane (HFC-32) + 1,1,1,2-tetrafluoroethane (HFC-134a)} mixed-gas hydrate system were measured at the temperatures 274.15 K, 279.15 K, and 283.15 K. The heterogeneous azeotropic-like behaviour derived from the structural phase transition of (HFC-32 + HFC-134a) mixed-gas hydrates appears over the whole temperature range of the present study. In addition to the heterogeneous azeotropic-like behaviour, the isothermal phase equilibrium curves of the (HFC-32 + HFC-134a) mixed-gas hydrate system exhibit the negative homogeneous azeotropic-like behaviour at temperatures 279.15 K and 283.15 K. The negative azeotropic-like behaviour, which becomes more remarkable at higher temperatures, results in the lower equilibrium pressure of (HFC-32 + HFC-134a) mixed-gas hydrates than those of both simple HFC-32 and HFC-134a hydrates. Although the HFC-134a molecule forms the simple structure-II hydrate at the temperatures, the present findings reveal that HFC-134a molecules occupy a part of the large cages of the structure-I mixed-gas hydrate.

  18. An Introduction to the Gas Phase

    Science.gov (United States)

    Vallance, Claire

    2017-11-01

    'An Introduction to the Gas Phase' is adapted from a set of lecture notes for a core first year lecture course in physical chemistry taught at the University of Oxford. The book is intended to give a relatively concise introduction to the gas phase at a level suitable for any undergraduate scientist. After defining the gas phase, properties of gases such as temperature, pressure, and volume are discussed. The relationships between these properties are explained at a molecular level, and simple models are introduced that allow the various gas laws to be derived from first principles. Finally, the collisional behaviour of gases is used to explain a number of gas-phase phenomena, such as effusion, diffusion, and thermal conductivity.

  19. A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals

    International Nuclear Information System (INIS)

    Mizuno, Nobuhiro; Makino, Masatomo; Kumasaka, Takashi

    2013-01-01

    A convenient gas-derivatization tool for protein crystals is presented in combination with a fine-needle capillary and a gas-pressure regulator. Gas derivatization of protein crystals is useful not only to analyse gas-binding proteins but also to solve the phase problem of X-ray crystallography by using noble gases. However, the gas pressurization tools for these experiments are often elaborate and need to release the gas before flash-cooling. To simplify this step, a procedure using a fine-needle capillary to mount and flash-cool protein crystals under the pressurization of gases has been developed. After the crystals are picked up with the capillary, the capillary is sealed with an adhesive and then connected directly to a gas regulator. The quality of the diffraction data using this method is comparable with that of data from conventional pressurization procedures. The preparation of xenon-derivatives of hen egg-white lysozyme using this method was a success. In the derivatives, two new xenon binding sites were found and one of their sites vanished by releasing the gas. This observation shows the availability of flash-cooling under gas pressurization. This procedure is simple and useful for preparing gas-derivative crystals

  20. TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.

    Science.gov (United States)

    Iwayanagi, Takao; Miyamoto, Sei; Konno, Takeshi; Mizutani, Hisashi; Hirai, Tomohiro; Shigemoto, Yasumasa; Gojobori, Takashi; Sugawara, Hideaki

    2012-09-01

    The Targeted Proteins Research Program (TPRP) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan is the phase II of structural biology project (2007-2011) following the Protein 3000 Project (2002-2006) in Japan. While the phase I Protein 3000 Project put partial emphasis on the construction and maintenance of pipelines for structural analyses, the TPRP is dedicated to revealing the structures and functions of the targeted proteins that have great importance in both basic research and industrial applications. To pursue this objective, 35 Targeted Proteins (TP) Projects selected in the three areas of fundamental biology, medicine and pharmacology, and food and environment are tightly collaborated with 10 Advanced Technology (AT) Projects in the four fields of protein production, structural analyses, chemical library and screening, and information platform. Here, the outlines and achievements of the 35 TP Projects are summarized in the system named TP Atlas. Progress in the diversified areas is described in the modules of Graphical Summary, General Summary, Tabular Summary, and Structure Gallery of the TP Atlas in the standard and unified format. Advances in TP Projects owing to novel technologies stemmed from AT Projects and collaborative research among TP Projects are illustrated as a hallmark of the Program. The TP Atlas can be accessed at http://net.genes.nig.ac.jp/tpatlas/index_e.html .

  1. Structure Elucidation of Dimethylformamide-Solvated Alkylzinc Cations in the Gas Phase

    NARCIS (Netherlands)

    Dreiocker, F.; Oomens, J.; Meijer, Ajhm; Pickup, B. T.; Jackson, R. F. W.; Schafer, M.

    2010-01-01

    Organozinc iodides, useful for the synthesis of nonproteinogenic amino acids, are investigated in the gas phase by a combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, and infrared multiphoton dissociation (IRMPD) spectroscopy employing a free electron laser. ESI allowed the

  2. Structure elucidation of dimethylformamide-solvated alkylzinc cations in the gas phase

    NARCIS (Netherlands)

    Dreiocker, F.; Oomens, J.; Meijer, A.J.H.M.; Pickup, B.T.; Jackson, R.F.W.; Schäfer, M.

    2010-01-01

    Organozinc iodides, useful for the synthesis of nonproteinogenic amino acids, are investigated in the gas phase by a combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, and infrared multiphoton dissociation (IRMPD) spectroscopy employing a free electron laser. ESI allowed the

  3. Iodine removal from a gas phase

    International Nuclear Information System (INIS)

    Vikis, A. Ch.

    1982-01-01

    Iodine, e.g. radioactive iodine, present as one or more organic iodides, optionally with elemental iodine, in a gas phase (e.g. air) are removed by photochemically decomposing the organic iodides to elemental iodine, reacting the iodine produced, and any initially present with excess ozone, preferably photochemically produced in situ in the gas phase to produce solid iodine oxides, and removing the solid oxides from the gas phase. (author)

  4. Iodine removal from a gas phase

    International Nuclear Information System (INIS)

    Vikis, A.C.

    1984-01-01

    Iodine, e.g. radioactive iodine, present as one or more organic iodides, optionally with elemental iodine, in a gas phase (e.g. air) are removed by photochemically decomposing the organic iodides to elemental iodine, reacting the iodine produced, and any initially present with excess ozone, preferably photochemically produced in situ in the gas phase to produce solid iodine oxides, and removing the solid oxides from the gas phase

  5. Gas Phase Sulfur, Chlorine and Potassium Chemistry in Biomass Combustion

    DEFF Research Database (Denmark)

    Løj, Lusi Hindiyarti

    2007-01-01

    Gas Phase Sulfur, Chlorine and Alkali Metal Chemistry in Biomass Combustion Concern about aerosols formation, deposits, corrosion, and gaseous emissions during biomass combustion, especially straw, continues to be a driving force for investigation on S, Cl, K-containing species under combustions...... conditions. These trace species contained in the biomass structure will be released to the gas phase during combustion and contribute to the problems generated during the process. The investigation during this PhD project is done to stepwise improve the understanding in the chemistry and reduce...... the uncertainties. In the present work, the detailed kinetic model for gas phase sulfur, chlorine, alkali metal, and their interaction has been updated. The K/O/H/Cl chemistry, S chemistry, and their interaction can reasonably predict a range of experimental data. In general, understanding of the interaction...

  6. UPS and DFT investigation of the electronic structure of gas-phase trimesic acid

    Energy Technology Data Exchange (ETDEWEB)

    Reisberg, L., E-mail: rebban@ut.ee [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Pärna, R. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund (Sweden); Kikas, A.; Kuusik, I.; Kisand, V. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Hirsimäki, M.; Valden, M. [Surface Science Laboratory, Optoelectronics Research Centre, Tampere University of Technology, FIN-33101 Tampere (Finland); Nõmmiste, E. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia)

    2016-11-15

    Highlights: • In the current study outer valence band electronic structure of benzene-1,3,5-tricarboxylic acid was interpreted. • Experimental and calculated trimesic acid (TMA) spectrum were compared to ones of benzene and benzoic acid. • It is shown that similarities between MO energies and shapes for benzene and TMA exists. • Addition of carboxyl groups to the benzene ring clearly correlates with increasing binding energy of HOMO. - Abstract: Benzene-1,3,5-tricarboxylic acid (trimesic acid, TMA) molecules in gas-phase have been investigated by using valence band photoemission. The photoelectron spectrum in the binding energy region from 9 to 22 eV is interpreted by using density functional theory calculations. The electronic structure of TMA is compared with benzene and benzoic acid in order to demonstrate changes in molecular orbital energies induced by addition of carboxyl groups to benzene ring.

  7. Effects of plasticization and shear stress on phase structure development and properties of soy protein blends.

    Science.gov (United States)

    Chen, Feng; Zhang, Jinwen

    2010-11-01

    In this study, soy protein concentrate (SPC) was used as a plastic component to blend with poly(butylene adipate-co-terephthalate) (PBAT). Effects of SPC plasticization and blend composition on its deformation during mixing were studied in detail. Influence of using water as the major plasticizer and glycerol as the co-plasticizer on the deformation of the SPC phase during mixing was explored. The effect of shear stress, as affected by SPC loading level, on the phase structure of SPC in the blends was also investigated. Quantitative analysis of the aspect ratio of SPC particles was conducted by using ImageJ software, and an empirical model predicting the formation of percolated structure was applied. The experimental results and the model prediction showed a fairly good agreement. The experimental results and statistic analysis suggest that both SPC loading level and its water content prior to compounding had significant influences on development of the SPC phase structure and were correlated in determining the morphological structures of the resulting blends. Consequently, physical and mechanical properties of the blends greatly depended on the phase morphology and PBAT/SPC ratio of the blends.

  8. Liquid-gas phase transition in asymmetric nuclear matter at finite temperature

    Science.gov (United States)

    Maruyama, Toshiki; Tatsumi, Toshitaka; Chiba, Satoshi

    2010-03-01

    Liquid-gas phase transition is discussed in warm asymmetric nuclear matter. Some peculiar features are figured out from the viewpoint of the basic thermodynamics about the phase equilibrium. We treat the mixed phase of the binary system based on the Gibbs conditions. When the Coulomb interaction is included, the mixed phase is no more uniform and the sequence of the pasta structures appears. Comparing the results with those given by the simple bulk calculation without the Coulomb interaction, we extract specific features of the pasta structures at finite temperature.

  9. Liquid-gas phase transition in asymmetric nuclear matter at finite temperature

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Tatsumi, Toshitaka; Chiba, Satoshi

    2010-01-01

    Liquid-gas phase transition is discussed in warm asymmetric nuclear matter. Some peculiar features are figured out from the viewpoint of the basic thermodynamics about the phase equilibrium. We treat the mixed phase of the binary system based on the Gibbs conditions. When the Coulomb interaction is included, the mixed phase is no more uniform and the sequence of the pasta structures appears. Comparing the results with those given by the simple bulk calculation without the Coulomb interaction, we extract specific features of the pasta structures at finite temperature.

  10. Liquid phase separation of proteins based on electrophoretic effects in an electrospray setup during sample introduction into a gas-phase electrophoretic mobility molecular analyzer (CE–GEMMA/CE–ES–DMA)

    Science.gov (United States)

    Weiss, Victor U.; Kerul, Lukas; Kallinger, Peter; Szymanski, Wladyslaw W.; Marchetti-Deschmann, Martina; Allmaier, Günter

    2014-01-01

    Nanoparticle characterization is gaining importance in food technology, biotechnology, medicine, and pharmaceutical industry. An instrument to determine particle electrophoretic mobility (EM) diameters in the single-digit to double-digit nanometer range receiving increased attention is the gas-phase electrophoretic mobility molecular analyzer (GEMMA) separating electrophoretically single charged analytes in the gas-phase at ambient pressure. A fused-silica capillary is used for analyte transfer to the gas-phase by means of a nano electrospray (ES) unit. The potential of this capillary to separate analytes electrophoretically in the liquid phase due to different mobilities is, at measurement conditions recommended by the manufacturer, eliminated due to elevated pressure applied for sample introduction. Measurements are carried out upon constant feeding of analytes to the system. Under these conditions, aggregate formation is observed for samples including high amounts of non-volatile components or complex samples. This makes the EM determination of individual species sometimes difficult, if not impossible. With the current study we demonstrate that liquid phase electrophoretic separation of proteins (as exemplary analytes) occurs in the capillary (capillary zone electrophoresis, CE) of the nano ES unit of the GEMMA. This finding was consecutively applied for on-line desalting allowing EM diameter determination of analytes despite a high salt concentration within samples. The present study is to our knowledge the first report on the use of the GEMMA to determine EM diameters of analytes solubilized in the ES incompatible electrolyte solutions by the intended use of electrophoresis (in the liquid phase) during sample delivery. Results demonstrate the proof of concept of such an approach and additionally illustrate the high potential of a future on-line coupling of a capillary electrophoresis to a GEMMA instrument. PMID:25109866

  11. Escherichia coli MltA : MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (vol D61, pg 613, 2005)

    NARCIS (Netherlands)

    Barends, Thomas R.M.; Jong, René M. de; Straaten, Karin E. van; Thunnissen, Andy-Mark W.H.; Dijkstra, Bauke W.

    Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 Å resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found

  12. cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein-DNA ladders.

    Science.gov (United States)

    Andreeva, Liudmila; Hiller, Björn; Kostrewa, Dirk; Lässig, Charlotte; de Oliveira Mann, Carina C; Jan Drexler, David; Maiser, Andreas; Gaidt, Moritz; Leonhardt, Heinrich; Hornung, Veit; Hopfner, Karl-Peter

    2017-09-21

    Cytosolic DNA arising from intracellular pathogens triggers a powerful innate immune response. It is sensed by cyclic GMP-AMP synthase (cGAS), which elicits the production of type I interferons by generating the second messenger 2'3'-cyclic-GMP-AMP (cGAMP). Endogenous nuclear or mitochondrial DNA can also be sensed by cGAS under certain conditions, resulting in sterile inflammation. The cGAS dimer binds two DNA ligands shorter than 20 base pairs side-by-side, but 20-base-pair DNA fails to activate cGAS in vivo and is a poor activator in vitro. Here we show that cGAS is activated in a strongly DNA length-dependent manner both in vitro and in human cells. We also show that cGAS dimers form ladder-like networks with DNA, leading to cooperative sensing of DNA length: assembly of the pioneering cGAS dimer between two DNA molecules is ineffective; but, once formed, it prearranges the flanking DNA to promote binding of subsequent cGAS dimers. Remarkably, bacterial and mitochondrial nucleoid proteins HU and mitochondrial transcription factor A (TFAM), as well as high-mobility group box 1 protein (HMGB1), can strongly stimulate long DNA sensing by cGAS. U-turns and bends in DNA induced by these proteins pre-structure DNA to nucleate cGAS dimers. Our results suggest a nucleation-cooperativity-based mechanism for sensitive detection of mitochondrial DNA and pathogen genomes, and identify HMGB/TFAM proteins as DNA-structuring host factors. They provide an explanation for the peculiar cGAS dimer structure and suggest that cGAS preferentially binds incomplete nucleoid-like structures or bent DNA.

  13. Gas phase ion chemistry

    CERN Document Server

    Bowers, Michael T

    1979-01-01

    Gas Phase Ion Chemistry, Volume 1 covers papers on the advances of gas phase ion chemistry. The book discusses the advances in flow tubes and the measurement of ion-molecule rate coefficients and product distributions; the ion chemistry of the earth's atmosphere; and the classical ion-molecule collision theory. The text also describes statistical methods in reaction dynamics; the state selection by photoion-photoelectron coincidence; and the effects of temperature and pressure in the kinetics of ion-molecule reactions. The energy distribution in the unimolecular decomposition of ions, as well

  14. Structure and dynamics of gas phase ions: Interplay between experiments and computations in IRMPD spectroscopy

    Science.gov (United States)

    Coletti, Cecilia; Corinti, Davide; Paciotti, Roberto; Re, Nazzareno; Crestoni, Maria Elisa; Fornarini, Simonetta

    2017-11-01

    The investigation of the molecular structure and dynamics of ions in gas phase is an item of increasing interest, due the role such species play in many areas of chemistry and physics, not to mention that they often represent elusive intermediates in more complex reaction mechanisms. Infrared Multiple Photon Dissociation spectroscopy is today one of the most advanced technique to this purpose, because of its high sensitivity to even small structure changes. The interpretation of IRMPD spectra strongly relies on high level quantum mechanical computations, so that a close interplay is needed for a detailed understanding of structure and kinetics properties which can be gathered from the many applications of this powerful technique. Recent advances in experiment and theory in this field are here illustrated, with emphasis on recent progresses for the elucidation of the mechanism of action of cisplatin, one of the most widely used anticancer drugs.

  15. The structural phase diagram and oxygen equilibrium partial pressure of YBa2CU3O6+x studied by neutron powder diffraction and gas volumetry

    DEFF Research Database (Denmark)

    Andersen, N.H.; Lebech, B.; Poulsen, H.F.

    1990-01-01

    An experimental technique based on neutron powder diffraction and gas volumetry is presented and used to study the structural phase diagram of YBa2Cu3O6+x under equilibrium conditions in an extended part of (x, T)-phase (0.15

  16. CASCADER: An M-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Cawlfield, D.E.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-09-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or dispersion. Additionally during the transport of parent and daughter radionuclides in soil, radionuclide decay may occur. This version of CASCADER called CASCADR9 starts with the concepts presented in volumes one and three of this series. For a proper understanding of how the model works, the reader should read volume one first. Also presented in this volume is a set of realistic scenarios for buried sources of radon gas, and the input and output file structure for CASCADER9

  17. CASCADER: An m-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Cawlfield, D.E.; Been, K.B.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. This is volume two to the CASCADER series, titled CASCADR8. It embodies the concepts presented in volume one of this series. To properly understand how the CASCADR8 model works, the reader should read volume one first. This volume presents the input and output file structure for CASCADR8, and a set of realistic scenarios for buried sources of radon gas

  18. Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

    Science.gov (United States)

    Mawhorter, Richard J., Jr.

    A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

  19. Closed-cage tungsten oxide clusters in the gas phase.

    Science.gov (United States)

    Singh, D M David Jeba; Pradeep, T; Thirumoorthy, Krishnan; Balasubramanian, Krishnan

    2010-05-06

    During the course of a study on the clustering of W-Se and W-S mixtures in the gas phase using laser desorption ionization (LDI) mass spectrometry, we observed several anionic W-O clusters. Three distinct species, W(6)O(19)(-), W(13)O(29)(-), and W(14)O(32)(-), stand out as intense peaks in the regular mass spectral pattern of tungsten oxide clusters suggesting unusual stabilities for them. Moreover, these clusters do not fragment in the postsource decay analysis. While trying to understand the precursor material, which produced these clusters, we found the presence of nanoscale forms of tungsten oxide. The structure and thermodynamic parameters of tungsten clusters have been explored using relativistic quantum chemical methods. Our computed results of atomization energy are consistent with the observed LDI mass spectra. The computational results suggest that the clusters observed have closed-cage structure. These distinct W(13) and W(14) clusters were observed for the first time in the gas phase.

  20. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    Science.gov (United States)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  1. The structure optimization of gas-phase surface discharge and its application for dye degradation

    Science.gov (United States)

    Ying, CAO; Jie, LI; Nan, JIANG; Yan, WU; Kefeng, SHANG; Na, LU

    2018-05-01

    A gas-phase surface discharge (GSD) was employed to optimize the discharge reactor structure and investigate the dye degradation. A dye mixture of methylene blue, acid orange and methyl orange was used as a model pollutant. The results indicated that the reactor structure of the GSD system with the ratio of tube inner surface area and volume of 2.48, screw pitch between a high-voltage electrode of 9.7 mm, high-voltage electrode wire diameter of 0.8 mm, dielectric tube thickness of 2.0 mm and tube inner diameter of 16.13 mm presented a better ozone (O3) generation efficiency. Furthermore, a larger screw pitch and smaller wire diameter enhanced the O3 generation. After the dye mixture degradation by the optimized GSD system, 73.21% and 50.74% of the chemical oxygen demand (COD) and total organic carbon removal rate were achieved within 20 min, respectively, and the biochemical oxygen demand (BOD) and biodegradability (BOD/COD) improved.

  2. Local gas- and liquid-phase measurements for air-water two-phase flows in a rectangular channel

    International Nuclear Information System (INIS)

    Zhou, X.; Sun, X.; Williams, M.; Fu, Y.; Liu, Y.

    2014-01-01

    Local gas- and liquid-phase measurements of various gas-liquid two-phase flows, including bubbly, cap-bubbly, slug, and churn-turbulent flows, were performed in an acrylic vertical channel with a rectangular cross section of 30 mm x 10 mm and height of 3.0 m. All the measurements were carried out at three measurement elevations along the flow channel, with z/D h = 9, 72, and 136, respectively, to study the flow development. The gas-phase velocity, void fraction, and bubble number frequency were measured using a double-sensor conductivity probe. A high-speed imaging system was utilized to perform the flow regime visualization and to provide additional quantitative information of the two-phase flow structure. An image processing scheme was developed to obtain the gas-phase velocity, void fraction, Sauter mean diameter, bubble number density, and interfacial area concentration. The liquid-phase velocity and turbulence measurements were conducted using a particle image velocimetry-planar laser-induced fluorescence (PIV-PLIF) system, which enables whole-field and high-resolution data acquisition. An optical phase separation method, which uses fluorescent particles and optical filtration technique, is adopted to extract the velocity information of the liquid phase. An image pre-processing scheme is imposed on the raw PIV images acquired to remove noises due to the presence of bubble residuals and optically distorted particles in the images captured by the PIV-PLIF system. Due to the better light access and less bubble distortion in the narrow rectangular channel, the PIV-PLIF system were able to perform reasonably well in flows of even higher void fractions as compared to the situations with circular pipe test sections. The flow conditions being studied covered various flow regime transitions, void fractions, and liquid-phase flow Reynolds numbers. The obtained experimental data can also be used to validate two-phase CFD results. (author)

  3. Computational phase diagrams of noble gas hydrates under pressure

    Energy Technology Data Exchange (ETDEWEB)

    Teeratchanan, Pattanasak, E-mail: s1270872@sms.ed.ac.uk; Hermann, Andreas, E-mail: a.hermann@ed.ac.uk [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD (United Kingdom)

    2015-10-21

    We present results from a first-principles study on the stability of noble gas-water compounds in the pressure range 0-100 kbar. Filled-ice structures based on the host water networks ice-I{sub h}, ice-I{sub c}, ice-II, and C{sub 0} interacting with guest species He, Ne, and Ar are investigated, using density functional theory (DFT) with four different exchange-correlation functionals that include dispersion effects to various degrees: the non-local density-based optPBE-van der Waals (vdW) and rPW86-vdW2 functionals, the semi-empirical D2 atom pair correction, and the semi-local PBE functional. In the He-water system, the sequence of stable phases closely matches that seen in the hydrogen hydrates, a guest species of comparable size. In the Ne-water system, we predict a novel hydrate structure based on the C{sub 0} water network to be stable or at least competitive at relatively low pressure. In the Ar-water system, as expected, no filled-ice phases are stable; however, a partially occupied Ar-C{sub 0} hydrate structure is metastable with respect to the constituents. The ability of the different DFT functionals to describe the weak host-guest interactions is analysed and compared to coupled cluster results on gas phase systems.

  4. Capacitive Structures for Gas and Biological Sensing

    KAUST Repository

    Sapsanis, Christos

    2015-04-01

    The semiconductor industry was benefited by the advances in technology in the last decades. This fact has an impact on the sensors field, where the simple transducer was evolved into smart miniaturized multi-functional microsystems. However, commercially available gas and biological sensors are mostly bulky, expensive, and power-hungry, which act as obstacles to mass use. The aim of this work is gas and biological sensing using capacitive structures. Capacitive sensors were selected due to its design simplicity, low fabrication cost, and no DC power consumption. In the first part, the dominant structure among interdigitated electrodes (IDEs), fractal curves (Peano and Hilbert) and Archimedean spiral was investigated from capacitance density perspective. The investigation consists of geometrical formula calculations, COMSOL Multiphysics simulations and cleanroom fabrication of the capacitors on a silicon substrate. Moreover, low-cost fabrication on flexible plastic PET substrate was conducted outside cleanroom with rapid prototyping using a maskless laser etching. The second part contains the humidity, Volatile Organic compounds (VOCs) and Ammonia sensing of polymers, Polyimide and Nafion, and metal-organic framework (MOF), Cu(bdc)2.xH2O using IDEs and tested in an automated gas setup for experiment control and data extraction. The last part includes the biological sensing of C - reactive protein (CRP) quantification, which is considered as a biomarker of being prone to cardiac diseases and Bovine serum albumin (BSA) protein quantification, which is used as a reference for quantifying unknown proteins.

  5. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins.

    Science.gov (United States)

    Habka, S; Sohn, W Y; Vaquero-Vara, V; Géléoc, M; Tardivel, B; Brenner, V; Gloaguen, E; Mons, M

    2018-01-31

    Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

  6. EDM-DEDM and protein crystal structure solution.

    Science.gov (United States)

    Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Anna Maria; Siliqi, Dritan

    2009-05-01

    Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249-256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM-DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed.

  7. GAS PHASE STRUCTURE AND STABILITY OF COMPLEX FORMED BY H2O, NH3, H2S AND THEIR METHYL DERIVATIVES WITH THE CATION CO2+

    Directory of Open Access Journals (Sweden)

    Cahyorini Kusumawardani

    2010-06-01

    Full Text Available Ab initio molecular orbital calculations at the Hartree-Fock-Self Consistent Field (HF-SCF have been performed in order to determine the structure and gas phase energies of complex formed by the Lewis bases of H2O, NH3, H2S and their methyl derivatives with the cation Co2+. The relative basicities of the base studied depend on both the substituent. The gas-phase interaction energies computed by the SCF method including electron correlation Møller-Plesset 2 (MP2 dan Configuration Iteration (CI were comparable in accuracy. The binding energies computed by these two methods reach the targeted chemical accuracy.   Keywords: ab initio calculation, cobalt complex, structure stability

  8. Preconcentration in gas or liquid phases using adsorbent thin films

    Directory of Open Access Journals (Sweden)

    Antonio Pereira Nascimento Filho

    2006-03-01

    Full Text Available The possibility of preconcentration on microchannels for organic compounds in gas or liquid phases was evaluated. Microstructures with different geometries were mechanically machined using poly(methyl methacrylate - PMMA as substrates and some cavities were covered with cellulose. The surfaces of the microchannels were modified by plasma deposition of hydrophilic or hydrophobic films using 2-propanol and hexamethyldisilazane (HMDS, respectively. Double layers of HMDS + 2-propanol were also used. Adsorption characterization was made by Quartz Crystal Measurements (QCM technique using reactants in a large polarity range that showed the adsorption ability of the structures depends more on the films used than on the capillary phenomena. Cellulose modified by double layer film showed a high retention capacity for all gaseous compounds tested. However, structures without plasma deposition showed low retention capacity. Microchannels modified with double layers or 2-propanol plasma films showed higher retention than non-modified ones on gas or liquid phase.

  9. Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

    Science.gov (United States)

    Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A; Gordeliy, Valentin; Popov, Alexander

    2017-05-01

    We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.

  10. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

    Science.gov (United States)

    Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

    2014-06-01

    The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

  11. Gas-Phase Thermolyses

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge

    1982-01-01

    The unimolecular gas-phase thermolyses of the four methyl and ethyl monothioacetates (5)–(8) have been studied by the flash vacuum thermolysis–field ionization mass spectrometry technique in the temperature range 883–1 404 K. The types of reactions verified were keten formation, thiono–thiolo rea...

  12. FORTRAN program for calculating liquid-phase and gas-phase thermal diffusion column coefficients

    International Nuclear Information System (INIS)

    Rutherford, W.M.

    1980-01-01

    A computer program (COLCO) was developed for calculating thermal diffusion column coefficients from theory. The program, which is written in FORTRAN IV, can be used for both liquid-phase and gas-phase thermal diffusion columns. Column coefficients for the gas phase can be based on gas properties calculated from kinetic theory using tables of omega integrals or on tables of compiled physical properties as functions of temperature. Column coefficients for the liquid phase can be based on compiled physical property tables. Program listings, test data, sample output, and users manual are supplied for appendices

  13. OAS proteins and cGAS: unifying concepts in sensing and responding to cytosolic nucleic acids.

    Science.gov (United States)

    Hornung, Veit; Hartmann, Rune; Ablasser, Andrea; Hopfner, Karl-Peter

    2014-08-01

    Recent discoveries in the field of innate immunity have highlighted the existence of a family of nucleic acid-sensing proteins that have similar structural and functional properties. These include the well-known oligoadenylate synthase (OAS) family proteins and the recently identified OAS homologue cyclic GMP-AMP (cGAMP) synthase (cGAS). The OAS proteins and cGAS are template-independent nucleotidyltransferases that, once activated by double-stranded nucleic acids in the cytosol, produce unique classes of 2'-5'-linked second messenger molecules, which - through distinct mechanisms - have crucial antiviral functions. 2'-5'-linked oligoadenylates limit viral propagation through the activation of the enzyme RNase L, which degrades host and viral RNA, and 2'-5'-linked cGAMP activates downstream signalling pathways to induce de novo antiviral gene expression. In this Progress article, we describe the striking functional and structural similarities between OAS proteins and cGAS, and highlight their roles in antiviral immunity.

  14. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase; Determinacao da estrutura molecular do ciclooctano por metodos Ab Initio e difracao de eletrons na fase gasosa

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Wagner B. de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica

    2000-10-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  15. Reactor for tracking catalyst nanoparticles in liquid at high temperature under a high-pressure gas phase with X-ray absorption spectroscopy.

    Science.gov (United States)

    Nguyen, Luan; Tao, Franklin Feng

    2018-02-01

    Structure of catalyst nanoparticles dispersed in liquid phase at high temperature under gas phase of reactant(s) at higher pressure (≥5 bars) is important for fundamental understanding of catalytic reactions performed on these catalyst nanoparticles. Most structural characterizations of a catalyst performing catalysis in liquid at high temperature under gas phase at high pressure were performed in an ex situ condition in terms of characterizations before or after catalysis since, from technical point of view, access to the catalyst nanoparticles during catalysis in liquid phase at high temperature under high pressure reactant gas is challenging. Here we designed a reactor which allows us to perform structural characterization using X-ray absorption spectroscopy including X-ray absorption near edge structure spectroscopy and extended X-ray absorption fine structure spectroscopy to study catalyst nanoparticles under harsh catalysis conditions in terms of liquid up to 350 °C under gas phase with a pressure up to 50 bars. This reactor remains nanoparticles of a catalyst homogeneously dispersed in liquid during catalysis and X-ray absorption spectroscopy characterization.

  16. Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV

    DEFF Research Database (Denmark)

    Goulet, Adeline; Vestergaard, Gisle Alberg; Felisberto-Rodrigues, Catarina

    2010-01-01

    The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 A wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structu...... on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization....

  17. Multiple Multidentate Halogen Bonding in Solution, in the Solid State, and in the (Calculated) Gas Phase.

    Science.gov (United States)

    Jungbauer, Stefan H; Schindler, Severin; Herdtweck, Eberhardt; Keller, Sandro; Huber, Stefan M

    2015-09-21

    The binding properties of neutral halogen-bond donors (XB donors) bearing two multidentate Lewis acidic motifs toward halides were investigated. Employing polyfluorinated and polyiodinated terphenyl and quaterphenyl derivatives as anion receptors, we obtained X-ray crystallographic data of the adducts of three structurally related XB donors with tetraalkylammonium chloride, bromide, and iodide. The stability of these XB complexes in solution was determined by isothermal titration calorimetry (ITC), and the results were compared to X-ray analyses as well as to calculated binding patterns in the gas phase. Density functional theory (DFT) calculations on the gas-phase complexes indicated that the experimentally observed distortion of the XB donors during multiple multidentate binding can be reproduced in 1:1 complexes with halides, whereas adducts with two halides show a symmetric binding pattern in the gas phase that is markedly different from the solid state structures. Overall, this study demonstrates the limitations in the transferability of binding data between solid state, solution, and gas phase in the study of complex multidentate XB donors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

    Science.gov (United States)

    Rajabi, Khadijeh

    2015-01-01

    A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

  19. Multiple scales and phases in discrete chains with application to folded proteins

    Science.gov (United States)

    Sinelnikova, A.; Niemi, A. J.; Nilsson, Johan; Ulybyshev, M.

    2018-05-01

    Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein. Here we address this impending problem. We develop a methodology with the potential to systematically identify different length scales, in the general case of a linear polymer chain. For this we introduce and analyze the properties of an order parameter that can both reveal the presence of different length scales and can also probe the phase structure. We first develop our concepts in the case of chiral homopolymers. We introduce a variant of Kadanoff's block-spin transformation to coarse grain piecewise linear chains, such as the C α backbone of a protein. We derive analytically, and then verify numerically, a number of properties that the order parameter can display, in the case of a chiral polymer chain. In particular, we propose that in the case of a chiral heteropolymer the order parameter can reveal traits of several different phases, contingent on the length scale at which it is scrutinized. We confirm that this is the case with crystallographic protein structures in the Protein Data Bank. Thus our results suggest relations between the scales, the phases, and the complexity of folding pathways.

  20. Gas flow headspace liquid phase microextraction.

    Science.gov (United States)

    Yang, Cui; Qiu, Jinxue; Ren, Chunyan; Piao, Xiangfan; Li, Xifeng; Wu, Xue; Li, Donghao

    2009-11-06

    There is a trend towards the use of enrichment techniques such as microextraction in the analysis of trace chemicals. Based on the theory of ideal gases, theory of gas chromatography and the original headspace liquid phase microextraction (HS-LPME) technique, a simple gas flow headspace liquid phase microextraction (GF-HS-LPME) technique has been developed, where the extracting gas phase volume is increased using a gas flow. The system is an open system, where an inert gas containing the target compounds flows continuously through a special gas outlet channel (D=1.8mm), and the target compounds are trapped on a solvent microdrop (2.4 microL) hanging on the microsyringe tip, as a result, a high enrichment factor is obtained. The parameters affecting the enrichment factor, such as the gas flow rate, the position of the microdrop, the diameter of the gas outlet channel, the temperatures of the extracting solvent and of the sample, and the extraction time, were systematically optimized for four types of polycyclic aromatic hydrocarbons. The results were compared with results obtained from HS-LPME. Under the optimized conditions (where the extraction time and the volume of the extracting sample vial were fixed at 20min and 10mL, respectively), detection limits (S/N=3) were approximately a factor of 4 lower than those for the original HS-LPME technique. The method was validated by comparison of the GF-HS-LPME and HS-LPME techniques using data for PAHs from environmental sediment samples.

  1. Laser spectroscopy of a halocarbocation in the gas phase: CH2I+.

    Science.gov (United States)

    Tao, Chong; Mukarakate, Calvin; Reid, Scott A

    2006-07-26

    We report the first gas-phase observation of the electronic spectrum of a simple halocarbocation, CH2I+. The ion was generated rotationally cold (Trot approximately 20 K) using pulsed discharge methods and was detected via laser spectroscopy. The identity of the spectral carrier was confirmed by modeling the rotational contour observed in the excitation spectra and by comparison of ground state vibrational frequencies determined by single vibronic level emission spectroscopy with Density Functional Theory (DFT) predictions. The transition was assigned as 3A1 gas phase should open new avenues for study of the structure and reactivity of these important ions.

  2. Experimental on two sensors combination used in horizontal pipe gas-water two-phase flow

    International Nuclear Information System (INIS)

    Wu, Hao; Dong, Feng

    2014-01-01

    Gas-water two phase flow phenomenon widely exists in production and living and the measurement of it is meaningful. A new type of long-waist cone flow sensor has been designed to measure two-phase mass flow rate. Six rings structure of conductance probe is used to measure volume fraction and axial velocity. The calibration of them have been made. Two sensors have been combined in horizontal pipeline experiment to measure two-phase flow mass flow rate. Several model of gas-water two-phase flow has been discussed. The calculation errors of total mass flow rate measurement is less than 5% based on the revised homogeneous flow model

  3. Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

    Science.gov (United States)

    Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

    2010-11-25

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

  4. Conformational Study of DNA Sugars: from the Gas Phase to Solution

    Science.gov (United States)

    Uriarte, Iciar; Vallejo-López, Montserrat; Cocinero, Emilio J.; Corzana, Francisco; Davis, Benjamin G.

    2017-06-01

    Sugars are versatile molecules that play a variety of roles in the organism. For example, they are important in energy storage processes or as structural scaffolds. Here, we focus on the monosaccharide present in DNA by addressing the conformational and puckering properties in the gas phase of α- and β-methyl-2-deoxy-ribofuranoside and α- and β-methyl-2-deoxy-ribopiranoside. Other sugars have been previously studied in the gas phase The work presented here stems from a combination of chemical synthesis, ultrafast vaporization methods, supersonic expansions, microwave spectroscopy (both chirped-pulsed and Balle-Flygare cavity-based spectrometers) and NMR spectroscopy. Previous studies in the gas phase had been performed on 2-deoxyribose, but only piranose forms were detected. However, thanks to the combination of these techniques, we have isolated and characterized for the first time the conformational landscape of the sugar present in DNA in its biologically relevant furanose form. Our gas phase study serves as a probe of the conformational preferences of these biomolecules under isolation conditions. Thanks to the NMR experiments, we can characterize the favored conformations in solution and extract the role of the solvent in the structure and puckering of the monosaccharides. E. J. Cocinero, A. Lesarri, P. Écija, F. J. Basterretxea, J.-U. Grabow, J. A. Fernández, F. Castaño, Angew. Chem. Int. Edit. 2012, 51, 3119. P. Écija, I. Uriarte, L. Spada, B. G. Davis, W. Caminati, F. J. Basterretxea, A. Lesarri, E. J. Cocinero, Chem. Commun. 2016, 52, 6241. I. Peña, E. J. Cocinero, C. Cabezas, A. Lesarri, S. Mata, P. Écija, A. M. Daly, Á. Cimas, C. Bermúdez, F. J. Basterretxea, S. Blanco, J. A. Fernández, J. C. López, F. Castaño, J. L. Alonso, Angew. Chem. Int. Edit. 2013, 52, 11840.

  5. Analyte induced water adsorbability in gas phase biosensors: the influence of ethinylestradiol on the water binding protein capacity.

    Science.gov (United States)

    Snopok, Borys; Kruglenko, Ivanna

    2015-05-07

    An ultra-sensitive gas phase biosensor/tracer/bio-sniffer is an emerging technology platform designed to provide real-time information on air-borne analytes, or those in liquids, through classical headspace analysis. The desired bio-sniffer measures gaseous 17α- ethinylestradiol (ETED) as frequency changes on a quartz crystal microbalance (QCM), which is a result of the interactions of liquid sample components in the headspace (ETED and water) with a biorecognition layer. The latter was constructed by immobilization of polyclonal antiserum against a phenolic A-ring of estrogenic receptors through protein A. The QCM response exhibited stretched exponential kinetics of negative frequency shifts with reversible and "irreversible" components of mass uptake onto the sensor surface in static headspace conditions when exposed to water solutions of ETED over the sensor working range, from 10(-10) to 10(-17) g L(-1). It was shown that the variations in the QCM response characteristics are due to the change of the water-binding capacity of the sensing layer induced by protein transformations initiated by the binding of ETED molecules. This result is well correlated with the natural physiological function of estrogens in controlling the homeostasis of body fluids in living beings.

  6. Posttranslational modification of bioaerosol protein by common gas pollutants: NO2 and O3

    Science.gov (United States)

    Abdullahi Mahmood, Marliyyah; Bloss, William; Pope, Francis

    2016-04-01

    Air pollution can exacerbate several medical conditions, for example, hay fever and asthma. The global incidence of hay fever has been rising for decades; however, the underlying reasons behind this rise remain unclear. It is hypothesized that the exposure of pollen to common gas phase pollutants, such as nitrogen dioxide (NO2) and ozone (O3), increases the allergenicity of the pollen and thus increases hay fever incidence (Reinmuth-Selzle et al., 2014, Franze, et al., 2005). Since atmospheric pollutants often have greater concentrations within urban areas (in particular NO2) the hypothesis suggests that greater allergenicity should occur in urban areas. Certainly, several studies do suggest higher hay fever incidence within urban areas compared to rural areas (Schröder et al., 2015). Previous published work suggests a link between increased allergies and changes in the chemical composition of pollen protein via posttranslational modification of the protein (Reinmuth-Selzle et al., 2014). This study investigates the posttranslational modification of two highly allergenic pollen species (Birch and Ragweed) that are common in Europe. Within the laboratory, we expose pollen grains to atmospherically relevant exposures of gas phase NO2, O3 and other common gas phase oxidants under a range of environmentally relevant conditions. The effects of the exposures on the biochemistry of the pollen grains were probed using a proteomic approach (liquid chromatography coupled ultra-high resolution spectrometer). Our findings indicate the interaction between gas phase pollutants and pollen cause protein specific modifications; in particular nitration that occurs upon tyrosine residues and nitrosylation on cysteine residues. These modifications may affect human immune response to the pollen protein, which may suggest a possible reason for increased allergies in reaction to such chemically altered protein. Quantification of the relative degree of PTMs, from a variety of

  7. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

    Science.gov (United States)

    Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

    2015-07-30

    Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

  8. Analyses of liquid-gas two-phase flow in fermentation tanks

    International Nuclear Information System (INIS)

    Toi, Takashi; Serizawa, Akimi; Takahashi, Osamu; Kawara, Zensaku; Gofuku, Akio; Kataoka, Isao.

    1993-01-01

    The understanding of two-phase flow is one of the important problems for both design and safety analyses of various engineering systems. For example, the flow conditions in beer fermentation tanks have an influence on the quality of production and productivity of tank. In this study, a two-dimensional numerical calculation code based on the one-pressure two-fluid model is developed to understand the circulation structure of low quality liquid-gas two-phase flows induced by bubble plume in a tank. (author)

  9. Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies.

    Science.gov (United States)

    Rodgers, Mary T; Armentrout, Peter B

    2016-01-01

    Quantitative insight into the structures and thermodynamics of alkali metal cations interacting with biological molecules can be obtained from studies in the gas phase combined with theoretical work. In this chapter, the fundamentals of the experimental and theoretical techniques are first summarized and results for such work on complexes of alkali metal cations with amino acids, small peptides, and nucleobases are reviewed. Periodic trends in how these interactions vary as the alkali metal cations get heavier are highlighted.

  10. Gas-Phase Thermolyses

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge

    1982-01-01

    The unimolecular gas-phase thermolyses of 1,2,3-oxadithiolan 2-oxide and thiiran 1-oxide have been studied by the flash vacuum thermolysis–field ionization mass spectrometry (f.v.t.–f.i.m.s.) technique in the temperature range from 1 043 to 1 404 K. The reactions are rationalized in terms of sulp...

  11. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation.

    Science.gov (United States)

    Straus, Rita N; Jockusch, Rebecca A

    2017-02-01

    An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.

  12. Taking MAD to the extreme: ultrafast protein structure determination

    International Nuclear Information System (INIS)

    Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

    1999-01-01

    Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

  13. Phasing and structure of bestrophin-1: a case study in the use of heavy-atom cluster compounds with multi-subunit transmembrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Dickson, Veronica Kane (Cambridge)

    2016-03-01

    The purification and three-dimensional crystallization of membrane proteins are commonly affected by a cumulation of pathologies that are less prevalent in their soluble counterparts. This may include severe anisotropy, poor spot shape, poor to moderate-resolution diffraction, crystal twinning, translational pseudo-symmetry and poor uptake of heavy atoms for derivatization. Such challenges must be circumvented by adaptations in the approach to crystallization and/or phasing. Here, an example of a protein that exhibited all of the above-mentioned complications is presented. Bestrophin-1 is a eukaryotic calcium-activated chloride channel, the structure of which was recently determined in complex with monoclonal antibody fragments using SAD phasing with tantalum bromide clusters (Ta6Br12·Br2). Some of the obstacles to obtaining improved diffraction and phasing for this particular channel are discussed, as well as the approach and adaptations that were key to determining the structure.

  14. Exploring the Photoreduction of Au(III) Complexes in the Gas-Phase

    Science.gov (United States)

    Marcum, Jesse C.; Kaufman, Sydney H.; Weber, J. Mathias

    2010-06-01

    We have used photodissociation spectroscopy to probe the electronic structure and photoreduction of Au(III) in gas-phase complexes containing Cl- and OH-. The gas-phase electronic spectrum of [AuCl_4]- closely resembles the aqueous solution spectrum, showing a lack of strong solvatochromic shifts. Substitution of Cl- ligands with OH- results in a strong blue shift, in agreement with ligand-field theory. Upon excitation, [AuCl_4]- can dissociate by loss of either one or two neutral Cl atoms, resulting in the reduction of gold from Au(III) to Au(II) and Au(I) respectively. The hydroxide substituted complex, [AuCl_2(OH)_2]-, demonstrates similar behavior but the only observable fragment channel is the loss of two neutral OH ligands, leading only to Au(I).

  15. Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

    DEFF Research Database (Denmark)

    Boll, Rebecca; Rouzee, Arnaud; Adolph, Marcus

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular...

  16. Gas-phase photocatalysis in μ-reactors

    DEFF Research Database (Denmark)

    Vesborg, Peter Christian Kjærgaard; Olsen, Jakob Lind; Henriksen, Toke Riishøj

    2010-01-01

    Gas-phase photocatalysis experiments may benefit from the high sensitivity and good time response in product detection offered by μ-reactors. We demonstrate this by carrying out CO oxidation and methanol oxidation over commercial TiO2 photocatalysts in our recently developed high-sensitivity reac......Gas-phase photocatalysis experiments may benefit from the high sensitivity and good time response in product detection offered by μ-reactors. We demonstrate this by carrying out CO oxidation and methanol oxidation over commercial TiO2 photocatalysts in our recently developed high...

  17. Thiobenzamide: Structure of a free molecule as studied by gas electron diffraction and quantum chemical calculations

    Science.gov (United States)

    Kolesnikova, Inna N.; Putkov, Andrei E.; Rykov, Anatolii N.; Shishkov, Igor F.

    2018-06-01

    The equilibrium (re) molecular structure of thiobenzamide along with rh1 structure has been determined in gas phase using gas electron-diffraction (GED) at about 127 °C and quantum-chemical calculations (QC). Rovibrational distance corrections to the thermal averaged GED structure have been computed with anharmonic force constants obtained at the MP2/cc-pVTZ level of theory. According to the results of GED and QC thiobenzamide exists as mixture of two non-planar enantiomers of C1 symmetry. The selected equilibrium geometrical parameters of thiobenzamide (re, Å and ∠e, deg) are the following: (Cdbnd S) = 1.641(4), (Csbnd N) = 1.352(2), (Csbnd C) = 1.478(9), (Cdbnd C)av = 1.395(2), CCN = 114.7(5), CCS = 123.4(5), C2C1C7S = 31(4), C6C1C7N = 29(4). The structure of thiobenzamide in the gas phase is markedly different to that in the literature for the single crystal. The differences between the gas and the solid structures are ascribed to the presence of intermolecular hydrogen bonding in the solid phase.

  18. Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1.

    Science.gov (United States)

    de Oliveira Mann, Carina C; Kiefersauer, Reiner; Witte, Gregor; Hopfner, Karl-Peter

    2016-06-08

    The exceptionally conserved metazoan MAB21 proteins are implicated in cell fate decisions and share considerable sequence homology with the cyclic GMP-AMP synthase. cGAS is the major innate immune sensor for cytosolic DNA and produces the second messenger 2'-5', 3'-5' cyclic GMP-AMP. Little is known about the structure and biochemical function of other proteins of the cGAS-MAB21 subfamily, such as MAB21L1, MAB21L2 and MAB21L3. We have determined the crystal structure of human full-length MAB21L1. Our analysis reveals high structural conservation between MAB21L1 and cGAS but also uncovers important differences. Although monomeric in solution, MAB21L1 forms a highly symmetric double-pentameric oligomer in the crystal, raising the possibility that oligomerization could be a feature of MAB21L1. In the crystal, MAB21L1 is in an inactive conformation requiring a conformational change - similar to cGAS - to develop any nucleotidyltransferase activity. Co-crystallization with NTP identified a putative ligand binding site of MAB21 proteins that corresponds to the DNA binding site of cGAS. Finally, we offer a structure-based explanation for the effects of MAB21L2 mutations in patients with eye malformations. The underlying residues participate in fold-stabilizing interaction networks and mutations destabilize the protein. In summary, we provide a first structural framework for MAB21 proteins.

  19. Modeling the Phase Composition of Gas Condensate in Pipelines

    Science.gov (United States)

    Dudin, S. M.; Zemenkov, Yu D.; Shabarov, A. B.

    2016-10-01

    Gas condensate fields demonstrate a number of thermodynamic characteristics to be considered when they are developed, as well as when gas condensate is transported and processed. A complicated phase behavior of the gas condensate system, as well as the dependence of the extracted raw materials on the phase state of the deposit other conditions being equal, is a key aspect. Therefore, when designing gas condensate lines the crucial task is to select the most appropriate methods of calculating thermophysical properties and phase equilibrium of the transported gas condensate. The paper describes a physical-mathematical model of a gas-liquid flow in the gas condensate line. It was developed based on balance equations of conservation of mass, impulse and energy of the transported medium within the framework of a quasi-1D approach. Constitutive relationships are given separately, and practical recommendations on how to apply the research results are provided as well.

  20. Differential Mobility Spectrometry-Hydrogen Deuterium Exchange (DMS-HDX) as a Probe of Protein Conformation in Solution.

    Science.gov (United States)

    Zhu, Shaolong; Campbell, J Larry; Chernushevich, Igor; Le Blanc, J C Yves; Wilson, Derek J

    2016-06-01

    Differential mobility spectrometry (DMS) is an ion mobility technique that has been adopted chiefly as a pre-filter for small- to medium-sized analytes (DMS-field asymmetric waveform ion mobility spectroscopy (FAIMS)-the application of DMS to intact biomacromolecules remains largely unexplored. In this work, we employ DMS combined with gas-phase hydrogen deuterium exchange (DMS-HDX) to probe the gas-phase conformations generated from proteins that were initially folded, partially-folded, and unfolded in solution. Our findings indicate that proteins with distinct structural features in solution exhibit unique deuterium uptake profiles as function of their optimal transmission through the DMS. Ultimately we propose that DMS-HDX can, if properly implemented, provide rapid measurements of liquid-phase protein structural stability that could be of use in biopharmaceuticals development. Graphical Abstract ᅟ.

  1. Controlled in meso phase crystallization--a method for the structural investigation of membrane proteins.

    Directory of Open Access Journals (Sweden)

    Jan Kubicek

    Full Text Available We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i the stabilization of membrane proteins in the meso phase, (ii the control of hydration level and additive concentration by vapor diffusion. The new technology (iii significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII from Halobacterium salinarum for the first time.

  2. Protein-mediated surface structuring in biomembranes

    Directory of Open Access Journals (Sweden)

    Maggio B.

    2005-01-01

    Full Text Available The lipids and proteins of biomembranes exhibit highly dissimilar conformations, geometrical shapes, amphipathicity, and thermodynamic properties which constrain their two-dimensional molecular packing, electrostatics, and interaction preferences. This causes inevitable development of large local tensions that frequently relax into phase or compositional immiscibility along lateral and transverse planes of the membrane. On the other hand, these effects constitute the very codes that mediate molecular and structural changes determining and controlling the possibilities for enzymatic activity, apposition and recombination in biomembranes. The presence of proteins constitutes a major perturbing factor for the membrane sculpturing both in terms of its surface topography and dynamics. We will focus on some results from our group within this context and summarize some recent evidence for the active involvement of extrinsic (myelin basic protein, integral (Folch-Lees proteolipid protein and amphitropic (c-Fos and c-Jun proteins, as well as a membrane-active amphitropic phosphohydrolytic enzyme (neutral sphingomyelinase, in the process of lateral segregation and dynamics of phase domains, sculpturing of the surface topography, and the bi-directional modulation of the membrane biochemical reactivity.

  3. Structural analysis of a set of proteins resulting from a bacterial genomics project.

    Science.gov (United States)

    Badger, J; Sauder, J M; Adams, J M; Antonysamy, S; Bain, K; Bergseid, M G; Buchanan, S G; Buchanan, M D; Batiyenko, Y; Christopher, J A; Emtage, S; Eroshkina, A; Feil, I; Furlong, E B; Gajiwala, K S; Gao, X; He, D; Hendle, J; Huber, A; Hoda, K; Kearins, P; Kissinger, C; Laubert, B; Lewis, H A; Lin, J; Loomis, K; Lorimer, D; Louie, G; Maletic, M; Marsh, C D; Miller, I; Molinari, J; Muller-Dieckmann, H J; Newman, J M; Noland, B W; Pagarigan, B; Park, F; Peat, T S; Post, K W; Radojicic, S; Ramos, A; Romero, R; Rutter, M E; Sanderson, W E; Schwinn, K D; Tresser, J; Winhoven, J; Wright, T A; Wu, L; Xu, J; Harris, T J R

    2005-09-01

    The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Copyright 2005 Wiley-Liss, Inc.

  4. The nuclear liquid gas phase transition and phase coexistence

    International Nuclear Information System (INIS)

    Chomaz, Ph.

    2001-01-01

    In this talk we will review the different signals of liquid gas phase transition in nuclei. From the theoretical side we will first discuss the foundations of the concept of equilibrium, phase transition and critical behaviors in infinite and finite systems. From the experimental point of view we will first recall the evidences for some strong modification of the behavior of hot nuclei. Then we will review quantitative detailed analysis aiming to evidence phase transition, to define its order and phase diagram. Finally, we will present a critical discussion of the present status of phase transitions in nuclei and we will draw some lines for future development of this field. (author)

  5. The nuclear liquid gas phase transition and phase coexistence

    Energy Technology Data Exchange (ETDEWEB)

    Chomaz, Ph

    2001-07-01

    In this talk we will review the different signals of liquid gas phase transition in nuclei. From the theoretical side we will first discuss the foundations of the concept of equilibrium, phase transition and critical behaviors in infinite and finite systems. From the experimental point of view we will first recall the evidences for some strong modification of the behavior of hot nuclei. Then we will review quantitative detailed analysis aiming to evidence phase transition, to define its order and phase diagram. Finally, we will present a critical discussion of the present status of phase transitions in nuclei and we will draw some lines for future development of this field. (author)

  6. Entropy feature extraction on flow pattern of gas/liquid two-phase flow based on cross-section measurement

    International Nuclear Information System (INIS)

    Han, J; Dong, F; Xu, Y Y

    2009-01-01

    This paper introduces the fundamental of cross-section measurement system based on Electrical Resistance Tomography (ERT). The measured data of four flow regimes of the gas/liquid two-phase flow in horizontal pipe flow are obtained by an ERT system. For the measured data, five entropies are extracted to analyze the experimental data according to the different flow regimes, and the analysis method is examined and compared in three different perspectives. The results indicate that three different perspectives of entropy-based feature extraction are sensitive to the flow pattern transition in gas/liquid two-phase flow. By analyzing the results of three different perspectives with the changes of gas/liquid two-phase flow parameters, the dynamic structures of gas/liquid two-phase flow is obtained, and they also provide an efficient supplementary to reveal the flow pattern transition mechanism of gas/liquid two-phase flow. Comparison of the three different methods of feature extraction shows that the appropriate entropy should be used for the identification and prediction of flow regimes.

  7. Ultrafast protein structure-based virtual screening with Panther

    Science.gov (United States)

    Niinivehmas, Sanna P.; Salokas, Kari; Lätti, Sakari; Raunio, Hannu; Pentikäinen, Olli T.

    2015-10-01

    Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.

  8. Molecular simulation of excess isotherm and excess enthalpy change in gas-phase adsorption.

    Science.gov (United States)

    Do, D D; Do, H D; Nicholson, D

    2009-01-29

    We present a new approach to calculating excess isotherm and differential enthalpy of adsorption on surfaces or in confined spaces by the Monte Carlo molecular simulation method. The approach is very general and, most importantly, is unambiguous in its application to any configuration of solid structure (crystalline, graphite layer or disordered porous glass), to any type of fluid (simple or complex molecule), and to any operating conditions (subcritical or supercritical). The behavior of the adsorbed phase is studied using the partial molar energy of the simulation box. However, to characterize adsorption for comparison with experimental data, the isotherm is best described by the excess amount, and the enthalpy of adsorption is defined as the change in the total enthalpy of the simulation box with the change in the excess amount, keeping the total number (gas + adsorbed phases) constant. The excess quantities (capacity and energy) require a choice of a reference gaseous phase, which is defined as the adsorptive gas phase occupying the accessible volume and having a density equal to the bulk gas density. The accessible volume is defined as the mean volume space accessible to the center of mass of the adsorbate under consideration. With this choice, the excess isotherm passes through a maximum but always remains positive. This is in stark contrast to the literature where helium void volume is used (which is always greater than the accessible volume) and the resulting excess can be negative. Our definition of enthalpy change is equivalent to the difference between the partial molar enthalpy of the gas phase and the partial molar enthalpy of the adsorbed phase. There is no need to assume ideal gas or negligible molar volume of the adsorbed phase as is traditionally done in the literature. We illustrate this new approach with adsorption of argon, nitrogen, and carbon dioxide under subcritical and supercritical conditions.

  9. Structural and magnetic properties of FePt nanoparticles from the gas phase; Strukturelle und magnetische Eigenschaften von FePt-Nanopartikeln aus der Gasphase

    Energy Technology Data Exchange (ETDEWEB)

    Dmitrieva, O.

    2007-09-21

    In this work, we present the structural and magnetic characterization of FePt nanoparticles. The nanoparticles with mean size of about 6 nm were prepared by sputtering in the gas and subsequent inert gas condensation. The particles are annealed in the furnace during their flight prior to deposition on a substrate. The aim of this work is to prepare magnetically hard FePt nanoparticles in the L1{sub 0}-ordered phase. The structure of the particles was investigated by high-resolution transmission electron microscopy, and the investigations were supported by contrast simulations. The morphology of the particles varies with the sputter-gas pressure and with the annealing temperature. At a pressure of 0.5 mbar, the FePt-nanoparticles are multiply-twinned with an icosahedral structure and exhibit no formation of the L1{sub 0}-ordered phase. At a higher pressure of 1 mbar and an annealing temperature of 1000 C, the particles are partially single-crystalline. About 36 % of the particles are found to be in the L1{sub 0}-ordered state as was estimated by statistical counting supported by simulations. In order to activate the volume diffusion in the particles and to stabilize the formation of the L1{sub 0}-ordered state, the addition of nitrogen was used during the sputtering phase. In this phase, atomic nitrogen is incorporated interstitially into the structure of the primary particles. After annealing nitrogen effuses out of the particles and, thereby, increases the volume diffusion of the Fe and Pt atoms. The incorporation of nitrogen atoms during nucleation and their effusion at an annealing temperature of 1000 C was verified by electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS). Structural investigations on particles prepared in the presence of nitrogen shows that most of the particles are single-crystalline and about 70 % of them are L1{sub 0}-ordered. Detailed structural analysis of the nanoparticles was done by the exit wave

  10. Photoelectron spectroscopy an introduction to ultraviolet photoelectron spectroscopy in the gas phase

    CERN Document Server

    Eland, J H D

    2013-01-01

    Photoelectron Spectroscopy: An Introduction to Ultraviolet Photoelectronspectroscopy in the Gas Phase, Second Edition Photoelectron Spectroscopy: An Introduction to Ultraviolet PhotoelectronSpectroscopy in the Gas Phase, Second Edition aims to give practical approach on the subject of photoelectron spectroscopy, as well as provide knowledge on the interpretation of the photoelectron spectrum. The book covers topics such as the principles and literature of photoelectron microscopy; the main features and analysis of photoelectron spectra; ionization techniques; and energies from the photoelectron spectra. Also covered in the book are topics suc as photoelectron band structure and the applications of photoelectron spectroscopy in chemistry. The text is recommended for students and practitioners of chemistry who would like to be familiarized with the concepts of photoelectron spectroscopy and its importance in the field.

  11. Structure analysis of turbulent liquid phase by POD and LSE techniques

    International Nuclear Information System (INIS)

    Munir, S.; Muthuvalu, M. S.; Siddiqui, M. I.; Heikal, M. R.; Aziz, A. Rashid A.

    2014-01-01

    In this paper, vortical structures and turbulence characteristics of liquid phase in both single liquid phase and two-phase slug flow in pipes were studied. Two dimensional velocity vector fields of liquid phase were obtained by Particle image velocimetry (PIV). Two cases were considered one single phase liquid flow at 80 l/m and second slug flow by introducing gas at 60 l/m while keeping liquid flow rate same. Proper orthogonal decomposition (POD) and Linear stochastic estimation techniques were used for the extraction of coherent structures and analysis of turbulence in liquid phase for both cases. POD has successfully revealed large energy containing structures. The time dependent POD spatial mode coefficients oscillate with high frequency for high mode numbers. The energy distribution of spatial modes was also achieved. LSE has pointed out the coherent structured for both cases and the reconstructed velocity fields are in well agreement with the instantaneous velocity fields

  12. Structure analysis of turbulent liquid phase by POD and LSE techniques

    Energy Technology Data Exchange (ETDEWEB)

    Munir, S., E-mail: shahzad-munir@comsats.edu.pk; Muthuvalu, M. S.; Siddiqui, M. I. [Department of Fundamental and Applied Science, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia); Heikal, M. R., E-mail: morgan.heikal@petronas.com.my; Aziz, A. Rashid A., E-mail: morgan.heikal@petronas.com.my [Department of Mechanical Engineering, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia)

    2014-10-24

    In this paper, vortical structures and turbulence characteristics of liquid phase in both single liquid phase and two-phase slug flow in pipes were studied. Two dimensional velocity vector fields of liquid phase were obtained by Particle image velocimetry (PIV). Two cases were considered one single phase liquid flow at 80 l/m and second slug flow by introducing gas at 60 l/m while keeping liquid flow rate same. Proper orthogonal decomposition (POD) and Linear stochastic estimation techniques were used for the extraction of coherent structures and analysis of turbulence in liquid phase for both cases. POD has successfully revealed large energy containing structures. The time dependent POD spatial mode coefficients oscillate with high frequency for high mode numbers. The energy distribution of spatial modes was also achieved. LSE has pointed out the coherent structured for both cases and the reconstructed velocity fields are in well agreement with the instantaneous velocity fields.

  13. Protein Structure Prediction by Protein Threading

    Science.gov (United States)

    Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

    The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

  14. Energy Demodulation Algorithm for Flow Velocity Measurement of Oil-Gas-Water Three-Phase Flow

    Directory of Open Access Journals (Sweden)

    Yingwei Li

    2014-01-01

    Full Text Available Flow velocity measurement was an important research of oil-gas-water three-phase flow parameter measurements. In order to satisfy the increasing demands for flow detection technology, the paper presented a gas-liquid phase flow velocity measurement method which was based on energy demodulation algorithm combing with time delay estimation technology. First, a gas-liquid phase separation method of oil-gas-water three-phase flow based on energy demodulation algorithm and blind signal separation technology was proposed. The separation of oil-gas-water three-phase signals which were sampled by conductance sensor performed well, so the gas-phase signal and the liquid-phase signal were obtained. Second, we used the time delay estimation technology to get the delay time of gas-phase signals and liquid-phase signals, respectively, and the gas-phase velocity and the liquid-phase velocity were derived. At last, the experiment was performed at oil-gas-water three-phase flow loop, and the results indicated that the measurement errors met the need of velocity measurement. So it provided a feasible method for gas-liquid phase velocity measurement of the oil-gas-water three-phase flow.

  15. Visualization of velocity field and phase distribution in gas-liquid two-phase flow by NMR imaging

    International Nuclear Information System (INIS)

    Matsui, G.; Monji, H.; Obata, J.

    2004-01-01

    NMR imaging has been applied in the field of fluid mechanics, mainly single phase flow, to visualize the instantaneous flow velocity field. In the present study, NMR imaging was used to visualize simultaneously both the instantaneous phase structure and velocity field of gas-liquid two-phase flow. Two methods of NMR imaging were applied. One is useful to visualize both the one component of liquid velocity and the phase distribution. This method was applied to horizontal two-phase flow and a bubble rising in stagnant oil. It was successful in obtaining some pictures of velocity field and phase distribution on the cross section of the pipe. The other is used to visualize a two-dimensional velocity field. This method was applied to a bubble rising in a stagnant water. The velocity field was visualized after and before the passage of a bubble at the measuring cross section. Furthermore, the distribution of liquid velocity was obtained. (author)

  16. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    Science.gov (United States)

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-11-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

  17. Understanding Gas-Phase Ammonia Chemistry in Protoplanetary Disks

    Science.gov (United States)

    Chambers, Lauren; Oberg, Karin I.; Cleeves, Lauren Ilsedore

    2017-01-01

    Protoplanetary disks are dynamic regions of gas and dust around young stars, the remnants of star formation, that evolve and coagulate over millions of years in order to ultimately form planets. The chemical composition of protoplanetary disks is affected by both the chemical and physical conditions in which they develop, including the initial molecular abundances in the birth cloud, the spectrum and intensity of radiation from the host star and nearby systems, and mixing and turbulence within the disk. A more complete understanding of the chemical evolution of disks enables a more complete understanding of the chemical composition of planets that may form within them, and of their capability to support life. One element known to be essential for life on Earth is nitrogen, which often is present in the form of ammonia (NH3). Recent observations by Salinas et al. (2016) reveal a theoretical discrepancy in the gas-phase and ice-phase ammonia abundances in protoplanetary disks; while observations of comets and protostars estimate the ice-phase NH3/H2O ratio in disks to be 5%, Salinas reports a gas-phase NH3/H2O ratio of ~7-84% in the disk surrounding TW Hydra, a young nearby star. Through computational chemical modeling of the TW Hydra disk using a reaction network of over 5000 chemical reactions, I am investigating the possible sources of excess gas-phase NH3 by determining the primary reaction pathways of NH3 production; the downstream chemical effects of ionization by ultraviolet photons, X-rays, and cosmic rays; and the effects of altering the initial abundances of key molecules such as N and N2. Beyond providing a theoretical explanation for the NH3 ice/gas discrepancy, this new model may lead to fuller understanding of the gas-phase formation processes of all nitrogen hydrides (NHx), and thus fuller understanding of the nitrogen-bearing molecules that are fundamental for life as we know it.

  18. Analysis of volatile phase transport in soils using natural radon gas as a tracer

    International Nuclear Information System (INIS)

    Chen, C.; Thomas, D.M.

    1992-01-01

    We have conducted a field study of soil gas transport processes using radon gas as a naturally occurring tracer. The experiment monitored soil gas radon activity, soil moisture, and soil temperature at three depths in the shallow soil column; barometric pressure, rainfall and wind speed were monitored at the soil surface. Linear and multiple regression analysis of the data sets has shown that the gas phase radon activities under natural environmental conditions are influenced by soil moisture content, barometric pressure variations, soil temperature and soil structure. The effect of wind speed on subsurface radon activities under our field conditions has not been demonstrated

  19. Structural deformation upon protein-protein interaction: a structural alphabet approach.

    Science.gov (United States)

    Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

    2008-02-28

    In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

  20. Structural deformation upon protein-protein interaction: A structural alphabet approach

    Directory of Open Access Journals (Sweden)

    Lecornet Hélène

    2008-02-01

    Full Text Available Abstract Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%. This proportion is even greater in the interface regions (41%. Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

  1. Gas-Phase Thermolysis

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge; Schaumann, Ernst

    1980-01-01

    The unimolecular gas-phase thermolytic decomposition of three silylated thionocarboxylic acid derivatives (2b), (3), and (8) have been studied by the flash vacuum thermolysis–field ionization mass spectrometry technique in the temperature range from 783 to 1 404 K in order to elucidate its possible...... applicability as a route to thioketens. Only very minor amounts of the expected thioketens were found, whereas the corresponding ketens were obtained as the major products. A possible mechanism for keten formation is discussed....

  2. Tuning Catalytic Performance through a Single or Sequential Post-Synthesis Reaction(s) in a Gas Phase

    Energy Technology Data Exchange (ETDEWEB)

    Shan, Junjun [Department; Department; Zhang, Shiran [Department; Department; Choksi, Tej [Department; Nguyen, Luan [Department; Department; Bonifacio, Cecile S. [Department; Li, Yuanyuan [Department; Zhu, Wei [Department; Department; College; Tang, Yu [Department; Department; Zhang, Yawen [College; Yang, Judith C. [Department; Greeley, Jeffrey [Department; Frenkel, Anatoly I. [Department; Tao, Franklin [Department; Department

    2016-12-05

    Catalytic performance of a bimetallic catalyst is determined by geometric structure and electronic state of the surface or even the near-surface region of the catalyst. Here we report that single and sequential postsynthesis reactions of an as-synthesized bimetallic nanoparticle catalyst in one or more gas phases can tailor surface chemistry and structure of the catalyst in a gas phase, by which catalytic performance of this bimetallic catalyst can be tuned. Pt–Cu regular nanocube (Pt–Cu RNC) and concave nanocube (Pt–Cu CNC) are chosen as models of bimetallic catalysts. Surface chemistry and catalyst structure under different reaction conditions and during catalysis were explored in gas phase of one or two reactants with ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The newly formed surface structures of Pt–Cu RNC and Pt–Cu CNC catalysts strongly depend on the reactive gas(es) used in the postsynthesis reaction(s). A reaction of Pt–Cu RNC-as synthesized with H2 at 200 °C generates a near-surface alloy consisting of a Pt skin layer, a Cu-rich subsurface, and a Pt-rich deep layer. This near-surface alloy of Pt–Cu RNC-as synthesized-H2 exhibits a much higher catalytic activity in CO oxidation in terms of a low activation barrier of 39 ± 4 kJ/mol in contrast to 128 ± 7 kJ/mol of Pt–Cu RNC-as synthesized. Here the significant decrease of activation barrier demonstrates a method to tune catalytic performances of as-synthesized bimetallic catalysts. A further reaction of Pt–Cu RNC-as synthesized-H2 with CO forms a Pt–Cu alloy surface, which exhibits quite different catalytic performance in CO oxidation. It suggests the capability of generating a different surface by using another gas. The capability of tuning surface chemistry and structure of bimetallic catalysts was also demonstrated in restructuring of Pt–Cu CNC-as synthesized.

  3. Analytical study of solids-gas two phase flow

    International Nuclear Information System (INIS)

    Hosaka, Minoru

    1977-01-01

    Fundamental studies were made on the hydrodynamics of solids-gas two-phase suspension flow, in which very small solid particles are mixed in a gas flow to enhance the heat transfer characteristics of gas cooled high temperature reactors. Especially, the pressure drop due to friction and the density distribution of solid particles are theoretically analyzed. The friction pressure drop of two-phase flow was analyzed based on the analytical result of the single-phase friction pressure drop. The calculated values of solid/gas friction factor as a function of solid/gas mass loading are compared with experimental results. Comparisons are made for Various combinations of Reynolds number and particle size. As for the particle density distribution, some factors affecting the non-uniformity of distribution were considered. The minimum of energy dispersion was obtained with the variational principle. The suspension density of particles was obtained as a function of relative distance from wall and was compared with experimental results. It is concluded that the distribution is much affected by the particle size and that the smaller particles are apt to gather near the wall. (Aoki, K.)

  4. Improved machine learning method for analysis of gas phase chemistry of peptides

    Directory of Open Access Journals (Sweden)

    Ahn Natalie

    2008-12-01

    Full Text Available Abstract Background Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS of peptides from complex digests with theoretically derived spectra from a database of protein sequences. Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra. Results We employed a robust data mining strategy using new feature annotation functions of MAE software, which revealed under-prediction of the frequency of occurrence in fragmentation of the second peptide bond. We applied methods of exploratory data analysis to pre-process the information in the MS/MS spectra, including data normalization and attribute selection, to reduce the attributes to a smaller, less correlated set for machine learning studies. We then compared our rule building machine learning program, DataSqueezer, with commonly used association rules and decision tree algorithms. All used machine learning algorithms produced similar results that were consistent with expected properties for a second gas phase mechanism at the second peptide bond. Conclusion The results provide compelling evidence that we have identified underlying chemical properties in the data that suggest the existence of an additional gas phase mechanism for the second peptide bond. Thus, the methods described in this study provide a valuable approach for analyses of this kind in the future.

  5. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.

    Science.gov (United States)

    Bravaya, Ksenia; Bochenkova, Anastasia; Granovsky, Alexander; Nemukhin, Alexander

    2007-10-31

    We considered a series of model systems for treating the photoabsorption of the 11-cis retinal chromophore in the protonated Schiff-base form in vacuum, solutions, and the protein environment. A high computational level, including the quantum mechanical-molecular mechanical (QM/MM) approach for solution and protein was utilized in simulations. The S0-S1 excitation energies in quantum subsystems were evaluated by means of an augmented version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) with the ground-state geometry parameters optimized in the density functional theory PBE0/cc-pVDZ approximation. The computed positions of absorption bands lambdamax, 599(g), 448(s), and 515(p) nm for the gas phase, solution, and protein, respectively, are in excellent agreement with the corresponding experimental data, 610(g), 445(s), and 500(p) nm. Such consistency provides a support for the formulated qualitative conclusions on the role of the chromophore geometry, environmental electrostatic field, and the counterion in different media. An essentially nonplanar geometry conformation of the chromophore group in the region of the C14-C15 bond was obtained for the protein, in particular, owing to the presence of the neighboring charged amino acid residue Glu181. Nonplanarity of the C14-C15 bond region along with the influence of the negatively charged counterions Glu181 and Glu113 are found to be important to reproduce the spectroscopic features of retinal chromophore inside the Rh cavity. Furthermore, the protein field is responsible for the largest bond-order decrease at the C11-C12 double bond upon excitation, which may be the reason for the 11-cis photoisomerization specificity.

  6. Gas Phase Chromatography of some Group 4, 5, and 6 Halides

    Energy Technology Data Exchange (ETDEWEB)

    Sylwester, Eric Robert [Univ. of California, Berkeley, CA (United States)

    1998-10-01

    Gas phase chromatography using The Heavy Element Volatility Instrument (HEVI) and the On Line Gas Apparatus (OLGA III) was used to determine volatilities of ZrBr4, HfBr4, RfBr4, NbBr5, TaOBr3, HaCl5, WBr6, FrBr, and BiBr3. Short-lived isotopes of Zr, Hf, Rf, Nb, Ta, Ha, W, and Bi were produced via compound nucleus reactions at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and transported to the experimental apparatus using a He gas transport system. The isotopes were halogenated, separated from the other reaction products, and their volatilities determined by isothermal gas phase chromatography. Adsorption Enthalpy (ΔHa) values for these compounds were calculated using a Monte Carlo simulation program modeling the gas phase chromatography column. All bromides showed lower volatility than molecules of similar molecular structures formed as chlorides, but followed similar trends by central element. Tantalum was observed to form the oxybromide, analogous to the formation of the oxychloride under the same conditions. For the group 4 elements, the following order in volatility and ΔHa was observed: RfBr4 > ZrBr4 > HfBr4. The ΔHa values determined for the group 4, 5, and 6 halides are in general agreement with other experimental data and theoretical predictions. Preliminary experiments were performed on Me-bromides. A new measurement of the half-life of 261Rf was performed. 261Rf was produced via the 248Cm(18O, 5n) reaction and observed with a half-life of 74-6+7 seconds, in excellent agreement with the previous measurement of 78-6+11 seconds. We recommend a new half-life of 75±7 seconds for 261Rf based on these two measurements. Preliminary studies in transforming HEVI from an isothermal (constant

  7. Gas phase pulse radiolysis

    International Nuclear Information System (INIS)

    Jonah, C.D.; Andong Liu; Mulac, W.A.

    1987-01-01

    Gas phase pulse radiolysis, a technique which can be used to study many different phenomena in chemistry and physics, is discussed. As a source of small radicals, pulse radiolysis is important to the field of chemistry, particularly to combustion and atmospheric kinetics. The reactions of 1,3-butadiene, allene, ethylene and acetylene with OH are presented. 52 refs., 1 fig., 1 tab

  8. Laser spectroscopy and gas-phase chemistry in CVD

    International Nuclear Information System (INIS)

    Ho, P.; Breiland, W.G.; Coltrin, M.E.

    1986-01-01

    The experimental work involves the use of laser spectroscopic techniques for in situ measurements on the gas phase in a chemical vapor deposition reactor. The theoretical part of the program consists of a computer model of the coupled fluid mechanics and gas-phase chemical kinetics of silane decomposition and subsequent reactions of intermediate species. The laser measurements provide extensive data for thoroughly testing the predictive capabilities of the model

  9. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

    Science.gov (United States)

    2014-01-01

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

  10. Ionic liquid stationary phases for gas chromatography.

    Science.gov (United States)

    Poole, Colin F; Poole, Salwa K

    2011-04-01

    This article provides a summary of the development of ionic liquids as stationary phases for gas chromatography beginning with early work on packed columns that established details of the retention mechanism and established working methods to characterize selectivity differences compared with molecular stationary phases through the modern development of multi-centered cation and cross-linked ionic liquids for high-temperature applications in capillary gas chromatography. Since there are many reviews on ionic liquids dealing with all aspects of their chemical and physical properties, the emphasis in this article is placed on the role of gas chromatography played in the design of ionic liquids of low melting point, high thermal stability, high viscosity, and variable selectivity for separations. Ionic liquids provide unprecedented opportunities for extending the selectivity range and temperature-operating range of columns for gas chromatography, an area of separation science that has otherwise been almost stagnant for over a decade. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Monoolein lipid phases as incorporation and enrichment materials for membrane protein crystallization.

    Directory of Open Access Journals (Sweden)

    Ellen Wallace

    Full Text Available The crystallization of membrane proteins in amphiphile-rich materials such as lipidic cubic phases is an established methodology in many structural biology laboratories. The standard procedure employed with this methodology requires the generation of a highly viscous lipidic material by mixing lipid, for instance monoolein, with a solution of the detergent solubilized membrane protein. This preparation is often carried out with specialized mixing tools that allow handling of the highly viscous materials while minimizing dead volume to save precious membrane protein sample. The processes that occur during the initial mixing of the lipid with the membrane protein are not well understood. Here we show that the formation of the lipidic phases and the incorporation of the membrane protein into such materials can be separated experimentally. Specifically, we have investigated the effect of different initial monoolein-based lipid phase states on the crystallization behavior of the colored photosynthetic reaction center from Rhodobacter sphaeroides. We find that the detergent solubilized photosynthetic reaction center spontaneously inserts into and concentrates in the lipid matrix without any mixing, and that the initial lipid material phase state is irrelevant for productive crystallization. A substantial in-situ enrichment of the membrane protein to concentration levels that are otherwise unobtainable occurs in a thin layer on the surface of the lipidic material. These results have important practical applications and hence we suggest a simplified protocol for membrane protein crystallization within amphiphile rich materials, eliminating any specialized mixing tools to prepare crystallization experiments within lipidic cubic phases. Furthermore, by virtue of sampling a membrane protein concentration gradient within a single crystallization experiment, this crystallization technique is more robust and increases the efficiency of identifying productive

  12. Acute-phase proteins: As diagnostic tool

    Directory of Open Access Journals (Sweden)

    Sachin Jain

    2011-01-01

    Full Text Available The varied reactions of the host to infection, inflammation, or trauma are collectively known as the acute-phase response and encompass a wide range of pathophysiological responses such as pyrexia, leukocytosis, hormone alterations, and muscle protein depletion combining to minimize tissue damage while enhancing the repair process. The mechanism for stimulation of hepatic production of acute-phase proteins is by proinflammatory cytokines. The functions of positive acute-phase proteins (APP are regarded as important in optimization and trapping of microorganism and their products, in activating the complement system, in binding cellular remnants like nuclear fractions, in neutralizing enzymes, scavenging free hemoglobin and radicals, and in modulating the host′s immune response. APP can be used as diagnostic tool in many diseases like bovine respiratory syncytial virus, prostate cancer, bronchopneumonia, multiple myeloma, mastitis, Streptococcus suis infection, starvation, or lymphatic neoplasia. Thus, acute-phase proteins may provide an alternative means of monitoring animal health.

  13. Effect of biochar on soil structural characteristics: water retention and gas transport

    DEFF Research Database (Denmark)

    Sun, Zhencai; Møldrup, Per; Vendelboe, Anders Lindblad

    Biochar addition to agricultural soil has been reported to reduce climate gas emission, as well as improve soil fertility and crop productivity. Little, however, is known about biochar effects on soil structural characteristics. This study investigates if biochar-application changes soil structural...... characteristics, as indicated from water retention and gas transport measurements on intact soil samples. Soil was sampled from a field experiment on a sandy loam with four control plots (C) without biochar and four plots (B) with incorporated biochar at a rate of 20 tons per hectare (plot size, 6 x 8 m). The C......-gas diffusivity on intact 100cm3 soil samples (5 replicates in each plot). We found that biochar application significantly decreased soil bulk density, hereby creating higher porosity. At the same soil-water matric potential, all the soil-gas phase parameters (air-filled porosity, air permeability and gas...

  14. Identification of dominant structures and their flow dynamics in the turbulent two-phase flow using POD technique

    Energy Technology Data Exchange (ETDEWEB)

    Munir, Shahzad; Siddiqui, Muhammad Israr; Heikal, Morgan; Aziz, Abdul Rashid Abdul [Universiti Teknologi PETRONAS, Bander Seri Iskandar (Malaysia); Sercey, Guillaume de [University of Brighton, Brighton (United Kingdom)

    2015-11-15

    The Proper orthogonal decomposition (POD) method has seen increasingly used in the last two decades and has a lot of applications for the comparison of experimental and numerically simulated data. The POD technique is often used to extract information about coherent structures dominating the flow. The two-dimensional and two-component instantaneous velocity fields of both liquid and gas phases of a slug flow were obtained by Particle image velocimetry (PIV) combined with Laser induced fluorescence (LIF). POD was applied to the velocity fields of both phases separately to identify the coherent flow structures. We focused on POD eigenmodes and their corresponding energy contents of both liquid and gas phases. The sum of first few eigenmodes that contain maximum turbulent kinetic energy of the flow represents the coherent structures. In the case of liquid phase the first eigenmode contained 42% of the total energy, while in the gas phase the decaying energy distribution was flat. The POD results showed that the coefficient of mode 1 for the liquid phase oscillated between positive and negative values and had the highest amplitude. For the visualization of coherent motion different linear combinations of eigenmodes for liquid and gas phases were used. The phenomena of turbulent bursting events associated with Q2 events (low momentum fluid moving away from the wall) and Q4 events (high momentum flow moving towards the wall) were also discussed to assess its contribution in turbulence production.

  15. Multiphase flow and transport caused by spontaneous gas phase growth in the presence of dense non-aqueous phase liquid.

    Science.gov (United States)

    Roy, James W; Smith, James E

    2007-01-30

    Disconnected bubbles or ganglia of trapped gas may occur below the top of the capillary fringe through a number of mechanisms. In the presence of dense non-aqueous phase liquid (DNAPL), the disconnected gas phase experiences mass transfer of dissolved gases, including volatile components from the DNAPL. The properties of the gas phase interface can also change. This work shows for the first time that when seed gas bubbles exist spontaneous gas phase growth can be expected to occur and can significantly affect water-gas-DNAPL distributions, fluid flow, and mass transfer. Source zone behaviour was observed in three different experiments performed in a 2-dimensional flow cell. In each case, a DNAPL pool was created in a zone of larger glass beads over smaller glass beads, which served as a capillary barrier. In one experiment effluent water samples were analyzed to determine the vertical concentration profile of the plume above the pool. The experiments effectively demonstrated a) a cycle of spontaneous gas phase expansion and vertical advective mobilization of gas bubbles and ganglia above the DNAPL source zone, b) DNAPL redistribution caused by gas phase growth and mobilization, and c) that these processes can significantly affect mass transport from a NAPL source zone.

  16. Gas-phase synthesis and structure of monomeric ZnOH: a model species for metalloenzymes and catalytic surfaces.

    Science.gov (United States)

    Zack, Lindsay N; Sun, Ming; Bucchino, Matthew P; Clouthier, Dennis J; Ziurys, Lucy M

    2012-02-16

    Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems.

  17. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    International Nuclear Information System (INIS)

    Jorge, Nelly Lidia; Romero, Jorge Marcelo; Grand, André; Hernández-Laguna, Alfonso

    2012-01-01

    Highlights: ► Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. ► Gas chromatography and computational potential energy surfaces were performed. ► A mechanism in steps looked like the most probable mechanism. ► A spin–orbit coupling appeared at the singlet and triple diradical open structures. ► A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463–503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 ± 0.8 kcal/mol and 5.2 × 10 13 s −1 , respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G ∗∗ level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin–orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  18. Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

    Science.gov (United States)

    Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

    2018-02-01

    Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

  19. A probabilistic fragment-based protein structure prediction algorithm.

    Directory of Open Access Journals (Sweden)

    David Simoncini

    Full Text Available Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].

  20. Wigner Distribution Functions as a Tool for Studying Gas Phase Alkali Metal Plus Noble Gas Collisions

    Science.gov (United States)

    2014-03-27

    WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR STUDYING GAS PHASE ALKALI METAL PLUS NOBLE GAS COLLISIONS THESIS Keith A. Wyman, Second Lieutenant, USAF...the U.S. Government and is not subject to copyright protection in the United States. AFIT-ENP-14-M-39 WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR...APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED AFIT-ENP-14-M-39 WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR STUDYING GAS PHASE ALKALI METAL PLUS

  1. The Genealogical Tree of Ethanol: Gas-phase Formation of Glycolaldehyde, Acetic Acid, and Formic Acid

    Science.gov (United States)

    Skouteris, Dimitrios; Balucani, Nadia; Ceccarelli, Cecilia; Vazart, Fanny; Puzzarini, Cristina; Barone, Vincenzo; Codella, Claudio; Lefloch, Bertrand

    2018-02-01

    Despite the harsh conditions of the interstellar medium, chemistry thrives in it, especially in star-forming regions where several interstellar complex organic molecules (iCOMs) have been detected. Yet, how these species are synthesized is a mystery. The majority of current models claim that this happens on interstellar grain surfaces. Nevertheless, evidence is mounting that neutral gas-phase chemistry plays an important role. In this paper, we propose a new scheme for the gas-phase synthesis of glycolaldehyde, a species with a prebiotic potential and for which no gas-phase formation route was previously known. In the proposed scheme, the ancestor is ethanol and the glycolaldehyde sister species are acetic acid (another iCOM with unknown gas-phase formation routes) and formic acid. For the reactions of the new scheme with no available data, we have performed electronic structure and kinetics calculations deriving rate coefficients and branching ratios. Furthermore, after a careful review of the chemistry literature, we revised the available chemical networks, adding and correcting several reactions related to glycolaldehyde, acetic acid, and formic acid. The new chemical network has been used in an astrochemical model to predict the abundance of glycolaldehyde, acetic acid, and formic acid. The predicted abundance of glycolaldehyde depends on the ethanol abundance in the gas phase and is in excellent agreement with the measured one in hot corinos and shock sites. Our new model overpredicts the abundance of acetic acid and formic acid by about a factor of 10, which might imply a yet incomplete reaction network.

  2. Gas-phase water-mediated equilibrium between methylglyoxal and its geminal diol

    Science.gov (United States)

    Axson, Jessica L.; Takahashi, Kaito; De Haan, David O.; Vaida, Veronica

    2010-01-01

    In aqueous solution, aldehydes, and to a lesser extent ketones, hydrate to form geminal diols. We investigate the hydration of methylglyoxal (MG) in the gas phase, a process not previously considered to occur in water-restricted environments. In this study, we spectroscopically identified methylglyoxal diol (MGD) and obtained the gas-phase partial pressures of MG and MGD. These results, in conjunction with the relative humidity, were used to obtain the equilibrium constant, KP, for the water-mediated hydration of MG in the gas phase. The Gibbs free energy for this process, ΔG°, obtained as a result, suggests a larger than expected gas-phase diol concentration. This may have significant implications for understanding the role of organics in atmospheric chemistry. PMID:20142510

  3. Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

    Directory of Open Access Journals (Sweden)

    Srinivasan Narayanaswamy

    2010-06-01

    Full Text Available Abstract Background Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. Results In the present analysis, starting from Cα positions of low resolution cryo electron microscopic structures the residue level details of protein-protein interaction interfaces of dengue virus coat proteins have been predicted. By comparing the preexisting structures of virus in different phases of life cycle, the changes taking place in these predicted protein-protein interaction interfaces were followed as a function of maturation process of the virus. Besides changing the current notion about the presence of only homodimers in the mature viral coat, the present analysis indicated presence of a proline-rich motif at the protein-protein interaction interface of the coat protein. Investigating the conservation status of these seemingly functionally crucial residues across other members of flaviviridae family enabled dissecting common mechanisms used for infections by these viruses. Conclusions Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens.

  4. Nanoparticles from the Gas Phase as Building Blocks for Electrical Devices

    International Nuclear Information System (INIS)

    Fissan, H.; Kennedy, M.K.; Krinke, T.J.; Kruis, F.E.

    2003-01-01

    Electrical device development is driven by miniaturization and possibilities to use new chemical and physical effects. Nanotechnology offers both aspects. The structural dimensions of materials and devices are small and because of that large exchange surfaces are provided but also effects like quantum effects may occur and be used to get new or at least improved properties of nanostructured materials and devices.Nanoparticles are of special interest because of their nanodimensions in all three directions, so that nanoeffects become most prominent. They can be synthesized in solid materials, in liquids and in gases. Gas synthesis has several advantages compared to the other phases, especially the high cleanliness which can be achieved. In case of electrical devices the particles have to be deposited onto substrates in a structured way.The substrate may consist out of microelectronic devices in which the deposited nanoparticles are introduced for the basic function. In case of a transistor this would be the gate function, in case of a sensor this would be the sensing layer, where the contact with the measurement object takes place. For two kinds of particles SnO 2 and PbS, synthesized in the gas phase, we demonstrate the way how to create devices with improved sensor properties

  5. Gas-liquid two-phase flows in double inlet cyclones for natural gas separation

    DEFF Research Database (Denmark)

    Yang, Yan; Wang, Shuli; Wen, Chuang

    2017-01-01

    The gas-liquid two-phase flow within a double inlet cyclone for natural gasseparation was numerically simulated using the discrete phase model. The numericalapproach was validated with the experimental data, and the comparison resultsagreed well with each other. The simulation results showed...... that the strong swirlingflow produced a high centrifugal force to remove the particles from the gas mixture.The larger particles moved downward on the internal surface and were removeddue to the outer vortex near the wall. Most of the tiny particles went into the innervortex zones and escaped from the up...

  6. SILP catalysis in gas-phase hydroformylation and carbonylation

    Energy Technology Data Exchange (ETDEWEB)

    Riisager, A.; Fehrmann, R. [Technical Univ. of Denmark, Lyngby (Denmark). Dept. of Chemistry; Haumann, M.; Wasserscheid, P. [Univ. Erlangen-Nuernberg (Germany). Lehrstuhl fuer Chemische Reaktionstechnik

    2006-07-01

    Supported ionic liquid phase (SILP) catalysts are new materials consisting of an ionic liquid-metal catalyst solution highly dispersed on a porous support. The use of a non-volatile, ionic liquid catalyst phase in SILP catalysts results in a stable heterogeneous-type material with selectivity and efficiency like homogeneous catalysts. The silica-supported SILP Rh-bisphosphine hydroformylation catalyst exhibited good activities and excellent selectivities in gas phase hydroformylation with stability exceeding 700 hours time-on-stream. Spectroscopic and kinetic data confirmed the homogeneous nature of the catalyst. In the Rh- SILP catalysed carbonylation of methanol the formation of undesired by-products could be suppressed by variation of residence time and gas pressure. (orig.)

  7. Comparison of catalytic ethylene polymerization in slurry and gas phase

    NARCIS (Netherlands)

    Daftaribesheli, Majid

    2009-01-01

    Polyethylene (PE) with the annual consumption of 70 million tones in 2007 is mostly produced in slurry, gas-phase or combination of both processes. This work focuses on a comparison between the slurry and gas phase processes. Why does PE produced in theses two processes can show extremely different

  8. Gas holdup in a reciprocating plate bioreactor: Non-Newtonian - liquid phase

    Directory of Open Access Journals (Sweden)

    Naseva Olivera S.

    2002-01-01

    Full Text Available The gas holdup was studied in non-newtonian liquids in a gas-liquid and gas-liquid-solid reciprocating plate bioreactor. Aqueous solutions of carboxy methyl cellulose (CMC; Lucel, Lučane, Yugoslavia of different degrees of polymerization (PP 200 and PP 1000 and concentration (0,5 and 1%, polypropylene spheres (diameter 8.3 mm; fraction of spheres: 3.8 and 6.6% by volume and air were used as the liquid, solid and gas phase. The gas holdup was found to be dependent on the vibration rate, the superficial gas velocity, volume fraction of solid particles and Theological properties of the liquid ohase. Both in the gas-liquid and gas-liquid-solid systems studied, the gas holdup increased with increasing vibration rate and gas flow rate. The gas holdup was higher in three-phase systems than in two-phase ones under otter operating conditions being the same. Generally the gas holdup increased with increasing the volume fraction of solid particles, due to the dispersion action of the solid particles, and decreased with increasing non-Newtonian behaviour (decreasing flow index i.e. with increasing degree of polymerization and solution concentration of CMC applied, as a result of gas bubble coalescence.

  9. The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

    Science.gov (United States)

    Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

    2018-03-01

    The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

  10. Experimental station for gas phase fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Stankiewicz, M.; Garcia, E. Melero; Ruiz, J. Alvarez; Erman, P.; Hatherly, P.A.; Kivimaeki, A.; Rachlew, E.; Rius i Riu, J.

    2004-01-01

    The details of an experimental setup for gas phase atomic and molecular fluorescence measurements using synchrotron radiation are described in this article. The most significant part of the apparatus is an optical arrangement, which allows for simultaneous measurements of dispersed as well as total fluorescence intensity using an effusive gas jet and an inbuilt gas cell assembled in a convenient plug and measure configuration. The first measurements concerning fluorescence of the N 2 molecule around the N 1s edge obtained with this setup are presented

  11. Post-flame gas-phase sulfation of potassium chloride

    DEFF Research Database (Denmark)

    Li, Bo; Sun, Zhiwei; Li, Zhongshan

    2013-01-01

    The sulfation of KCl during biomass combustion has implications for operation and emissions: it reduces the rates of deposition and corrosion, it increases the formation of aerosols, and it leads to higher concentrations of HCl and lower concentrations of SO2 in the gas phase. Rigorously homogene......The sulfation of KCl during biomass combustion has implications for operation and emissions: it reduces the rates of deposition and corrosion, it increases the formation of aerosols, and it leads to higher concentrations of HCl and lower concentrations of SO2 in the gas phase. Rigorously...

  12. Nonlinear analysis of gas-water/oil-water two-phase flow in complex networks

    CERN Document Server

    Gao, Zhong-Ke; Wang, Wen-Xu

    2014-01-01

    Understanding the dynamics of multi-phase flows has been a challenge in the fields of nonlinear dynamics and fluid mechanics. This chapter reviews our work on two-phase flow dynamics in combination with complex network theory. We systematically carried out gas-water/oil-water two-phase flow experiments for measuring the time series of flow signals which is studied in terms of the mapping from time series to complex networks. Three network mapping methods were proposed for the analysis and identification of flow patterns, i.e. Flow Pattern Complex Network (FPCN), Fluid Dynamic Complex Network (FDCN) and Fluid Structure Complex Network (FSCN). Through detecting the community structure of FPCN based on K-means clustering, distinct flow patterns can be successfully distinguished and identified. A number of FDCN’s under different flow conditions were constructed in order to reveal the dynamical characteristics of two-phase flows. The FDCNs exhibit universal power-law degree distributions. The power-law exponent ...

  13. Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

    Science.gov (United States)

    Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

    2012-12-01

    Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

  14. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Jorge, Nelly Lidia [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain); Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Romero, Jorge Marcelo [Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Grand, Andre [INAC, SCIB, Laboratoire ' Lesions des Acides Nucleiques' , UMR CEA-UJF E3, CEA-Grenoble, 17 Rue des Martyrs, 38054 Grenoble cedex 9 (France); Hernandez-Laguna, Alfonso, E-mail: ahlaguna@ugr.es [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain)

    2012-01-17

    Highlights: Black-Right-Pointing-Pointer Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. Black-Right-Pointing-Pointer Gas chromatography and computational potential energy surfaces were performed. Black-Right-Pointing-Pointer A mechanism in steps looked like the most probable mechanism. Black-Right-Pointing-Pointer A spin-orbit coupling appeared at the singlet and triple diradical open structures. Black-Right-Pointing-Pointer A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463-503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 {+-} 0.8 kcal/mol and 5.2 Multiplication-Sign 10{sup 13} s{sup -1}, respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G{sup Asterisk-Operator Asterisk-Operator} level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin-orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  15. [Study of the phase transformation of TiO2 with in-situ XRD in different gas].

    Science.gov (United States)

    Ma, Li-Jing; Guo, Lie-Jin

    2011-04-01

    TiO2 sample was prepared by sol-gel method from chloride titanium. The phase transformation of the prepared TiO2 sample was studied by in-situ XRD and normal XRD in different gas. The experimental results showed that the phase transformation temperatures of TiO2 were different under in-situ or normal XRD in different kinds of gas. The transformation of amorphous TiO2 to anatase was controlled by kinetics before 500 degrees C. In-situ XRD showed that the growth of anatase was inhibited, but the transformation of anatase to rutile was accelerated under inactive nitrogen in contrast to air. Also better crystal was obtained under hydrogen than in argon. These all showed that external oxygen might accelerate the growth of TiO2, but reduced gas might partly counteract the negative influence of lack of external oxygen. The mechanism of phase transformation of TiO2 was studied by in-situ XRD in order to control the structure in situ.

  16. Application of structured illumination to gas phase thermometry using thermographic phosphor particles: a study for averaged imaging

    Science.gov (United States)

    Zentgraf, Florian; Stephan, Michael; Berrocal, Edouard; Albert, Barbara; Böhm, Benjamin; Dreizler, Andreas

    2017-07-01

    Structured laser illumination planar imaging (SLIPI) is combined with gas phase thermometry measurements using thermographic phosphor (TGP) particles. The technique is applied to a heated jet surrounded by a coflow which is operated at ambient temperature. The respective air flows are seeded with a powder of BaMgAl10O17:Eu2+ (BAM) which is used as temperature-sensitive gas phase tracer. Upon pulsed excitation in the ultraviolet spectral range, the temperature is extracted based on the two-color ratio method combined with SLIPI. The main advantage of applying the SLIPI approach to phosphor thermometry is the reduction of particle-to-particle multiple light scattering and diffuse wall reflections, yielding a more robust calibration procedure as well as improving the measurement accuracy, precision, and sensitivity. For demonstration, this paper focuses on sample-averaged measurements of temperature fields in a jet-in-coflow configuration. Using the conventional approach, which in contrast to SLIPI is based on imaging with an unmodulated laser light sheet, we show that for the present setup typically 40% of the recorded signal is affected by the contribution of multiply scattered photons. At locations close to walls even up to 75% of the apparent signal is due to diffuse reflection and wall luminescence of BAM sticking at the surface. Those contributions lead to erroneous temperature fields. Using SLIPI, an unbiased two-color ratio field is recovered allowing for two-dimensional mean temperature reconstructions which exhibit a more realistic physical behavior. This is in contrast to results deduced by the conventional approach. Furthermore, using the SLIPI approach it is shown that the temperature sensitivity is enhanced by a factor of up to 2 at 270 °C. Finally, an outlook towards instantaneous SLIPI phosphorescence thermometry is provided.

  17. C-terminal peptide extension via gas-phase ion/ion reactions

    Science.gov (United States)

    Peng, Zhou; McLuckey, Scott A.

    2015-01-01

    The formation of peptide bonds is of great importance from both a biological standpoint and in routine organic synthesis. Recent work from our group demonstrated the synthesis of peptides in the gas-phase via ion/ion reactions with sulfo-NHS reagents, which resulted in conjugation of individual amino acids or small peptides to the N-terminus of an existing ‘anchor’ peptide. Here, we demonstrate a complementary approach resulting in the C-terminal extension of peptides. Individual amino acids or short peptides can be prepared as reagents by incorporating gas phase-labile protecting groups to the reactive C-terminus and then converting the N-terminal amino groups to the active ketenimine reagent. Gas-phase ion/ion reactions between the anionic reagents and doubly protonated “anchor” peptide cations results in extension of the “anchor” peptide with new amide bond formation at the C-terminus. We have demonstrated that ion/ion reactions can be used as a fast, controlled, and efficient means for C-terminal peptide extension in the gas phase. PMID:26640400

  18. Device to remove hydrogen isotopes from a gas phase

    International Nuclear Information System (INIS)

    Morlock, G.; Wiesemes, J.; Bachner, D.

    1977-01-01

    The device described here guarantees the selective removal of hydrogen isotopes from gas phases in order to prevent the occurence of explosive H 2 gas mixtures, or to separate off radioactive tritium in nuclear plants from the gas phase. It consists of a closed container whose walls are selectively penetrable by hydrogen isotopes. It is simultaneously filled compactly and presssure-resistant with a metal bulk (e.g. powder, sponges or the like of titanium or other hydrogen isotope binding metal). Walling and bulk are maintained at suitable working temperatures by means of a system according to the Peltier effect. The whole thing is safeguarded by protective walling. (RB) [de

  19. Exceptionally High Proton and Lithium Cation Gas-Phase Basicity of the Anti-Diabetic Drug Metformin.

    Science.gov (United States)

    Raczyńska, Ewa D; Gal, Jean-François; Maria, Pierre-Charles; Michalec, Piotr; Zalewski, Marcin

    2017-11-16

    Substituted biguanides are known for their biological effect, and a few of them are used as drugs, the most prominent example being metformin (1,1-dimethylbiguanide, IUPAC name: N,N-dimethylimidodicarbonimidic diamide). Because of the presence of hydrogen atoms at the amino groups, biguanides exhibit a multiple tautomerism. This aspect of their structures was examined in detail for unsubstituted biguanide and metformin in the gas phase. At the density functional theory (DFT) level {essentially B3LYP/6-311+G(d,p)}, the most stable structures correspond to the conjugated, push-pull, system (NR 2 )(NH 2 )C═N-C(═NH)NH 2 (R = H, CH 3 ), further stabilized by an internal hydrogen bond. The structural and energetic aspects of protonation and lithium cation adduct formation of biguanide and metformin was examined at the same level of theory. The gas-phase protonation energetics reveal that the more stable tautomer is protonated at the terminal imino C═NH site, still with an internal hydrogen bond maintaining the structure of the neutral system. The calculated proton affinity and gas-phase basicity of the two molecules reach the domain of superbasicity. By contrast, the lithium cation prefers to bind the less stable, not fully conjugated, tautomer (NR 2 )C(═NH)-NH-C(═NH)NH 2 of biguanides, in which the two C═NH groups are separated by NH. This less stable form of biguanides binds Li + as a bidentate ligand, in agreement with what was reported in the literature for other metal cations in the solid phase. The quantitative assessment of resonance in biguanide, in metformin and in their protonated forms, using the HOMED and HOMA indices, reveals an increase in electron delocalization upon protonation. On the contrary, the most stable lithium cation adducts are less conjugated than the stable neutral biguanides, because the metal cation is better coordinated by the not-fully conjugated bidentate tautomer.

  20. Liquid-gas phase transition and isospin fractionation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Xing Yongzhong; Liu Jianye; Guo Wenjun

    2004-01-01

    The liquid-gas phase transition in the heavy ion collisions and nuclear matter has been an important topic and got achievements, such as, based on the studies by H.Q. Song et al the critical temperature of liquid-gas phase transition enhances with increasing the mass of system and reduces as the increase of the neutron proton ratio of system. As authors know that both the liquid-gas phase transition and the isospin fractionation occur in the spinodal instability region at the nuclear density below the normal nuclear density. In particular, these two dynamical processes lead to the separation of nuclear matter into the liquid phase and gas phase. In this case to compare their dynamical behaviors is interested. The authors investigate the dependence of isospin fractionation degree on the mass and neutron proton ratio of system by using the isospin dependent quantum molecular dynamics model. The authors found that the degree of isospin fractionation (N/Z) n /(N/Z) imf decreases with increasing the mass of the system. This is just similar to the enhance of the critical temperature of liquid-gas phase transition T c as the increase of system mass. Because the enhance of T c is not favorable for the liquid-gas transition taking place, which reduces the isospin fractionation process and leads to decrease of (N/Z) n /(N/Z) imf . However the degree of isospin fractionation enhances with increasing the neutron proton ratio of the system. It is just corresponding to the reduce of T c of the liquid-gas phase transition as the increase of the isospin fractionation of the system. Because the reduce of T c enhances the liquid-gas phase transition process and also prompts the isospin fractionation process leading the increase of the isospin fractionation degree. To sum up, there are very similar dynamical behaviors for the degree of isospin fractionation and the critical temperature of the liquid-gas phase transition. So dynamical properties of the liquid-gas phase transition can

  1. Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

    Science.gov (United States)

    Kinjo, Akira R; Nakamura, Haruki

    2013-01-01

    Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

  2. SVOC partitioning between the gas phase and settled dust indoors

    Science.gov (United States)

    Weschler, Charles J.; Nazaroff, William W.

    2010-09-01

    Semivolatile organic compounds (SVOCs) are a major class of indoor pollutants. Understanding SVOC partitioning between the gas phase and settled dust is important for characterizing the fate of these species indoors and the pathways by which humans are exposed to them. Such knowledge also helps in crafting measurement programs for epidemiological studies designed to probe potential associations between exposure to these compounds and adverse health effects. In this paper, we analyze published data from nineteen studies that cumulatively report measurements of dustborne and airborne SVOCs in more than a thousand buildings, mostly residences, in seven countries. In aggregate, measured median data are reported in these studies for 66 different SVOCs whose octanol-air partition coefficients ( Koa) span more than five orders of magnitude. We use these data to test a simple equilibrium model for estimating the partitioning of an SVOC between the gas phase and settled dust indoors. The results demonstrate, in central tendency, that a compound's octanol-air partition coefficient is a strong predictor of its abundance in settled dust relative to its gas phase concentration. Using median measured results for each SVOC in each study, dustborne mass fractions predicted using Koa and gas-phase concentrations correlate reasonably well with measured dustborne mass fractions ( R2 = 0.76). Combined with theoretical understanding of SVOC partitioning kinetics, the empirical evidence also suggests that for SVOCs with high Koa values, the mass fraction in settled dust may not have sufficient time to equilibrate with the gas phase concentration.

  3. Ground-State Gas-Phase Structures of Inorganic Molecules Predicted by Density Functional Theory Methods

    KAUST Repository

    Minenkov, Yury

    2017-11-29

    We tested a battery of density functional theory (DFT) methods ranging from generalized gradient approximation (GGA) via meta-GGA to hybrid meta-GGA schemes as well as Møller–Plesset perturbation theory of the second order and a single and double excitation coupled-cluster (CCSD) theory for their ability to reproduce accurate gas-phase structures of di- and triatomic molecules derived from microwave spectroscopy. We obtained the most accurate molecular structures using the hybrid and hybrid meta-GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion interactions play an insignificant role. The structures that the CCSD method predicts are of similar quality although at considerably larger computational cost. The structures that GGA and meta-GGA schemes predict are less accurate with the largest absolute errors detected with BLYP and M11-L, suggesting that these methods should not be used if accurate three-dimensional molecular structures are required. Because of numerical problems related to the integration of the exchange–correlation part of the functional and large scattering of errors, most of the Minnesota models tested, particularly MN12-L, M11, M06-L, SOGGA11, and VSXC, are also not recommended for geometry optimization. When maintaining a low computational budget is essential, the nonseparable gradient functional N12 might work within an acceptable range of error. As expected, the DFT-D3 dispersion correction had a negligible effect on the internuclear distances when combined with the functionals tested on nonweakly bonded di- and triatomic inorganic molecules. By contrast, the dispersion correction for the APF-D functional has been found to shorten the bonds significantly, up to 0.064 Å (AgI), in Ag halides, BaO, BaS, BaF, BaCl, Cu halides, and Li and

  4. Infrared spectroscopy of gas-phase clusters using a free-electron laser

    International Nuclear Information System (INIS)

    Heijnsbergen, D. van; Helden, G. von; Meijer, G.

    2002-01-01

    Most clusters produced in the gas phase, especially those containing metals, remain largely uncharaterized, among these are transition metal - carbide, -oxide and -nitride clusters. A method for recording IR spectra of strongly bound gas-phase clusters is presented. It is based on a free-electron laser called Felix, characterized by wide wavelength tuning range, covering almost the full 'molecular finger print' region, high power and fluence which make it suited to excite gas-phase species i.e. gas -phase clusters. Neutral clusters were generated by laser vaporization technique, ions that were created after the interaction with the free-electron laser were analyzed in a flight mass spectrometer. Experiments were run with titanium carbide clusters and their IR spectra given. It was shown that this method is suited to strongly bound clusters with low ionization energies, a condition met for many pure metal clusters and metal compound clusters. (nevyjel)

  5. The Structure and Function of Non-Collagenous Bone Proteins

    Science.gov (United States)

    Hook, Magnus

    1997-01-01

    The long-term goal for this program is to determine the structural and functional relationships of bone proteins and proteins that interact with bone. This information will used to design useful pharmacological compounds that will have a beneficial effect in osteoporotic patients and in the osteoporotic-like effects experienced on long duration space missions. The first phase of this program, funded under a cooperative research agreement with NASA through the Texas Medical Center, aimed to develop powerful recombinant expression systems and purification methods for production of large amounts of target proteins. Proteins expressed in sufficient'amount and purity would be characterized by a variety of structural methods, and made available for crystallization studies. In order to increase the likelihood of crystallization and subsequent high resolution solution of structures, we undertook to develop expression of normal and mutant forms of proteins by bacterial and mammalian cells. In addition to the main goals of this program, we would also be able to provide reagents for other related studies, including development of anti-fibrotic and anti-metastatic therapeutics.

  6. Interaction of lysozyme protein with different sized silica nanoparticles and their resultant structures

    Energy Technology Data Exchange (ETDEWEB)

    Yadav, Indresh, E-mail: iykumarindresh288@gmail.com; Aswal, V. K. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India); Kohlbrecher, J. [Laboratory for Neutron Scattering, Paul Scherrer Institut, CH-5232 PSI Villigen (Switzerland)

    2016-05-23

    The interaction of model protein-lysozyme with three different sized anionic silica nanoparticles has been studied by UV-vis spectroscopy, dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The surface area and curvature of the nanoparticles change with size, which significantly influence their interaction with protein. The lysozyme adsorbs on the surface of the nanoparticles due to electrostatic attraction and leads to the phase transformation from one phase (clear) to two-phase (turbid) of the nanoparticle-protein system. The dominance of lysozyme induced short-range attraction over long-range electrostatic repulsion between nanoparticles is responsible for phase transformation and modeled by the two-Yukawa potential. The magnitude of the attractive interaction increases with the size of the nanoparticles as a result the phase transformation commences relatively at lower concentration of lysozyme. The structure of the nanoparticle-protein system in two-phase is characterized by the diffusion limited aggregate type of mass fractal morphology.

  7. Growth arrest specific protein (GAS) 6

    DEFF Research Database (Denmark)

    Haase, T N; Rasmussen, Morten; Jaksch, C A M

    2013-01-01

    using RNA microarray and quantitative PCR. The role of a differentially expressed gene, growth arrest specific protein 6 (GAS6), was evaluated in vitro using neonatal rat islets. Results The mRNA level of Gas6, known to be mitogenic in other tissues, was reduced in LP offspring. The mRNA content of Mafa...... was increased in LP offspring suggesting an early maturation of beta cells. When applied in vitro, GAS6 increased proliferation of neonatal pancreatic beta cells, while reducing glucose-stimulated insulin secretion without changing the total insulin content of the islets. In addition, GAS6 decreased the m......RNA content of Mafa. Conclusions/interpretation We propose a role for GAS6 in the regulation of pancreatic beta cells in the critical period around the time of birth. Our results support the hypothesis that the reduced beta cell mass seen in LP offspring is caused by a change in the intra-uterine environment...

  8. Atomic and molecular physics in the gas phase

    International Nuclear Information System (INIS)

    Toburen, L.H.

    1990-09-01

    The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets

  9. Gas phase decontamination of gaseous diffusion process equipment

    International Nuclear Information System (INIS)

    Bundy, R.D.; Munday, E.B.; Simmons, D.W.; Neiswander, D.W.

    1994-01-01

    D ampersand D of the process facilities at the gaseous diffusion plants (GDPs) will be an enormous task. The EBASCO estimate places the cost of D ampersand D of the GDP at the K-25 Site at approximately $7.5 billion. Of this sum, nearly $4 billion is associated with the construction and operation of decontamination facilities and the dismantlement and transport of contaminated process equipment to these facilities. In situ long-term low-temperature (LTLT) gas phase decontamination is being developed and demonstrated at the K-25 site as a technology that has the potential to substantially lower these costs while reducing criticality and safeguards concerns and worker exposure to hazardous and radioactive materials. The objective of gas phase decontamination is to employ a gaseous reagent to fluorinate nonvolatile uranium deposits to form volatile LJF6, which can be recovered by chemical trapping or freezing. The LTLT process permits the decontamination of the inside of gas-tight GDP process equipment at room temperature by substituting a long exposure to subatmospheric C1F for higher reaction rates at higher temperatures. This paper outlines the concept for applying LTLT gas phase decontamination, reports encouraging laboratory experiments, and presents the status of the design of a prototype mobile system. Plans for demonstrating the LTLT process on full-size gaseous diffusion equipment are also outlined briefly

  10. Raman study of vibrational dynamics of aminopropylsilanetriol in gas phase

    Science.gov (United States)

    Volovšek, V.; Dananić, V.; Bistričić, L.; Movre Šapić, I.; Furić, K.

    2014-01-01

    Raman spectrum of aminopropylsilanetriol (APST) in gas phase has been recorded at room temperature in macro chamber utilizing two-mirror technique over the sample tube. Unlike predominantly trans molecular conformation in condensed phase, the spectra of vapor show that the molecules are solely in gauche conformation with intramolecular hydrogen bond N⋯Hsbnd O which reduces the molecular energy in respect to trans conformation by 0.152 eV. The assignment of the molecular spectra based on the DFT calculation is presented. The strong vibrational bands at 354 cm-1, 588 cm-1 and 3022 cm-1 are proposed for verifying the existence of the ring like, hydrogen bonded structure. Special attention was devoted to the high frequency region, where hydrogen bond vibrations are coupled to stretchings of amino and silanol groups.

  11. Holographic entanglement entropy and the extended phase structure of STU black holes

    International Nuclear Information System (INIS)

    Caceres, Elena; Nguyen, Phuc H.; Pedraza, Juan F.

    2015-01-01

    We study the extended thermodynamics, obtained by considering the cosmological constant as a thermodynamic variable, of STU black holes in 4-dimensions in the fixed charge ensemble. The associated phase structure is conjectured to be dual to an RG-flow on the space of field theories. We find that for some charge configurations the phase structure resembles that of a Van der Waals gas: the system exhibits a family of first order phase transitions ending in a second order phase transition at a critical temperature. We calculate the holographic entanglement entropy for several charge configurations and show that for the cases where the gravity background exhibits Van der Waals behavior, the entanglement entropy presents a transition at the same critical temperature. To further characterize the phase transition we calculate appropriate critical exponents and show that they coincide. Thus, the entanglement entropy successfully captures the information of the extended phase structure. Finally, we discuss the physical interpretation of the extended space in terms of the boundary QFT and construct various holographic heat engines dual to STU black holes.

  12. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

    International Nuclear Information System (INIS)

    Blomberg, Sara; Gustafson, Johan; Lundgren, Edvin; Zhou, Jianfeng; Zetterberg, Johan

    2016-01-01

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  13. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

    Science.gov (United States)

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-01

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  14. Effect of geometric parameters of liquid-gas separator units on phase separation performance

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Songping; Chen, Xueqing; Chen, Ying [Guangdong University of Technology, Seoul (China); Yang, Zhen [Tsinghua University, Beijing (China)

    2015-07-15

    Five liquid-gas separator units were designed and constructed based on a new concept of a validated high-performance condenser. Each separator unit consists of two united T-junctions and an apertured baffle. The separator units have different header diameters or different baffles with different diameters of the liquid-gas separation hole. The phase separation characteristics of the units were investigated at inlet air superficial velocities from 1.0m/s to 33.0m/s and water superficial velocities from 0.0015 m/s to 0..50 m/s. The experimental results showed that the liquid height, liquid flow rate through the separation hole, and liquid separation efficiency increased with increased header diameter and decreased diameter of the separation hole. The geometric structures of the separator units affected the phase separation characteristics by influencing the liquid height in the header and the liquid flow rate through the separation hole.

  15. Long-lived gas-phase radicals from combustion

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Takashi; Furusawa, Koji; Amano, Toshiji; Okubo, Yoichi; Tsuchiya, Jun' ichi; Yoshizawa, Fujiroku; Akutsu, Yoshiaki; Tamura, Masamitsu; Yoshida, Tadao (Univ. of Tokyo (Japan))

    1989-04-20

    On indoor air pollution or fire, it is feared that the gas-phase radicals from the combustion of inflammables or fuel seriously exert an influence on the organisms as harmful matter. The gas-phase radicals were studied using the electron spin resonance (ESR) spin-trapping technique. For the spin trap solution, 0.1 mol solution of {alpha}-phenyl-N-t-butylnitron in benzene was used. As a result, apparently long-lived and highly reactive oxygen-centered radicals were detected in the smoke from polyethylene, polypropylene, polystyrene, polymethylmethacrylate, cellulose, kerosene, benzene, acetone, methanol and butylalcohol. It is suggested that the production mechanism for the radicals should be different from olefin-NOx-air system reaction, which is considered for the radicals from cigarette smoke. 11 refs., 6 figs., 2 tabs.

  16. Fischer Indole Synthesis in the Gas Phase, the Solution Phase, and at the Electrospray Droplet Interface.

    Science.gov (United States)

    Bain, Ryan M; Ayrton, Stephen T; Cooks, R Graham

    2017-07-01

    Previous reports have shown that reactions occurring in the microdroplets formed during electrospray ionization can, under the right conditions, exhibit significantly greater rates than the corresponding bulk solution-phase reactions. The observed acceleration under electrospray ionization could result from a solution-phase, a gas-phase, or an interfacial reaction. This study shows that a gas-phase ion/molecule (or ion/ion) reaction is not responsible for the observed rate enhancement in the particular case of the Fischer indole synthesis. The results show that the accelerated reaction proceeds in the microdroplets, and evidence is provided that an interfacial process is involved. Graphical Abstract GRAPHICAL ABSTRACT TEXT HERE] -->.

  17. Phase transition in the hadron gas model

    International Nuclear Information System (INIS)

    Gorenstein, M.I.; Petrov, V.K.; Zinov'ev, G.M.

    1981-01-01

    A class of statistical models of hadron gas allowing an analytical solution is considered. A mechanism of a possible phase transition in such a system is found and conditions for its occurence are determined [ru

  18. Severe slugging in gas-liquid two-phase pipe flow

    NARCIS (Netherlands)

    Malekzadeh, R.

    2012-01-01

    transportation facilities. In an offshore oil and gas production facility, pipeline-riser systems are required to transport two-phase hydrocarbons from subsurface oil and gas wells to a central production platform. Severe slugs reaching several thousands pipe diameters may occur when transporting

  19. MOLECULAR SPECTROSCPY AND REACTIONS OF ACTINIDES IN THE GAS PHASE AND CRYOGENIC MATRICES

    Energy Technology Data Exchange (ETDEWEB)

    Heaven, Michael C.; Gibson, John K.; Marcalo, Joaquim

    2009-02-01

    temperature or below. For many spectroscopic measurements, low temperatures have been achieved by co-condensing the actinide vapor in rare gas or inert molecule host matrices. Spectra recorded in matrices are usually considered to be minimally perturbed. Trapping the products from gas-phase reactions that occur when trace quantities of reactants are added to the inert host gas has resulted in the discovery of many new actinide species. Selected aspects of the matrix isolation data were discussed in chapter 17. In the present chapter we review the spectroscopic matrix data in terms of its relationship to gas-phase measurements, and update the description of the new reaction products found in matrices to reflect the developments that have occurred during the past two years. Spectra recorded in matrix environments are usually considered to be minimally perturbed, and this expectation is borne out for many closed shell actinide molecules. However, there is growing evidence that significant perturbations can occur for open shell molecules, resulting in geometric distortions and/or electronic state reordering. Studies of actinide reactions in the gas phase provide an opportunity to probe the relationship between electronic structure and reactivity. Much of this work has focused on the reactions of ionic species, as these may be selected and controlled using various forms of mass spectrometry. As an example of the type of insight derived from reaction studies, it has been established that the reaction barriers for An+ ions are determined by the promotion energies required to achieve the 5fn6d7s configuration. Gas-phase reaction studies also provide fundamental thermodynamic properties such as bond dissociation and ionization energies. In recent years, an increased number of gas-phase ion chemistry studies of bare (atomic) and ligated (molecular) actinide ions have appeared, in which relevant contributions to fundamental actinide chemistry have been made. These studies were initiated

  20. Phase transitions and steady-state microstructures in a two-temperature lattice-gas model with mobile active impurities

    DEFF Research Database (Denmark)

    Henriksen, Jonas Rosager; Sabra, Mads Christian; Mouritsen, Ole G.

    2000-01-01

    The nonequilibrium, steady-state phase transitions and the structure of the different phases of a two-dimensional system with two thermodynamic temperatures are studied via a simple lattice-gas model with mobile active impurities ("hot/cold spots'') whose activity is controlled by an external drive...... on the temperatures, microstructured phases of both lamellar and droplet symmetry arise, described by a length scale that is determined by the characteristic temperature controlling the diffusive motion of the active impurities....

  1. The porcine acute phase response to infection with Actinobacillus pleuropneumoniae. Haptoglobin, C-reactive protein, major acute phase protein and serum amyloid a protein are sensitive indicators of infection

    DEFF Research Database (Denmark)

    Heegaard, Peter M. H.; Klausen, Joan; Nielsen, J.P.

    1998-01-01

    response peaking at around 2 days after infection. Haptoglobin, C-reactive protein (CRP), and major acute phase protein (MAP) responded with large increases in serum levels, preceding the development of specific antibodies by 4-5 days. Serum amyloid A protein (SAA) was also strongly induced. The increase......, kinetics of induction and normalization were different between these proteins. It is concluded that experimental Ap-infection by the aerosol route induces a typical acute phase reaction in the pig, and that pig Hp, CRP, MAP, and SAA are major acute phase reactants. These findings indicate the possibility...

  2. Continuous fixed-bed gas-phase hydroformylation using supported ionic liquid-phase (SILP) Rh catalysts

    DEFF Research Database (Denmark)

    Riisager, Anders; Wasserscheid, Peter; Van Hal, R.

    2003-01-01

    Continuous flow gas-phase hydroformylation of propene was performed using novel supported ionic liquid-phase (SILP) catalysts containing immobilized Rh complexes of the biphosphine ligand sulfoxantphos in the ionic liquids 1-n-butyl-3-methylimidazolium hexafluorophosphate and halogen-free 1-n-butyl...

  3. Reactive intermediates in the gas phase generation and monitoring

    CERN Document Server

    Setser, D W

    2013-01-01

    Reactive Intermediates in the Gas Phase: Generation and Monitoring covers methods for reactive intermediates in the gas phase. The book discusses the generation and measurement of atom and radical concentrations in flow systems; the high temperature flow tubes, generation and measurement of refractory species; and the electronically excited long-lived states of atoms and diatomic molecules in flow systems. The text also describes the production and detection of reactive species with lasers in static systems; the production of small positive ions in a mass spectrometer; and the discharge-excite

  4. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

    Science.gov (United States)

    Li, Jun; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2017-10-01

    The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. [Figure not available: see fulltext.

  5. PIV Measurement of Transient 3-D (Liquid and Gas Phases) Flow Structures Created by a Spreading Flame over 1-Propanol

    Science.gov (United States)

    Hassan, M. I.; Kuwana, K.; Saito, K.

    2001-01-01

    In the past, we measured three-D flow structure in the liquid and gas phases that were created by a spreading flame over liquid fuels. In that effort, we employed several different techniques including our original laser sheet particle tracking (LSPT) technique, which is capable of measuring transient 2-D flow structures. Recently we obtained a state-of-the-art integrated particle image velocimetry (IPIV), whose function is similar to LSPT, but it has an integrated data recording and processing system. To evaluate the accuracy of our IPIV system, we conducted a series of flame spread tests using the same experimental apparatus that we used in our previous flame spread studies and obtained a series of 2-D flow profiles corresponding to our previous LSPT measurements. We confirmed that both LSPT and IPIV techniques produced similar data, but IPIV data contains more detailed flow structures than LSPT data. Here we present some of newly obtained IPIV flow structure data, and discuss the role of gravity in the flame-induced flow structures. Note that the application of IPIV to our flame spread problems is not straightforward, and it required several preliminary tests for its accuracy including this IPIV comparison to LSPT.

  6. The gas industry in Britain: future structures

    International Nuclear Information System (INIS)

    McKinnon, J.

    1993-01-01

    This paper is intended to provide a summary of the kind of structural changes to British Gas that can be considered in order to enable effective competition to develop in the gas market. It draws on an extensive analysis undertaken by the Office of Gas Supply (OFGAS) of recent developments in the gas market, the need to ensure the safety, efficiency and security of gas supplies under different structures and how regulation may change with different structures. Many of these issues covered are complex, and can each be discussed at length, but the intention of this paper is to provide an overview of the key options for a restructured gas market. OFGAS has also examined the regulatory environment within which competitors to British Gas who have emerged or who are likely to emerge in the future may be expected to operate. This paper describes the range of structural options we see. At one end of the spectrum there is the option of continuing with a vertically integrated but more heavily regulated monopoly; at the other end is a fully competitive structure with no or much reduced regulation. In between, there are various combinations between the degree of regulation and the extent of competition that can be considered. In analysing future structural options, we believe it necessary to consider the complete gas supply chain. The analysis therefore considers the offshore production or importation of gas, its purchase at the beach, its reception and processing at terminals, its transportation from terminal meters to customers' meters, its storage and sale to final customers. (author)

  7. Mechanisms of gas phase decomposition of C-nitro compounds from quantum chemical data

    International Nuclear Information System (INIS)

    Khrapkovskii, Grigorii M; Shamov, Alexander G; Nikolaeva, E V; Chachkov, D V

    2009-01-01

    Data on the mechanisms of gas-phase monomolecular decomposition of nitroalkanes, nitroalkenes and nitroarenes obtained using modern quantum chemical methods are described systematically. The attention is focused on the discussion of multistage decomposition of nitro compounds to elementary experimentally observed products. Characteristic features of competition of different mechanisms and the effect of molecular structure on the change in the Arrhenius parameters of the primary reaction step are considered.

  8. Mechanisms of gas phase decomposition of C-nitro compounds from quantum chemical data

    Energy Technology Data Exchange (ETDEWEB)

    Khrapkovskii, Grigorii M; Shamov, Alexander G; Nikolaeva, E V; Chachkov, D V [Kazan State Technological University, Kazan (Russian Federation)

    2009-10-31

    Data on the mechanisms of gas-phase monomolecular decomposition of nitroalkanes, nitroalkenes and nitroarenes obtained using modern quantum chemical methods are described systematically. The attention is focused on the discussion of multistage decomposition of nitro compounds to elementary experimentally observed products. Characteristic features of competition of different mechanisms and the effect of molecular structure on the change in the Arrhenius parameters of the primary reaction step are considered.

  9. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Aboul-Magd Mohammed O

    2009-07-01

    Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input

  10. Structure dynamics. Determination of the coupled relationships in solid-fluid-gas dynamics

    International Nuclear Information System (INIS)

    Hofmann, H.; Huber, A.; Naehring, T.; Bonakdarzadeh, S.; Faass, E.; Gaschen, J.P.; Kniffka, K.; Pilz, H.

    1980-06-01

    In the present paper the code concept SAN (Structure ANalysis) is presented. SAN is designed according to the modular principle using describing and coordinating modules. SAN is based on the discreetizing method. It uses compatible forms of description. The method of finite elements is applied. Solid-fluid-gas structures may be described as well as their interrelations in the linear and nonlinear region, including phase transitions with the associated descriptions of material and state. (orig./RW) [de

  11. Two-phase gas bubble-liquid boundary layer flow along vertical and inclined surfaces

    International Nuclear Information System (INIS)

    Cheung, F.B.; Epstein, M.

    1985-01-01

    The behavior of a two-phase gas bubble liquid boundary layer along vertical and inclined porous surfaces with uniform gas injection is investigated experimentally and analytically. Using argon gas and water as the working fluids, a photographical study of the two-phase boundary layer flow has been performed for various angles of inclination ranging from 45 0 to 135 0 and gas injection rates ranging from 0.01 to 0.1 m/s. An integral method has been employed to solve the system of equations governing the two-phase motion. The effects of the gas injection rate and the angle of inclination on the growth of the boundary layer have been determined

  12. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  13. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  14. Measurement of phase interaction in dispersed gas-particle two-phase flow by phase-doppler anemometry

    Directory of Open Access Journals (Sweden)

    Mergheni Ali Mohamed

    2008-01-01

    Full Text Available For simultaneous measurement of size and velocity distributions of continuous and dispersed phases in a two-phase flow a technique phase-Doppler anemometry was used. Spherical glass particles with a particle diameter range from 102 up to 212 µm were used. In this two-phase flow an experimental results are presented which indicate a significant influence of the solid particles on the flow characteristics. The height of influence of these effects depends on the local position in the jet. Near the nozzle exit high gas velocity gradients exist and therefore high turbulence production in the shear layer of the jet is observed. Here the turbulence intensity in the two-phase jet is decreased compared to the single-phase jet. In the developed zone the velocity gradient in the shear layer is lower and the turbulence intensity reduction is higher. .

  15. Continuous gas-phase hydroformylation of 1-butene using supported ionic liquid phase (SILP) catalysts

    DEFF Research Database (Denmark)

    Haumann, Marco; Dentler, Katharina; Joni, Joni

    2007-01-01

    The concept of supported ionic liquid phase (SILP) catalysis has been extended to 1-butene hydroformylation. A rhodium-sulfoxantphos complex was dissolved in [BMIM][n-C8H17OSO3] and this solution was highly dispersed on silica. Continuous gas-phase experiments in a fixed-bed reactor revealed...

  16. Two-phase gas bubble-liquid boundary layer flow along vertical and inclined surfaces

    International Nuclear Information System (INIS)

    Cheung, F.B.; Epstein, M.

    1985-01-01

    The behavior of a two-phase gas bubble-liquid boundary layer along vertical and inclined porous surfaces with uniform gas injection is investigated experimentally and analytically. Using argon gas and water as the working fluids, a photographical study of the two-phase boundary layer flow has been performed for various angles of inclination ranging from 45 0 to 135 0 and gas injection rates ranging from 0.01 to 0.1 m/s. An integral method has been employed to solve the system of equations governing the two-phase motion. The effects of the gas injection rate and the angle of inclination on the growth of the boundary layer have been determined. The predicted boundary layer thickness is found to be in good agreement with the experimental results. The calculated axial liquid velocity and the void fraction in the two-phase region are also presented along with the observed flow behavior

  17. Heat transfer characteristics of liquid-gas Taylor flows incorporating microencapsulated phase change materials

    International Nuclear Information System (INIS)

    Howard, J A; Walsh, P A

    2014-01-01

    This paper presents an investigation on the heat transfer characteristics associated with liquid-gas Taylor flows in mini channels incorporating microencapsulated phase change materials (MPCM). Taylor flows have been shown to result in heat transfer enhancements due to the fluid recirculation experienced within liquid slugs which is attributable to the alternating liquid slug and gas bubble flow structure. Microencapsulated phase change materials (MPCM) also offer significant potential with increased thermal capacity due to the latent heat required to cause phase change. The primary aim of this work was to examine the overall heat transfer potential associated with combining these two novel liquid cooling technologies. By investigating the local heat transfer characteristics, the augmentation/degradation over single phase liquid cooling was quantified while examining the effects of dimensionless variables, including Reynolds number, liquid slug length and gas void fraction. An experimental test facility was developed which had a heated test section and allowed MPCM-air Taylor flows to be subjected to a constant heat flux boundary condition. Infrared thermography was used to record high resolution experimental wall temperature measurements and determine local heat transfer coefficients from the thermal entrance point. 30.2% mass particle concentration of the MPCM suspension fluid was examined as it provided the maximum latent heat for absorption. Results demonstrate a significant reduction in experimental wall temperatures associated with MPCM-air Taylor flows when compared with the Graetz solution for conventional single phase coolants. Total enhancement in the thermally developed region is observed to be a combination of the individual contributions due to recirculation within the liquid slugs and also absorption of latent heat. Overall, the study highlights the potential heat transfer enhancements that are attainable within heat exchange devices employing MPCM

  18. Modularity in protein structures: study on all-alpha proteins.

    Science.gov (United States)

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  19. The structural phase diagram and oxygen equilibrium partial pressure of YBa 2Cu 3O 6+ x studied by neutron powder diffraction and gas volumetry

    Science.gov (United States)

    Andersen, N. H.; Lebech, B.; Poulsen, H. F.

    1990-12-01

    An experimental technique based on neutron powder diffraction and gas volumetry is presented and used to study the structural phase diagram of YBa 2Cu 3O 6+ x under equilibrium conditions in an extended part of ( x, T)-phase (0.15< x<0.92 and 25° C< T<725°C). Our experimental observations lend strong support to a recent two-dimensional anisotropic next-nearest-neighbour Ising model calculation (the ASYNNNI model) of the basal plane oxygen ordering based of first principle interaction parameters. Simultaneous measurements of the oxygen equilibrium partial pressure show anomalies, one of which proves the thermodynamic stability of the orthorhombic OII double cell structure. Striking similarity with predictions of recent model calculations support that another anomaly may be interpreted to result from local one-dimensional fluctuations in the distribution of oxygen atoms in the basal plane of tetragonal YBCO. Our pressure data also indicate that x=0.92 is a maximum obtainable oxygen concentration for oxygen pressures below 760 Torr.

  20. Two-phase xenon detector with gas amplification and electroluminescent signal detection

    International Nuclear Information System (INIS)

    Akimov, D.Yu.; Burenkov, A.A.; Grishkin, Yu.L.; Kovalenko, A.G.; Lebedenko, V.N.; Stekhanov, V.N.

    2008-01-01

    An optical technique for detecting ionization electrons produced during ionization of the liquid phase has been experimentally tested in two-phase (liquid-gas) xenon. The effects of gas and electroluminescent amplifications at the wire anode are simultaneously used for detection. This method allows construction of a supersensitive detector of small ionization signals-down to those corresponding to the detection of single electrons [ru

  1. Two-phase modeling of DDT: Structure of the velocity-relaxation zone

    International Nuclear Information System (INIS)

    Kapila, A.K.; Son, S.F.; Bdzil, J.B.; Menikoff, R.; Stewart, D.S.

    1997-01-01

    The structure of the velocity relaxation zone in a hyperbolic, nonconservative, two-phase model is examined in the limit of large drag, and in the context of the problem of deflagration-to-detonation transition in a granular explosive. The primary motivation for the study is the desire to relate the end states across the relaxation zone, which can then be treated as a discontinuity in a reduced, equivelocity model, that is computationally more efficient than its parent. In contrast to a conservative system, where end states across thin zones of rapid variation are determined principally by algebraic statements of conservation, the nonconservative character of the present system requires an explicit consideration of the structure. Starting with the minimum admissible wave speed, the structure is mapped out as the wave speed increases. Several critical wave speeds corresponding to changes in the structure are identified. The archetypal structure is partly dispersed, monotonic, and involves conventional hydrodynamic shocks in one or both phases. The picture is reminiscent of, but more complex than, what is observed in such (simpler) two-phase media as a dusty gas. copyright 1997 American Institute of Physics

  2. Mapping monomeric threading to protein-protein structure prediction.

    Science.gov (United States)

    Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

    2013-03-25

    The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

  3. Homolytic iodination and nitration of some benzene derivatives in the gas phase

    International Nuclear Information System (INIS)

    Vonk, W.F.M.

    1980-01-01

    Two gas phase reactions, involving the iodination and nitration of benzene derivatives, are described. The experimental techniques of the apparatus and the methods used are outlined. The kinetic H/D isotope effect in the gas phase nitration of benzene with NO 2 is determined. (C.F.)

  4. Constructing a unique two-phase compressibility factor model for lean gas condensates

    Energy Technology Data Exchange (ETDEWEB)

    Moayyedi, Mahmood; Gharesheikhlou, Aliashghar [Research Institute of Petroleum Industry (RIPI), Tehran (Iran, Islamic Republic of); Azamifard, Arash; Mosaferi, Emadoddin [Amirkabir University of Technology (AUT), Tehran (Iran, Islamic Republic of)

    2015-02-15

    Generating a reliable experimental model for two-phase compressibility factor in lean gas condensate reservoirs has always been demanding, but it was neglected due to lack of required experimental data. This study presents the main results of constructing the first two-phase compressibility factor model that is completely valid for Iranian lean gas condensate reservoirs. Based on a wide range of experimental data bank for Iranian lean gas condensate reservoirs, a unique two-phase compressibility factor model was generated using design of experiments (DOE) method and neural network technique (ANN). Using DOE, a swift cubic response surface model was generated for two-phase compressibility factor as a function of some selected fluid parameters for lean gas condensate fluids. The proposed DOE and ANN models were finally validated using four new independent data series. The results showed that there is a good agreement between experimental data and the proposed models. In the end, a detailed comparison was made between the results of proposed models.

  5. Constructing a unique two-phase compressibility factor model for lean gas condensates

    International Nuclear Information System (INIS)

    Moayyedi, Mahmood; Gharesheikhlou, Aliashghar; Azamifard, Arash; Mosaferi, Emadoddin

    2015-01-01

    Generating a reliable experimental model for two-phase compressibility factor in lean gas condensate reservoirs has always been demanding, but it was neglected due to lack of required experimental data. This study presents the main results of constructing the first two-phase compressibility factor model that is completely valid for Iranian lean gas condensate reservoirs. Based on a wide range of experimental data bank for Iranian lean gas condensate reservoirs, a unique two-phase compressibility factor model was generated using design of experiments (DOE) method and neural network technique (ANN). Using DOE, a swift cubic response surface model was generated for two-phase compressibility factor as a function of some selected fluid parameters for lean gas condensate fluids. The proposed DOE and ANN models were finally validated using four new independent data series. The results showed that there is a good agreement between experimental data and the proposed models. In the end, a detailed comparison was made between the results of proposed models

  6. Protein Loop Structure Prediction Using Conformational Space Annealing.

    Science.gov (United States)

    Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

    2017-05-22

    We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

  7. Reactions of newly formed fission products in the gas phase

    International Nuclear Information System (INIS)

    Strickert, R.G.

    1976-01-01

    A dynamic gas-flow system was constructed which stopped fission products in the gas phase and rapidly separated (in less than 2 sec) volatile compounds from non-volatile ones. The filter assembly designed and used was shown to stop essentially all non-volatile fission products. Between 5 percent and 20 percent of tellurium fission-product isotopes reacted with several hydrocarbon gases to form volatile compounds, which passed through the filter. With carbon monoxide gas, volatile tellurium compound(s) (probably TeCO) were also formed with similar efficiencies. The upper limits for the yields of volatile compounds formed between CO and tin and antimony fission products were shown to be less than 0.3 percent, so tellurium nuclides, not their precursors, reacted with CO. It was found that CO reacted preferentially with independently produced tellurium atoms; the reaction efficiency of beta-produced atoms was only 27 +- 3 percent of that of the independently formed atoms. The selectivity, which was independent of the over-all reaction efficiency, was shown to be due to reaction of independently formed atoms in the gas phase. The gas phase reactions are believed to occur mainly at thermal energies because of the independence of the yield upon argon moderator mole-fraction (up to 80 percent). It was shown in some experiments that about one-half of the TeCO decomposed in passing through a filter and that an appreciable fraction (approximately 20 percent) of the tellurium atoms deposited on the filter reacted agin with CO. Other tellurium atoms on the filter surface (those formed by beta decay and those formed independently but not reacting in the gas phase) also reacted with CO, but probably somewhat less efficiently than atoms formed by TeCO decomposition. No evidence was found for formation of TeCO as a direct result of beta-decay

  8. Role of isospin in nuclear-matter liquid-gas phase transition

    International Nuclear Information System (INIS)

    Ducoin, C.

    2006-10-01

    Nuclear matter presents a phase transition of the liquid-gas type. This well-known feature is due to the nuclear interaction profile (mean-range attractive, short-range repulsive). Symmetric-nuclear-matter thermodynamics is thus analogous to that of a Van der Waals fluid. The study shows up to be more complex in the case of asymmetric matter, composed of neutrons and protons in an arbitrary proportion. Isospin, which distinguishes both constituents, gives a measure of this proportion. Studying asymmetric matter, isospin is an additional degree of freedom, which means one more dimension to consider in the space of observables. The nuclear liquid-gas transition is associated with the multi-fragmentation phenomenon observed in heavy-ion collisions, and to compact-star physics: the involved systems are neutron rich, so they are affected by the isospin degree of freedom. The present work is a theoretical study of isospin effects which appear in the asymmetric nuclear matter liquid-gas phase transition. A mean-field approach is used, with a Skyrme nuclear effective interaction. We demonstrate the presence of a first-order phase transition for asymmetric matter, and study the isospin distillation phenomenon associated with this transition. The case of phase separation at thermodynamic equilibrium is compared to spinodal decomposition. Finite size effects are addressed, as well as the influence of the electron gas which is present in the astrophysical context. (author)

  9. Theoretical Investigation of the Structural Stabilities of Ceria Surfaces and Supported Metal Nanocluster in Vapor and Aqueous Phases

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Zhibo [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Liu, Ning [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Chen, Biaohua [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Li, Jianwei [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Mei, Donghai [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States

    2018-01-25

    Understanding the structural stability and dynamics at the interface between the solid metal oxide and aqueous phase is significant in a variety of industrial applications including heterogeneous catalysis and environmental remediation. In the present work, the stabilities of three low-index ceria (CeO2) surfaces, i.e., (111), (110) and (100) in vapor and aqueous phases were studied using ab initio molecular dynamics simulations and density functional theory (DFT) calculations. Gibbs surface free energies as a function of temperature, water partial pressure, and water coverages were calculated using DFT based atomistic thermodynamic approach. On the basis of surface free energies, the morphology and exposed surface structures of the CeO2 nanoparticle were predicted using Wulff construction principle. It is found that the partially hydroxylated (111) and (100) are two major surface structures of CeO2 nanoparticles in vapor phase at ambient temperature (300 K). As the temperature increases, the fully dehydrated (111) surface gradually becomes the most dominant surface structure. While in aqueous phase, the exposed surface of the CeO2 nanoparticle is dominated by the hydroxylated (110) structure at 393 K. Finally, the morphology and stability of a cuboctahedron Pt13 nanocluster supported on CeO2 surfaces in both gas and aqueous phases were investigated. In gas phase, the supported Pt13 nanocluster has the tendency to wetting the CeO2 surface due to the strong metal-support interaction. The calculated interaction energies suggest the CeO2(110) surface provides the best stability for the Pt13 nanocluster. The CeO2 supported Pt13 nanoclusters are oxidized. Compared to the gas phase, the morphology of the CeO2 supported Pt13 nanocluster is less distorted due to the solvation effect provided by surrounding water molecules in aqueous phase. More electrons are transferred from the Pt13 nanocluster to the CeO2 support, implying the supported Pt13 nanocluster is further

  10. Gas phase adsorption technology for nitrogen isotope separation and its feasibility for highly enriched nitrogen gas production

    International Nuclear Information System (INIS)

    Inoue, Masaki; Asaga, Takeo

    2000-04-01

    Highly enriched nitrogen-15 gas is favorable to reduce radioactive carbon-14 production in reactor. The cost of highly enriched nitrogen-15 gas in mass production is one of the most important subject in nitride fuel option in 'Feasibility Study for FBR and Related Fuel Cycle'. In this work gas phase adsorption technology was verified to be applicable for nitrogen isotope separation and feasible to produce highly enriched nitrogen-15 gas in commercial. Nitrogen isotopes were separated while ammonia gas flows through sodium-A type zeolite column using pressure swing adsorption process. The isotopic ratio of eight samples were measured by high resolution mass spectrometry and Fourier transform microwave spectroscopy. Gas phase adsorption technology was verified to be applicable for nitrogen isotope separation, since the isotopic ratio of nitrogen-15 and nitrogen-14 in samples were more than six times as high as in natural. The cost of highly enriched nitrogen-15 gas in mass production were estimated by the factor method. It revealed that highly enriched nitrogen-15 gas could be supplied in a few hundred yen per gram in mass production. (author)

  11. Online Measurements of Highly Oxidized Organics in the Gas and Particle phase during SOAS and SENEX

    Science.gov (United States)

    Lopez-Hilfiker, F.; Lee, B. H.; Mohr, C.; Ehn, M.; Rubach, F.; Mentel, T. F.; Kleist, E.; Thornton, J. A.

    2014-12-01

    We present measurements of a large suite of gas and particle phase organic compounds made with a Filter Inlet for Gas and AEROsol (FIGAERO) coupled to a high resolution time of flight chemical ionization mass spectrometer (HR-ToF-CIMS) developed at the University of Washington and with airborne HR-ToF-CIMS measurements. The FIGAERO instrument was deployed on the Jülich Plant Atmosphere Chamber to study α-pinene oxidation, and subsequently at the SMEAR II forest station in Hyytiälä, Finland and the SOAS ground site, in Brent Alabama. During the Southern Atmosphere Study, a gas-phase only version of the HR-ToF-CIMS was deployed on the NOAA WP-3 aircraft as part of SENEX. We focus here on highly oxygenated organic compounds derived from monoterpene oxidation detected both aloft during SENEX and at the ground-based site during SOAS. In both chamber and the atmosphere, many highly oxidized, low volatility compounds were observed in the gas and particles and many of the same compositions detected in the gas-phase were detected in the particles upon temperature programmed thermal desorption. The fraction of a given compound measured in the particle phase follows expected trends with elemental composition such as O/C ratios, but many compounds would not be well described by an absorptive partitioning model assuming unity activity coefficients. The detailed structure in the thermograms reveals a significant contribution from large molecular weight organics and/or oligomers in both chamber and ambient aerosol samples. Approximately 50% of the measured organics in the particle phase are associated with compounds having effective vapour pressures 4 or more orders of magnitude lower than commonly measured monoterpene oxidation products. We discuss the implications of these findings for measurements of gas-particle partitioning and for evaluating the contribution of monoterpene oxidation to organic aerosol formation and growth. We also use the aircraft measurements and a

  12. Comparison of catalytic ethylene polymerization in slurry and gas phase

    OpenAIRE

    Daftaribesheli, Majid

    2009-01-01

    Polyethylene (PE) with the annual consumption of 70 million tones in 2007 is mostly produced in slurry, gas-phase or combination of both processes. This work focuses on a comparison between the slurry and gas phase processes. Why does PE produced in theses two processes can show extremely different properties and extremely different reaction behaviour even if the same Ziegler-Natta (ZN) catalyst is used? Generally, it is known that the reason can be found in the differences of local condition...

  13. Optical processes in the performance and recovery of gas-phase switches

    International Nuclear Information System (INIS)

    Gundersen, M.

    1982-01-01

    In this paper several optical processes that may be used to affect gas-phase switch performance and operation are discussed, and approaches using a laser to increase recovery rates of switches are presented. In the latter the laser is used during the recovery phase rather than the conductive or closure phase. This papper suggests that it should be possible to use a low-power laser (e.g., one that is technologically feasible to use as part of a switch) to assist in opening the switch by quenching excited atomic and/or molecular species. The application of laser-induced energy extraction to gas-phase switches is also discussed

  14. Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.

    Science.gov (United States)

    Abbass, Jad; Nebel, Jean-Christophe

    2017-01-01

    Protein structure prediction is considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh experiment that free modelling target predictions are still beyond reliable accuracy, therefore, much effort should be made to improve ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments. Generally, the structure with the lowest energy score, also known as first model, is chosen to be the "predicted one". A thorough study has been conducted on the role and diversity of 3-mers involved in Rosetta's model "refinement" phase. Usage of the standard number of 3-mers - i.e. 200 - has been shown to degrade alpha and alpha-beta protein conformations initially achieved by assembling 9-mers. Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction. Over 8% improvement in terms of first model structure accuracy is reported for alpha and alpha-beta classes when decreasing the number of 3- mers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  15. DEMONSTRATION BULLETIN: GAS-PHASE CHEMICAL REDUCTION - ECO LOGIC INTERNATIONAL, INC.

    Science.gov (United States)

    The patented Eco Logic Process employs a gas-phase reduction reaction of hydrogen with organic and chlorinated organic compounds at elevated temperatures to convert aqueous and oily hazardous contaminants into a hydrocarbon-rich gas product. After passing through a scrubber, the ...

  16. The electron spectrum of UF6 recorded in the gas phase

    Science.gov (United States)

    Mârtensson, N.; Malmquist, P.-Å.; Svensson, S.; Johansson, B.

    1984-06-01

    Gas phase core and valence electron spectra from UF6, excited by AlKα monochromatized x rays, in the binding energy range 0-1000 eV are presented. It is shown that the AlKα excited valence electron spectrum can be used to reassign the highest occupied molecular orbital (HOMO) in UF6. Many-body effects on the core levels are discussed and core level lifetimes are determined. The shift between solid phase and gas phase electron binding energies for core lines is used to discuss the U5 f population in UF6.

  17. Experimental and numerical investigation of shock wave propagation through complex geometry, gas continuous, two-phase media

    Energy Technology Data Exchange (ETDEWEB)

    Chien-Chih Liu, James [Univ. of California, Berkeley, CA (United States)

    1993-01-01

    The work presented here investigates the phenomenon of shock wave propagation in gas continuous, two-phase media. The motivation for this work stems from the need to understand blast venting consequences in the HYLIFE inertial confinement fusion (ICF) reactor. The HYLIFE concept utilizes lasers or heavy ion beams to rapidly heat and compress D-T targets injected into the center of a reactor chamber. A segmented blanket of falling molten lithium or Li2BeF4 (Flibe) jets encircles the reactor`s central cavity, shielding the reactor structure from radiation damage, absorbing the fusion energy, and breeding more tritium fuel. X-rays from the fusion microexplosion will ablate a thin layer of blanket material from the surfaces which face toward the fusion site. This generates a highly energetic vapor, which mostly coalesces in the central cavity. The blast expansion from the central cavity generates a shock which propagates through the segmented blanket - a complex geometry, gas-continuous two-phase medium. The impulse that the blast gives to the liquid as it vents past, the gas shock on the chamber wall, and ultimately the liquid impact on the wall are all important quantities to the HYLIFE structural designers.

  18. Prediction of turbulent mixing rates of both gas and liquid phases between adjacent subchannels in a two-phase slug-churn flow

    International Nuclear Information System (INIS)

    Kawahara, A.; Sadatomi, M.; Tomino, T.; Sato, Y.

    1998-01-01

    This paper presents a slug-churn flow model for predicting turbulent mixing rates of both gas and liquid phase between adjacent subchannels in a BWR fuel rod bundle. In the model, the mixing rate of the liquid phase is calculated as the sum of the three components, i.e., turbulent diffusion, convective transfer and pressure difference fluctuations between the subchannels. The compenents of turbulent diffusion and convective transfer are calculated from Sadatomi et al.'s (1996) method, applicable to single-phase turbulent mixing by considering the effect of the increment of liquid velocity due to the presence of gas phase. The component of the pressure difference fluctuations is evaluated from a newly developed correlations. The mixing rate of the gas phase, on the other side, is calculated from a simple relation of mixing rate between gas and liquid phases. The validity of the proposed model has been confirmed with the turbulent mixing rates data of Rudzinski et al. as well as the present authors

  19. Gas Dynamics in Planetary Nebulae: From Macro-structures to FLIERs

    Science.gov (United States)

    Perinotto, Mario

    2000-10-01

    Purpose of this paper is to clarify how Planetary Nebulae (PNe) are very interesting laboratories to study cosmic gas dynamics. I first recall the history of PNe which are generated from low and intermediate mass stars through successive mass loss processes starting in the Reg Giant phase of evolution and continuing also after the termination of the pulsed AGB phase, where most of the nebular mass is believed to be ejected. The correponding stellar winds are the ingredients of the nebula. Their initial properties and subsequent mutual interactions, under the action of the evolving stellar radiation field, are responsible for the properties of the nebula. The observed structures of PNe are considered in detail. Larger scale macroscopic structures (MACS) are examined separately from quite smaller scale microscopic structures (MICS). The formation of MACS, at least in cases of round to moderately elliptical PNe, is shown to be reasonably well understood in terms of existing hydrodynamical models. Considering the kinematical behaviour, MICS can be separated into FLIERs (Fast Low Ionization Emitting Regions) and SLOWERs (slowly moving). Attention is focussed on FLIERs and on the proposed mechanisms to interpret them. Recent observations with the Hubble Space Telescope have provided us with a wealth of detailed (subarcsec) information on the nebular structures. The inner structure of FLIERs is here illustrated to consist of substructures of various shapes with an high degree of individually from object to object, also within the same PN. These new data call for deeper thoretical efforts to solve the problems of cosmic gas dynamics, posed by their observed properties. An ample account is given of the most relevant original works, in an effort to allow the non specialist reader to quickly become acquainted with the status of art in the various aspects of the subject.

  20. Structural test of the parameterized-backbone method for protein design.

    Science.gov (United States)

    Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

    2004-09-03

    Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

  1. Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles

    Science.gov (United States)

    Wei, Ming-Tzo; Elbaum-Garfinkle, Shana; Holehouse, Alex S.; Chen, Carlos Chih-Hsiung; Feric, Marina; Arnold, Craig B.; Priestley, Rodney D.; Pappu, Rohit V.; Brangwynne, Clifford P.

    2017-11-01

    Many intracellular membraneless organelles form via phase separation of intrinsically disordered proteins (IDPs) or regions (IDRs). These include the Caenorhabditis elegans protein LAF-1, which forms P granule-like droplets in vitro. However, the role of protein disorder in phase separation and the macromolecular organization within droplets remain elusive. Here, we utilize a novel technique, ultrafast-scanning fluorescence correlation spectroscopy, to measure the molecular interactions and full coexistence curves (binodals), which quantify the protein concentration within LAF-1 droplets. The binodals of LAF-1 and its IDR display a number of unusual features, including 'high concentration' binodal arms that correspond to remarkably dilute droplets. We find that LAF-1 and other in vitro and intracellular droplets are characterized by an effective mesh size of ∼3-8 nm, which determines the size scale at which droplet properties impact molecular diffusion and permeability. These findings reveal how specific IDPs can phase separate to form permeable, low-density (semi-dilute) liquids, whose structural features are likely to strongly impact biological function.

  2. Monoterpene oxidation in an oxidative flow reactor: SOA yields and the relationship between bulk gas-phase properties and organic aerosol growth

    Science.gov (United States)

    Friedman, B.; Link, M.; Farmer, D.

    2016-12-01

    We use an oxidative flow reactor (OFR) to determine the secondary organic aerosol (SOA) yields of five monoterpenes (alpha-pinene, beta-pinene, limonene, sabinene, and terpinolene) at a range of OH exposures. These OH exposures correspond to aging timescales of a few hours to seven days. We further determine how SOA yields of beta-pinene and alpha-pinene vary as a function of seed particle type (organic vs. inorganic) and seed particle mass concentration. We hypothesize that the monoterpene structure largely accounts for the observed variance in SOA yields for the different monoterpenes. We also use high-resolution time-of-flight chemical ionization mass spectrometry to calculate the bulk gas-phase properties (O:C and H:C) of the monoterpene oxidation systems as a function of oxidant concentrations. Bulk gas-phase properties can be compared to the SOA yields to assess the capability of the precursor gas-phase species to inform the SOA yields of each monoterpene oxidation system. We find that the extent of oxygenated precursor gas-phase species corresponds to SOA yield.

  3. Highly Selective Continuous Gas-Phase Methoxycarbonylation of Ethylene with Supported Ionic Liquid Phase (SILP) Catalysts

    DEFF Research Database (Denmark)

    Khokarale, Santosh Govind; Garcia Suárez, Eduardo José; Fehrmann, Rasmus

    2017-01-01

    Supported ionic liquid phase (SILP) technology was applied for the first time to the Pd-catalyzed continuous, gas-phase methoxycarbonylation of ethylene to selectively produce methyl propanoate (MP) in high yields. The influence of catalyst and reaction parameters such as, for example, ionic liquid...

  4. Protein enriched pasta: structure and digestibility of its protein network.

    Science.gov (United States)

    Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

    2016-02-01

    Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

  5. Zpif's law in the liquid gas phase transition of nuclei

    International Nuclear Information System (INIS)

    Ma, Y.G.

    1999-01-01

    Zpif's law in the field of linguistics is tested in the nuclear disassembly within the framework of isospin dependent lattice gas model. It is found that the average cluster charge (or mass) of rank n in the charge (or mass) list shows exactly inversely to its rank, i.e., there exists Zpif's law, at the phase transition temperature. This novel criterion shall be helpful to search the nuclear liquid gas phase transition experimentally and theoretically. In addition, the finite size scaling of the effective phase transition temperature at which the Zpif's law appears is studied for several systems with different mass and the critical exponents of ν and β are tentatively extracted. (orig.)

  6. Structure-based barcoding of proteins.

    Science.gov (United States)

    Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

    2014-01-01

    A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

  7. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    Science.gov (United States)

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

  8. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    International Nuclear Information System (INIS)

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-01-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ 1 and ϕ 2 ) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ DS list as a criterion to select optimized phases ϕ am from ϕ 1 or ϕ 2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ SAD has been developed. Based on this work, reflections with an angle θ DS in the range 35–145° are selected for an optimized improvement, where θ DS is the angle between the initial phase ϕ SAD and a preliminary density-modification (DM) phase ϕ DM NHL . The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination

  9. Quantification of Protein Hydration, Glass Transitions, and Structural Relaxations of Aqueous Protein and Carbohydrate-Protein Systems.

    Science.gov (United States)

    Roos, Yrjö H; Potes, Naritchaya

    2015-06-11

    Water distribution and miscibility of carbohydrate and protein components in biological materials and their structural contributions in concentrated solids are poorly understood. In the present study, structural relaxations and a glass transition of protein hydration water and antiplasticization of the hydration water at low temperatures were measured using dynamic mechanical analysis (DMA) and differential scanning calorimetry (DSC) for bovine whey protein (BWP), aqueous glucose-fructose (GF), and their mixture. Thermal transitions of α-lactalbumin and β-lactoglobulin components of BWP included water-content-dependent endothermic but reversible dehydration and denaturation, and exothermic and irreversible aggregation. An α-relaxation assigned to hydration water in BWP appeared at water-content-dependent temperatures and increased to over the range of 150-200 K at decreasing water content and in the presence of GF. Two separate glass transitions and individual fractions of unfrozen water of ternary GF-BWP-water systems contributed to uncoupled α-relaxations, suggesting different roles of protein hydration water and carbohydrate vitrification in concentrated solids during freezing and dehydration. Hydration water in the BWP fraction of GF-BWP systems was derived from equilibrium water sorption and glass transition data of the GF fraction, which gave a significant universal method to quantify (i) protein hydration water and (ii) the unfrozen water in protein-carbohydrate systems for such applications as cryopreservation, freezing, lyophilization, and dehydration of biological materials. A ternary supplemented phase diagram (state diagram) established for the GF-BWP-water system can be used for the analysis of the water distribution across carbohydrate and protein components in such applications.

  10. Zwitterionic states in gas-phase polypeptide ions revealed by 157-nm ultra-violet photodissociation

    DEFF Research Database (Denmark)

    Kjeldsen, Frank; Silivra, Oleg A; Zubarev, Roman A

    2006-01-01

    carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+)...(-)...(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding...... of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm...

  11. Condensation in gas transmission pipelines. Phase behavior of mixtures of hydrogen with natural gas

    Energy Technology Data Exchange (ETDEWEB)

    Schouten, J.A.; Michels, J.P.J. [Amsterdam Univ. (Netherlands). Van der Waals-Zeeman Inst.; Rosmalen, R.J. van [Energy, Roden (Netherlands)

    2005-05-01

    Several pressure and temperature reductions occur along gas transmission lines. Since the pressure and temperature conditions of the natural gas in the pipeline are often close to the dew point curve, liquid dropout can occur. Injection of hydrogen into the natural gas will change the phase envelope and thus the liquid dropout. This condensation of the heavy hydrocarbons requires continuous operational attention and a positive effect of hydrogen may affect the decision to introduce hydrogen. In this paper we report on calculations of the amount of condensate in a natural gas and in this natural gas mixed with 16.7% hydrogen. These calculations have been performed at conditions prevailing in gas transport lines. The results will be used to discuss the difference in liquid dropout in a natural gas and in a mixture with hydrogen at pressure reduction stations, at crossings under waterways, at side-branching, and at separators in the pipelines. (author)

  12. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng

    2016-06-15

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

  13. Importance of the gas phase role to the prediction of energetic material behavior: An experimental study

    International Nuclear Information System (INIS)

    Ali, A.N.; Son, S.F.; Asay, B.W.; Sander, R.K.

    2005-01-01

    Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6 mm±0.4 mm exists below which ignition by CO 2 laser is not possible at the tested irradiances of 29 W/cm 2 and 38 W/cm 2 for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials

  14. Importance of the gas phase role to the prediction of energetic material behavior: An experimental study

    Science.gov (United States)

    Ali, A. N.; Son, S. F.; Asay, B. W.; Sander, R. K.

    2005-03-01

    Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6mm±0.4mm exists below which ignition by CO2 laser is not possible at the tested irradiances of 29W /cm2 and 38W/cm2 for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials.

  15. Simple setup for gas-phase h/d exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale

    DEFF Research Database (Denmark)

    Mistarz, Ulrik Hvid; Brown, Jeffery M; Haselmann, Kim F

    2014-01-01

    gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3....../D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium...

  16. Supercharging Protein Complexes from Aqueous Solution Disrupts their Native Conformations

    Science.gov (United States)

    Sterling, Harry J.; Kintzer, Alexander F.; Feld, Geoffrey K.; Cassou, Catherine A.; Krantz, Bryan A.; Williams, Evan R.

    2012-02-01

    The effects of aqueous solution supercharging on the solution- and gas-phase structures of two protein complexes were investigated using traveling-wave ion mobility-mass spectrometry (TWIMS-MS). Low initial concentrations of m-nitrobenzyl alcohol ( m-NBA) in the electrospray ionization (ESI) solution can effectively increase the charge of concanavalin A dimers and tetramers, but at higher m-NBA concentrations, the increases in charge are accompanied by solution-phase dissociation of the dimers and up to a ~22% increase in the collision cross section (CCS) of the tetramers. With just 0.8% m-NBA added to the ESI solution of a ~630 kDa anthrax toxin octamer complex, the average charge is increased by only ~4% compared with the "native" complex, but it is sufficiently destabilized so that extensive gas-phase fragmentation occurs in the relatively high pressure regions of the TWIMS device. Anthrax toxin complexes exist in either a prechannel or a transmembrane channel state. With m-NBA, the prechannel state of the complex has the same CCS/charge ratio in the gas phase as the transmembrane channel state of the same complex formed without m-NBA, yet undergoes extensive dissociation, indicating that destabilization from supercharging occurs in the ESI droplet prior to ion formation and is not a result of Coulombic destabilization in the gas phase as a result of higher charging. These results demonstrate that the supercharging of large protein complexes is the result of conformational changes induced by the reagents in the ESI droplets, where enrichment of the supercharging reagent during droplet evaporation occurs.

  17. Gas-phase polynuclear aromatic hydrocarbons (PAH) in vehicle exhaust: A method for collection and analysis

    International Nuclear Information System (INIS)

    Seigl, W.O.; Chladek, E.

    1990-01-01

    Gas-phase polynuclear aromatic hydrocarbons (PAH) are emitted at low levels in vehicle exhaust compared to other hydrocarbon emissions. A method has been developed involving the trapping of gas phase emissions on Tenax, a macrorecticular porous polymer, followed by thermal desorption onto a capillary gas chromatography column. Gas chromatography/mass spectrometry (GC/MS) was used for the chemical analysis. A detection limit of 0.05 ng was achieved for several gas-phase PAH. This high sensitivity enables the speciation and quantitation of gas-phase PAH collected from a dilution tube during standard driving (test) cycles. The method was demonstrated for the analysis of 9 PAH in the exhaust from a 1987 vehicle (with and without catalyst) during the hot start transient phase of the EPA urban dynamometer driving schedule. The PAH measured include naphthalene, 2-methyl- and 1-methylnaphthalene, biphenyl, fluorene, phenanthrene, anthracene, fluoranthene and pyrene. The four most abundant PAH observed are naphthalene, 2-methyl and 1-methylnaphthalene, and biphenyl, in that order

  18. The Ultrafast Wolff Rearrangement in the Gas Phase

    Science.gov (United States)

    Steinbacher, Andreas; Roeding, Sebastian; Brixner, Tobias; Nuernberger, Patrick

    The Wolff rearrangement of gas-phase 5-diazo Meldrum's acid is disclosed with femtosecond ion spectroscopy. Distinct differences are found for 267 nm and 200 nm excitation, the latter leading to even two ultrafast rearrangement reactions.

  19. Gas-phase fragmentation of peptides to increase the spatial resolution of the Hydrogen Exchange Mass Spectrometry experiment

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Rand, Kasper Dyrberg

    2016-01-01

    are produced after precursor ion selection and thus do not add complexity to the LC-MS analysis. The key to obtaining optimal spatial resolution in a hydrogen exchange mass spectrometry (HX-MS) experiment is the fragmentation efficiency. This chapter discusses common fragmentation techniques like collision....../D scrambling, thus making them suitable for HX applications. By combining the classic bottom-up HX-MS workflow with gas-phase fragmentation by ETD, detailed information on protein HX can be obtained....

  20. Measurement of pressure fluctuation in gas-liquid two-phase vortex street

    International Nuclear Information System (INIS)

    Sun Zhiqiang; Sang Wenhui; Zhang Hongjian

    2009-01-01

    The pressure fluctuation in the wake is an important parameter to characterize the shedding process of gas-liquid two-phase Karman vortex street. This paper investigated such pressure fluctuations in a horizontal pipe using air and water as the tested fluid media. The dynamic signal representing the pressure fluctuation was acquired by the duct-wall differential pressure method. Results show that in the wake of the gas-liquid two-phase Karman vortex street, the frequency of the pressure fluctuation is linear with the Reynolds number when the volume void fraction is within the range of 18%. Moreover, the mean amplitude of the pressure fluctuation decreases with the volume void fraction, and the mean amplitude is larger at higher water flowrates under the same volume void fraction. These findings contribute to an in-depth understanding of the gas-liquid two-phase Karman vortex street.

  1. Design of functional guanidinium ionic liquid aqueous two-phase systems for the efficient purification of protein.

    Science.gov (United States)

    Ding, Xueqin; Wang, Yuzhi; Zeng, Qun; Chen, Jing; Huang, Yanhua; Xu, Kaijia

    2014-03-07

    A series of novel cationic functional hexaalkylguanidinium ionic liquids and anionic functional tetraalkylguanidinium ionic liquids have been devised and synthesized based on 1,1,3,3-tetramethylguanidine. The structures of the ionic liquids (ILs) were confirmed by (1)H nuclear magnetic resonance ((1)H NMR) and 13C nuclear magnetic resonance (13C NMR) and the production yields were all above 90%. Functional guanidinium ionic liquid aqueous two-phase systems (FGIL-ATPSs) have been first designed with these functional guanidinium ILs and phosphate solution for the purification of protein. After phase separation, proteins had transferred into the IL-rich phase and the concentrations of proteins were determined by measuring the absorbance at 278 nm using an ultra violet visible (UV-vis) spectrophotometer. The advantages of FGIL-ATPSs were compared with ordinary ionic liquid aqueous two-phase systems (IL-ATPSs). The proposed FGIL-ATPS has been applied to purify lysozyme, trypsin, ovalbumin and bovine serum albumin. Single factor experiments were used to research the effects of the process, such as the amount of ionic liquid (IL), the concentration of salt solution, temperature and the amount of protein. The purification efficiency reaches to 97.05%. The secondary structure of protein during the experimental process was observed upon investigation using UV-vis spectrophotometer, Fourier-transform infrared spectroscopy (FT-IR) and circular dichroism spectrum (CD spectrum). The precision, stability and repeatability of the process were investigated. The mechanisms of purification were researched by dynamic light scattering (DLS), determination of the conductivity and transmission electron microscopy (TEM). It was suggested that aggregation and embrace phenomenon play a significant role in the purification of proteins. All the results show that FGIL-ATPSs have huge potential to offer new possibility in the purification of proteins. Copyright © 2014 Elsevier B.V. All rights

  2. Temperature dependence of the particle/gas partition coefficient: An application to predict indoor gas-phase concentrations of semi-volatile organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Wenjuan, E-mail: Wenjuan.Wei@cstb.fr [University of Paris-Est, Scientific and Technical Center for Building (CSTB), Health and Comfort Department, French Indoor Air Quality Observatory (OQAI), 84 Avenue Jean Jaurès, Champs sur Marne, 77447 Marne la Vallée Cedex 2 (France); Mandin, Corinne [University of Paris-Est, Scientific and Technical Center for Building (CSTB), Health and Comfort Department, French Indoor Air Quality Observatory (OQAI), 84 Avenue Jean Jaurès, Champs sur Marne, 77447 Marne la Vallée Cedex 2 (France); INSERM-U1085, Irset-Research Institute for Environmental and Occupational Health, Rennes (France); LERES-Environment and Health Research Laboratory (Irset and EHESP Technologic Platform), Rennes (France); Blanchard, Olivier [EHESP-School of Public Health, Sorbonne Paris Cité, Rennes (France); INSERM-U1085, Irset-Research Institute for Environmental and Occupational Health, Rennes (France); Mercier, Fabien [EHESP-School of Public Health, Sorbonne Paris Cité, Rennes (France); LERES-Environment and Health Research Laboratory (Irset and EHESP Technologic Platform), Rennes (France); INSERM-U1085, Irset-Research Institute for Environmental and Occupational Health, Rennes (France); Pelletier, Maud [EHESP-School of Public Health, Sorbonne Paris Cité, Rennes (France); INSERM-U1085, Irset-Research Institute for Environmental and Occupational Health, Rennes (France); Le Bot, Barbara [EHESP-School of Public Health, Sorbonne Paris Cité, Rennes (France); LERES-Environment and Health Research Laboratory (Irset and EHESP Technologic Platform), Rennes (France); INSERM-U1085, Irset-Research Institute for Environmental and Occupational Health, Rennes (France); and others

    2016-09-01

    The indoor gas-phase concentrations of semi-volatile organic compounds (SVOCs) can be predicted from their respective concentrations in airborne particles by applying the particle/gas partitioning equilibrium. The temperature used for partitioning is often set to 25 °C. However, indoor temperatures frequently differ from this reference value. This assumption may result in errors in the predicted equilibrium gas-phase SVOC concentrations. To improve the prediction model, the temperature dependence of the particle/gas partition coefficient must be addressed. In this paper, a theoretical relationship between the particle/gas partition coefficient and temperature was developed based on the SVOC absorptive mechanism. The SVOC particle/gas partition coefficients predicted by employing the derived theoretical relationship agree well with the experimental data retrieved from the literature (R > 0.93). The influence of temperature on the equilibrium gas-phase SVOC concentration was quantified by a dimensionless analysis of the derived relationship between the SVOC particle/gas partition coefficient and temperature. The predicted equilibrium gas-phase SVOC concentration decreased by between 31% and 53% when the temperature was lowered by 6 °C, while it increased by up to 750% when the indoor temperature increased from 15 °C to 30 °C. - Highlights: • A theoretical relationship between K{sub p} and temperature was developed. • The relationship was based on the SVOC absorptive mechanism. • The temperature impact was quantified by a dimensionless analysis.

  3. Additional phase information from UV damage of selenomethionine labelled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Sanctis, Daniele de [ESRF, Structural Biology Group, 6 rue Jules Horowitz, 38043 Grenoble Cedex (France); Tucker, Paul A.; Panjikar, Santosh, E-mail: panjikar@embl-hamburg.de [EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg (Germany)

    2011-05-01

    Successful examples of ultraviolet radiation-damage-induced phasing with anomalous scattering from selenomethionine protein crystals have been demonstrated. Currently, selenium is the most widely used phasing vehicle for experimental phasing, either by single anomalous scattering or multiple-wavelength anomalous dispersion (MAD) procedures. The use of the single isomorphous replacement anomalous scattering (SIRAS) phasing procedure with selenomethionine containing proteins is not so commonly used, as it requires isomorphous native data. Here it is demonstrated that isomorphous differences can be measured from intensity changes measured from a selenium labelled protein crystal before and after UV exposure. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment. The phasing procedure for two selenomethionine proteins, the feruloyl esterase module of xylanase 10B from Clostridium thermocellum and the Mycobacterium tuberculosis chorismate synthase, have been investigated using datasets collected near the absorption edge of selenium before and after UV radiation. The utility of UV radiation in measuring radiation damage data for isomorphous differences is highlighted and it is shown that, after such measurements, the UV-RIPAS procedure yields comparable phase sets with those obtained from the conventional MAD procedure. The results presented are encouraging for the development of alternative phasing approaches for selenomethionine proteins in difficult cases.

  4. IRMPD Action Spectroscopy of Alkali Metal Cation-Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation

    NARCIS (Netherlands)

    Yang, B.; Wu, R.R.; Polfer, N.C.; Berden, G.; Oomens, J.; Rodgers, M.T.

    2013-01-01

    The gas-phase structures of alkali metal cation-cytosine complexes generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra of five alkali metal cation-cytosine complexes exhibit both

  5. The liquid protein phase in crystallization: a case study—intact immunoglobulins

    Science.gov (United States)

    Kuznetsov, Yurii G.; Malkin, Alexander J.; McPherson, Alexander

    2001-11-01

    A common observation by protein chemists has been the appearance, for many proteins in aqueous solutions, of oil like droplets, or in more extreme cases the formation of a second oil like phase. These may accompany the formation of precipitate in "salting out" or "salting in' procedures, but more commonly appear in place of any precipitate. Such phase separations also occur, with even greater frequency, in the presence of polymeric precipitants such as polyethyleneglycol (PEG). In general the appearance of a second liquid phase has been taken as indicative of protein aggregation, though an aggregate state distinctly different from that characteristic of amorphous precipitate. While the latter is thought to be composed of linear and branched assemblies, polymers of a sort, the oil phase suggests a more compact, three-dimensional, but fluid state. An important property of an alternate, fluid phase is that it can mediate transitions between other states, for example, between protein molecules free in solution and protein molecules immobilized in amorphous precipitate or crystals. The "liquid protein" phase can be readily observed in many crystallization experiments either prior to the appearance of visible crystals, or directly participating in the crystal growth process. In some cases the relationship between the liquid phase and developing crystals is intimate. Crystals grow directly from the liquid phase, or appear only after the visible formation of the liquid phase. We describe here our experience with a class of macromolecules, immunoglobulins, and particularly IDEC-151, an IgG specific for CD4 on human lymphocytes. This protein has been crystallized from a Jeffamine-LiSO 4 mother liquor and, its crystallization illustrates many of the features associated with the liquid protein, or protein rich phase.

  6. Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

    Directory of Open Access Journals (Sweden)

    Zhen Huang

    2008-03-01

    Full Text Available Selenium derivatization (via selenomethionine of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2’-position of the ribose. All the synthesis of 2’-SeMe modified phosphoramidite building blocks (U, C, T, A, G and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

  7. Monitoring gas-phase CO2 in the headspace of champagne glasses through combined diode laser spectrometry and micro-gas chromatography analysis.

    Science.gov (United States)

    Moriaux, Anne-Laure; Vallon, Raphaël; Parvitte, Bertrand; Zeninari, Virginie; Liger-Belair, Gérard; Cilindre, Clara

    2018-10-30

    During Champagne or sparkling wine tasting, gas-phase CO 2 and volatile organic compounds invade the headspace above glasses, thus progressively modifying the chemical space perceived by the consumer. Gas-phase CO 2 in excess can even cause a very unpleasant tingling sensation perturbing both ortho- and retronasal olfactory perception. Monitoring as accurately as possible the level of gas-phase CO 2 above glasses is therefore a challenge of importance aimed at better understanding the close relationship between the release of CO 2 and a collection of various tasting parameters. Here, the concentration of CO 2 found in the headspace of champagne glasses served under multivariate conditions was accurately monitored, all along the 10 min following pouring, through a new combined approach by a CO 2 -Diode Laser Sensor and micro-gas chromatography. Our results show the strong impact of various tasting conditions (volume dispensed, intensity of effervescence, and glass shape) on the release of gas-phase CO 2 above the champagne surface. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Possibilities of gas-phase radio-chromatography application to permanent-gas analysis

    International Nuclear Information System (INIS)

    Dupuis, M.C.; Charrier, G.; Alba, C.; Massimino, D.

    1970-01-01

    The gas-phase radio-chromatography technique has been applied to the rapid analysis of permanent gases (H 2 , O 2 , N 2 , A, Kr, Xe, CO, CH 4 ) labelled with radioactive indicators ( 3 H, 37 A, 85 Kr, 133 Xe). After calibration, the components of such a mixture can be identified and their concentrations measured in less than two hours, using a sample volume of from 0.1 to 10 cm 3 . The minimum detectable activity is of the order of 10 -4 μC for each radioactive isotope. The measurements are reproducible to about 2 to 3 per cent. This work has been mainly concerned with the influence of parameters affecting the response of the radioactivity detector (ionization chamber or gas flow proportional counter). The method has very numerous applications both theoretically, for the study of chromatographic phenomena under ideal conditions (infinitesimal concentrations made possible by the use of radioactive tracers), and practically, for rapid and accurate radiochemical analysis of radioactive gas mixtures. (authors) [fr

  9. Design of functional guanidinium ionic liquid aqueous two-phase systems for the efficient purification of protein

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Xueqin; Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn; Zeng, Qun; Chen, Jing; Huang, Yanhua; Xu, Kaijia

    2014-03-01

    Graphical abstract: - Highlights: • A series of novel cationic functional hexaalkylguanidinium ionic liquids and anionic functional tetraalkylguanidinium ionic liquids have been synthesized. • Functional guanidinium ionic liquid aqueous two-phase systems have been first designed for the purification of protein. • Mechanisms and performances of the process were researched. • Simple, green, safety and presents better purified ability than ordinary process. • A potential efficient platform for protein purification and related studies. - Abstract: A series of novel cationic functional hexaalkylguanidinium ionic liquids and anionic functional tetraalkylguanidinium ionic liquids have been devised and synthesized based on 1,1,3,3-tetramethylguanidine. The structures of the ionic liquids (ILs) were confirmed by {sup 1}H nuclear magnetic resonance ({sup 1}H NMR) and 13C nuclear magnetic resonance (13C NMR) and the production yields were all above 90%. Functional guanidinium ionic liquid aqueous two-phase systems (FGIL-ATPSs) have been first designed with these functional guanidinium ILs and phosphate solution for the purification of protein. After phase separation, proteins had transferred into the IL-rich phase and the concentrations of proteins were determined by measuring the absorbance at 278 nm using an ultra violet visible (UV–vis) spectrophotometer. The advantages of FGIL-ATPSs were compared with ordinary ionic liquid aqueous two-phase systems (IL-ATPSs). The proposed FGIL-ATPS has been applied to purify lysozyme, trypsin, ovalbumin and bovine serum albumin. Single factor experiments were used to research the effects of the process, such as the amount of ionic liquid (IL), the concentration of salt solution, temperature and the amount of protein. The purification efficiency reaches to 97.05%. The secondary structure of protein during the experimental process was observed upon investigation using UV–vis spectrophotometer, Fourier-transform infrared

  10. Infrared multiple photon dissociation action spectroscopy of alkali metal cation-cyclen complexes: Effects of alkali metal cation size on gas-phase conformation

    NARCIS (Netherlands)

    Austin, C.A.; Chen, Y.; Kaczan, C.M.; Berden, G.; Oomens, J.; Rodgers, M.T.

    2013-01-01

    The gas-phase structures of alkali metal cationized complexes of cyclen (1,4,7,10-tetraazacyclododecane) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure theory calculations. The measured IRMPD action spectra of four M+(cyclen) complexes are

  11. Photocatalytic Activity of Nanotubular TiO2 Films Obtained by Anodic Oxidation: A Comparison in Gas and Liquid Phase

    Directory of Open Access Journals (Sweden)

    Beatriz Eugenia Sanabria Arenas

    2018-03-01

    Full Text Available The availability of immobilized nanostructured photocatalysts is of great importance in the purification of both polluted air and liquids (e.g., industrial wastewaters. Metal-supported titanium dioxide films with nanotubular morphology and good photocatalytic efficiency in both environments can be produced by anodic oxidation, which avoids release of nanoscale materials in the environment. Here we evaluate the effect of different anodizing procedures on the photocatalytic activity of TiO2 nanostructures in gas and liquid phases, in order to identify the most efficient and robust technique for the production of TiO2 layers with different morphologies and high photocatalytic activity in both phases. Rhodamine B and toluene were used as model pollutants in the two media, respectively. It was found that the role of the anodizing electrolyte is particularly crucial, as it provides substantial differences in the oxide specific surface area: nanotubular structures show remarkably different activities, especially in gas phase degradation reactions, and within nanotubular structures, those produced by organic electrolytes lead to better photocatalytic activity in both conditions tested.

  12. Numerical simulation of gas-solid two-phase flow in U-beam separator

    International Nuclear Information System (INIS)

    Zhou, X Y; Chen, X P; Dou, H S; Zhang, H Z; Ruan, J M

    2015-01-01

    Numerical simulation is carried out for gas-solid two-phase flow in a U-beam separator. In this study, the U-beam is altered with the inlet fins in order to improve the performance of the separator. The inlet fin angle of the separator are 30°, 35°, 40°, 45°, 50°, 55 ° and 60°. The governing equations are the Reynolds-Averaged Navier-Stokes equation with the standard k-ε model and the discrete phase model (DPM) describing the discrete two - phase flow as well as stochastic tracking model. Results show that the pressure drop deviation with fins is within 3% from those without fins. It is found that there is a maximum separation efficiency at the fin angle of 35°. Fin induces generation of a stagnation region which could collect particles and lead to change of vortical structures. The fin induced flow also causes the turbulent intensity inside the baffle to decrease to facilitate separation

  13. Diode Laser Raman Scattering Prototype Gas-Phase Environmental Monitoring

    National Research Council Canada - National Science Library

    Benner, Robert

    1999-01-01

    We proposed developing a diode-laser-based, full spectrum Raman scattering instrument incorporating a multipass, external cavity enhancement cell for full spectrum, gas phase analysis of environmental pollutants...

  14. New set-up for high-quality soft-X-ray absorption spectroscopy of large organic molecules in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Holch, Florian; Huebner, Dominique [Universitaet Wuerzburg, Experimentelle Physik VII, Am and Roentgen Reasearch Center for Complex Materials (RCCM) Hubland, 97074 Wuerzburg (Germany); Fink, Rainer [Universitaet Erlangen-Nuernberg, ICMM and CENEM, Egerlandstrasse 3, 91058 Erlangen (Germany); Schoell, Achim, E-mail: achim.schoell@physik.uni-wuerzburg.de [Universitaet Wuerzburg, Experimentelle Physik VII, Am and Roentgen Reasearch Center for Complex Materials (RCCM) Hubland, 97074 Wuerzburg (Germany); Umbach, Eberhard [Karlsruhe Institute of Technology, 76021 Karlsruhe (Germany)

    2011-11-15

    Highlights: {yields} We present a new set-up for x-ray absorption (NEXAFS) on large molecules in the gas-phase. {yields} The cell has a confined volume and can be heated. {yields} The spectra can be acquired fast, are of very high quality with respect tosignal-to-noise ratio and energy resolution. {yields} This allowsthe analysis of spectroscopic details (e.g. solid state effects by comparing gas- and condensed phase data). - Abstract: We present a new experimental set-up for the investigation of large (>128 amu) organic molecules in the gas-phase by means of near-edge X-ray absorption fine structure spectroscopy in the soft X-ray range. Our approach uses a gas cell, which is sealed off against the surrounding vacuum and which can be heated above the sublimation temperature of the respective molecular compound. Using a confined volume rather than a molecular beam yields short acquisition times and intense signals due to the high molecular density, which can be tuned by the container temperature. In turn, the resulting spectra are of very high quality with respect to signal-to-noise ratio and energy resolution, which are the essential aspects for the analysis of fine spectroscopic details. Using the examples of ANQ, NTCDA, and PTCDA, specific challenges of gas phase measurements on large organic molecules with high sublimation temperatures are addressed in detail with respect to the presented set-up and possible ways to tackle them are outlined.

  15. SDSL-ESR-based protein structure characterization.

    Science.gov (United States)

    Strancar, Janez; Kavalenka, Aleh; Urbancic, Iztok; Ljubetic, Ajasja; Hemminga, Marcus A

    2010-03-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.

  16. Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

    Science.gov (United States)

    Wang, Guanbo; Kaltashov, Igor A

    2014-08-05

    Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

  17. Gas-phase nitrosation of ethylene and related events in the C2H4NO+ landscape.

    Science.gov (United States)

    Gerbaux, Pascal; Dechamps, Noemie; Flammang, Robert; Nam, Pham Cam; Nguyen, Minh Tho; Djazi, Fayçal; Berruyer, Florence; Bouchoux, Guy

    2008-06-19

    The C2H4NO(+) system has been examined by means of quantum chemical calculations using the G2 and G3B3 approaches and tandem mass spectrometry experiments. Theoretical investigation of the C2H4NO(+) potential-energy surface includes 19 stable C2H4NO(+) structures and a large set of their possible interconnections. These computations provide insights for the understanding of the (i) addition of the nitrosonium cation NO(+) to the ethylene molecule, (ii) skeletal rearrangements evidenced in previous experimental studies on comparable systems, and (iii) experimental identification of new C2H4NO(+) structures. It is predicted from computation that gas-phase nitrosation of ethylene may produce C2H4(*)NO(+) adducts, the most stable structure of which is a pi-complex, 1, stabilized by ca. 65 kJ/mol with respect to its separated components. This complex was produced in the gas phase by a transnitrosation process involving as reactant a complex between water and NO(+) (H2O.NO(+)) and the ethylene molecule and fully characterized by collisional experiments. Among the other C 2H 4NO (+) structures predicted by theory to be protected against dissociation or isomerization by significant energy barriers, five were also experimentally identified. These finding include structures CH3CHNO(+) (5), CH 3CNOH (+) ( 8), CH3NHCO(+) (18), CH3NCOH(+) (19), and an ion/neutral complex CH2O...HCNH(+) (12).

  18. Numerical simulation for gas-liquid two-phase flow in pipe networks

    International Nuclear Information System (INIS)

    Li Xiaoyan; Kuang Bo; Zhou Guoliang; Xu Jijun

    1998-01-01

    The complex pipe network characters can not directly presented in single phase flow, gas-liquid two phase flow pressure drop and void rate change model. Apply fluid network theory and computer numerical simulation technology to phase flow pipe networks carried out simulate and compute. Simulate result shows that flow resistance distribution is non-linear in two phase pipe network

  19. Phase equilibria and phase structures of polymer blends

    International Nuclear Information System (INIS)

    Chalykh, Anatolii E; Gerasimov, Vladimir K

    2004-01-01

    Experimental, methodical and theoretical studies dealing with phase equilibria and phase structures of polymer blends are generalised. The general and specific features of the change in solubility of polymers with changes in the molecular mass and copolymer composition and upon the formation of three-dimensional cross-linked networks are described. The results of the effect of the prehistory on the phase structure and the non-equilibrium state of polymer blends are considered in detail.

  20. Silica, alumina and aluminosilicates as solid stationary phases in gas chromatography

    Directory of Open Access Journals (Sweden)

    S. Faramawy

    2016-09-01

    Full Text Available Silica, alumina and Aluminosilicates of different Si/Al ratios were prepared by conventional precipitation or co-precipitation methods and then subjected to thermal treatment at 800 °C. The parent and thermally treated materials were characterized by means of FTIR, SEM and thermal analysis (DTA and TGA in order to elucidate the main structural properties. Surface textural characteristics were investigated by means of nitrogen adsorption–desorption isotherms at −196 °C. Pore size distribution curves indicated the presence of mesopores (10–150 Å exhibiting maxima at 35 Å. The maxima were shifted toward higher values by increasing the alumina content. Thermodynamic parameters, ΔH, ΔG and ΔS, were determined by means of inverse gas chromatography using n-hexane as a probe. The untreated and thermally treated materials were tested as solid stationary phases in gas chromatography. The separation efficiency of various non polar and polar compounds was explained in terms of surface texture and thermodynamic parameters.

  1. Structure and non-structure of centrosomal proteins.

    Science.gov (United States)

    Dos Santos, Helena G; Abia, David; Janowski, Robert; Mortuza, Gulnahar; Bertero, Michela G; Boutin, Maïlys; Guarín, Nayibe; Méndez-Giraldez, Raúl; Nuñez, Alfonso; Pedrero, Juan G; Redondo, Pilar; Sanz, María; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, José M; Gonzalez, Cayetano; Reina, José; Valpuesta, José M; Vernos, Isabelle; Zabala, Juan C; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis

    2013-01-01

    Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

  2. The Stability of CI02 as a Product of Gas Phase Decontamination Treatments

    International Nuclear Information System (INIS)

    Simmons, D. W.

    1994-01-01

    The gas phase decontamination project is investigating the use of chlorine trifluoride (ClF 3 ) to fluorinate nonvolatile uranium deposits to produce uranium hexafluoride (UF 6 ) gas. The potential existence of chlorine dioxide (ClO 2 ) during gas phase decontamination with ClF 3 has been the subject of recent safety discussions. Some of the laboratory data collected during feasibility studies of the gas phase process has been evaluated for the presence of ClO 2 in the product gas stream. The preliminary evidence to date can be summarized as follows: (1) ClO 2 was not detected in the flow loop in the absence of ClF 3 ; (2) ClO 2 was not detected in the static reactors in the absence of both ClF 3 and ClF; and (3) ClO 2 was detected in a static reactor in the absence of all fluorinating gases. The experimental evidence suggests that ClO 2 will not exist in the presence of ClF 3 , ClF, or UF 6 . The data analyzed to date is insufficient to determine the stability of ClO 2 in the presence of ClO 2 F. Thermodynamic calculations of the ClF 3 + H 2 O system support the experimental evidence, and suggest that ClO 2 will not exist in the presence of ClO 2 F. Additional experimental efforts are needed to provide a better understanding of the gas phase ClF 3 treatments and the product gases. However, preliminary evidence to date suggests that ClO 2 should not be present as a product during the normal operations of the gas phase decontamination project

  3. The gas-phase bis-uranyl nitrate complex ((UO2)2(NO3)5)-: infrared spectrum and structure

    International Nuclear Information System (INIS)

    Groenewold, Gary S.; van Stipdonk, Michael J.; Oomens, Jos; de Jong, Wibe; McIlwain, Michael E.

    2011-01-01

    The infrared spectrum of the bis-uranyl nitrate complex ((UO 2 ) 2 (NO 3 ) 5 ) - was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate nu3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex ((UO 2 ) 2 (NO 3 ) 5 ) - compared to the mono-complex (UO 2 (NO 3 ) 3 ) - , as indicated by a higher O-U-O asymmetric stretching (nu3) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the ν 3 frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The structure was calculated using density functional theory (B3LYP functional), which produced a structure in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  4. Development of techniques in magnetic resonance and structural studies of the prion protein

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, Hans-Marcus L. [Univ. of California, Berkeley, CA (United States)

    2000-07-01

    Magnetic resonance is the most powerful analytical tool used by chemists today. Its applications range from determining structures of large biomolecules to imaging of human brains. Nevertheless, magnetic resonance remains a relatively young field, in which many techniques are currently being developed that have broad applications. In this dissertation, two new techniques are presented, one that enables the determination of torsion angles in solid-state peptides and proteins, and another that involves imaging of heterogenous materials at ultra-low magnetic fields. In addition, structural studies of the prion protein via solid-state NMR are described. More specifically, work is presented in which the dependence of chemical shifts on local molecular structure is used to predict chemical shift tensors in solid-state peptides with theoretical ab initio surfaces. These predictions are then used to determine the backbone dihedral angles in peptides. This method utilizes the theoretical chemicalshift tensors and experimentally determined chemical-shift anisotropies (CSAs) to predict the backbone and side chain torsion angles in alanine, leucine, and valine residues. Additionally, structural studies of prion protein fragments are described in which conformationally-dependent chemical-shift measurements were made to gain insight into the structural differences between the various conformational states of the prion protein. These studies are of biological and pathological interest since conformational changes in the prion protein are believed to cause prion diseases. Finally, an ultra-low field magnetic resonance imaging technique is described that enables imaging and characterization of heterogeneous and porous media. The notion of imaging gases at ultra-low fields would appear to be very difficult due to the prohibitively low polarization and spin densities as well as the low sensitivities of conventional Faraday coil detectors. However, Chapter 5 describes how gas imaging

  5. Mainstream Smoke Gas Phase Filtration Performance of Adsorption Materials Evaluated With A Puff-by-Puff Multiplex GC-MS Method

    Directory of Open Access Journals (Sweden)

    Xue L

    2014-12-01

    Full Text Available The mainstream smoke filtration performance of activated carbon, silica gel and polymeric aromatic resins for gas-phase components was evaluated using a puff-by-puff multiplex gas chromatography-mass spectrometry (GC-MS analysis method (1. The sample 1R4F Kentucky reference cigarettes were modified by placing the adsorbents in a plug/space/plug filter configuration. Due to differences in surface area and structural characteristics, the adsorbent materials studied showed different levels of filtration activities for the twenty-six constituents monitored. Activated carbon had significant adsorption activity for all the gas-phase smoke constituents observed except ethane and carbon dioxide, while silica gel had significant activities for polar components such as aldehydes, acrolein, ketones, and diacetyl. XAD-16 polyaromatic resins showed varied levels of activity for aromatic compounds, cyclic dienes and ketones.

  6. Phase space analysis of some interacting Chaplygin gas models

    Energy Technology Data Exchange (ETDEWEB)

    Khurshudyan, M. [Academy of Sciences of Armenia, Institute for Physical Research, Ashtarak (Armenia); Tomsk State University of Control Systems and Radioelectronics, Laboratory for Theoretical Cosmology, Tomsk (Russian Federation); Tomsk State Pedagogical University, Department of Theoretical Physics, Tomsk (Russian Federation); Myrzakulov, R. [Eurasian National University, Eurasian International Center for Theoretical Physics, Astana (Kazakhstan)

    2017-02-15

    In this paper we discuss a phase space analysis of various interacting Chaplygin gas models in general relativity. Linear and nonlinear sign changeable interactions are considered. For each case appropriate late time attractors of field equations are found. The Chaplygin gas is one of the dark fluids actively considered in modern cosmology due to the fact that it is a joint model of dark energy and dark matter. (orig.)

  7. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  8. A gas-phase reactor powered by solar energy and ethanol for H2 production

    International Nuclear Information System (INIS)

    Ampelli, Claudio; Genovese, Chiara; Passalacqua, Rosalba; Perathoner, Siglinda; Centi, Gabriele

    2014-01-01

    In the view of H 2 as the future energy vector, we presented here the development of a homemade photo-reactor working in gas phase and easily interfacing with fuel cell devices, for H 2 production by ethanol dehydrogenation. The process generates acetaldehyde as the main co-product, which is more economically advantageous with respect to the low valuable CO 2 produced in the alternative pathway of ethanol photoreforming. The materials adopted as photocatalysts are based on TiO 2 substrates but properly modified with noble (Au) and not-noble (Cu) metals to enhance light harvesting in the visible region. The samples were characterized by BET surface area analysis, Transmission Electron Microscopy (TEM) and UV–visible Diffusive Reflectance Spectroscopy, and finally tested in our homemade photo-reactor by simulated solar irradiation. We discussed about the benefits of operating in gas phase with respect to a conventional slurry photo-reactor (minimization of scattering phenomena, no metal leaching, easy product recovery, etc.). Results showed that high H 2 productivity can be obtained in gas phase conditions, also irradiating titania photocatalysts doped with not-noble metals. - Highlights: • A gas-phase photoreactor for H 2 production by ethanol dehydrogenation was developed. • The photocatalytic behaviours of Au and Cu metal-doped TiO 2 thin layers are compared. • Benefits of operating in gas phase with respect to a slurry reactor are presented. • Gas phase conditions and use of not-noble metals are the best economic solution

  9. Acute Phase Proteins and Variables of Protein Metabolism in Dairy Cows during the Pre- and Postpartal Period

    Directory of Open Access Journals (Sweden)

    Cs. Tóthová

    2008-01-01

    Full Text Available The objective of the present study was to compare the concentrations of acute phase proteins and selected variables of protein metabolism in dairy cows of the Slovak Spotted breed from 4 weeks before parturition to 10 weeks after parturition. Acute phase proteins - haptoglobin (Hp and serum amyloid A (SAA - and variables of protein metabolism - total proteins, albumin, urea, creatinine, total immunoglobulins - were evaluated in blood serum. Significant differences were found in average values of the Hp and SAA concentrations in several groups during the monitored period (P P P P P P P P P < 0.001. The above mentioned results indicate that in the time around parturition there are significant changes in concentrations of acute phase proteins, as well as in the whole protein metabolism of dairy cows. These facts suggest that the postparturient period is a critical biological phase, throughout which there is the highest incidence of metabolic disorders.

  10. GAS PHASE SELECTIVE PHOTOXIDATION OF ALCOHOLS USING LIGHT-ACTIVATED TITANIUM DIOXIDE AND MOLECULAR OXYGEN

    Science.gov (United States)

    Gas Phase Selective Oxidation of Alcohols Using Light-Activated Titanium Dioxide and Molecular Oxygen Gas phase selective oxidations of various primary and secondary alcohols are studied in an indigenously built stainless steel up-flow photochemical reactor using ultravi...

  11. Numerical Method based on SIMPLE Algorithm for a Two-Phase Flow with Non-condensable Gas

    International Nuclear Information System (INIS)

    Kim, Jong Tae

    2009-08-01

    In this study, a numerical method based on SIMPLE algorithm for a two-phase flow with non-condensable gas has been developed in order to simulate thermal hydraulics in a containment of a nuclear power plant. As governing equations, it adopts a two-fluid three-field model for the two-phase flows. The three fields include gas, drops, and continuous liquid. The gas field can contains vapor and non-condensable gases such as air and hydrogen. In order to resolve mixing phenomena of gas species, gas transport equations for each species base on the gas mass fractions are solved with gas phase governing equations such as mass, momentum and energy equations. Methods to evaluate the properties of the gas species were implemented in the code. They are constant or polynomial function based a user input and a property library from Chemkin and JANAF table for gas specific heat. Properties for the gas mixture which are dependent on mole fractions of the gas species were evaluated by a mix rule

  12. Fundamental research of two-phase flows with high liquid/gas density ratios

    International Nuclear Information System (INIS)

    Mishima, Kaichiro; Hibiki, Takashi; Saito, Yasushi; Tobita, Yoshiharu; Konishi, Kensuke; Suzuki, Tohru

    2000-07-01

    In order to analyze the boiling of a fuel-steel mixture pool formed during the core disruptive accident in a fast breeder reactor, it is important to understand the flow characteristics of gas-liquid two-phase pools containing molten reactor materials. Since the liquid/gas density ratio is high, the characteristics of such two-phase flows may differ from those of ordinary flows such as water/air flow. In this study, as a fundamental research of two-phase flows with a high liquid/gas density ratio, the experiments were performed to visualize and measure molten metal (lead-bismuth)/nitrogen gas two-phase flows using a neutron radiography technique. From these experiments, fundamental data such as bubble shapes, void fractions and liquid velocity fields were obtained. In addition, the momentum exchange model of SIMMER-III, which has been developed by JNC, was assessed and improved using the experimental data. In the visualization by neutron radiography, it was found that deformed ellipsoidal bubbles could be seen with smaller gas flux or lower void fractions, and spherical cap bubbles could be seen with larger gas flux or higher void fractions. In addition, a correlation applicable to SIMMER-III was proposed through a comparison between the experimental data and traditional empirical correlations. Furthermore, a visualization experiment using gold-cadmium tracer particles showed that the image processing technique used in the quantification of void fractions is applicable to the measurement of the liquid velocity fields. On the other hand, in the analysis by SIMMER-III, it was confirmed that the original momentum exchange model was appropriate for ellipsoidal bobby flows and that the accuracy of SIMMER-III for cap bubbly flows was much improved with the proposed correlation. Moreover, a new procedure, in which the appropriate drag coefficient could be automatically selected according to bubble shape, was developed. The SIMMER-III code improved through this study can

  13. Conformational Preferences of Glycerol in the Gas Phase and in Water

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Keun Hong [Korea Military Academy, Seoul (Korea, Republic of); Byun, Byung Jin; Kang, Young Kee [Chungbuk National University, Cheongju (Korea, Republic of)

    2012-03-15

    The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two C{sub 5} hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory

  14. Deliberate and Accidental Gas-Phase Alkali Doping of Chalcogenide Semiconductors: Cu(In,Ga)Se2.

    Science.gov (United States)

    Colombara, Diego; Berner, Ulrich; Ciccioli, Andrea; Malaquias, João C; Bertram, Tobias; Crossay, Alexandre; Schöneich, Michael; Meadows, Helene J; Regesch, David; Delsante, Simona; Gigli, Guido; Valle, Nathalie; Guillot, Jérome; El Adib, Brahime; Grysan, Patrick; Dale, Phillip J

    2017-02-24

    Alkali metal doping is essential to achieve highly efficient energy conversion in Cu(In,Ga)Se 2 (CIGSe) solar cells. Doping is normally achieved through solid state reactions, but recent observations of gas-phase alkali transport in the kesterite sulfide (Cu 2 ZnSnS 4 ) system (re)open the way to a novel gas-phase doping strategy. However, the current understanding of gas-phase alkali transport is very limited. This work (i) shows that CIGSe device efficiency can be improved from 2% to 8% by gas-phase sodium incorporation alone, (ii) identifies the most likely routes for gas-phase alkali transport based on mass spectrometric studies, (iii) provides thermochemical computations to rationalize the observations and (iv) critically discusses the subject literature with the aim to better understand the chemical basis of the phenomenon. These results suggest that accidental alkali metal doping occurs all the time, that a controlled vapor pressure of alkali metal could be applied during growth to dope the semiconductor, and that it may have to be accounted for during the currently used solid state doping routes. It is concluded that alkali gas-phase transport occurs through a plurality of routes and cannot be attributed to one single source.

  15. BLAST-based structural annotation of protein residues using Protein Data Bank.

    Science.gov (United States)

    Singh, Harinder; Raghava, Gajendra P S

    2016-01-25

    In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

  16. Molecular structure of tetramethylgermane from gas electron diffraction

    Science.gov (United States)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  17. Resolving Gas-Phase Metallicity In Galaxies

    Science.gov (United States)

    Carton, David

    2017-06-01

    Chapter 2: As part of the Bluedisk survey we analyse the radial gas-phase metallicity profiles of 50 late-type galaxies. We compare the metallicity profiles of a sample of HI-rich galaxies against a control sample of HI-'normal' galaxies. We find the metallicity gradient of a galaxy to be strongly correlated with its HI mass fraction {M}{HI}) / {M}_{\\ast}). We note that some galaxies exhibit a steeper metallicity profile in the outer disc than in the inner disc. These galaxies are found in both the HI-rich and control samples. This contradicts a previous indication that these outer drops are exclusive to HI-rich galaxies. These effects are not driven by bars, although we do find some indication that barred galaxies have flatter metallicity profiles. By applying a simple analytical model we are able to account for the variety of metallicity profiles that the two samples present. The success of this model implies that the metallicity in these isolated galaxies may be in a local equilibrium, regulated by star formation. This insight could provide an explanation of the observed local mass-metallicity relation. Chapter 3 We present a method to recover the gas-phase metallicity gradients from integral field spectroscopic (IFS) observations of barely resolved galaxies. We take a forward modelling approach and compare our models to the observed spatial distribution of emission line fluxes, accounting for the degrading effects of seeing and spatial binning. The method is flexible and is not limited to particular emission lines or instruments. We test the model through comparison to synthetic observations and use downgraded observations of nearby galaxies to validate this work. As a proof of concept we also apply the model to real IFS observations of high-redshift galaxies. From our testing we show that the inferred metallicity gradients and central metallicities are fairly insensitive to the assumptions made in the model and that they are reliably recovered for galaxies

  18. Laboratory investigations of the alpha-pinene/ozone gas-phase reaction

    International Nuclear Information System (INIS)

    Benner, C.L.

    1985-01-01

    In order to provide more insight into terpene photooxidation or ozonolysis reaction mechanisms, a radiotracer technique was developed. This technique was applied to an investigation of the 14 C-alpha-pinene/ozone reaction. In the first phase of the research, the carbon distribution at the conclusion of the ozonolysis reaction was determined by separating carbon-14-labelled gaseous products from labelled aerosols, and counting each phase by liquid scintillation methods. The resulting carbon balance was 38% to 60% filtered aerosols, 6% to 20% gas phase compounds, and 11% to 29% products absorbed on the reaction chamber walls. Recoveries of the alpha-pinene carbon-14 ranging from 79% to 97% were achieved using this method. The alpha-pinene concentrations in these experiments were close to ambient (1 part per billion), yet the carbon balance was similar to that observed at much higher concentrations (>1 part per million). In the second phase of the alpha-pinene study, both gas and aerosol products of the ozonolysis reaction were collected on cartridges impregnated with 2,4-dinitrophenylhydrazine, then analyzed by HPLC. In the final experiments, alpha-pinene aerosol was reacted with a silylating agent to improve the detection of organic acids and alcohols. The gas chromatographic/mass spectrometric analysis of the silylated aerosol products showed evidence of dimer/polymer formation occurring in the ozonolysis reaction

  19. Modeling and simulation of a pseudo-two-phase gas-liquid column reactor for thermal hydrocracking of petroleum heavy fractions

    Directory of Open Access Journals (Sweden)

    E.M. Matos

    2002-07-01

    Full Text Available This work presents a model to predict the behavior of velocity, gas holdup and local concentration fields in a pseudo-two-phase gas-liquid column reactor applied for thermal hydrocracking of petroleum heavy fractions. The model is based on the momentum and mass balances for the system, using an Eulerian-Eulerian approach. Using the k-epsilon model,fluid dynamics accounts for both laminar and turbulent flows, with discrete small bubbles (hydrogen flowing in a continuous pseudohomogeneous liquid phase (oil and catalyst particles. The petroleum is assumed to be a mixture of pseudocomponents, grouped by similar chemical structural properties, and the thermal hydrocracking is taken into account using a kinetic network based on these pseudocomponents.

  20. Mixed-mode reversed phase/positively charged repulsion chromatography for intact protein separation.

    Science.gov (United States)

    Ding, Ling; Guo, Zhimou; Hu, Zhuo; Liang, Xinmiao

    2017-05-10

    A mixed-mode reversed phase/positively charged repulsion stationary phase C8PN composed of octyl and amino group has been developed for separation of intact protein. Before the separation of proteins, a set of probe compounds were employed to evaluate the chromatographic properties of C8PN, demonstrating typical reversed phase/positively charged repulsion interaction on this stationary phase as estimated. Then the new C8PN stationary phase was used to separate a standard protein mixture on the reversed phase mode. Compared with a commercial C4 stationary phase, it showed different selectivity for some proteins. In order to better understand the properties of C8PN, the effect of acetonitrile content was investigated based on retention equation. Higher values of the equation parameters on C8PN demonstrated that the protein retentions were more sensitive to the change of acetonitrile content. Besides, the influences of buffer salt additives on the protein retentions were also studied. The retention factors of the proteins got larger with the increase of buffer salt concentration, which confirmed the positively charged repulsion interaction on the column. Finally, the C8PN was further applied to separate oxidized- and reduced- forms of Recombinant Human Growth Hormone. Our study indicated the advantages and application potential of mixed-mode reversed phase/positively charged repulsion stationary phase for intact protein separation. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Preconceptual design of the gas-phase decontamination demonstration cart

    International Nuclear Information System (INIS)

    Munday, E.B.

    1993-12-01

    Removal of uranium deposits from the interior surfaces of gaseous diffusion equipment will be a major portion of the overall multibillion dollar effort to decontaminate and decommission the gaseous diffusion plants. Long-term low-temperature (LTLT) gas-phase decontamination is being developed at the K-25 Site as an in situ decontamination process that is expected to significantly lower the decontamination costs, reduce worker exposure to radioactive materials, and reduce safeguard concerns. This report documents the preconceptual design of the process equipment that is necessary to conduct a full-scale demonstration of the LTLT method in accordance with the process steps listed above. The process equipment and method proposed in this report are not intended to represent a full-scale production campaign design and operation, since the gas evacuation, gas charging, and off-gas handling systems that would be cost effective in a production campaign are not cost effective for a first-time demonstration. However, the design presented here is expected to be applicable to special decontamination projects beyond the demonstration, which could include the Deposit Recovery Program. The equipment will therefore be sized to a 200 ft size 1 converter (plus a substantial conservative design margin), which is the largest item of interest for gas phase decontamination in the Deposit Recovery Program. The decontamination equipment will allow recovery of the UF 6 , which is generated from the reaction of ClF 3 with the uranium deposits, by use of NaF traps

  2. The Stability of CI02 as a Product of Gas Phase Decontamination Treatments

    Energy Technology Data Exchange (ETDEWEB)

    D. W. Simmons

    1994-09-01

    The gas phase decontamination project is investigating the use of chlorine trifluoride (ClF{sub 3}) to fluorinate nonvolatile uranium deposits to produce uranium hexafluoride (UF{sub 6}) gas. The potential existence of chlorine dioxide (ClO{sub 2}) during gas phase decontamination with ClF{sub 3} has been the subject of recent safety discussions. Some of the laboratory data collected during feasibility studies of the gas phase process has been evaluated for the presence of ClO{sub 2} in the product gas stream. The preliminary evidence to date can be summarized as follows: (1) ClO{sub 2} was not detected in the flow loop in the absence of ClF{sub 3}; (2) ClO{sub 2} was not detected in the static reactors in the absence of both ClF{sub 3} and ClF; and (3) ClO{sub 2} was detected in a static reactor in the absence of all fluorinating gases. The experimental evidence suggests that ClO{sub 2} will not exist in the presence of ClF{sub 3}, ClF, or UF{sub 6}. The data analyzed to date is insufficient to determine the stability of ClO{sub 2} in the presence of ClO{sub 2}F. Thermodynamic calculations of the ClF{sub 3} + H{sub 2}O system support the experimental evidence, and suggest that ClO{sub 2} will not exist in the presence of ClO{sub 2}F. Additional experimental efforts are needed to provide a better understanding of the gas phase ClF{sub 3} treatments and the product gases. However, preliminary evidence to date suggests that ClO{sub 2} should not be present as a product during the normal operations of the gas phase decontamination project.

  3. Dynamic Modeling Strategy for Flow Regime Transition in Gas-Liquid Two-Phase Flows

    Directory of Open Access Journals (Sweden)

    Xia Wang

    2012-12-01

    Full Text Available In modeling gas-liquid two-phase flows, the concept of flow regimes has been widely used to characterize the global interfacial structure of the flows. Nearly all constitutive relations that provide closures to the interfacial transfers in two-phase flow models, such as the two-fluid model, are flow regime dependent. Current nuclear reactor safety analysis codes, such as RELAP5, classify flow regimes using flow regime maps or transition criteria that were developed for steady-state, fully-developed flows. As two-phase flows are dynamic in nature, it is important to model the flow regime transitions dynamically to more accurately predict the two-phase flows. The present work aims to develop a dynamic modeling strategy to determine flow regimes in gas-liquid two-phase flows through introduction of interfacial area transport equations (IATEs within the framework of a two-fluid model. The IATE is a transport equation that models the interfacial area concentration by considering the creation of the interfacial area, fluid particle (bubble or liquid droplet disintegration, boiling and evaporation, and the destruction of the interfacial area, fluid particle coalescence and condensation. For flow regimes beyond bubbly flows, a two-group IATE has been proposed, in which bubbles are divided into two groups based on their size and shapes, namely group-1 and group-2 bubbles. A preliminary approach to dynamically identify the flow regimes is discussed, in which discriminators are based on the predicted information, such as the void fraction and interfacial area concentration. The flow regime predicted with this method shows good agreement with the experimental observations.

  4. Gas-Phase IR Spectroscopy of Deprotonated Amino Acids

    NARCIS (Netherlands)

    Oomens, J.; Steill, J. D.; Redlich, B.

    2009-01-01

    Gas-phase infrared multiple photon dissociation (IRMPD) spectra have been recorded for the conjugate bases of a series of amino acids (Asp, Cys, Glu, Phe, Set, Trp, Tyr). The spectra are dominated by strong symmetric and antisymmetric carboxylate stretching modes around 1300 and 1600 cm(-1),

  5. Evolution of the Normal State of a Strongly Interacting Fermi Gas from a Pseudogap Phase to a Molecular Bose Gas

    International Nuclear Information System (INIS)

    Perali, A.; Palestini, F.; Pieri, P.; Strinati, G. C.; Stewart, J. T.; Gaebler, J. P.; Drake, T. E.; Jin, D. S.

    2011-01-01

    Wave-vector resolved radio frequency spectroscopy data for an ultracold trapped Fermi gas are reported for several couplings at T c , and extensively analyzed in terms of a pairing-fluctuation theory. We map the evolution of a strongly interacting Fermi gas from the pseudogap phase into a fully gapped molecular Bose gas as a function of the interaction strength, which is marked by a rapid disappearance of a remnant Fermi surface in the single-particle dispersion. We also show that our theory of a pseudogap phase is consistent with a recent experimental observation as well as with quantum Monte Carlo data of thermodynamic quantities of a unitary Fermi gas above T c .

  6. The nature of the apolar phase influences the structure of the protein emulsifier in oil-in-water emulsions stabilized by bovine serum albumin. A front-surface fluorescence study.

    Science.gov (United States)

    Rampon, Vincent; Brossard, Chantal; Mouhous-Riou, Nadine; Bousseau, Benoît; Llamas, Geneviève; Genot, Claude

    2004-05-20

    Proteins are widely used as emulsifiers in food emulsions. Model emulsions, designed to study emulsifying properties of proteins and their conformation at the interfaces often contain a hydrocarbon as apolar phase instead of natural triglycerides as found in food products. Yet, some results indicate that the protein conformation at the interface depends on the nature of the apolar phase. Front-surface fluorescence spectroscopy was used to evidence differences in the structure of bovine serum albumin (BSA) adsorbed at the interface of emulsions prepared with different apolar phases: an hydrocarbon (n-dodecane), a synthetic medium-chain triglyceride (miglyol) and a natural vegetable oil (sunflower oil). Emulsions had similar size distributions of oil droplets. Front-surface fluorescence emission spectra of tryptophanyl residues of the protein (Trp) in emulsions, creams and serums varied as a function of the nature of hydrophobic phase. In emulsions and creams, wavelength of the maximum fluorescence intensities was blue-shifted as compared to the BSA solution. The shift was larger in creams than in emulsions and in samples containing dodecane than with the other apolar phases. Fourth derivative spectra of emulsions and creams exhibited two peaks assigned, respectively, to Trp located in hydrophilic and hydrophobic environments. The peaks were slightly red-shifted in the presence of sunflower oil as compared to miglyol and dodecane and the relative intensity of the "hydrophobic peak" was higher in dodecane. The effects were greater in creams than in emulsions. Fluorescence intensity of Trp was the highest in the serums of emulsions prepared with dodecane as compared to serums issued from sunflower oil and miglyol emulsions. Thus, proportion of adsorbed protein was lower in dodecane emulsions than with the other apolar phases. These results evidence that the mean environment of Trp was more hydrophobic in emulsions and creams than in solutions due to a displacement of

  7. In Situ Environmental TEM in Imaging Gas and Liquid Phase Chemical Reactions for Materials Research.

    Science.gov (United States)

    Wu, Jianbo; Shan, Hao; Chen, Wenlong; Gu, Xin; Tao, Peng; Song, Chengyi; Shang, Wen; Deng, Tao

    2016-11-01

    Gas and liquid phase chemical reactions cover a broad range of research areas in materials science and engineering, including the synthesis of nanomaterials and application of nanomaterials, for example, in the areas of sensing, energy storage and conversion, catalysis, and bio-related applications. Environmental transmission electron microscopy (ETEM) provides a unique opportunity for monitoring gas and liquid phase reactions because it enables the observation of those reactions at the ultra-high spatial resolution, which is not achievable through other techniques. Here, the fundamental science and technology developments of gas and liquid phase TEM that facilitate the mechanistic study of the gas and liquid phase chemical reactions are discussed. Combined with other characterization tools integrated in TEM, unprecedented material behaviors and reaction mechanisms are observed through the use of the in situ gas and liquid phase TEM. These observations and also the recent applications in this emerging area are described. The current challenges in the imaging process are also discussed, including the imaging speed, imaging resolution, and data management. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. NAPS: Network Analysis of Protein Structures

    Science.gov (United States)

    Chakrabarty, Broto; Parekh, Nita

    2016-01-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  9. A local leaky-box model for the local stellar surface density-gas surface density-gas phase metallicity relation

    Science.gov (United States)

    Zhu, Guangtun Ben; Barrera-Ballesteros, Jorge K.; Heckman, Timothy M.; Zakamska, Nadia L.; Sánchez, Sebastian F.; Yan, Renbin; Brinkmann, Jonathan

    2017-07-01

    We revisit the relation between the stellar surface density, the gas surface density and the gas-phase metallicity of typical disc galaxies in the local Universe with the SDSS-IV/MaNGA survey, using the star formation rate surface density as an indicator for the gas surface density. We show that these three local parameters form a tight relationship, confirming previous works (e.g. by the PINGS and CALIFA surveys), but with a larger sample. We present a new local leaky-box model, assuming star-formation history and chemical evolution is localized except for outflowing materials. We derive closed-form solutions for the evolution of stellar surface density, gas surface density and gas-phase metallicity, and show that these parameters form a tight relation independent of initial gas density and time. We show that, with canonical values of model parameters, this predicted relation match the observed one well. In addition, we briefly describe a pathway to improving the current semi-analytic models of galaxy formation by incorporating the local leaky-box model in the cosmological context, which can potentially explain simultaneously multiple properties of Milky Way-type disc galaxies, such as the size growth and the global stellar mass-gas metallicity relation.

  10. Propagation characteristics of pulverized coal and gas two-phase flow during an outburst.

    Science.gov (United States)

    Zhou, Aitao; Wang, Kai; Fan, Lingpeng; Tao, Bo

    2017-01-01

    Coal and gas outbursts are dynamic failures that can involve the ejection of thousands tons of pulverized coal, as well as considerable volumes of gas, into a limited working space within a short period. The two-phase flow of gas and pulverized coal that occurs during an outburst can lead to fatalities and destroy underground equipment. This article examines the interaction mechanism between pulverized coal and gas flow. Based on the role of gas expansion energy in the development stage of outbursts, a numerical simulation method is proposed for investigating the propagation characteristics of the two-phase flow. This simulation method was verified by a shock tube experiment involving pulverized coal and gas flow. The experimental and simulated results both demonstrate that the instantaneous ejection of pulverized coal and gas flow can form outburst shock waves. These are attenuated along the propagation direction, and the volume fraction of pulverized coal in the two-phase flow has significant influence on attenuation of the outburst shock wave. As a whole, pulverized coal flow has a negative impact on gas flow, which makes a great loss of large amounts of initial energy, blocking the propagation of gas flow. According to comparison of numerical results for different roadway types, the attenuation effect of T-type roadways is best. In the propagation of shock wave, reflection and diffraction of shock wave interact through the complex roadway types.

  11. Heterometallic molecular precursors for a lithium-iron oxide material: synthesis, solid state structure, solution and gas-phase behaviour, and thermal decomposition.

    Science.gov (United States)

    Han, Haixiang; Wei, Zheng; Barry, Matthew C; Filatov, Alexander S; Dikarev, Evgeny V

    2017-05-02

    Three heterometallic single-source precursors with a Li : Fe = 1 : 1 ratio for a LiFeO 2 oxide material are reported. Heterometallic compounds LiFeL 3 (L = tbaoac (1), ptac (2), and acac(3)) have been obtained on a large scale, in nearly quantitative yields by one-step reactions that employ readily available reagents. The heterometallic precursor LiFe(acac) 3 (3) with small, symmetric substituents on the ligand (acac = pentane-2,4-dionate), maintains a 1D polymeric structure in the solid state that limits its volatility and prevents solubility in non-coordinating solvents. The application of the unsymmetrical ligands, tbaoac (tert-butyl acetoacetate) and ptac (1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate), that exhibit different bridging properties at the two ends of the ligand, allowed us to change the connectivity pattern within the heterometallic assembly. The latter was demonstrated by structural characterization of heterometallic complexes LiFe(tbaoac) 3 (1) and LiFe(ptac) 3 (2) that consist of discrete heterocyclic tetranuclear molecules Li 2 Fe 2 L 6 . The compounds are highly volatile and exhibit a congruent sublimation character. DART mass spectrometric investigation revealed the presence of heterometallic molecules in the gas phase. The positive mode spectra are dominated by the presence of [M - L] + peaks (M = Li 2 Fe 2 L 6 ). In accord with their discrete molecular structure, complexes 1 and 2 are highly soluble in nearly all common solvents. In order to test the retention of the heterometallic structure in solution, the diamagnetic analog of 1, LiMg(tbaoac) 3 (4), has been isolated. Its tetranuclear molecular structure was found to be isomorphous to that of the iron counterpart. 1 H and 7 Li NMR spectroscopy unambiguously confirmed the presence of heterometallic molecules in solutions of non-coordinating solvents. The heterometallic precursor 1 was shown to exhibit clean thermal decomposition in air that results in phase-pure

  12. Investigation of the resistive phase in high power gas switching. Research and development report

    International Nuclear Information System (INIS)

    O'Rourke, R.C.

    1977-01-01

    A theoretical study was made of the resistive phase in high pressure gas switching with the regime of interest being (10 to 50) kV from (1J, 10ns, 100KHz) to (100J, 10μs, 1KHz). The resistive phase was examined as a function of applied field, gap spacing, inductance, gas type and pressure, and electrode material. The initiating and quenching phases as regards system performance (e.g., the jitter problem) were examined. The cooling and electrode debris removal effects of the vortex gas flow on the operating characteristics of the system were considered

  13. Oxidative potential of gas phase combustion emissions - An underestimated and potentially harmful component of air pollution from combustion processes

    Science.gov (United States)

    Stevanovic, S.; Vaughan, A.; Hedayat, F.; Salimi, F.; Rahman, M. M.; Zare, A.; Brown, R. A.; Brown, R. J.; Wang, H.; Zhang, Z.; Wang, X.; Bottle, S. E.; Yang, I. A.; Ristovski, Z. D.

    2017-06-01

    The oxidative potential (OP) of the gas phase is an important and neglected aspect of environmental toxicity. Whilst prolonged exposure to particulate matter (PM) associated reactive oxygen species (ROS) have been shown to lead to negative health effects, the potential for compounds in gas phase to cause similar effects is yet to be understood. In this study we describe: the significance of the gas phase OP generated through vehicle emissions; discuss the origin and evolution of species contributing to measured OP; and report on the impact of gas phase OP on human lung cells. The model aerosol for this study was exhaust emitted from a Euro III Common-rail diesel engine fuelled with different blends of diesel and biodiesel. The gas phase of these emissions was found to be potentially as hazardous as the particle phase. Fuel oxygen content was found to negatively correlate with the gas phase OP, and positively correlate with particle phase OP. This signifies a complex interaction between reactive species present in gas and particle phase. Furthermore, this interaction has an overarching effect on the OP of both particle and gas phase, and therefore the toxicity of combustion emissions.

  14. Imaging and structural studies of DNA–protein complexes and membrane ion channels

    KAUST Repository

    Marini, Monica; Limongi, Tania; Falqui, Andrea; Genovese, Alessandro; Allione, Marco; Moretti, Manola; Lopatin, Sergei; Tirinato, Luca; Das, Gobind; Torre, Bruno; Giugni, Andrea; Cesca, F.; Benfenati, F.; Di Fabrizio, Enzo M.

    2017-01-01

    In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K+ and GABA(A) channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 angstrom, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

  15. Imaging and structural studies of DNA–protein complexes and membrane ion channels

    KAUST Repository

    Marini, Monica

    2017-01-17

    In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K+ and GABA(A) channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 angstrom, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

  16. Heavy haze in winter Beijing driven by fast gas phase oxidation

    Science.gov (United States)

    Lu, K.; Tan, Z.; Wang, H.; Li, X.; Wu, Z.; Chen, Q.; Wu, Y.; Ma, X.; Liu, Y.; Chen, X.; Shang, D.; Dong, H.; Zeng, L.; Shao, M.; Hu, M.; Fuchs, H.; Novelli, A.; Broch, S.; Hofzumahaus, A.; Holland, F.; Rohrer, F.; Bohn, B.; Georgios, G.; Schmitt, S. H.; Schlag, P.; Kiendler-Scharr, A.; Wahner, A.; Zhang, Y.

    2017-12-01

    Heavy haze conditions were frequently presented in the airsheds of Beijing and surrounding areas, especially during winter time. To explore the trace gas oxidation and the subsequent formation of aerosols, a comprehensive field campaign was performed at a regional site (in the campus of University of Chinese Academy of Science, UCAS) in Beijing winter 2016. Serious haze pollution processes were often observed with the fast increase of inorganic salt (especially nitrate) and these pollutions were always associated with enhanced humidity and the concentrations of PAN (PeroxyAcyl Nitrates) which is normally a marker of gas phase oxidations from NOx and VOCs. Moreover, based on the measurements of OH, HO2, RO2, total OH reactivity, N2O5, NO, NO2, SO2, particle concentrations/distributions/chemical compositions, and meteorological parameters, the gas phase oxidation rates that leads to the formation of sulfate, nitrate and secondary organic aerosols were estimated. These determined formation rates were clearly enhanced by several folds during pollution episodes compared to that of the clean air masses. Preliminary analysis result showed that the gas phase formation potential of nitrate and secondary organic aerosols were larger than the observed concentrations of nitrate and SOA of which the excess production may be explained by deposition and dilution.

  17. Gas phase toluene isopropylation over high silica mordenite

    Indian Academy of Sciences (India)

    Mordenite (HM) catalysts with three different Si/Al ratios were compared for their activity and selectivities in gas phase toluene isopropylation with isopropanol. Catalyst with Si/Al ratio 44.9 offered better cumene selectivity, hence, it was chosen for detailed kinetic investigations. The influence of various process parameters ...

  18. G protein-membrane interactions II: Effect of G protein-linked lipids on membrane structure and G protein-membrane interactions.

    Science.gov (United States)

    Casas, Jesús; Ibarguren, Maitane; Álvarez, Rafael; Terés, Silvia; Lladó, Victoria; Piotto, Stefano P; Concilio, Simona; Busquets, Xavier; López, David J; Escribá, Pablo V

    2017-09-01

    G proteins often bear myristoyl, palmitoyl and isoprenyl moieties, which favor their association with the membrane and their accumulation in G Protein Coupled Receptor-rich microdomains. These lipids influence the biophysical properties of membranes and thereby modulate G protein binding to bilayers. In this context, we showed here that geranylgeraniol, but neither myristate nor palmitate, increased the inverted hexagonal (H II ) phase propensity of phosphatidylethanolamine-containing membranes. While myristate and palmitate preferentially associated with phosphatidylcholine membranes, geranylgeraniol favored nonlamellar-prone membranes. In addition, Gαi 1 monomers had a higher affinity for lamellar phases, while Gβγ and Gαβγ showed a marked preference for nonlamellar prone membranes. Moreover, geranylgeraniol enhanced the binding of G protein dimers and trimers to phosphatidylethanolamine-containing membranes, yet it decreased that of monomers. By contrast, both myristate and palmitate increased the Gαi 1 preference for lamellar membranes. Palmitoylation reinforced the binding of the monomer to PC membranes and myristoylation decreased its binding to PE-enriched bilayer. Finally, binding of dimers and trimers to lamellar-prone membranes was decreased by palmitate and myristate, but it was increased in nonlamellar-prone bilayers. These results demonstrate that co/post-translational G protein lipid modifications regulate the membrane lipid structure and that they influence the physico-chemical properties of membranes, which in part explains why G protein subunits sort to different plasma membrane domains. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

    Science.gov (United States)

    Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2015-01-01

    Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

  20. Identification of isomers in the gas phase and as adsorbates by near-edge X-ray absorption fine structure spectroscopy: Cis- and trans-stilbene

    International Nuclear Information System (INIS)

    Püttner, Ralph; Schmidt-Weber, Philipp; Kampen, Thorsten; Kolczewski, Christine; Hermann, Klaus; Horn, Karsten

    2017-01-01

    Highlights: • NEXAFS spectra of the cis- and trans-isomer of stilbene reveal distinct differences by which the isomers can be distinguished. • DFT calculations using the transition potential approach assign specific transitions that are different in the two isomers. • On Si(100), these differences in NEXAFS are also observed, suggesting that their conformations survive in the bonding situation. • NEXAFS is thus shown to be a sensitive tool to distinguish isomers in adsorbed species. - Abstract: Near-edge x-ray absorption fine structure spectra of the cis- and trans-isomers of stilbene in the gas phase reveal clear differences, which are analyzed by results from density-functional theory calculations using the transition potential approach. The differences between the two species also occur in stilbene adsorbed on Si(100), opening the way towards studying structural changes in molecules in different surface environments, and configurational switching in organic molecules on surfaces in particular.

  1. Identification of isomers in the gas phase and as adsorbates by near-edge X-ray absorption fine structure spectroscopy: Cis- and trans-stilbene

    Energy Technology Data Exchange (ETDEWEB)

    Püttner, Ralph [Department of Physics, Freie Universität Berlin, 14195 Berlin (Germany); Schmidt-Weber, Philipp [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany); Kampen, Thorsten [SPECS Surface Nano Analysis GmbH, 13355 Berlin (Germany); Kolczewski, Christine [Deutsches Museum München, 80538 Munich (Germany); Hermann, Klaus [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany); Horn, Karsten, E-mail: horn@fhi-berlin.mpg.de [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany)

    2017-02-15

    Highlights: • NEXAFS spectra of the cis- and trans-isomer of stilbene reveal distinct differences by which the isomers can be distinguished. • DFT calculations using the transition potential approach assign specific transitions that are different in the two isomers. • On Si(100), these differences in NEXAFS are also observed, suggesting that their conformations survive in the bonding situation. • NEXAFS is thus shown to be a sensitive tool to distinguish isomers in adsorbed species. - Abstract: Near-edge x-ray absorption fine structure spectra of the cis- and trans-isomers of stilbene in the gas phase reveal clear differences, which are analyzed by results from density-functional theory calculations using the transition potential approach. The differences between the two species also occur in stilbene adsorbed on Si(100), opening the way towards studying structural changes in molecules in different surface environments, and configurational switching in organic molecules on surfaces in particular.

  2. Transport of Gas Phase Radionuclides in a Fractured, Low-Permeability Reservoir

    Science.gov (United States)

    Cooper, C. A.; Chapman, J.

    2001-12-01

    The U.S. Atomic Energy Commission (predecessor to the Department of Energy, DOE) oversaw a joint program between industry and government in the 1960s and 1970s to develop technology to enhance production from low-permeability gas reservoirs using nuclear stimulation rather than conventional means (e.g., hydraulic and/or acid fracturing). Project Rio Blanco, located in the Piceance Basin, Colorado, was the third experiment under the program. Three 30-kiloton nuclear explosives were placed in a 2134 m deep well at 1780, 1899, and 2039 m below the land surface and detonated in May 1973. Although the reservoir was extensively fractured, complications such as radionuclide contamination of the gas prevented production and subsequent development of the technology. Two-dimensional numerical simulations were conducted to identify the main transport processes that have occurred and are currently occurring in relation to the detonations, and to estimate the extent of contamination in the reservoir. Minor modifications were made to TOUGH2, the multiphase, multicomponent reservoir simulator developed at Lawrence Berkeley National Laboratories. The simulator allows the explicit incorporation of fractures, as well as heat transport, phase change, and first order radionuclide decay. For a fractured two-phase (liquid and gas) reservoir, the largest velocities are of gases through the fractures. In the gas phase, tritium and one isotope of krypton are the principle radionuclides of concern. However, in addition to existing as a fast pathway, fractures also permit matrix diffusion as a retardation mechanism. Another retardation mechanism is radionuclide decay. Simulations show that incorporation of fractures can significantly alter transport rates, and that radionuclides in the gas phase can preferentially migrate upward due to the downward gravity drainage of liquid water in the pores. This project was funded by the National Nuclear Security Administration, Nevada Operations Office

  3. Nanocrystalline AL2 O2 powders produced by laser induced gas phase reactions

    International Nuclear Information System (INIS)

    Borsella, E.; Botti, S.; Martelli, S.; Zappa, G.; Giorgi, R.; Turt, S.

    1993-01-01

    Nanocrystalline Al 2 O 3 powders were successfully synthesized by a CO 2 laser-driven gas-phase reaction involving trimethylaluminium (Al(CH 3 ) 3 ) and nitrous-oxide (N 2 O). Ethylene (C 2 H 4 ) was added as gas sensitizer. The as-synthesized powder particles showed a considerable carbon contamination and an amorphous-like structure. After thermal treatment at 1200-1400 degrees C, the powder was transformed to hexagonal a-Al 2 O 3 with very low carbon contamination as confirmed by X-ray diffraction, X-ray photo-electron spectroscopy and chemical analysis. The calcinated powders resulted to be spherical single crystal nanoparticles with a mean size of 15-20 nm, as determined by X-ray diffraction, electron microscopy and B.E.T. specific surface measurements. The laser synthesized Al 2 O 3 particles are well suited dispersoids for intermetallic alloy technology

  4. Novel X-ray phase-contrast tomography method for quantitative studies of heat induced structural changes in meat

    DEFF Research Database (Denmark)

    Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur

    2014-01-01

    The objective of this study was to evaluate the use of X-ray phase-contrast tomography combined with 3D image segmentation to investigate the heat induced structural changes in meat. The measurements were performed at the Swiss synchrotron radiation light source using a grating interferometric...... and separated into a water phase and a gel phase formed by the sarcoplasmic proteins in the exudate. The results show that X-ray phase contrast tomography offers unique possibilities in studies both the meat structure and the different meat component such as water, fat, connective tissue and myofibrils...

  5. Theoretical modeling and design of photonic structures in zeolite nanocomposites for gas sensing. Part I: surface relief gratings.

    Science.gov (United States)

    Cody, D; Naydenova, I

    2017-12-01

    The suitability of holographic structures fabricated in zeolite nanoparticle-polymer composite materials for gas sensing applications has been investigated. Theoretical modeling of the sensor response (i.e., change in hologram readout due to a change in refractive index modulation or thickness as a result of gas adsorption) of different sensor designs was carried out using Raman-Nath theory and Kogelnik's coupled wave theory. The influence of a range of parameters on the sensor response of holographically recorded surface and volume photonic grating structures has been studied, namely the phase difference between the diffracted and probe beam introduced by the grating, grating geometry, thickness, spatial frequency, reconstruction wavelength, and zeolite nanoparticle refractive index. From this, the optimum fabrication conditions for both surface and volume holographic gas sensor designs have been identified. Here, in part I, results from theoretical modeling of the influence of design on the sensor response of holographically inscribed surface relief structures for gas sensing applications is reported.

  6. The gas chimney formation during the steam explosion premixing phase

    International Nuclear Information System (INIS)

    Leskovar, M.

    2001-01-01

    The crucial part in isothermal premixing experiment simulation is the correct prediction of the gas chimney, which forms when the spheres penetrate into water. The first simulation results with the developed original combined multiphase model showed that the gas chimney starts to close at the wrong place at the top of the chimney and not in the middle, like it was observed in the experiments. To find the physical explanation for this identified weakness of our numerical model a comprehensive parametric analysis (mesh size, initial water-air surface thickness, water density, momentum coupling starting position) has been performed. It was established that the reason for the unphysical gas chimney closing at the top could be the gradual air-water density transition in the experiment model, since there is due to the finite differences description always a transition layer with intermediate phases density over the pure water phase. It was shown that this difference between our numerical model and the experiment can be somewhat compensated if the spheres interfacial drag coefficient at the upmost mesh plane of the unphysical air-water transition layer is artificially risen. On this way a more correct gas chimney formation can be obtained.(author)

  7. Fast loop modeling for protein structures

    Science.gov (United States)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  8. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping

    2013-06-05

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  9. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

    2013-01-01

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  10. Study of Iodine Behavior in the Gas Phase during a Severe Accident

    International Nuclear Information System (INIS)

    Kim, Hanchul; Cho, Yeonghun; Ryu, Myunghyun

    2014-01-01

    Among the iodine species, the organic iodides produced from the reaction between iodine and organics such as paint, are not easily trapped by the filters during the containment venting following a severe accident. Korea Institute of Nuclear Safety (KINS) has been studying this issue, joining international research programs such as ISTP-EPICUR, OECDBIP and OECD-STEM. In the course of this study, a simple iodine model, RAIM (Radio-Active Iodine chemistry Model) has been developed (Oh et al., 2011), based on the IMOD methodology, and other previous studies. This paper deals with our recent activities on this study, including the development of the model for the iodine reactions in gas phase. Iodine reactions in gas phase were modeled and added to the RAIM code, taking into account several relevant reactions such as formation of ARP, iodine oxide, and organic iodides in gas phase. RAIM was then applied to analyze the S2-6-5-2 test for which iodine-loaded coupons were tested in gas phase. The analysis results show a reasonable estimation of volatile iodine concentration with the desorption rate constant of about 10 -6 s -1 , while those of the other iodine species overestimated for the whole period of the test. It reveals the need to determine appropriate values for the rate constants for formation of iodine oxides and organic iodides

  11. Synthesizing lattice structures in phase space

    International Nuclear Information System (INIS)

    Guo, Lingzhen; Marthaler, Michael

    2016-01-01

    In one dimensional systems, it is possible to create periodic structures in phase space through driving, which is called phase space crystals (Guo et al 2013 Phys. Rev. Lett. 111 205303). This is possible even if for particles trapped in a potential without periodicity. In this paper we discuss ultracold atoms in a driven optical lattice, which is a realization of such a phase space crystals. The corresponding lattice structure in phase space is complex and contains rich physics. A phase space lattice differs fundamentally from a lattice in real space, because its coordinate system, i.e., phase space, has a noncommutative geometry, which naturally provides an artificial gauge (magnetic) field. We study the behavior of the quasienergy band structure and investigate the dissipative dynamics. Synthesizing lattice structures in phase space provides a new platform to simulate the condensed matter phenomena and study the intriguing phenomena of driven systems far away from equilibrium. (paper)

  12. Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

    International Nuclear Information System (INIS)

    Tuncbag, Nurcan; Gursoy, Attila; Keskin, Ozlem

    2011-01-01

    The vast majority of the chores in the living cell involve protein–protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein–protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations

  13. Research in Korea on Gas Phase Synthesis and Control of Nanoparticles

    International Nuclear Information System (INIS)

    Choi, Mansoo

    2001-01-01

    Research activity into the gas phase synthesis of nanoparticles has witnessed rapid growth on a worldwide basis, which is also reflected by Korean research efforts. Nanoparticle research is inherently a multi-disciplinary activity involving both science and engineering. In this paper, the recent studies undertaken in Korea on the gas phase synthesis and control of nanoparticles are reviewed. Studies on the synthesis of various kinds of nanoparticles are first discussed with a focus on the different types of reactors used. Recent experimental and theoretical studies and newly developed methods of measuring and modeling nanoparticle growth are also reviewed

  14. Structural anatomy of telomere OB proteins.

    Science.gov (United States)

    Horvath, Martin P

    2011-10-01

    Telomere DNA-binding proteins protect the ends of chromosomes in eukaryotes. A subset of these proteins are constructed with one or more OB folds and bind with G+T-rich single-stranded DNA found at the extreme termini. The resulting DNA-OB protein complex interacts with other telomere components to coordinate critical telomere functions of DNA protection and DNA synthesis. While the first crystal and NMR structures readily explained protection of telomere ends, the picture of how single-stranded DNA becomes available to serve as primer and template for synthesis of new telomere DNA is only recently coming into focus. New structures of telomere OB fold proteins alongside insights from genetic and biochemical experiments have made significant contributions towards understanding how protein-binding OB proteins collaborate with DNA-binding OB proteins to recruit telomerase and DNA polymerase for telomere homeostasis. This review surveys telomere OB protein structures alongside highly comparable structures derived from replication protein A (RPA) components, with the goal of providing a molecular context for understanding telomere OB protein evolution and mechanism of action in protection and synthesis of telomere DNA.

  15. Protein Structure and the Sequential Structure of mRNA

    DEFF Research Database (Denmark)

    Brunak, Søren; Engelbrecht, Jacob

    1996-01-01

    entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment, By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets, These signals do not originate from......A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed, We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting...... protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain, A complete search for GenBank nucleotide sequences coding for structural...

  16. Shear viscosity of neutron-rich nucleonic matter near its liquid–gas phase transition

    International Nuclear Information System (INIS)

    Xu, Jun; Chen, Lie-Wen; Ko, Che Ming; Li, Bao-An; Ma, Yu Gang

    2013-01-01

    Within a relaxation time approach using free nucleon–nucleon cross sections modified by the in-medium nucleon masses that are determined from an isospin- and momentum-dependent effective nucleon–nucleon interaction, we investigate the specific shear viscosity (η/s) of neutron-rich nucleonic matter near its liquid–gas phase transition. It is found that as the nucleonic matter is heated at fixed pressure or compressed at fixed temperature, its specific shear viscosity shows a valley shape in the temperature or density dependence, with the minimum located at the boundary of the phase transition. Moreover, the value of η/s drops suddenly at the first-order liquid–gas phase transition temperature, reaching as low as 4–5 times the KSS bound of ℏ/4π. However, it varies smoothly for the second-order liquid–gas phase transition. Effects of the isospin degree of freedom and the nuclear symmetry energy on the value of η/s are also discussed

  17. Chlorination of some eliphatic organic compounds in liquid and gas phase

    International Nuclear Information System (INIS)

    Hassan, A.A.

    1990-01-01

    The photochlorination of different organic compounds and the relative slectivities of different positions have been investigated in both gaseous and liquid phases at different temperatures. The results have shown that the relative selectivity generally decreased with increasing temperature and in the gas phase has a higher value. Polar solvents increase the selectivity relative to the chlorination of pure liquid phases. The differences in activation energy between two positions were much higher in the gas phases chlorination, relative to that in the liquid phase. It was also found that the functional groups have great influence on the rate of chlorine free radical attack on different positions, for example the electron withdrawing groups decreasing the selectivity on the first position, but the electron donating groups increase the selectivity on the first position, but the electron donating groups increase the selectivity on the first position. Furthermore it was found that the polar solvents, which stabilize the resonance between oxygen and carbon atoms, increases the selectivity on that position. 23 tabs.; 16 figs.; 50 refs

  18. Gas phase collision dynamics by means of pulse-radiolysis methods

    International Nuclear Information System (INIS)

    Hatano, Yoshihiko

    1989-01-01

    After a brief survey of recent advances in gas-phase collision dynamics studies using pulse radiolysis methods, the following two topics in our research programs are presented with emphasis on the superior advantages of the pulse radiolysis methods over the various methods of gas-phase collision dynamics, such as beam methods, swarm methods and flow methods. One of the topics is electron attachment to van der Waals molecules. The attachment rates of thermal electrons to O 2 and other molecules in dense gases have been measured in wide ranges of both gas temperatures and pressures, from which experimental evidence has been obtained for electron attachment to van der Waals molecules. The results have been compared with theories and discussed in terms of the effect of van der Waals interaction on the electron attachment resonance. The obtained conclusions have been related with investigations of electron attachment, solvation and localization in the condensed phase. The other is Penning ionization and its related processes. The rate constants for the de-excitation of He(2 1 P), He(2 3 S), Ne( 3 P 0 ), Ne( 3 P 1 ), Ne( 3 P 2 ), Ar( 1 P 1 ), Ar( 3 P 1 ), by atoms and molecules have been measured in the temperature range from 100 to 300 K, thus obtaining the collisional energy dependence of the de-excitation cross sections. The results are compared in detail with theories classified according to the excited rare gas atoms in the metastable and resonance states. (author)

  19. Reticulated Vitreous Carbon Electrodes for Gas Phase Pulsed Corona Reactors

    National Research Council Canada - National Science Library

    Locke, B

    1998-01-01

    A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon electrodes is demonstrated to be effective for the removal of nitrogen oxides from synthetic air mixtures...

  20. Reticulated Vitreous Carbon Electrodes for Gas Phase Pulsed Corona Reactors

    National Research Council Canada - National Science Library

    LOCKE, B

    1999-01-01

    A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon electrodes is demonstrated to be effective for the removal of nitrogen oxides from synthetic air mixtures...

  1. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

    Science.gov (United States)

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

  2. Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

    OpenAIRE

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of appl...

  3. Gas phase enthalpies of formation of nitrobenzamides using combustion calorimetry and thermal analysis

    International Nuclear Information System (INIS)

    Ximello, Arturo; Flores, Henoc; Rojas, Aarón; Adriana Camarillo, E.; Patricia Amador, M.

    2014-01-01

    Graphical abstract: - Highlights: • Formation enthalpies of the nitrobenzamides were derived from combustion calorimetry. • Enthalpies of vaporisation and sublimation were calculated by thermogravimetry. • From gas phase enthalpies of formation the stability of the isomers is studied. • Stability of isomers is not driven by a steric hindrance between functional groups. - Abstract: The standard molar energies of combustion of 2-nitrobenzamide, 3-nitrobenzamide and 4-nitrobenzamide were determined with an isoperibolic, static-bomb, combustion calorimeter. From the combustion results, the standard molar enthalpies of combustion and formation for these compounds in the condensed phase at T = 298.15 K were derived. Subsequently, to determine the enthalpies of sublimation, the vapour pressure data as a function of the temperature for the compounds under investigation were estimated using thermogravimetry by applying Langmuir’s equation, and the enthalpies of vaporisation were derived. Standard enthalpies of fusion were measured by differential scanning calorimetry then added to those of vaporisation to obtain reliable results for the enthalpy of sublimation. From the combustion and sublimation data, the gas phase enthalpies of formation were determined to be (−138.9 ± 3.5) kJ · mol −1 , (−122.9 ± 2.9) kJ · mol −1 and (−108.5 ± 3.7) kJ · mol −1 for the ortho, meta and para isomers of nitrobenzamide, respectively. The meaning of these results with regard to the enthalpic stability of these molecular structures is discussed herein

  4. Maxwell's Law Based Models for Liquid and Gas Phase Diffusivities in Variably-Saturated Soil

    DEFF Research Database (Denmark)

    Mamamoto, Shoichiro; Møldrup, Per; Kawamoto, Ken

    2012-01-01

    -s,D-l). Different percolation threshold terms adopted from recent studies for gas (D-s,D-g) and solute (D-s,D-l) diffusion were applied. For gas diffusion, epsilon(th) was a function of bulk density (total porosity), while for solute diffusion theta(th) was best described by volumetric content of finer soil...... particles (clay and organic matter), FINESvol. The resulting LIquid and GAs diffusivity and tortuosity (LIGA) models were tested against D-s,D-g and D-s,D-l data for differently-textured soils and performed well against the measured data across soil types. A sensitivity analysis using the new Maxwell's Law...... based LIGA models implied that the liquid phase but not the gaseous-phase tortuosity was controlled by soil type. The analyses also suggested very different pathways and fluid-phase connectivity for gas and solute diffusion in unsaturated soil...

  5. Gas-phase advanced oxidation as an integrated air pollution control technique

    Directory of Open Access Journals (Sweden)

    Getachew A. Adnew

    2016-03-01

    Full Text Available Gas-phase advanced oxidation (GPAO is an emerging air cleaning technology based on the natural self-cleaning processes that occur in the Earth’s atmosphere. The technology uses ozone, UV-C lamps and water vapor to generate gas-phase hydroxyl radicals that initiate oxidation of a wide range of pollutants. In this study four types of GPAO systems are presented: a laboratory scale prototype, a shipping container prototype, a modular prototype, and commercial scale GPAO installations. The GPAO systems treat volatile organic compounds, reduced sulfur compounds, amines, ozone, nitrogen oxides, particles and odor. While the method covers a wide range of pollutants, effective treatment becomes difficult when temperature is outside the range of 0 to 80 °C, for anoxic gas streams and for pollution loads exceeding ca. 1000 ppm. Air residence time in the system and the rate of reaction of a given pollutant with hydroxyl radicals determine the removal efficiency of GPAO. For gas phase compounds and odors including VOCs (e.g. C6H6 and C3H8 and reduced sulfur compounds (e.g. H2S and CH3SH, removal efficiencies exceed 80%. The method is energy efficient relative to many established technologies and is applicable to pollutants emitted from diverse sources including food processing, foundries, water treatment, biofuel generation, and petrochemical industries.

  6. Optimisation of anomalous scattering and structural studies of proteins using synchrotron radiation

    International Nuclear Information System (INIS)

    Helliwell, J.R.

    1979-01-01

    Measurements from crystalline protein samples using SR can be conveniently divided into two classes. Firstly, small samples, large unit cells, the rapid collection of accurate high resolution data and dynamical studies can all benefit from the high intensity. Secondly, an important extension of the classical methods of protein structure determination arises from use of the tunability of SR for optimization of anomalous scattering and subsequent phase determination. This paper concentrates on this area of application. (author)

  7. Beta-structures in fibrous proteins.

    Science.gov (United States)

    Kajava, Andrey V; Squire, John M; Parry, David A D

    2006-01-01

    The beta-form of protein folding, one of the earliest protein structures to be defined, was originally observed in studies of silks. It was then seen in early studies of synthetic polypeptides and, of course, is now known to be present in a variety of guises as an essential component of globular protein structures. However, in the last decade or so it has become clear that the beta-conformation of chains is present not only in many of the amyloid structures associated with, for example, Alzheimer's Disease, but also in the prion structures associated with the spongiform encephalopathies. Furthermore, X-ray crystallography studies have revealed the high incidence of the beta-fibrous proteins among virulence factors of pathogenic bacteria and viruses. Here we describe the basic forms of the beta-fold, summarize the many different new forms of beta-structural fibrous arrangements that have been discovered, and review advances in structural studies of amyloid and prion fibrils. These and other issues are described in detail in later chapters.

  8. Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

    Science.gov (United States)

    Tokatli, A.; Ucun, F.; Sütçü, K.; Osmanoğlu, Y. E.; Osmanoğlu, Ş.

    2018-02-01

    In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6-31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

  9. Diagnostical meaning acute phase proteins in cerebrospinal liquid in children with neuroinfections

    OpenAIRE

    L. A. Alekseeva; N. V. Skripchenko; T. V. Bessonova

    2010-01-01

    In the article presented results of the examination of acute phase proteins in cerebrospinal liquid in 237 children with meningitis and encephalitis viral and bacterial etiology. The dependence between the level of acute phase proteins in cerebrospinal liquid and etiology of neuroinfectional process, the severity of brain damage and the process stage was determined. Diagnostic and prognostic efficiency of the acute phase proteins (C-reactive protein, albumin, alpha-1-antitripsin, alpha-2-macr...

  10. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  11. GIS: a comprehensive source for protein structure similarities.

    Science.gov (United States)

    Guerler, Aysam; Knapp, Ernst-Walter

    2010-07-01

    A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. alpha-helices and beta-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10,000 protein domains yielding about 55 x 10(6) possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

  12. Structure Prediction of Outer Membrane Protease Protein of Salmonella typhimurium Using Computational Techniques

    Directory of Open Access Journals (Sweden)

    Rozina Tabassum

    2016-03-01

    Full Text Available Salmonella typhimurium, a facultative gram-negative intracellular pathogen belonging to family Enterobacteriaceae, is the most frequent cause of human gastroenteritis worldwide. PgtE gene product, outer membrane protease emerges important in the intracellular phases of salmonellosis. The pgtE gene product of S. typhimurium was predicted to be capable of proteolyzing T7 RNA polymerase and localize in the outer membrane of these gram negative bacteria. PgtE product of S. enterica and OmpT of E. coli, having high sequence similarity have been revealed to degrade macrophages, causing salmonellosis and other diseases. The three-dimensional structure of the protein was not available through Protein Data Bank (PDB creating lack of structural information about E protein. In our study, by performing Comparative model building, the three dimensional structure of outer membrane protease protein was generated using the backbone of the crystal structure of Pla of Yersinia pestis, retrieved from PDB, with MODELLER (9v8. Quality of the model was assessed by validation tool PROCHECK, web servers like ERRAT and ProSA are used to certify the reliability of the predicted model. This information might offer clues for better understanding of E protein and consequently for developmet of better therapeutic treatment against pathogenic role of this protein in salmonellosis and other diseases.

  13. Neural Networks for protein Structure Prediction

    DEFF Research Database (Denmark)

    Bohr, Henrik

    1998-01-01

    This is a review about neural network applications in bioinformatics. Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones...

  14. Peptide-tagged proteins in aqueous two-phase systems

    OpenAIRE

    Nilsson, Anna

    2002-01-01

    This thesis deals with proteins containing peptide tags for improved partitioning in aqueous two-phase systems. Qualitatively the peptide-tagged protein partitioning could be predicted from peptide data, i.e. partitioning trends found for peptides were also found for the peptide-tagged proteins. However, full effect of the tag as expected from peptide partitioning was not found in the tagged protein. When alkyl-ethylene oxide surfactant was included in a two-polymer system, almost full effect...

  15. Zpif's law in the liquid gas phase transition of nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Y.G. [China Center of Advanced Science and Technology (CCAST), Beijing, BJ (China). World Lab.; Shanghai Institute of Nuclear Research, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800 (China)

    1999-12-01

    Zpif's law in the field of linguistics is tested in the nuclear disassembly within the framework of isospin dependent lattice gas model. It is found that the average cluster charge (or mass) of rank n in the charge (or mass) list shows exactly inversely to its rank, i.e., there exists Zpif's law, at the phase transition temperature. This novel criterion shall be helpful to search the nuclear liquid gas phase transition experimentally and theoretically. In addition, the finite size scaling of the effective phase transition temperature at which the Zpif's law appears is studied for several systems with different mass and the critical exponents of {nu} and {beta} are tentatively extracted. (orig.)

  16. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  17. Pharmaceutical Perspective on Opalescence and Liquid-Liquid Phase Separation in Protein Solutions.

    Science.gov (United States)

    Raut, Ashlesha S; Kalonia, Devendra S

    2016-05-02

    Opalescence in protein solutions reduces aesthetic appeal of a formulation and can be an indicator of the presence of aggregates or precursor to phase separation in solution signifying reduced product stability. Liquid-liquid phase separation of a protein solution into a protein-rich and a protein-poor phase has been well-documented for globular proteins and recently observed for monoclonal antibody solutions, resulting in physical instability of the formulation. The present review discusses opalescence and liquid-liquid phase separation (LLPS) for therapeutic protein formulations. A brief discussion on theoretical concepts based on thermodynamics, kinetics, and light scattering is presented. This review also discusses theoretical concepts behind intense light scattering in the vicinity of the critical point termed as "critical opalescence". Both opalescence and LLPS are affected by the formulation factors including pH, ionic strength, protein concentration, temperature, and excipients. Literature reports for the effect of these formulation factors on attractive protein-protein interactions in solution as assessed by the second virial coefficient (B2) and the cloud-point temperature (Tcloud) measurements are also presented. The review also highlights pharmaceutical implications of LLPS in protein solutions.

  18. TAM receptors, Gas6, and protein S: roles in inflammation and hemostasis.

    Science.gov (United States)

    van der Meer, Jonathan H M; van der Poll, Tom; van 't Veer, Cornelis

    2014-04-17

    TAM receptors (Tyro3, Axl, and Mer) belong to a family of receptor tyrosine kinases that have important effects on hemostasis and inflammation. Also, they affect cell proliferation, survival, adhesion, and migration. TAM receptors can be activated by the vitamin K-dependent proteins Gas6 and protein S. Protein S is more commonly known as an important cofactor for protein C as well as a direct inhibitor of multiple coagulation factors. To our knowledge, the functions of Gas6 are limited to TAM receptor activation. When activated, the TAM receptors have effects on primary hemostasis and coagulation and display an anti-inflammatory or a proinflammatory effect, depending on cell type. To comprehend the effects that the TAM receptors and their ligands have on hemostasis and inflammation, we compare studies that report the different phenotypes displayed by mice with deficiencies in the genes of this receptor family and its ligands (protein S(+/-), Gas6(-/-), TAM(-/-), and variations of these). In this manner, we aim to display which features are attributable to the different ligands. Because of the effects TAM receptors have on hemostasis, inflammation, and cancer growth, their modulation could make interesting therapeutic targets in thromboembolic disease, atherosclerosis, sepsis, autoimmune disease, and cancer.

  19. The Gas-Phase Formation of Methyl Formate in Hot Molecular Cores

    Science.gov (United States)

    Horn, Anne; Møllendal, Harald; Sekiguchi, Osamu; Uggerud, Einar; Roberts, Helen; Herbst, Eric; Viggiano, A. A.; Fridgen, Travis D.

    2004-08-01

    Methyl formate, HCOOCH3, is a well-known interstellar molecule prominent in the spectra of hot molecular cores. The current view of its formation is that it occurs in the gas phase from precursor methanol, which is synthesized on the surfaces of grain mantles during a previous colder era and evaporates while temperatures increase during the process of high-mass star formation. The specific reaction sequence thought to form methyl formate, the ion-molecule reaction between protonated methanol and formaldehyde followed by dissociative recombination of the protonated ion [HCO(H)OCH3]+, has not been studied in detail in the laboratory. We present here the results of both a quantum chemical study of the ion-molecule reaction between [CH3OH2]+ and H2CO as well as new experimental work on the system. In addition, we report theoretical and experimental studies for a variety of other possible gas-phase reactions leading to ion precursors of methyl formate. The studied chemical processes leading to methyl formate are included in a chemical model of hot cores. Our results show that none of these gas-phase processes produces enough methyl formate to explain its observed abundance.

  20. Loading and stress analysis of gas pipeline structures; Analise de esforcos e tensoes em estruturas de gasodutos durante despressurizacoes

    Energy Technology Data Exchange (ETDEWEB)

    Frisoli, Caetano [TRANSPETRO - PETROBRAS Transporte S.A., Rio de Janeiro, RJ (Brazil); Frota, Cristiane Souto [TBG - Transportadora Brasileira Gasoduto Bolivia Brasil S.A., Rio de Janeiro, RJ (Brazil); Silva, Luis Fernando Figueira da; Carvalho, Marcio da Silveira [Pontificia Univ. Catolica do Rio de Janeiro, RJ (Brazil). Dept. de Engenharia Mecanica; Savi, Marcelo Amorim [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Dept. de Engenharia Mecanica; Pacheco, Pedro Manuel Calas Lopes [Centro Federal de Educacao Tecnologica do Rio de Janeiro (CEFET-RJ), Rio de Janeiro, RJ (Brazil)

    2003-07-01

    Repairing and maintenance activities on Bolivia-Brazil gas pipeline often need blow down lines. During the blow down process, the high speed of discharging gases imposes great efforts to the structures. A detailed analysis of this situation is essential for a safe operation. This paper describes two phases of a project, developed under TBG coordination. It consists in analyzing the stress and forces involved in this operation, in order to design facilities to blow down pipes and develop a safe blow down procedure for the gas pipeline. The first phase consists of a supersonic flowing simulation in the blow down gas pipeline device. The pressure behavior, mass flow and the speed at the device's ending point are calculated for different operational conditions. In the second phase, the equivalent loading caused by blow down operations is used as input in a stress analysis program to determine stress, critical sessions evaluation and material recommendations for blow down devices. (author)

  1. Structure based alignment and clustering of proteins (STRALCP)

    Science.gov (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  2. Validation-driven protein-structure improvement

    NARCIS (Netherlands)

    Touw, W.G.

    2016-01-01

    High-quality protein structure models are essential for many Life Science applications, such as protein engineering, molecular dynamics, drug design, and homology modelling. The WHAT_CHECK model validation project and the PDB_REDO model optimisation project have shown that many structure models in

  3. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

    Science.gov (United States)

    Morrison, Lindsay J; Chai, Wenrui; Rosenberg, Jake A; Henkelman, Graeme; Brodbelt, Jennifer S

    2017-08-02

    Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

  4. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation...... to score the likelihood of the interaction between two proteins and to develop a method for the prediction of PPIs. We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable...

  5. Serum protein capillary electrophoresis and measurement of acute phase proteins in a captive cheetah (Acinonyx jubatus) population.

    Science.gov (United States)

    Depauw, Sarah; Delanghe, Joris; Whitehouse-Tedd, Katherine; Kjelgaard-Hansen, Mads; Christensen, Michelle; Hesta, Myriam; Tugirimana, Pierrot; Budd, Jane; Dermauw, Veronique; Janssens, Geert P J

    2014-09-01

    Renal and gastrointestinal pathologies are widespread in the captive cheetah (Acinonyx jubatus) population but are often diagnosed at a late stage, because diagnostic tools are limited to the evaluation of clinical signs or general blood examination. Presently, no data are available on serum proteins and acute-phase proteins in cheetahs during health or disease, although they might be important to improve health monitoring. This study aimed to quantify serum proteins by capillary electrophoresis in 80 serum samples from captive cheetahs, categorized according to health status and disease type. Moreover, serum amyloid A concentrations were measured via a turbidimetric immunoassay validated in domestic cats, whereas haptoglobin and C-reactive protein were determined by non-species-specific functional tests. Cheetahs classified as healthy had serum protein and acute phase protein concentrations within reference ranges for healthy domestic cats. In contrast, unhealthy cheetahs had higher (P cheetahs suffering from chronic kidney disease were significantly greater compared to the reportedly healthy cheetahs. Our study indicates that serum proteins in the cheetah can be analyzed by routine capillary electrophoresis, whereas acute-phase proteins can be measured using available immunoassays or non-species-specific techniques, which are also likely to be applicable in other exotic felids. Moreover, results suggest that serum amyloid A and haptoglobin are important acute-phase proteins in the diseased cheetah and highlight the need to evaluate their role as early-onset markers for disease.

  6. Angular intensity of a gas-phase field ionization source

    International Nuclear Information System (INIS)

    Orloff, J.; Swanson, L.W.

    1979-01-01

    Angular intensities of 1 μA sr -1 have been measured for a gas-phase field ionization source in an optical column under practical operating conditions. The source, which was differentially pumped and cooled to 77 K, utilized a -oriented iridium emitter and precooled hydrogen gas at 10 -2 Torr. The ion beam was collimated with an electrostatic lens and detected below an aperture subtending 0.164 msr. A transmitted current of approx.10 -10 A was measured at voltages corresponding to a field of approx. =2.2 V/A at the emitter

  7. Magnetic resonance velocity imaging of liquid and gas two-phase flow in packed beds.

    Science.gov (United States)

    Sankey, M H; Holland, D J; Sederman, A J; Gladden, L F

    2009-02-01

    Single-phase liquid flow in porous media such as bead packs and model fixed bed reactors has been well studied by MRI. To some extent this early work represents the necessary preliminary research to address the more challenging problem of two-phase flow of gas and liquid within these systems. In this paper, we present images of both the gas and liquid velocities during stable liquid-gas flow of water and SF(6) within a packing of 5mm spheres contained within columns of diameter 40 and 27 mm; images being acquired using (1)H and (19)F observation for the water and SF(6), respectively. Liquid and gas flow rates calculated from the velocity images are in agreement with macroscopic flow rate measurements to within 7% and 5%, respectively. In addition to the information obtained directly from these images, the ability to measure liquid and gas flow fields within the same sample environment will enable us to explore the validity of assumptions used in numerical modelling of two-phase flows.

  8. Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media

    Science.gov (United States)

    Huber, Patrick

    2015-03-01

    Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

  9. Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins.

    Science.gov (United States)

    Dzuricky, Michael; Roberts, Stefan; Chilkoti, Ashutosh

    2018-05-01

    A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.

  10. The gas-phase bis-uranyl nitrate complex ((UO2)2(NO3)5)-: infrared spectrum and structure

    International Nuclear Information System (INIS)

    Groenewold, G.S.; van Stipdonk, Michael J.; Oomens, Jos; De Jong, Wibe A.; McIlwain, Michael E.

    2011-01-01

    The infrared spectrum of the bis-uranyl nitrate complex ((UO 2 ) 2 (NO 3 ) 5 ) - was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate v 3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex ((UO 2 ) 2 (NO 3 ) 5 ) - compared to the mono-complex (UO 2 (NO 3 ) 3 ) - , as indicated by a higher O-U-O asymmetric stretching (v 3 ) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the v 3 frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The lowest energy structure predicted by density functional theory (B3LYP functional) calculations was one in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  11. Two-phase behavior and compression effects in the PEFC gas diffusion medium

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, Partha P [Los Alamos National Laboratory; Kang, Qinjun [Los Alamos National Laboratory; Schulz, Volker P [APL-LANDAU GMBH; Wang, Chao - Yang [PENN STATE UNIV; Becker, Jurgen [NON LANL; Wiegmann, Andreas [NON LANL

    2009-01-01

    A key performance limitation in the polymer electrolyte fuel cell (PEFC), manifested in terms of mass transport loss, originates from liquid water transport and resulting flooding phenomena in the constituent components. A key contributor to the mass transport loss is the cathode gas diffusion layer (GDL) due to the blockage of available pore space by liquid water thus rendering hindered oxygen transport to the active reaction sites in the electrode. The GDL, therefore, plays an important role in the overall water management in the PEFC. The underlying pore-morphology and the wetting characteristics have significant influence on the flooding dynamics in the GDL. Another important factor is the role of cell compression on the GDL microstructural change and hence the underlying two-phase behavior. In this article, we present the development of a pore-scale modeling formalism coupled With realistic microstructural delineation and reduced order compression model to study the structure-wettability influence and the effect of compression on two-phase behavior in the PEFC GDL.

  12. Efficient protein structure search using indexing methods.

    Science.gov (United States)

    Kim, Sungchul; Sael, Lee; Yu, Hwanjo

    2013-01-01

    Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

  13. A 'periodic table' for protein structures.

    Science.gov (United States)

    Taylor, William R

    2002-04-11

    Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

  14. A robust quantitative solid phase immunoassay for the acute phase protein C-reactive protein (CRP) based on cytidine 5 '-diphosphocholine coupled dendrimers

    DEFF Research Database (Denmark)

    Heegaard, Peter M. H.; Pedersen, H. G.; Jensen, A. L.

    2009-01-01

    C-reactive protein (CRP) is an important acute phase protein, being used as a sensitive indicator of inflammation and infection and is also associated with the risk of cardiovascular problems. The present paper describes a robust and sensitive ELISA for CRP, based on the affinity of CRP for phosp......C-reactive protein (CRP) is an important acute phase protein, being used as a sensitive indicator of inflammation and infection and is also associated with the risk of cardiovascular problems. The present paper describes a robust and sensitive ELISA for CRP, based on the affinity of CRP...... was applied to determination of pig and human CRP using commercially available antibodies against human CRP. The assay was shown to be more sensitive than previously published immunoassays employing albumin-coupled cytidine diphosphocholine. The coating was stable for at least 30 days at room temperature...

  15. Comprehensive Analysis of the Gas- and Particle-Phase Products of VOC Oxidation

    Science.gov (United States)

    Bakker-Arkema, J.; Ziemann, P. J.

    2017-12-01

    Controlled environmental chamber studies are important for determining atmospheric reaction mechanisms and gas and aerosol products formed in the oxidation of volatile organic compounds (VOCs). Such information is necessary for developing detailed chemical models for use in predicting the atmospheric fate of VOCs and also secondary organic aerosol (SOA) formation. However, complete characterization of atmospheric oxidation reactions, including gas- and particle-phase product yields, and reaction branching ratios, are difficult to achieve. In this work, we investigated the reactions of terminal and internal alkenes with OH radicals in the presence of NOx in an attempt to fully characterize the chemistry of these systems while minimizing and accounting for the inherent uncertainties associated with environmental chamber experiments. Gas-phase products (aldehydes formed by alkoxy radical decomposition) and particle-phase products (alkyl nitrates, β-hydroxynitrates, dihydroxynitrates, 1,4-hydroxynitrates, 1,4-hydroxycarbonyls, and dihydroxycarbonyls) formed through pathways involving addition of OH to the C=C double bond as well as H-atom abstraction were identified and quantified using a suite of analytical techniques. Particle-phase products were analyzed in real time with a thermal desorption particle beam mass spectrometer; and off-line by collection onto filters, extraction, and subsequent analysis of functional groups by derivatization-spectrophotometric methods developed in our lab. Derivatized products were also separated by liquid chromatography for molecular quantitation by UV absorbance and identification using chemical ionization-ion trap mass spectrometry. Gas phase aldehydes were analyzed off-line by collection onto Tenax and a 5-channel denuder with subsequent analysis by gas chromatography, or by collection onto DNPH-coated cartridges and subsequent analysis by liquid chromatography. The full product identification and quantitation, with careful

  16. Protein structure recognition: From eigenvector analysis to structural threading method

    Science.gov (United States)

    Cao, Haibo

    In this work, we try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. We found a strong correlation between amino acid sequence and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, we give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part include discussions of interactions among amino acids residues, lattice HP model, and the designablity principle. In the second part, we try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in our eigenvector study of protein contact matrix. We believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, we discuss a threading method based on the correlation between amino acid sequence and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, we list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  17. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Haibo [Iowa State Univ., Ames, IA (United States)

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  18. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    International Nuclear Information System (INIS)

    Haibo Cao

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches

  19. The Substitution Effect on Reaction Enthalpies of Antioxidant Mechanisms of Juglone and Its Derivatives in Gas and Solution Phase: DFT Study

    Directory of Open Access Journals (Sweden)

    Aymard Didier Tamafo Fouegue

    2018-01-01

    Full Text Available We examined the structure-reaction enthalpies-antioxidant activity relationship of the molecule library built around juglone and its derivatives at B3LYP/6-31+G(d,p level. Three major antioxidant mechanisms (hydrogen atom transfer (HAT, single electron transfer-proton transfer (SET-PT, and sequential proton loss electron transfer (SPLET have been investigated in five solvents and in the gas phase. The delocalization of the unpaired electrons in the radicals or cation radicals has been explored by the natural bond orbital analysis and the interpretation of spin density maps. The results obtained have proven that the HAT mechanism is the thermodynamically preferred mechanism in the gas phase. But, in the solution phase, the SPLET mechanism has been shown to be more predominant than HAT. The reactivity order of compounds towards selected reactive oxygen species has also been studied.

  20. Modeling of gas-phase chemistry in the chemical vapor deposition of polysilicon in a cold wall system

    Energy Technology Data Exchange (ETDEWEB)

    Toprac, A.J.; Edgar, T.F.; Trachtenberg, I. (Univ. of Texas, Austin, TX (United States). Dept. of Chemical Engineering)

    1993-06-01

    The relative contribution of gas-phase chemistry to deposition processes is an important issue both from the standpoint of operation and modeling of these processes. In polysilicon deposition from thermally activated silane in a cold wall rapid thermal chemical vapor deposition (RTCVD) system, the relative contribution of gas-phase chemistry to the overall deposition rate was examined by a mass-balance model. Evaluating the process at conditions examined experimentally, the model indicated that gas-phase reactions may be neglected to good accuracy in predicting polysilicon deposition rate. The model also provided estimates of the level of gas-phase generated SiH[sub 2] associated with deposition on the cold-process chamber walls.

  1. The structure and conformations of piracetam (2-oxo-1-pyrrolidineacetamide): Gas-phase electron diffraction and quantum chemical calculations

    Science.gov (United States)

    Ksenafontov, Denis N.; Moiseeva, Natalia F.; Khristenko, Lyudmila V.; Karasev, Nikolai M.; Shishkov, Igor F.; Vilkov, Lev V.

    2010-12-01

    The geometric structure of piracetam was studied by quantum chemical calculations (DFT and ab initio), gas electron diffraction (GED), and FTIR spectroscopy. Two stable mirror symmetric isomers of piracetam were found. The conformation of pyrrolidine ring is an envelope in which the C4 atom deviates from the ring plane, the angle between the planes (C3 sbnd C4 sbnd C5) and (C2 sbnd C3 sbnd C5) is 154.1°. The direction of the deviation is the same as that of the side acetamide group. The piracetam molecule is stabilized in the gas phase by an intramolecular hydrogen bond between the N9H 2 group and the oxygen O6, bonded to C2. The principal structural parameters ( re, Å and ∠e, degrees; uncertainties are 3 σLS values) were found to be: r(С3 sbnd С4) = 1.533(1), r(C4 sbnd C5) = 1.540(1), r(N1 sbnd C5) = 1.456(1), r(C2 sbnd C3) = 1.520(1), r(N1 sbnd C7) = 1.452(1), r(C7 sbnd C8) = 1.537(1), r(N1 sbnd C2) = 1.365(2), r(C8 sbnd N9) = 1.360(2), r(C2 dbnd O6) = 1.229(1), r(C8 dbnd O10) = 1.221(1), ∠C2 sbnd N1 sbnd C5 = 113.4(6), ∠N1 sbnd C2 sbnd C3 = 106.9(6), ∠N1 sbnd C7 sbnd C8 = 111.9(6), ∠C7 sbnd C8 sbnd N9 = 112.5(6), ∠N1 sbnd C2 sbnd O6 = 123.0(4), ∠C3 sbnd N1 sbnd C7 = 120.4(4), ∠C7 sbnd C8 sbnd O10 = 120.2(4), ∠C5 sbnd N1 sbnd C2 sbnd O6 = 170(6), ∠C3 sbnd C2 sbnd N1 sbnd C7 = 178(6), ∠C2 sbnd N1 sbnd C7 sbnd C8 = 84.2, ∠N1 sbnd C7 sbnd C8 sbnd O10 = 111.9.

  2. Tuning of Preparational Factors Affecting the Morphological Structure and Gas Separation Property of Asymmetric Polysulfone Membranes

    Science.gov (United States)

    Yuenyao, C.; Ruangdit, S.; Chittrakarn, T.

    2017-09-01

    The aim of this work was to study the effect of preparational factors such as solvent type, evaporation time (ET) and non-solvent additive, on the morphological structure, physical and gas separation properties of the prepared membrane samples by tuning of these parameters. Flat sheet asymmetric polysulfone (PSF) membranes were prepared by the dry/wet phase inversion process combined with the double coagulation bath method. The alteration of the prepared membranes were analyzed through scientific techniques such as Scanning Electron Microscope (SEM) and Dynamic Mechanical Thermal Analysis (DMTA). Furthermore, gas separation performance of membrane samples was measured in term of gas permeation and ideal selectivity of CO2/CH4. Experimental results showed that the change of preparational factors affected to the gas permeation of asymmetric PSF membranes. For example, the selective layer thickness increased with increasing of ET. This lead to increase significantly of ideal selectivity of CO2/CH4. The CO2/CH4 ideal selectivity was also increased with increase of ethanol (non-solvent additive) concentration in casting solution. In summary, the tuning of preparational factors affected to morphological structure, physical and gas separation properties of PSF membranes.

  3. Structures composing protein domains.

    Science.gov (United States)

    Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

    2013-08-01

    This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  4. Current strategies for protein production and purification enabling membrane protein structural biology.

    Science.gov (United States)

    Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E; Liu, Xiang-Qin; Rainey, Jan K

    2016-12-01

    Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

  5. Moisture effects on greenhouse gases generation in nitrifying gas-phase compost biofilters.

    Science.gov (United States)

    Maia, Guilherme D N; Day, George B; Gates, Richard S; Taraba, Joseph L; Coyne, Mark S

    2012-06-01

    Gas-phase compost biofilters are extensively used in concentrated animal feeding operations to remove odors and, in some cases, ammonia from air sources. The expected biochemical pathway for these predominantly aerobic systems is nitrification. However, non-uniform media with low oxygen levels can shift biofilter microbial pathways to denitrification, a source of greenhouse gases. Several factors contribute to the formation of anoxic/anaerobic zones: media aging, media and particle structure, air velocity distribution, compaction, biofilm thickness, and moisture content (MC) distribution. The present work studies the effects of media moisture conditions on ammonia (NH(3)) removal and greenhouse gas generation (nitrous oxide, N(2)O and methane, CH(4)) for gas-phase compost biofilters subject to a 100-day controlled drying process. Continuous recordings were made for the three gases and water vapor (2.21-h sampling cycle, each cycle consisted of three gas species, and water vapor, for a total of 10,050 data points). Media moisture conditions were classified into three corresponding media drying rate (DR) stages: Constant DR (wetter media), falling DR, and stable-dry system. The first-half of the constant DR period (0-750 h; MC=65-52%, w.b.) facilitated high NH(3) removal rates, but higher N(2)O generation and no CH(4) generation. At the drier stages of the constant DR (750-950 h; MC=52-48%, w.b.) NH(3) removal remained high but N(2)O net generation decreased to near zero. In the falling DR stage (1200-1480 h; MC=44-13%) N(2)O generation decreased, CH(4) increased, and NH(3) was no longer removed. No ammonia removal or greenhouse gas generation was observed in the stable-dry system (1500-2500 h; MC=13%). These results indicate that media should remain toward the drier region of the constant DR (in close proximity to the falling DR stage; MC=50%, approx.), to maintain high levels of NH(3) removal, reduced levels of N(2)O generation, and nullify levels of CH(4

  6. Simulation of phase structures

    International Nuclear Information System (INIS)

    Lawson, J.

    1995-01-01

    This memo outlines a procedure developed by the author to extract information from phase measurements and produce a simulated phase structure for use in modeling optical systems, including characteristic optics for the Beamlet and NIF laser systems. The report includes an IDL program listing

  7. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    Chou James

    2006-01-01

    Full Text Available Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum

  8. Phase transitions in a vortex gas

    International Nuclear Information System (INIS)

    Shah, P.A.

    1995-01-01

    It has been shown recently that the motion of solitons at couplings around a critical coupling can be reduced to the dynamics of particles (the zeros of the Higgs field) on a curved manifold with potential. The curvature gives a velocity-dependent force, and the magnitude of the potential is proportional to the distance from a critical coupling. In this paper we apply this approximation to determining the equation of state of a gas of vortices in the abelian Higgs model. We derive a virial expansion using certain known integrals of the metric, and the second virial coefficient is calculated, determining the behaviour of the gas at low densities. A formula for determining higher-order coefficients is given. At low densities and temperatures T >>λ the equation of state is of the Van der Waals form (P+b N 2 /A 2 )(A-aN) = NT with a=4π and b=-4.89πλ where λ is a measure of the distance from critical coupling. It is found that there is no phase transition in a low-density type-II gas, but there is a transition in the type-I case between a condensed and gaseous state. We conclude with a discussion of the relation of our results to vortex behaviour in superconductors. ((orig.))

  9. Methanol ice co-desorption as a mechanism to explain cold methanol in the gas-phase

    Science.gov (United States)

    Ligterink, N. F. W.; Walsh, C.; Bhuin, R. G.; Vissapragada, S.; van Scheltinga, J. Terwisscha; Linnartz, H.

    2018-05-01

    Context. Methanol is formed via surface reactions on icy dust grains. Methanol is also detected in the gas-phase at temperatures below its thermal desorption temperature and at levels higher than can be explained by pure gas-phase chemistry. The process that controls the transition from solid state to gas-phase methanol in cold environments is not understood. Aims: The goal of this work is to investigate whether thermal CO desorption provides an indirect pathway for methanol to co-desorb at low temperatures. Methods: Mixed CH3OH:CO/CH4 ices were heated under ultra-high vacuum conditions and ice contents are traced using RAIRS (reflection absorption IR spectroscopy), while desorbing species were detected mass spectrometrically. An updated gas-grain chemical network was used to test the impact of the results of these experiments. The physical model used is applicable for TW Hya, a protoplanetary disk in which cold gas-phase methanol has recently been detected. Results: Methanol release together with thermal CO desorption is found to be an ineffective process in the experiments, resulting in an upper limit of ≤ 7.3 × 10-7 CH3OH molecules per CO molecule over all ice mixtures considered. Chemical modelling based on the upper limits shows that co-desorption rates as low as 10-6 CH3OH molecules per CO molecule are high enough to release substantial amounts of methanol to the gas-phase at and around the location of the CO thermal desorption front in a protoplanetary disk. The impact of thermal co-desorption of CH3OH with CO as a grain-gas bridge mechanism is compared with that of UV induced photodesorption and chemisorption.

  10. Ultrafast electronic relaxation of excited state vitamin B12 in the gas phase

    International Nuclear Information System (INIS)

    Shafizadeh, Niloufar; Poisson, Lionel; Soep, Benoit

    2008-01-01

    The time evolution of electronically excited vitamin B 12 (cyanocobalamin) has been observed for the first time in the gas phase. It reveals an ultrafast decay to a state corresponding to metal excitation. This decay is interpreted as resulting from a ring to metal electron transfer. This opens the observation of the excited state of other complex biomimetic systems in the gas phase, the key to the characterisation of their complex evolution through excited electronic states

  11. Parents of two-phase flow and theory of "gas-lift"

    Science.gov (United States)

    Zitek, Pavel; Valenta, Vaclav

    2014-03-01

    This paper gives a brief overview of types of two-phase flow. Subsequently, it deals with their mutual division and problems with accuracy boundaries among particular types. It also shows the case of water flow through a pipe with external heating and the gradual origination of all kinds of flow. We have met it in solution of safety condition of various stages in pressurized and boiling water reactors. In the MSR there is a problem in the solution of gas-lift using helium as a gas and its secondary usage for clearing of the fuel mixture from gaseous fission products. Theory of gas-lift is described.

  12. Structural phase transitions and Huang scattering

    International Nuclear Information System (INIS)

    Yamada, Yasusada

    1980-01-01

    The usefulness of the application of the concept of Huang scattering to the understandings of the origin of diffuse scatterings near structural phase transitions are discussed. It is pointed out that in several phase transitions, the observed diffuse scatterings can not be interpreted in terms of critical fluctuations of the order parameters associated with the structural phase transitions, and that they are rather interpreted as Huang scattering due to random distribution of individual order parameter which is 'dressed' by strain fields. Examples to show effective applications of this concept to analyze the experimental X-ray data and whence to understand microscopic mechanisms of structural phase transitions are presented. (author)

  13. Modelling gas migration in compacted bentonite: gambit club phase 3. Final report

    International Nuclear Information System (INIS)

    Hoch, A.R.; Cliffe, K.A.; Swift, B.T.; Rodwell, W.R.

    2004-04-01

    This report describes the third phase of a programme of work to develop a computational model of gas migration through highly compacted water-saturated bentonite. One difficulty with this endeavour is the definitive determination of the mechanism of the gas migration from the available experimental data. The report contains a brief review of the experimental data and their interpretation. The model development work reported involves the investigation of two ways of enhancing a model proposed in the previous phase of the programme. This model was based on the concept that gas migration pathways were created by consolidating the clay fabric by application of gas pressure to create porosity through which the gas could flow. The two developments of this model that are separately explored in this work are: (a) The incorporation of a proper treatment of the stress-strain behaviour of the clay in (b) response to gas migration. The previous model had only considered stress effects through simple volume changes to the clay fabric. The inclusion of a dual-porosity feature into the model in an attempt to address the role that the clay fabric might play in gas migration through the clay, in particular the role that pre-existing interstack voids might have in gas migration. The consideration of hysteresis effects was also included in this study. As in previous GAMBIT Club work, the models are tested against the results of laboratory experiments. (orig.)

  14. Microfluidic and nanofluidic phase behaviour characterization for industrial CO2, oil and gas.

    Science.gov (United States)

    Bao, Bo; Riordon, Jason; Mostowfi, Farshid; Sinton, David

    2017-08-08

    Microfluidic systems that leverage unique micro-scale phenomena have been developed to provide rapid, accurate and robust analysis, predominantly for biomedical applications. These attributes, in addition to the ability to access high temperatures and pressures, have motivated recent expanded applications in phase measurements relevant to industrial CO 2 , oil and gas applications. We here present a comprehensive review of this exciting new field, separating microfluidic and nanofluidic approaches. Microfluidics is practical, and provides similar phase properties analysis to established bulk methods with advantages in speed, control and sample size. Nanofluidic phase behaviour can deviate from bulk measurements, which is of particular relevance to emerging unconventional oil and gas production from nanoporous shale. In short, microfluidics offers a practical, compelling replacement of current bulk phase measurement systems, whereas nanofluidics is not practical, but uniquely provides insight into phase change phenomena at nanoscales. Challenges, trends and opportunities for phase measurements at both scales are highlighted.

  15. SDSL-ESR-based protein structure characterization

    NARCIS (Netherlands)

    Strancar, J.; Kavalenka, A.A.; Urbancic, I.; Ljubetic, A.; Hemminga, M.A.

    2010-01-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be

  16. The phase transition of the first order in the critical region of the gas-liquid system

    Directory of Open Access Journals (Sweden)

    I.R. Yukhnovskii

    2014-12-01

    Full Text Available This is a summarising investigation of the events of the phase transition of the first order that occur in the critical region below the liquid-gas critical point. The grand partition function has been completely integrated in the phase-space of the collective variables. The basic density measure is the quartic one. It has the form of the exponent function with the first, second, third and fourth degree of the collective variables. The problem has been reduced to the Ising model in an external field, the role of which is played by the generalised chemical potential μ*. The line μ*(η =0, where η is the density, is the line of the phase transition. We consider the isothermal compression of the gas till the point where the phase transition on the line μ*(η =0 is reached. When the path of the pressing reaches the line μ* =0 in the gas medium, a droplet of liquid springs up. The work for its formation is obtained, the surface-tension energy is calculated. On the line μ* =0 we have a two-phase system: the gas and the liquid (the droplet one. The equality of the gas and of the liquid chemical potentials is proved. The process of pressing is going on. But the pressure inside the system has stopped, two fixed densities have arisen: one for the gas-phase ηG=ηc(1-d/2 and the other for the liquid-phase ηL=ηc(1+d/2 (symmetrically to the rectlinear diameter, where ηc=0.13044 is the critical density. Starting from that moment the external pressure works as a latent work of pressure. Its value is obtained. As a result, the gas-phase disappears and the whole system turns into liquid. The jump of the density is equal to ηc d, where d=(D/2G1/2 ~ τν/2. D and G are coefficients of the Hamiltonian in the last cell connected with the renormalisation-group symmetry. The equation of state is written.

  17. Measurement of gas-liquid two-phase flow in micro-pipes by a capacitance sensor.

    Science.gov (United States)

    Ji, Haifeng; Li, Huajun; Huang, Zhiyao; Wang, Baoliang; Li, Haiqing

    2014-11-26

    A capacitance measurement system is developed for the measurement of gas-liquid two-phase flow in glass micro-pipes with inner diameters of 3.96, 2.65 and 1.56 mm, respectively. As a typical flow regime in a micro-pipe two-phase flow system, slug flow is chosen for this investigation. A capacitance sensor is designed and a high-resolution and high-speed capacitance measurement circuit is used to measure the small capacitance signals based on the differential sampling method. The performance and feasibility of the capacitance method are investigated and discussed. The capacitance signal is analyzed, which can reflect the voidage variation of two-phase flow. The gas slug velocity is determined through a cross-correlation technique using two identical capacitance sensors. The simulation and experimental results show that the presented capacitance measurement system is successful. Research work also verifies that the capacitance sensor is an effective method for the measurement of gas liquid two-phase flow parameters in micro-pipes.

  18. Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures

    DEFF Research Database (Denmark)

    Hansen, Simon Boje; Laursen, Nick Stub; Andersen, Gregers Rom

    2017-01-01

    of the presence of free cysteines in the target protein could considerably facilitate the process of obtaining unbiased experimental phases. Nanobodies (single-domain antibodies) have recently been shown to promote the crystallization and structure determination of flexible proteins and complexes. To extend...... phased using single-wavelength anomalous dispersion (SAD) and single isomorphous replacement with anomalous signal (SIRAS), taking advantage of radiation-induced changes in Cys-Hg bonding. Importantly, Hg labelling influenced neither the interaction of Nb36 with its antigen complement C5 nor its...

  19. Phases of a polar spin-1 Bose gas in a magnetic field

    International Nuclear Information System (INIS)

    Kis-Szabo, Krisztian; Szepfalusy, Peter; Szirmai, Gergely

    2007-01-01

    The two Bose-Einstein condensed phases of a polar spin-1 gas at nonzero magnetizations and temperatures are investigated. The Hugenholtz-Pines theorem is generalized to this system. Crossover to a quantum phase transition is also studied. Results are discussed in a mean field approximation

  20. Possibility of determining the concentration of the gas phase in a two-phase stream by an acoustical method

    Energy Technology Data Exchange (ETDEWEB)

    Butenko, A N; Potapenko, A E; Chistyakov, E S

    1976-01-01

    The method is based on the recording of the amplitude-frequency characteristics of a circular piezoelectric resonator (sensor) during movement of a stream of a two-phase medium. It is shown that the electrical voltage drop across the transducer and the natural oscillating frequency of the transducer depend on the concentration of the gas phase in the two-phase mixture, allowing an instrument to be developed for measurement of this concentration.

  1. A modeling and experimental study of flue gas desulfurization in a dense phase tower

    International Nuclear Information System (INIS)

    Chang, Guanqin; Song, Cunyi; Wang, Li

    2011-01-01

    We used a dense phase tower as the reactor in a novel semi-dry flue gas desulfurization process to achieve a high desulfurization efficiency of over 95% when the Ca/S molar ratio reaches 1.3. Pilot-scale experiments were conducted for choosing the parameters of the full-scale reactor. Results show that with an increase in the flue gas flow rate the rate of the pressure drop in the dense phase tower also increases, however, the rate of the temperature drop decreases in the non-load hot gas. We chose a water flow rate of 0.6 kg/min to minimize the approach to adiabatic saturation temperature difference and maximize the desulfurization efficiency. To study the flue gas characteristics under different processing parameters, we simulated the desulfurization process in the reactor. The simulated data matched very well with the experimental data. We also found that with an increase in the Ca/S molar ratio, the differences between the simulation and experimental data tend to decrease; conversely, an increase in the flue gas flow rate increases the difference; this may be associated with the surface reactions caused by collision, coalescence and fragmentation between the dispersed phases.

  2. Industrial aspects of gas-liquid two-phase flow

    International Nuclear Information System (INIS)

    Hewitt, G.F.

    1977-01-01

    The lecture begins by reviewing the various types of plant in which two phase flow occurs. Specifically, boiling plant, condensing plant and pipelines are reviewed, and the various two phase flow problems occurring in them are described. Of course, many other kinds of chemical engineering plant involve two phase flow, but are somewhat outside the scope of this lecture. This would include distillation columns, vapor-liquid separators, absorption towers etc. Other areas of industrial two phase flow which have been omitted for space reasons from this lecture are those concerned with gas/solids, liquid/solid and liquid/liquid flows. There then follows a description of some of the two phase flow processes which are relevant in industrial equipment and where special problems occur. The topics chosen are as follows: (1) pressure drop; (2) horizontal tubes - separation effects non-uniformites in heat transfer coefficient, effect of bends on dryout; (3) multicomponent mixtures - effects in pool boiling, mass transfer effects in condensation and Marangoni effects; (4) flow distribution - manifold problems in single phase flow, separation effects at a single T-junction in two phase flow and distribution in manifolds in two phase flow; (5) instability - oscillatory instability, special forms of instability in cryogenic systems; (6) nucleate boiling - effect of variability of surface, unresolved problems in forced convective nucleate boiling; and (7) shell side flows - flow patterns, cross flow boiling, condensation in cross flow

  3. Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses

    Science.gov (United States)

    Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P.; Thibault, Pierre

    2018-04-01

    The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. [Figure not available: see fulltext.

  4. The constitutive distributed parameter model of multicomponent chemical processes in gas, fluid and solid phase

    International Nuclear Information System (INIS)

    Niemiec, W.

    1985-01-01

    In the literature of distributed parameter modelling of real processes is not considered the class of multicomponent chemical processes in gas, fluid and solid phase. The aim of paper is constitutive distributed parameter physicochemical model, constructed on kinetics and phenomenal analysis of multicomponent chemical processes in gas, fluid and solid phase. The mass, energy and momentum aspects of these multicomponent chemical reactions and adequate phenomena are utilized in balance operations, by conditions of: constitutive invariance for continuous media with space and time memories, reciprocity principle for isotropic and anisotropic nonhomogeneous media with space and time memories, application of definitions of following derivative and equation of continuity, to the construction of systems of partial differential constitutive state equations, in the following derivative forms for gas, fluid and solid phase. Couched in this way all physicochemical conditions of multicomponent chemical processes in gas, fluid and solid phase are new form of constitutive distributed parameter model for automatics and its systems of equations are new form of systems of partial differential constitutive state equations in sense of phenomenal distributed parameter control

  5. Metal-Organic Framework Thin Films as Stationary Phases in Microfabricated Gas-Chromatography Columns.

    Energy Technology Data Exchange (ETDEWEB)

    Read, Douglas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sillerud, Colin Halliday [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-01-01

    The overarching goal of this project is to integrate Sandia's microfabricated gas-chromatography ( GC) columns with a stationary phase material that is capable of retaining high-volatility chemicals and permanent gases. The successful integration of such a material with GCs would dramatically expand the repertoire of detectable compounds for Sandia's various microanalysis systems. One such promising class of candidate materials is metal-organic frameworks (MOFs). In this report we detail our methods for controlled deposition of HKUST-1 MOF stationary phases within GC columns. We demonstrate: the chromatographic separation of natural gas; a method for determining MOF film thickness from chromatography alone; and the first-reported GC x GC separation of natural gas -- in general -- let alone for two disparate MOF stationary phases. In addition we determine the fundamental thermodynamic constant for mass sorption, the partition coefficient, for HKUST-1 and several light hydrocarbons and select toxic industrial chemicals.

  6. Influence of gas-liquid two-phase flow on angiotensin-I converting enzyme inhibitory peptides separation by ultra-filtration.

    Science.gov (United States)

    Charoenphun, Narin; Youravong, Wirote

    2017-01-01

    Membrane fouling is a major problem in ultra-filtration systems and two-phase flow is a promising technique for permeate flux enhancement. The objective of this research was to study the use of an ultra-filtration (UF) system to enrich angiotensin-I converting enzyme (ACE) inhibitory peptides from tilapia protein hydrolysate. To select the most appropriate membrane and operating condition, the effects of membrane molecular weight cut-off (MWCO), transmembrane pressure (TMP) and cross-flow velocity (CFV) on permeate flux and ACE inhibitory peptide separation were studied. Additionally, the gas-liquid two-phase flow technique was applied to investigate its effect on the process capability. The results showed that the highest ACE inhibitory activity was obtained from permeate of the 1 kDa membrane. In terms of TMP and CFV, the permeate flux tended to increase with TMP and CFV. The use of gas-liquid two-phase flow as indicated by shear stress number could reduce membrane fouling and increase the permeate flux up to 42%, depending on shear stress number. Moreover, the use of a shear stress number of 0.039 led to an augmentation in ACE inhibitory activity of permeates. Operating conditions using a shear stress number of 0.039 were recommended for enrichment of ACE inhibitory peptides. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  7. Amino acid code of protein secondary structure.

    Science.gov (United States)

    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

  8. Surface adsorption of lattice HP proteins: Thermodynamics and structural transitions using Wang-Landau sampling

    International Nuclear Information System (INIS)

    Li Yingwai; Landau, David P; Wüst, Thomas

    2012-01-01

    Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a short HP sequence consisting of only 36 monomers interacting with a substrate which attracts all monomers in the sequence. The conformational “phase transitions” have been identified by a canonical analysis of the specific heat and suitable structural observables. Three major “transitions”, namely, adsorption, hydrophobic core formation and “flattening” of adsorbed structures, are observed. Depending on the surface attractive strength relative to the intra-protein attraction among the H monomers, these processes take place in different sequences upon cooling.

  9. The Influence of Mixing in High Temperature Gas Phase Reactions

    DEFF Research Database (Denmark)

    Østberg, Martin

    1996-01-01

    by injection of NH3 with carrier gas into the flue gas. NH3 can react with NO and form N2, but a competing reaction path is the oxidation of NH3 to NO.The SNR process is briefly described and it is shown by chemical kinetic modelling that OH radicals under the present conditions will initiate the reaction......The objective of this thesis is to describe the mixing in high temperature gas phase reactions.The Selective Non-Catalytic Reduction of NOx (referred as the SNR process) using NH3 as reductant was chosen as reaction system. This in-furnace denitrification process is made at around 1200 - 1300 K...... diffusion. The SNR process is simulated using the mixing model and an empirical kinetic model based on laboratory experiments.A bench scale reactor set-up has been built using a natural gas burner to provide the main reaction gas. The set-up has been used to perform an experimental investigation...

  10. Gas-phase synthesis of semiconductor nanocrystals and its applications

    Science.gov (United States)

    Mandal, Rajib

    Luminescent nanomaterials is a newly emerging field that provides challenges not only to fundamental research but also to innovative technology in several areas such as electronics, photonics, nanotechnology, display, lighting, biomedical engineering and environmental control. These nanomaterials come in various forms, shapes and comprises of semiconductors, metals, oxides, and inorganic and organic polymers. Most importantly, these luminescent nanomaterials can have different properties owing to their size as compared to their bulk counterparts. Here we describe the use of plasmas in synthesis, modification, and deposition of semiconductor nanomaterials for luminescence applications. Nanocrystalline silicon is widely known as an efficient and tunable optical emitter and is attracting great interest for applications in several areas. To date, however, luminescent silicon nanocrystals (NCs) have been used exclusively in traditional rigid devices. For the field to advance towards new and versatile applications for nanocrystal-based devices, there is a need to investigate whether these NCs can be used in flexible and stretchable devices. We show how the optical and structural/morphological properties of plasma-synthesized silicon nanocrystals (Si NCs) change when they are deposited on stretchable substrates made of polydimethylsiloxane (PDMS). Synthesis of these NCs was performed in a nonthermal, low-pressure gas phase plasma reactor. To our knowledge, this is the first demonstration of direct deposition of NCs onto stretchable substrates. Additionally, in order to prevent oxidation and enhance the luminescence properties, a silicon nitride shell was grown around Si NCs. We have demonstrated surface nitridation of Si NCs in a single step process using non?thermal plasma in several schemes including a novel dual-plasma synthesis/shell growth process. These coated NCs exhibit SiNx shells with composition depending on process parameters. While measurements including

  11. Laser diagnostics of a diamond depositing chemical vapour deposition gas-phase environment

    International Nuclear Information System (INIS)

    Smith, James Anthony

    2002-01-01

    Studies have been carried out to understand the gas-phase chemistry underpinning diamond deposition in hot filament and DC-arcjet chemical vapour deposition (CVD) systems. Resonance enhanced Multiphoton lonisation (REMPI) techniques were used to measure the relative H atom and CH 3 radical number densities and local gas temperatures prevalent in a hot filament reactor, operating on Ch 4 /H 2 and C 2 H 2 /H 2 gas mixtures. These results were compared to a 3D-computer simulation, and hence provided an insight into the nature of the gas-phase chemistry with particular reference to C 2 →C 1 species conversion. Similar experimental and theoretical studies were also carried out to explain the chemistry involved in NH 3 /CH 4 /H 2 and N 2 /CH 4 /H 2 gas mixtures. It was demonstrated that the reactive nature of the filament surface was dependent on the addition of NH 3 , influencing atomic hydrogen production, and thus the H/C/N gas-phase chemistry. Studies of the DC-arcjet diamond CVD reactor consisted of optical emission spectroscopic studies of the plume during deposition from an Ar/H 2 /CH 4 /N 2 gas mixture. Spatially resolved species emission intensity maps were obtained for C 2 (d→a), CN(B→X) and H β from Abel-inverted datasets. The C 2 (d→a) and CN(B→X) emission intensity maps both show local maxima near the substrate surface. SEM and Laser Raman analyses indicate that N 2 additions lead to a reduction in film quality and growth rate. Photoluminescence and SIMS analyses of the grown films provide conclusive evidence of nitrogen incorporation (as chemically bonded CN). Absolute column densities of C 2 (a) in a DC-arcjet reactor operating on an Ar/H 2 /CH 4 gas mixture, were measured using Cavity ring down spectroscopy. Simulations of the measured C 2 (v=0) transition revealed a rotational temperature of ∼3300 K. This gas temperature is similar to that deduced from optical emission spectroscopy studies of the C 2 (d→a) transition. (author)

  12. Quantum mechanics of the fractional-statistics gas: Random-phase approximation

    International Nuclear Information System (INIS)

    Dai, Q.; Levy, J.L.; Fetter, A.L.; Hanna, C.B.; Laughlin, R.B.

    1992-01-01

    A description of the fractional-statistics gas based on the complete summation of Hartree, Fock, ladder and bubble diagrams is presented. The superfluid properties identified previously in the random-phase-approximation (RPA) calculation of Fetter, Hanna, and Laughlin [Phys. Rev. B 39, 9679 (1989)] are substantially confirmed. The discrepancy between the RPA sound speed and the Hartree-Fock bulk modulus is found to be eliminated. The unusual Hall-effect behavior is found to vanish for the Bose gas test case but not for the fractional-statistics gas, implying that it is physically correct. Excellent agreement is obtained with the collective-mode dispersion obtained numerically by Xie, He, and Das Sarma [Phys. Rev. Lett. 65, 649 (1990)

  13. Single-step gas phase synthesis of stable iron aluminide nanoparticles with soft magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Vernieres, Jerome, E-mail: Jerome.vernieres@oist.jp; Benelmekki, Maria; Kim, Jeong-Hwan; Grammatikopoulos, Panagiotis; Diaz, Rosa E. [Nanoparticles by Design Unit, Okinawa Institute of Science and Technology (OIST) Graduate University, 1919-1 Tancha, Onna Son, Okinawa 904-0495 (Japan); Bobo, Jean-François [Centre d’Elaboration de Materiaux et d’Etudes Structurales (CEMES), 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4 (France); Sowwan, Mukhles, E-mail: Mukhles@oist.jp [Nanoparticles by Design Unit, Okinawa Institute of Science and Technology (OIST) Graduate University, 1919-1 Tancha, Onna Son, Okinawa 904-0495 (Japan); Nanotechnology Research Laboratory, Al-Quds University, P.O. Box 51000, East Jerusalem, Palestine (Country Unknown)

    2014-11-01

    Soft magnetic alloys at the nanoscale level have long generated a vivid interest as candidate materials for technological and biomedical purposes. Consequently, controlling the structure of bimetallic nanoparticles in order to optimize their magnetic properties, such as high magnetization and low coercivity, can significantly boost their potential for related applications. However, traditional synthesis methods stumble upon the long standing challenge of developing true nanoalloys with effective control over morphology and stability against oxidation. Herein, we report on a single-step approach to the gas phase synthesis of soft magnetic bimetallic iron aluminide nanoparticles, using a versatile co-sputter inert gas condensation technique. This method allowed for precise morphological control of the particles; they consisted of an alloy iron aluminide crystalline core (DO{sub 3} phase) and an alumina shell, which reduced inter-particle interactions and also prevented further oxidation and segregation of the bimetallic core. Remarkably, the as-deposited alloy nanoparticles show interesting soft magnetic properties, in that they combine a high saturation magnetization (170 emu/g) and low coercivity (less than 20 Oe) at room temperature. Additional functionality is tenable by modifying the surface of the particles with a polymer, to ensure their good colloidal dispersion in aqueous environments.

  14. Preparation of sulfur/multiple pore size porous carbon composite via gas-phase loading method for lithium-sulfur batteries

    International Nuclear Information System (INIS)

    Li, Long-Yan; Chen, Yan-Xiao; Guo, Xiao-Dong; Zhong, Ben-He; Zhong, Yan-Jun

    2014-01-01

    A porous carbon with multiple pore size distribution was synthesized, and regarded as a carrier to obtain the sulfur/carbon (S/C) composite via a gas-phase loading method. We proposed this novel gas-phase loading method by using a specially designed fluid-bed reactor to encapsulate and sequester gas-phase sulfur molecules into the porous carbon in current study. The nitrogen Brunauer-Emmett-Teller (BET), scanning electron microscopy (SEM) and X-ray powder diffraction (XRD) characterizations were investigated on both the porous carbon and the sulfur/carbon composite. The results show that the gas-phase loading method contributes to the combination of sulfur molecules and matrix porous carbon. Furthermore, the sulfur/multiple pore size distribution carbon composite based on the gas-phase loading method demonstrate an excellent electrochemical property. The initial specific discharge capacity is 795.0 mAh g −1 at 800 mA g −1 , with a capacity retention of 86.3% after 100 cycles

  15. Gas phase reactive collisions, experimental approach

    Directory of Open Access Journals (Sweden)

    Canosa A.

    2012-01-01

    Full Text Available Since 1937 when the first molecule in space has been identified, more than 150 molecules have been detected. Understanding the fate of these molecules requires having a perfect view of their photochemistry and reactivity with other partners. It is then crucial to identify the main processes that will produce and destroy them. In this chapter, a general view of experimental techniques able to deliver gas phase chemical kinetics data at low and very low temperatures will be presented. These techniques apply to the study of reactions between neutral reactants on the one hand and reactions involving charge species on the other hand.

  16. A New Void Fraction Measurement Method for Gas-Liquid Two-Phase Flow in Small Channels

    Directory of Open Access Journals (Sweden)

    Huajun Li

    2016-01-01

    Full Text Available Based on a laser diode, a 12 × 6 photodiode array sensor, and machine learning techniques, a new void fraction measurement method for gas-liquid two-phase flow in small channels is proposed. To overcome the influence of flow pattern on the void fraction measurement, the flow pattern of the two-phase flow is firstly identified by Fisher Discriminant Analysis (FDA. Then, according to the identification result, a relevant void fraction measurement model which is developed by Support Vector Machine (SVM is selected to implement the void fraction measurement. A void fraction measurement system for the two-phase flow is developed and experiments are carried out in four different small channels. Four typical flow patterns (including bubble flow, slug flow, stratified flow and annular flow are investigated. The experimental results show that the development of the measurement system is successful. The proposed void fraction measurement method is effective and the void fraction measurement accuracy is satisfactory. Compared with the conventional laser measurement systems using standard laser sources, the developed measurement system has the advantages of low cost and simple structure. Compared with the conventional void fraction measurement methods, the proposed method overcomes the influence of flow pattern on the void fraction measurement. This work also provides a good example of using low-cost laser diode as a competent replacement of the expensive standard laser source and hence implementing the parameter measurement of gas-liquid two-phase flow. The research results can be a useful reference for other researchers’ works.

  17. A New Void Fraction Measurement Method for Gas-Liquid Two-Phase Flow in Small Channels.

    Science.gov (United States)

    Li, Huajun; Ji, Haifeng; Huang, Zhiyao; Wang, Baoliang; Li, Haiqing; Wu, Guohua

    2016-01-27

    Based on a laser diode, a 12 × 6 photodiode array sensor, and machine learning techniques, a new void fraction measurement method for gas-liquid two-phase flow in small channels is proposed. To overcome the influence of flow pattern on the void fraction measurement, the flow pattern of the two-phase flow is firstly identified by Fisher Discriminant Analysis (FDA). Then, according to the identification result, a relevant void fraction measurement model which is developed by Support Vector Machine (SVM) is selected to implement the void fraction measurement. A void fraction measurement system for the two-phase flow is developed and experiments are carried out in four different small channels. Four typical flow patterns (including bubble flow, slug flow, stratified flow and annular flow) are investigated. The experimental results show that the development of the measurement system is successful. The proposed void fraction measurement method is effective and the void fraction measurement accuracy is satisfactory. Compared with the conventional laser measurement systems using standard laser sources, the developed measurement system has the advantages of low cost and simple structure. Compared with the conventional void fraction measurement methods, the proposed method overcomes the influence of flow pattern on the void fraction measurement. This work also provides a good example of using low-cost laser diode as a competent replacement of the expensive standard laser source and hence implementing the parameter measurement of gas-liquid two-phase flow. The research results can be a useful reference for other researchers' works.

  18. Visualization and measurement of liquid velocity field of gas-liquid metal two-phase flow using neutron radiography

    International Nuclear Information System (INIS)

    Saito, Yasushi; Suzuki, Tohru; Matsubayashi, Masahito

    2000-01-01

    In a core melt accident of a fast breeder reactor, a possibility of re-criticality is anticipated in the molten fuel-steel mixture pool. One of the mechanisms to suppress the re-criticality is the boiling of steel in the molten fuel-steel mixture pool because of the negative void reactivity effect. To evaluate the reactivity change due to boiling, it is necessary to know the characteristics of gas-liquid two-phase flow in the molten fuel-steel mixture pool. For this purpose, boiling bubbles in a molten fuel-steel mixture pool were simulated by adiabatic gas bubbles in a liquid metal pool to study the basic characteristics of gas-liquid metal two-phase mixture. Visualization of the two-phase mixture and measurements of liquid phase velocity and void fraction were conducted by using neutron radiography and image processing techniques. From these measurements, the basic characteristics of gas-liquid metal two-phase mixture were clarified. (author)

  19. Hydrate phase equilibrium and structure for (methane + ethane + tetrahydrofuran + water) system

    International Nuclear Information System (INIS)

    Sun Changyu; Chen Guangjin; Zhang Lingwei

    2010-01-01

    The separation of methane and ethane through forming hydrate is a possible choice in natural gas, oil processing, or ethylene producing. The hydrate formation conditions of five groups of (methane + ethane) binary gas mixtures in the presence of 0.06 mole fraction tetrahydrofuran (THF) in water were obtained at temperatures ranging from (277.7 to 288.2) K. In most cases, the presence of THF in water can lower the hydrate formation pressure of (methane + ethane) remarkably. However, when the composition of ethane is as high as 0.832, it is more difficult to form hydrate than without THF system. Phase equilibrium model for hydrates containing THF was developed based on a two-step hydrate formation mechanism. The structure of hydrates formed from (methane + ethane + THF + water) system was also determined by Raman spectroscopy. When THF concentration in initial aqueous solution was only 0.06 mole fraction, the coexistence of structure I hydrate dominated by ethane and structure II hydrate dominated by THF in the hydrate sample was clearly demonstrated by Raman spectroscopic data. On the contrary, only structure II hydrate existed in the hydrate sample formed from (methane + ethane + THF + water) system when THF concentration in initial aqueous solution was increased to 0.10 mole fraction. It indicated that higher THF concentration inhibited the formation of structure I hydrate dominated by ethane and therefore lowered the trapping of ethane in hydrate. It implies a very promising method to increase the separation efficiency of methane and ethane.

  20. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    Science.gov (United States)

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  1. Two-Phase Phenomena In Wet Flue Gas Desulfurization Process

    International Nuclear Information System (INIS)

    Minzer, U.; Moses, E.J.; Toren, M.; Blumenfeld, Y.

    1998-01-01

    In order to reduce sulfur oxides discharge, Israel Electric Corporation (IEC) is building a wet Flue Gas Desulfurization (FGD) facility at Rutenberg B power station. The primary objective of IEC is to minimize the occurrence of stack liquid discharge and avoid the discharge of large droplets, in order to prevent acid rain around the stack. Liquid discharge from the stack is the integrated outcome of two-phase processes, which are discussed in this work. In order to estimate droplets discharge the present investigation employs analytical models, empirical tests, and numerical calculations of two-phase phenomena. The two-phase phenomena are coupled and therefore cannot be investigated separately. The present work concerns the application of Computational Fluid Dynamic (CFD) as an engineering complementary tool in the IEC investigation

  2. FLUIDDYNAMIC ASPECTS OF GAS-PHASE ETHYLENE POLYMERIZATION REACTOR DESIGN

    Directory of Open Access Journals (Sweden)

    Guardani R.

    1998-01-01

    Full Text Available The relative importance of design variables affecting the fluiddynamic behavior of a fluidized bed reactor for the gas-phase ethylene polymerization is discussed, based on mathematical modeling. The three-phase bubbling fluidized bed model is based on axially distributed properties for the bubble, cloud and emulsion phases, combined with correlations for population balance and entrainment. Under the operating conditions adopted in most industrial processes, the reactor performance is affected mainly by the reaction rate and solids entrainment. Simulation results indicate that an adequate design of the freeboard and particle collecting equipment is of primary importance in order to produce polymeric particles with the desired size distribution, as well as to keep entrainment and catalyst feed rates at adequate levels.

  3. Fractionation of Hydrocarbons Between Oil and Gas Phases Fractionnement des hydrocarbures entre les phases huile et gaz

    Directory of Open Access Journals (Sweden)

    Ruffier-Meray V.

    2006-12-01

    Full Text Available The investigation of hydrocarbon fractionation between oil and gas phases is of interest for several purposes in reservoir exploitation. In reservoir geochemistry, the evolution of light hydrocarbon fractions of oils may explain some migration phenomena. In gas injection projects, the preferred dissolution of some components in gas may alter the composition as well as the properties of the oil. Underground gas storage in depleted oil reservoirs may also be concerned by these problems. Results of several IFP studies are described here to illustrate and to quantify the phenomenon. Two of them, using real reservoir fluids, concern reservoir geochemistry, while the third, which is a swelling test, aimed to study gas injection, investigated a synthetic reservoir fluid with hydrocarbon components up to C30. Two pieces of equipment were used: a sapphire cell with a maximum pressure rating of 400 bar and a high pressure apparatus called Hercule with a maximum pressure of 1500 bar. For each fluid, the saturation pressure was measured. For various pressure levels below saturation, the coexisting liquid and gas phases were sampled at constant pressure, and subsequently analyzed by gas chromatography. In the gas injection study, sampling was repeated with different quantities of injection gas. Compared to a n-paraffin with the same number of carbon atoms, aromatic hydrocarbons appear to stay preferentially in the liquid phase, as do cycloalkanes to a lesser extent. The gaseous phase is slightly enriched in isoalkanes. These fractionation effects are less pronounced near the critical region. These phenomena have been modeled with a cubic equation of state combined with a group contribution mixing rule. L'étude du fractionnement des hydrocarbures légers entre les phases gazeuses et liquides intéresse plusieurs domaines dans le cadre de l'exploitation des gisements. En géochimie de réservoir l'évolution de la composition de la fraction légère peut

  4. Gas phase fractionation method using porous ceramic membrane

    Science.gov (United States)

    Peterson, Reid A.; Hill, Jr., Charles G.; Anderson, Marc A.

    1996-01-01

    Flaw-free porous ceramic membranes fabricated from metal sols and coated onto a porous support are advantageously used in gas phase fractionation methods. Mean pore diameters of less than 40 .ANG., preferably 5-20 .ANG. and most preferably about 15 .ANG., are permeable at lower pressures than existing membranes. Condensation of gases in small pores and non-Knudsen membrane transport mechanisms are employed to facilitate and increase membrane permeability and permselectivity.

  5. Overcoming barriers to membrane protein structure determination.

    Science.gov (United States)

    Bill, Roslyn M; Henderson, Peter J F; Iwata, So; Kunji, Edmund R S; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G; Vogel, Horst

    2011-04-01

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.

  6. Gas Phase Hydrogenation of Levulinic Acid to gamma-Valerolactone

    NARCIS (Netherlands)

    Bonrath, Werner; Castelijns, Anna Maria Cornelia Francisca; de Vries, Johannes Gerardus; Guit, Rudolf Philippus Maria; Schuetz, Jan; Sereinig, Natascha; Vaessen, Henricus Wilhelmus Leonardus Marie

    The gas phase hydrogenation of levulinic acid to gamma-valerolactone over copper and ruthenium based catalysts in a continuous fixed-bed reactor system was investigated. Among the catalysts a copper oxide based one [50-75 % CuO, 20-25 % SiO2, 1-5 % graphite, 0.1-1 % CuCO3/Cu(OH)(2)] gave

  7. Serum protein capillary electrophoresis and measurement of acute phase proteins in a captive cheetah (Acinonyx jubatus) population

    DEFF Research Database (Denmark)

    Depauw, Sarah; Delanghe, Joris; Whitehouse-Tedd, Katherine

    2014-01-01

    Renal and gastrointestinal pathologies are widespread in the captive cheetah (Acinonyx jubatus) population but are often diagnosed at a late stage, because diagnostic tools are limited to the evaluation of clinical signs or general blood examination. Presently, no data are available on serum...... proteins and acute-phase proteins in cheetahs during health or disease, although they might be important to improve health monitoring. This study aimed to quantify serum proteins by capillary electrophoresis in 80 serum samples from captive cheetahs, categorized according to health status and disease type....... Moreover, serum amyloid A concentrations were measured via a turbidimetric immunoassay validated in domestic cats, whereas haptoglobin and C-reactive protein were determined by non-species-specific functional tests. Cheetahs classified as healthy had serum protein and acute phase protein concentrations...

  8. Axial dispersion of gas and solid phases in a gas—solid packed column at trickle flow

    NARCIS (Netherlands)

    Roes, A.W.M.; van Swaaij, Willibrordus Petrus Maria

    1979-01-01

    Axial dispersion of gas and solid phases in a gas—solid packed column at trickle flow, a promising new countercurrent operation, was evaluated using residence time distribution (RTD) experiments. The column was packed with dumped Pall rings, the gas phase was air at ambient conditions and the solid

  9. TAM receptors, Gas6, and protein S: roles in inflammation and hemostasis

    NARCIS (Netherlands)

    van der Meer, Jonathan H. M.; van der Poll, Tom; van 't Veer, Cornelis

    2014-01-01

    TAM receptors (Tyro3, Axl, andMer) belong to a family of receptor tyrosine kinases that have important effects on hemostasis and inflammation. Also, they affect cell proliferation, survival, adhesion, and migration. TAM receptors can be activated by the vitamin K-dependent proteins Gas6 and protein

  10. Quality assessment of protein model-structures based on structural and functional similarities.

    Science.gov (United States)

    Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

    2012-09-21

    Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and

  11. Acrolein Production by Gas-Phase Glycerol Dehydration Using PO₄/Nb₂O5 Catalysts.

    Science.gov (United States)

    Lee, Kyu Am; Ryoo, HeeKyoung; Ma, Byung Chol; Kim, Youngchul

    2018-02-01

    In this study, modified niobium oxide were prepared to study the addictive effects on the catalytic performance for gas-phase glycerol dehydration. The catalysts were characterized by N2 adsorption/desorption, XRD, NH3-TPD, FT-IR. The amount of phosphoric acid was up to 50 wt% in niobium. As a result, the highest glycerol conversion was achieved over 20 wt% PO4/Nb2O5. It indicates that the optimal amount of phosphoric acid leads the catalyst to have appropriate acidity which is an important factor for gas-phase glycerol dehydration.

  12. The nuclear liquid-gas phase transition: Present status and future perspectives

    International Nuclear Information System (INIS)

    Pochodzalla, J.; Imme, G.; Maddalena, V.

    1996-07-01

    More than two decades ago, the van der Waals behavior of the nucleon -nucleon force inspired the idea of a liquid-gas phase transition in nuclear matter. Heavy-ion reactions at relativistic energies offer the unique possibility for studying this phase transition in a finite, hadronic system. A general overview of this subject is given emphasizing the most recent results on nuclear calorimetry. (orig.)

  13. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

    2016-01-01

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment

  14. Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen, E-mail: huang@gsu.edu [Georgia State University, Atlanta, GA 30303 (United States)

    2014-02-01

    Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

  15. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  16. Elucidating the weak protein-protein interaction mechanisms behind the liquid-liquid phase separation of a mAb solution by different types of additives.

    Science.gov (United States)

    Wu, Guoliang; Wang, Shujing; Tian, Zhou; Zhang, Ning; Sheng, Han; Dai, Weiguo; Qian, Feng

    2017-11-01

    Liquid-liquid phase separation (LLPS) has long been observed during the physical stability investigation of therapeutic protein formulations. The buffer conditions and the presence of various excipients are thought to play important roles in the formulation development of monoclonal antibodies (mAbs). In this study, the effects of several small-molecule excipients (histidine, alanine, glycine, sodium phosphate, sodium chloride, sorbitol and sucrose) with diverse physical-chemical properties on LLPS of a model IgG1 (JM2) solutions were investigated by multiple techniques, including UV-vis spectroscopy, circular dichroism, differential scanning calorimetry/fluorimetry, size exclusion chromatography and dynamic light scattering. The LLPS of JM2 was confirmed to be a thermodynamic equilibrium process with no structural changes or irreversible aggregation of proteins. Phase diagrams of various JM2 formulations were constructed, suggesting that the phase behavior of JM2 was dependent on the solution pH, ionic strength and the presence of other excipients such as glycine, alanine, sorbitol and sucrose. Furthermore, we demonstrated that for this mAb, the interaction parameter (k D ) determined at low protein concentration appeared to be a good predictor for the occurrence of LLPS at high concentration. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Structural basis for target protein recognition by the protein disulfide reductase thioredoxin

    DEFF Research Database (Denmark)

    Maeda, Kenji; Hägglund, Per; Finnie, Christine

    2006-01-01

    Thioredoxin is ubiquitous and regulates various target proteins through disulfide bond reduction. We report the structure of thioredoxin (HvTrxh2 from barley) in a reaction intermediate complex with a protein substrate, barley alpha-amylase/subtilisin inhibitor (BASI). The crystal structure...... of this mixed disulfide shows a conserved hydrophobic motif in thioredoxin interacting with a sequence of residues from BASI through van der Waals contacts and backbone-backbone hydrogen bonds. The observed structural complementarity suggests that the recognition of features around protein disulfides plays...... a major role in the specificity and protein disulfide reductase activity of thioredoxin. This novel insight into the function of thioredoxin constitutes a basis for comprehensive understanding of its biological role. Moreover, comparison with structurally related proteins shows that thioredoxin shares...

  18. Photoisomerization action spectroscopy of the carbocyanine dye DTC+ in the gas phase.

    Science.gov (United States)

    Adamson, Brian D; Coughlan, Neville J A; da Silva, Gabriel; Bieske, Evan J

    2013-12-19

    Molecular photoisomerization plays a crucial role in diverse biological and technological contexts. Here, we combine ion mobility spectrometry and laser spectroscopy to characterize the photoisomerization of molecular cations in the gas phase. The target molecular ions, polymethine dye cations 3,3'-diethylthiacarbocyanine (DTC(+)), are propelled through helium buffer gas by an electric field and are photoisomerized by light from a tunable laser. Photoexcitation over the 450-570 nm range converts trans-DTC(+) to cis-DTC(+), noticeably modifying the ions' arrival time distribution. The photoisomerization action spectrum, which has a maximum at 535 nm, resembles the absorption spectrum of DTC(+) in solution but is shifted 25 nm to shorter wavelength. Comparisons between measured and calculated mobilities suggest that the photoisomer involves a twist about the second C-C bond in the methine chain (8,9-cis isomer) rather than a twist about the first methine C-C bond (2,8-cis isomer). It is postulated that the excited gas-phase ions internally convert from the S1 Franck-Condon region to the S0 manifold and explore the conformational landscape as they cool through He buffer gas collisions. Master equation simulations of the relaxation process in the S0 manifold suggest that the 8,9-cis isomer is preferred over the 2,8-cis isomer because it lies lower in energy and because it is separated from the trans isomer by a substantially higher barrier. The study demonstrates that the photoisomerization of molecular ions can be probed selectively in the gas phase, providing insights into photoisomerization mechanisms and information on the solvent-free absorption spectrum.

  19. Visualization for gas-liquid two-phase flow using wire mesh tomography

    International Nuclear Information System (INIS)

    Motegi, Yuichi; Wanjiraniran, Weerin; Kikura, Hiroshige; Aritomi, Masanori; Yamauchi, Toyoaki

    2003-01-01

    Wire Mesh Tomography (WMT), which is system to measure two-phase flow, has been developed in our laboratory. Measurement principle of WMT is detecting conductivity difference between gas and liquid. WMT measures void fraction as raw date, and calculates gas velocity and bubble volume etc. In this paper, this measurement technique was applied to vertical circular pipe of 50 mm diameter and about 7 m heights. New Wire Mesh Sensor (WMS), which is measurement part of WMT, for circular pipe, have been made. When experiment was performed, superficial gas and water velocity. The effect of each flow parameter was found for void fraction, true gas velocity and bubble volume and the results was in good agreement with the past research, qualitatively. (author)

  20. Protein structure: geometry, topology and classification

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, William R.; May, Alex C.W.; Brown, Nigel P.; Aszodi, Andras [Division of Mathematical Biology, National Institute for Medical Research, London (United Kingdom)

    2001-04-01

    The structural principals of proteins are reviewed and analysed from a geometric perspective with a view to revealing the underlying regularities in their construction. Computer methods for the automatic comparison and classification of these structures are then reviewed with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of the classification of proteins, more abstract geometric and topological representations are explored, including the occurrence of knotted topologies. The review concludes with a consideration of the origin of higher-level symmetries in protein structure. (author)

  1. Gas-phase salt bridge interactions between glutamic acid and arginine

    NARCIS (Netherlands)

    Jaeqx, S.; Oomens, J.; Rijs, A.M.

    2013-01-01

    The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in

  2. SVOC partitioning between the gas phase and settled dust indoors

    DEFF Research Database (Denmark)

    Weschler, Charles J.; Nazaroff, W. W.

    2010-01-01

    Semivolatile organic compounds (SVOCs) are a major class of indoor pollutants. Understanding SVOC partitioning between the gas phase and settled dust is important for characterizing the fate of these species indoors and the pathways by which humans are exposed to them. Such knowledge also helps...

  3. Effects of TT8 and HB12 Silencing on the Relations between the Molecular Structures of Alfalfa ( Medicago sativa) Plants and Their Nutritional Profiles and In Vitro Gas Production.

    Science.gov (United States)

    Lei, Yaogeng; Hannoufa, Abdelali; Prates, Luciana Louzada; Shi, Haitao; Wang, Yuxi; Biligetu, Bill; Christensen, David; Yu, Peiqiang

    2018-06-06

    The objective of this study was to investigate the effects of silencing the TT8 and HB12 genes on the nutritive profiles and in vitro gas production of alfalfa in relation to the spectral molecular structures of alfalfa. TT8-silenced (TT8i, n = 5) and HB12-silenced (HB12i, n = 11) alfalfa were generated by RNA interference (RNAi) and grown with nontransgenic wild type controls (WT, n = 4) in a greenhouse. Alfalfa plants were harvested at early-to-mid vegetative stage. Samples were analyzed for their chemical compositions, CNCPS fractions, and in vitro gas production. Correlations and regressions of the nutritional profiles and in vitro gas production with the molecular spectral structures were also determined. The results showed that the transformed alfalfa had higher digestible fiber and lower crude protein with higher proportions of indigestible protein than WT. HB12 RNAi had lower gas production compared with those of the others. Some chemical, CNCPS, and gas-production profiles were closely correlated with spectral structures and could be well predicted from spectral parameters. In conclusion, the RNAi silencing of TT8 and HB12 in alfalfa altered the chemical, CNCPS and gas-production profiles of alfalfa, and such alterations were closely correlated with the inherent spectral structures of alfalfa.

  4. Use of designed sequences in protein structure recognition.

    Science.gov (United States)

    Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

    2018-05-09

    Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

  5. Gas phase structure of transition metal dihydrides

    International Nuclear Information System (INIS)

    Demuynck, J.; Schaefer, H.F. III

    1980-01-01

    ESR and infrared spectroscopic measurements on matrix isolated MnH 2 and CrH 2 have recently suggested that these simple molecules may be bent. This result would be the opposite of that found experimentally for the transition metal dihalides MX 2 , known to be linear. Here the geometrical structure of MnH 2 has been investigated by molecular electronic structure theory. A large contracted Gaussian basis set [Mn(14s11p6p/9s8p3d), H(5s1p/3s1p)] was used in conjunction with self-consistent field and configuration interaction methods. These suggest that the 6 A 1 ground state of MnH 2 is linear. Further studies of the 3 A 1 state (one of several low-lying states) of TiH 2 also favor linearity, although this potential energy surface is extremely flat with respect to bending. Thus it appears probable that most MH 2 molecules, like the related MX 2 family, are linear

  6. A new method for determining gas phase heat of formation of aromatic energetic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Keshavarz, Mohammad H. [Department of Chemistry, Malek-ashtar University of Technology, Shahin-shahr P. O. Box 83145/115 (Iran); Tehrani, Masoud K. [Department of Physics, Malek-ashtar University of Technology, Shahin-shahr P. O. Box 83145/115 (Iran)

    2007-04-15

    A new correlation is introduced for desk calculation of gas phase heat of formation of aromatic energetic compounds that contain the elements of carbon, hydrogen, nitrogen and oxygen. Predicted gas phase heats of formation for 26 energetic compounds have a root mean square of deviation from experiment of 20.67 kJ/mol, which is in good agreement with respect to measured values of oxygen-lean and oxygen-rich aromatic energetic compounds. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  7. PDB2CD visualises dynamics within protein structures.

    Science.gov (United States)

    Janes, Robert W

    2017-10-01

    Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

  8. Simultaneous measurements of formaldehyde and nitrous acid in dews and gas phase in the atmosphere of Santiago, Chile

    Science.gov (United States)

    Rubio, María A.; Lissi, Eduardo; Villena, Guillermo; Elshorbany, Y. F.; Kleffmann, Jörg; Kurtenbach, Ralf; Wiesen, Peter

    2009-12-01

    The amounts of formaldehyde and nitrous acid (HONO) in gas phase and dews of Santiago de Chile were simultaneously measured. Formaldehyde concentrations values in the liquid phase (dews) correlate fairly well with those in the gaseous phase and are even higher than those expected from gas-dew equilibrium. On the other hand, nitrite concentrations in dews were considerably smaller (ca. 15 times) than those expected from the gas-phase concentrations. This under-saturation is attributed to diffusion limitations due to the relatively large HONO solubility. In agreement with this, under-saturation increases with the rate of dew formation and the pH of the collected waters, factors that should increase the rate of gas to liquid HONO transfer required to reach equilibrium.

  9. Recent progress of chiral stationary phases for separation of enantiomers in gas chromatography.

    Science.gov (United States)

    Xie, Sheng-Ming; Yuan, Li-Ming

    2017-01-01

    Chromatography techniques based on chiral stationary phases are widely used for the separation of enantiomers. In particular, gas chromatography has developed rapidly in recent years due to its merits such as fast analysis speed, lower consumption of stationary phases and analytes, higher column efficiency, making it a better choice for chiral separation in diverse industries. This article summarizes recent progress of novel chiral stationary phases based on cyclofructan derivatives and chiral porous materials including chiral metal-organic frameworks, chiral porous organic frameworks, chiral inorganic mesoporous materials, and chiral porous organic cages in gas chromatography, covering original research papers published since 2010. The chiral recognition properties and mechanisms of separation toward enantiomers are also introduced. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Gas-phase and liquid-phase pre-irradiation grafting of AAc onto LDPE and HDPE films for pervaporation membranes

    International Nuclear Information System (INIS)

    Rao Zhigong; Li Guixiang; Sugo, Takanobu; Okamoto, Jiro

    1992-01-01

    A study has been made on gas-phase and liquid-phase pre-irradiation grafting of acrylic acid onto LDPE and HDPE films for pervaporation membranes of ethanol-water mixtures. It was found that the degree of grafting, percent volume change of grafted membranes and length of grafting chains depend on the methods of grafting, crystal state of substrate films and diffusion rate of the monomer in the films. The pervaporation characteristics of grafted membranes is influenced directly by the surface hydrophilicity of grafted membranes, temperature of the feed, degree of grafting, crosslinking of grafted chains and alkaline metal ions in the functional groups. The potassium ion exchange membrane of HDPE synthesized by gas-phase grafting has better pervaporation efficiency. At 80 wt% ethanol in the feed, 25 o C feed temperature and 70% degree of grafting a grafted membrane has a 0.65 kg/m 2 h flux and a separation factor of 20. (Author)

  11. Berry's Phase and Fine Structure

    CERN Document Server

    Binder, B

    2002-01-01

    Irrational numbers can be assigned to physical entities based on iterative processes of geometric objects. It is likely that iterative round trips of vector signals include a geometric phase component. If so, this component will couple back to the round trip frequency or path length generating an non-linear feedback loop (i.e. induced by precession). In this paper such a quantum feedback mechanism is defined including generalized fine structure constants in accordance with the fundamental gravitomagnetic relation of spin-orbit coupling. Supported by measurements, the general relativistic and topological background allows to propose, that the deviation of the fine structure constant from 1/137 could be assigned to Berry's phase. The interpretation is straightforward: spacetime curvature effects can be greatly amplified by non-linear phase-locked feedback-loops adjusted to single-valued phase relationships in the quantum regime.

  12. The effect of a micro bubble dispersed gas phase on hydrogen isotope transport in liquid metals under nuclear irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Fradera, J., E-mail: jfradera@ubu.es; Cuesta-López, S., E-mail: scuesta@ubu.es

    2013-12-15

    The present work intend to be a first step towards the understanding and quantification of the hydrogen isotope complex phenomena in liquid metals for nuclear technology. Liquid metals under nuclear irradiation in, e.g., breeding blankets of a nuclear fusion reactor would generate tritium which is to be extracted and recirculated as fuel. At the same time that tritium is bred, helium is also generated and may precipitate in the form of nano bubbles. Other liquid metal systems of a nuclear reactor involve hydrogen isotope absorption processes, e.g., tritium extraction system. Hence, hydrogen isotope absorption into gas bubbles modelling and control may have a capital importance regarding design, operation and safety. Here general models for hydrogen isotopes transport in liquid metal and absorption into gas phase, that do not depend on the mass transfer limiting regime, are exposed and implemented in OpenFOAM® CFD tool for 0D–3D simulations. Results for a 0D case show the impact of a He dispersed phase of nano bubbles on hydrogen isotopes inventory at different temperatures as well as the inventory evolution during a He nucleation event. In addition, 1D and 2D axisymmetric cases are exposed showing the effect of a He dispersed gas phase on hydrogen isotope permeation through a lithium lead eutectic alloy and the effect of vortical structures on hydrogen isotope transport at a backward facing step. Exposed results give a valuable insight on current nuclear technology regarding the importance of controlling hydrogen isotope transport and its interactions with nucleation event through gas absorption processes.

  13. Humidity independent mass spectrometry for gas phase chemical analysis via ambient proton transfer reaction.

    Science.gov (United States)

    Zhu, Hongying; Huang, Guangming

    2015-03-31

    In this work, a humidity independent mass spectrometric method was developed for rapid analysis of gas phase chemicals. This method is based upon ambient proton transfer reaction between gas phase chemicals and charged water droplets, in a reaction chamber with nearly saturate humidity under atmospheric pressure. The humidity independent nature enables direct and rapid analysis of raw gas phase samples, avoiding time- and sample-consuming sample pretreatments in conventional mass spectrometry methods to control sample humidity. Acetone, benzene, toluene, ethylbenzene and meta-xylene were used to evaluate the analytical performance of present method. The limits of detection for benzene, toluene, ethylbenzene and meta-xylene are in the range of ∼0.1 to ∼0.3 ppbV; that of benzene is well below the present European Union permissible exposure limit for benzene vapor (5 μg m(-3), ∼1.44 ppbV), with linear ranges of approximately two orders of magnitude. The majority of the homemade device contains a stainless steel tube as reaction chamber and an ultrasonic humidifier as the source of charged water droplets, which makes this cheap device easy to assemble and facile to operate. In addition, potential application of this method was illustrated by the real time identification of raw gas phase chemicals released from plants at different physiological stages. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  15. Hydrodynamic characteristics of a two-phase gas-liquid flow upward through a fixed bed of spherical particles

    Directory of Open Access Journals (Sweden)

    VELIZAR D. STANKOVIC

    2001-01-01

    Full Text Available The influence of an electrochemically generated gas phase on the hydrodynamic characteristics of a three-phase system has been examined. The two-phase fluid, (gas-liquid, in which the liquid phase is the continuous one, flows through a packed bed with glass spheres. The influence of the liquid velocity was examined, as well as the gas velocity and particle diameter on the pressure drop through the fixed bed. It was found that with increasing liquid velocity (wl = 0.0162–0.03 m/s, the relative pressure drop decreases through the fixed bed. With increasing current density, the pressure drop increases, since greater gas quantities stay behind in the fixed bed. Besides, it was found that with decreasing diameter of the glass particles, the relative pressure drop also decreases. The relationship betweeen the experimentally obtained friction factor and the Reynolds number was established.

  16. Diagnostical meaning acute phase proteins in cerebrospinal liquid in children with neuroinfections

    Directory of Open Access Journals (Sweden)

    L. A. Alekseeva

    2010-01-01

    Full Text Available In the article presented results of the examination of acute phase proteins in cerebrospinal liquid in 237 children with meningitis and encephalitis viral and bacterial etiology. The dependence between the level of acute phase proteins in cerebrospinal liquid and etiology of neuroinfectional process, the severity of brain damage and the process stage was determined. Diagnostic and prognostic efficiency of the acute phase proteins (C-reactive protein, albumin, alpha-1-antitripsin, alpha-2-macroglobulin, gaptoglobin examination in children with neuroinfections was specified. Developed method of express diagnostics of the severity of inflammatory damage of the brain in bacterial meningitis in children by determination in cerebrospinal liquid alpha-2-macroglobulin is described.

  17. X-ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

    DEFF Research Database (Denmark)

    Küpper, Jochen; Stern, Stephan; Holmegaard, Lotte

    2014-01-01

    We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive...... imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural......-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules....

  18. Type 2 diabetes mellitus with early phase acute inflammatory protein on serum protein electrophoresis

    Directory of Open Access Journals (Sweden)

    ET Tuladhar

    2012-03-01

    Full Text Available Background: The onset of Type 2 diabetes has been associated with low grade systemic inflammation. The inflammatory status has been studied by measuring acute phase reactant proteins like hsCRP, α1- antitrypsin, α1-acid glycoprotein, ceruloplasmin, fibrinogen. Most of these acute phase reactants form α1 and α2 bands on electropherogram of serum proteins. The aim of this study was to evaluate inflammatory status in controlled and uncontrolled type 2 diabetes using cellulose acetate electrophoresis and to find the impact of glycemic status as indicated by HbA1c on inflammation process. Materials and Methods: Serum protein electrophoresis was done on serum samples of 60 cases of Diabetes [controlled and uncontrolled] using cellulose acetate paper technique. The electropherogram obtained was stained with Ponseu S and then quantitated using densitometer. Glycemic status was studied by HbA1c analysis. The density of α1and α2 bands in electropherogram were correlated with HbA1c level. Result: A significant increase in the percentage of α1 and α2 band proteins (0.765 and 0.716, p<0.001 were found with the increasing level of HbA1c. With cutoff of HbA1c 7% (American Diabetic Association recommended, the α1 and α2 serum proteins concentration are significantly higher (p<0.001 in uncontrolled diabetes mellitus compared to controlled diabetes mellitus Conclusion: Cellulose acetate electrophoresis of serum proteins show early phase acute inflammatory status in uncontrolled type 2 diabetes mellitus. The process of systemic inflammation worsens with uncontrolled glycemia as indicated by HbA1c. Inflammatory status should be studied adjunct to glycemic status. DOI: http://dx.doi.org/10.3126/jpn.v2i3.6024 JPN 2012; 2(3: 211-214

  19. Laser diagnostics of a diamond depositing chemical vapour deposition gas-phase environment

    Energy Technology Data Exchange (ETDEWEB)

    Smith, James Anthony

    2002-07-01

    Studies have been carried out to understand the gas-phase chemistry underpinning diamond deposition in hot filament and DC-arcjet chemical vapour deposition (CVD) systems. Resonance enhanced Multiphoton lonisation (REMPI) techniques were used to measure the relative H atom and CH{sub 3} radical number densities and local gas temperatures prevalent in a hot filament reactor, operating on Ch{sub 4}/H{sub 2} and C{sub 2}H{sub 2}/H{sub 2} gas mixtures. These results were compared to a 3D-computer simulation, and hence provided an insight into the nature of the gas-phase chemistry with particular reference to C{sub 2}{yields}C{sub 1} species conversion. Similar experimental and theoretical studies were also carried out to explain the chemistry involved in NH{sub 3}/CH{sub 4}/H{sub 2} and N{sub 2}/CH{sub 4}/H{sub 2} gas mixtures. It was demonstrated that the reactive nature of the filament surface was dependent on the addition of NH{sub 3}, influencing atomic hydrogen production, and thus the H/C/N gas-phase chemistry. Studies of the DC-arcjet diamond CVD reactor consisted of optical emission spectroscopic studies of the plume during deposition from an Ar/H{sub 2}/CH{sub 4}/N{sub 2} gas mixture. Spatially resolved species emission intensity maps were obtained for C{sub 2}(d{yields}a), CN(B{yields}X) and H{sub {beta}} from Abel-inverted datasets. The C{sub 2}(d{yields}a) and CN(B{yields}X) emission intensity maps both show local maxima near the substrate surface. SEM and Laser Raman analyses indicate that N{sub 2} additions lead to a reduction in film quality and growth rate. Photoluminescence and SIMS analyses of the grown films provide conclusive evidence of nitrogen incorporation (as chemically bonded CN). Absolute column densities of C{sub 2}(a) in a DC-arcjet reactor operating on an Ar/H{sub 2}/CH{sub 4} gas mixture, were measured using Cavity ring down spectroscopy. Simulations of the measured C{sub 2}(v=0) transition revealed a rotational temperature of {approx

  20. Application of epifluorescence scanning for monitoring the efficacy of protein removal by RF gas-plasma decontamination

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, Helen C; Richardson, Patricia R; Campbell, Gaynor A; Jones, Anita C; Baxter, Robert L [School of Chemistry, Joseph Black Chemistry Building, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Kovalev, Valeri I; Maier, Robert; Barton, James S [School of Engineering and Physical Science, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); DeLarge, Greg [Plasma Etch Inc, 3522 Arrowhead Drive, Carson City, NV 89706 (United States); Casey, Mark [Sterile Services Department, Royal Infirmary of Edinburgh, Edinburgh EH16 4AS (United Kingdom)], E-mail: r.baxter@ed.ac.uk

    2009-11-15

    The development of methods for measuring the efficiency of gas-plasma decontamination has lagged far behind application. An approach to measuring the efficiency of protein removal from solid surfaces using fluorescein-labelled bovine serum albumin and epifluorescence scanning (EFSCAN) is described. A method for fluorescently labelling proteins, which are adsorbed and denatured on metal surfaces, has been developed. Both approaches have been used to evaluate the efficiency of radio frequency (RF) gas-plasma decontamination protocols. Examples with 'real' surgical instruments demonstrate that an argon-oxygen RF gas-plasma treatment can routinely reduce the protein load by about three orders of magnitude beyond that achieved by current decontamination methods.

  1. Application of epifluorescence scanning for monitoring the efficacy of protein removal by RF gas-plasma decontamination

    International Nuclear Information System (INIS)

    Baxter, Helen C; Richardson, Patricia R; Campbell, Gaynor A; Jones, Anita C; Baxter, Robert L; Kovalev, Valeri I; Maier, Robert; Barton, James S; DeLarge, Greg; Casey, Mark

    2009-01-01

    The development of methods for measuring the efficiency of gas-plasma decontamination has lagged far behind application. An approach to measuring the efficiency of protein removal from solid surfaces using fluorescein-labelled bovine serum albumin and epifluorescence scanning (EFSCAN) is described. A method for fluorescently labelling proteins, which are adsorbed and denatured on metal surfaces, has been developed. Both approaches have been used to evaluate the efficiency of radio frequency (RF) gas-plasma decontamination protocols. Examples with 'real' surgical instruments demonstrate that an argon-oxygen RF gas-plasma treatment can routinely reduce the protein load by about three orders of magnitude beyond that achieved by current decontamination methods.

  2. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  3. Soil-gas phase transport and structure parameters for soils under different management regimes and at two moisture levels

    DEFF Research Database (Denmark)

    Eden, Marie; Møldrup, Per; Schjønning, Per

    2012-01-01

    Measurements of diffusive and convective gas transport parameters can be used to describe soil functional architecture and reveal key factors for soil structure development. Undisturbed 100-cm(3) soil samples were sampled at the Long-term Research on Agricultural Systems experiment located...... displayed markedly lower D-P/D-0 values at similar air-filled porosity, illustrating soil structure effects on D-P/D-0. The Currie tortuosity-connectivity parameter, X=Log(D-P/D-0)/Log(epsilon), decreased with increasing bulk density in the intact samples at both moisture conditions, suggesting less...

  4. Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

    Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and β-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (β-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein

  5. Protein interfacial structure and nanotoxicology

    Energy Technology Data Exchange (ETDEWEB)

    White, John W. [Research School of Chemistry, Australian National University, Canberra (Australia)], E-mail: jww@rsc.anu.edu.au; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M. [Research School of Chemistry, Australian National University, Canberra (Australia)

    2009-02-21

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between {beta}-casein and {kappa}-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a {beta}-casein monolayer is attacked by a {kappa}-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a {beta}-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

  6. Protein interfacial structure and nanotoxicology

    International Nuclear Information System (INIS)

    White, John W.; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M.

    2009-01-01

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between β-casein and κ-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a β-casein monolayer is attacked by a κ-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a β-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

  7. Parents of two-phase flow and theory of “gas-lift”

    Directory of Open Access Journals (Sweden)

    Zitek Pavel

    2014-03-01

    Full Text Available This paper gives a brief overview of types of two-phase flow. Subsequently, it deals with their mutual division and problems with accuracy boundaries among particular types. It also shows the case of water flow through a pipe with external heating and the gradual origination of all kinds of flow. We have met it in solution of safety condition of various stages in pressurized and boiling water reactors. In the MSR there is a problem in the solution of gas-lift using helium as a gas and its secondary usage for clearing of the fuel mixture from gaseous fission products. Theory of gas-lift is described.

  8. The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites

    Science.gov (United States)

    Chen, Hongda; Wang, Jihui; Ding, Anxin; Han, Xia; Sun, Ziheng

    2018-01-01

    In order to improve the efficiency of intumescent flame retardants (IFRs), a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine) (PETAT) with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP) in combination with ammonium polyphosphate (APP) via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR), and 1H nuclear magnetic resonance (NMR) spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG) and thermogravimetry–Fourier transform infrared spectroscopy (TG-FTIR). The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI) values before and after soaking, underwritten laboratory-94 (UL-94) vertical burning test, cone calorimetric test (CCT), scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS), and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR), total heat release (THR), and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

  9. The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites

    Directory of Open Access Journals (Sweden)

    Hongda Chen

    2018-01-01

    Full Text Available In order to improve the efficiency of intumescent flame retardants (IFRs, a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine (PETAT with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP in combination with ammonium polyphosphate (APP via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR, and 1H nuclear magnetic resonance (NMR spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG and thermogravimetry–Fourier transform infrared spectroscopy (TG-FTIR. The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI values before and after soaking, underwritten laboratory-94 (UL-94 vertical burning test, cone calorimetric test (CCT, scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS, and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR, total heat release (THR, and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

  10. The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites.

    Science.gov (United States)

    Chen, Hongda; Wang, Jihui; Ni, Aiqing; Ding, Anxin; Han, Xia; Sun, Ziheng

    2018-01-11

    In order to improve the efficiency of intumescent flame retardants (IFRs), a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine) (PETAT) with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP) in combination with ammonium polyphosphate (APP) via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR), and ¹H nuclear magnetic resonance (NMR) spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG) and thermogravimetry-Fourier transform infrared spectroscopy (TG-FTIR). The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI) values before and after soaking, underwritten laboratory-94 (UL-94) vertical burning test, cone calorimetric test (CCT), scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS), and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR), total heat release (THR), and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

  11. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  12. The structure of a cholesterol-trapping protein

    Science.gov (United States)

    cholesterol-trapping protein Contact: Dan Krotz, dakrotz@lbl.gov Berkeley Lab Science Beat Lab website index Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream. Knowing the structure of the protein, a cellular receptor that ensnares

  13. A Gas-Kinetic Method for Hyperbolic-Elliptic Equations and Its Application in Two-Phase Fluid Flow

    Science.gov (United States)

    Xu, Kun

    1999-01-01

    A gas-kinetic method for the hyperbolic-elliptic equations is presented in this paper. In the mixed type system, the co-existence and the phase transition between liquid and gas are described by the van der Waals-type equation of state (EOS). Due to the unstable mechanism for a fluid in the elliptic region, interface between the liquid and gas can be kept sharp through the condensation and evaporation process to remove the "averaged" numerical fluid away from the elliptic region, and the interface thickness depends on the numerical diffusion and stiffness of the phase change. A few examples are presented in this paper for both phase transition and multifluid interface problems.

  14. Protein structure determination by exhaustive search of Protein Data Bank derived databases.

    Science.gov (United States)

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

  15. Function and structure of GFP-like proteins in the protein data bank.

    Science.gov (United States)

    Ong, Wayne J-H; Alvarez, Samuel; Leroux, Ivan E; Shahid, Ramza S; Samma, Alex A; Peshkepija, Paola; Morgan, Alicia L; Mulcahy, Shawn; Zimmer, Marc

    2011-04-01

    The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

  16. Classification of proteins: available structural space for molecular modeling.

    Science.gov (United States)

    Andreeva, Antonina

    2012-01-01

    The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

  17. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  18. Measurement of gas-liquid two-phase flow around horizontal tube bundle using SF6-water. Simulating high-pressure high-temperature gas-liquid two-phase flow of PWR/SG secondary coolant side at normal pressure

    International Nuclear Information System (INIS)

    Ishikawa, Atsushi; Imai, Ryoj; Tanaka, Takahiro

    2014-01-01

    In order to improve prediction accuracy of analysis code used for design and development of industrial products, technology had been developed to create and evaluate constitutive equation incorporated in analysis code. The experimental facility for PWR/SG U tubes part was manufactured to measure local void fraction and gas-liquid interfacial velocity with forming gas-liquid upward two-phase flow simulating high-pressure high-temperature secondary coolant (water-steam) rising vertically around horizontal tube bundle. The experimental facility could reproduce flow field having gas-liquid density ratio equivalent to real system with no heating using SF6 (Sulfur Hexafluoride) gas at normal temperature and pressure less than 1 MPa, because gas-liquid density ratio, surface tension and gas-liquid viscosity ratio were important parameters to determine state of gas-liquid two-phase flow and gas-liquid density ratio was most influential. Void fraction was measured by two different methods of bi-optical probe and conductivity type probe. Test results of gas-liquid interfacial velocity vs. apparent velocity were in good agreement with existing empirical equation within 10% error, which could confirm integrity of experimental facility and appropriateness of measuring method so as to set up original constitutive equation in the future. (T. Tanaka)

  19. Functional classification of protein structures by local structure matching in graph representation.

    Science.gov (United States)

    Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

    2018-03-31

    As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  20. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  1. Reactive species output of a plasma jet with a shielding gas device—combination of FTIR absorption spectroscopy and gas phase modelling

    International Nuclear Information System (INIS)

    Schmidt-Bleker, A; Winter, J; Iseni, S; Dünnbier, M; Reuter, S; Weltmann, K-D

    2014-01-01

    In this work, a simple modelling approach combined with absorption spectroscopy of long living species generated by a cold atmospheric plasma jet yields insight into relevant gas phase chemistry. The reactive species output of the plasma jet is controlled using a shielding gas device. The shielding gas is varied using mixtures of oxygen and nitrogen at various humidity levels. Through the combination of Fourier transform infrared (FTIR) spectroscopy, computational fluid dynamics (CFD) simulations and zero dimensional kinetic modelling of the gas phase chemistry, insight into the underlying reaction mechanisms is gained. While the FTIR measurements yield absolute densities of ozone and nitrogen dioxide in the far field of the jet, the kinetic simulations give additional information on reaction pathways. The simulation is fitted to the experimentally obtained data, using the CFD simulations of the experimental setup to estimate the correct evaluation time for the kinetic simulation. It is shown that the ozone production of the plasma jet continuously rises with the oxygen content in the shielding gas, while it significantly drops as humidity is increased. The production of nitrogen dioxide reaches its maximum at about 30% oxygen content in the shielding gas. The underlying mechanisms are discussed based on the simulation results. (paper)

  2. CASCADER: An M-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1993-02-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one-space dimensional transport and fate model for M-chain radionuclides in very dry homogeneous or heterogeneous soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advection velocity is derived from an embedded air-pumping submodel. The air-pumping submodel is based on an assumption of isothermal conditions, which is driven by barometric pressure. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions are used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77

  3. CASCADER: An m-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1992-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes as they are advected and/or dispersed. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one space dimensional transport and fate model for an m-chain of radionuclides in very dry soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advocation velocity is derived from an embedded air-pumping submodel. The airpumping submodel is based on an assumption of isothermal conditions and is barometric pressure driven. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions is used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77

  4. Experimental redetermination of the gas-phase enthalpy of formation of ethyl 2-thiophenecarboxylate

    International Nuclear Information System (INIS)

    Santos, Ana Filipa L.O.M.; Ribeiro da Silva, Manuel A.V.

    2013-01-01

    The condensed phase standard (p° = 0.1 MPa) molar enthalpy of formation of ethyl-2-thiophenecarboxylate was derived from the remeasured standard molar energy of combustion, in oxygen, at T = 298.15 K, by rotating bomb combustion calorimetry and the standard molar enthalpy of vaporization, at T = 298.15 K, remeasured by Calvet microcalorimetry. Combining these two values, the following enthalpy of formation in the gas phase, at T = 298.15 K, was then derived for ethyl-2-thiophenecarboxylate: −(277.7 ± 2.9) kJ · mol −1 . The calculated gas-phase enthalpy of formation of the title compound, through the G3(MP2)//B3LYP approach was found to be 278.9 kJ · mol −1 , in excellent agreement with the experimental measured value

  5. Structure and function of nanoparticle-protein conjugates

    International Nuclear Information System (INIS)

    Aubin-Tam, M-E; Hamad-Schifferli, K

    2008-01-01

    Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle-protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Site-specific labeling is desirable in order to control the protein orientation on the nanoparticle, which is crucial in many applications such as fluorescence resonance energy transfer. We evaluate methods for successful site-specific attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed. We also examine how molecular dynamics simulations of conjugates would complete those experimental techniques in order to provide atomistic details on the effect of nanoparticle attachment. Characterization studies of nanoparticle-protein complexes show that the structure and function are influenced by the chemistry of the nanoparticle ligand, the nanoparticle size, the nanoparticle material, the stoichiometry of the conjugates, the labeling site on the protein and the nature of the linkage (covalent versus non-covalent)

  6. Protein Tertiary Structure Prediction Based on Main Chain Angle Using a Hybrid Bees Colony Optimization Algorithm

    Science.gov (United States)

    Mahmood, Zakaria N.; Mahmuddin, Massudi; Mahmood, Mohammed Nooraldeen

    Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.

  7. Gas-liquid two-phase flow behavior in terrain-inclined pipelines for gathering transport system of wet natural gas

    DEFF Research Database (Denmark)

    Yang, Yan; Li, Jingbo; Wang, Shuli

    2018-01-01

    The Volume of Fluid method and Re-Normalisation Group (RNG) k-ε turbulence model were employed to predict the gas-liquid two-phase flow in a terrain-inclined pipeline with deposited liquids. The simulation was carried out in a 22.5 m terrain-inclined pipeline with a 150 mm internal diameter...... on the liquid level under the suction force which caused by the negative pressure around the elbow, and then it touched to the top of the pipe. When the liquid blocked the pipe, the pressure drop between the upstream and downstream of the elbow increased with the increase of the gas velocity. At larger gas...

  8. Study of two-phase underexpanded jets by gas jet

    International Nuclear Information System (INIS)

    Uchida, Mitsunori; Someya, Satoshi; Okamoto, Koji

    2008-01-01

    When a heat exchange in a Fast Breeder Reactor cracks, a sodium-water reaction occurs. When a tube cracks, highly pressurized water or steam escapes into the surrounding liquid sodium and a sodium-water reaction occurs forming the disodium oxide. The disodium oxide caught in the steam jet strikes other tubes in the reactor. The struck disodium oxide can then cause these tubes to crack. The release of steam into the liquid sodium media is a two-phase flow involving underexpansion. In this paper qualitative measurement of the underexpanded gas jet which injected into water was carried our for the purpose of analyzing the behavior of the two-phase flow. (author)

  9. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

  10. Modeling protein structures: construction and their applications.

    Science.gov (United States)

    Ring, C S; Cohen, F E

    1993-06-01

    Although no general solution to the protein folding problem exists, the three-dimensional structures of proteins are being successfully predicted when experimentally derived constraints are used in conjunction with heuristic methods. In the case of interleukin-4, mutagenesis data and CD spectroscopy were instrumental in the accurate assignment of secondary structure. In addition, the tertiary structure was highly constrained by six cysteines separated by many residues that formed three disulfide bridges. Although the correct structure was a member of a short list of plausible structures, the "best" structure was the topological enantiomer of the experimentally determined conformation. For many proteases, other experimentally derived structures can be used as templates to identify the secondary structure elements. In a procedure called modeling by homology, the structure of a known protein is used as a scaffold to predict the structure of another related protein. This method has been used to model a serine and a cysteine protease that are important in the schistosome and malarial life cycles, respectively. The model structures were then used to identify putative small molecule enzyme inhibitors computationally. Experiments confirm that some of these nonpeptidic compounds are active at concentrations of less than 10 microM.

  11. Single-phase and two-phase gas-liquid turbulent mixing between subchannels in a simulated rod bundle

    International Nuclear Information System (INIS)

    Sadatomi, Michio; Kawahara, Akimaro; Sato, Yoshifusa; Tomino, Takayoshi.

    1996-01-01

    This study is concerned with turbulent mixing which is one of the three mechanisms of cross flows between subchannels in a nuclear fuel rod bundle. The channel used in this experiments was a vertical simulated rod bundle having two subchannels connected through 1 to 3 gaps between two rods and/or rod and channel wall. The number of the gaps was changed to investigate the effect of the number on the turbulent mixing. Turbulent mixing rates of air and water and fluctuations of pressure difference between the subchannels were measured for single-phase and two-phase gas-liquid flows under hydrodynamic equilibrium flow conditions. It has been confirmed that the turbulent mixing rate is affected strongly by the fluctuations especially for liquid phase in two-phase slug or churn flow. (author)

  12. Visualization and measurement of gas-liquid metal two-phase flow with large density difference using thermal neutrons as microscopic probes

    International Nuclear Information System (INIS)

    Mishima, K.; Hibiki, T.; Saito, Y.; Nishihara, H.; Tobita, Y.; Konishi, K.; Matsubayashi, M.

    1999-01-01

    In a core melt accident of a fast breeder reactor, there is a possibility of boiling of the fuel-steel mixture in the containment pool. In relation to safety evaluation on severe accident, it is indispensable to evaluate the possibility of re-criticality of melted core. Gas-liquid two-phase flow with a large liquid-to-gas density ratio is formed due to the boiling of fuel-steel mixture. Although it is anticipated that the large density ratio may affect the basic characteristics of two-phase flow, little work has been performed so far on two-phase flow with a large liquid-to-gas density ratio. In this study, visualization and void fraction measurement of gas-liquid metal two-phase flow were performed by using neutron radiography and image processing techniques. Then, the effect of large density difference between gas and liquid phases on the basic flow characteristics of two-phase flow was clarified

  13. Simulation of the Two-Phase Liquid – Gas Flow through Ultrasonic Transceivers Application in Ultrasonic Tomography

    Directory of Open Access Journals (Sweden)

    Zulkarnay Zakaria

    2010-01-01

    Full Text Available In this paper, ultrasonic transmission mode tomography was used to visualize the two phase liquid/gas flow in a pipe/vessel. The sensing element consists of 8, 16 and 32 units ultrasonic transceivers were used to cover the pipe cross-section at different time. The motivation of this paper is to analyze the optimum numbers of transceivers which can give the best performance in providing better image of the two phase liquid/gas flow. This paper also details the development of the system including the ultrasonic transduction circuits, the electronic measurement circuits, the data acquisition system and the image reconstruction techniques. Ten conditions of liquid-gas flow have been simulated. The system was found capable of visualizing the internal characteristics and provides the concentration profile for the corresponding liquid and gas phases while the 32 transceivers has provided the best image for the ten conditions applied.

  14. Long-term gas migration modelling in compacted bentonite using swelling/shrinkage-dependent two phase flow parameters

    International Nuclear Information System (INIS)

    Tawara, Y.; Mori, K.; Tada, K.; Shimura, T.; Sato, S.; Yamamoto, S.; Asano, H.; Namiki, K.

    2012-01-01

    Document available in extended abstract form only. After the completion of field-scaled Gas Migration Test (GMT) at the Grimsel Test Site (GTS Phase V Project, 1996-2004), an advanced gas migration modelling study has been implemented to increase the accuracy and reliability as a part of the R and D programs by the Radioactive Waste Management funding and research Center (RWMC) in Japan. The multiple gas migration modes which consist of diffusive transport of dissolved gas, conventional two phase flow, pore failure induced microscopic fissuring and macroscopic fracturing flow, were identified in GMT bentonite. However the required parameters and constitutive models governing those modes are still uncertain. To tackle this issue, an extended validation and scoping study aiming to generalize such gas migration behavior has been performed in the advanced gas migration modelling study. One of the main objectives of the validation study is to identify gas migration modes using laboratory test data and to qualify the alternative models and parameters. In the scoping study, we have extracted the specific THMC (Thermal, Hydrological, Mechanical and Chemical) coupled processes which have impacts on the performance measures such as the pressure built-up in EBS (Engineered Barrier System) and expelled water to the geosphere by gas generation and transport. The measured data of hydration tests and gas injection tests using bentonite specimens with different water contents were reproduced. Two phase flow parameters were estimated using the observed data of both types of tests, independently. The simulated results of the conventional two phase flow model were well-matched with the hydration test data. In the gas injection test, the extended two phase flow model which simulates the pressure-induced pore failure (pathway dilation), was able to reproduce observed data reasonably. However, we found that the identified parameters obtained from the hydration test data were

  15. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination.

    Science.gov (United States)

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-09-01

    Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (φ1 and φ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ(DS) list as a criterion to select optimized phases φ(am) from φ1 or φ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases φ(SAD) has been developed. Based on this work, reflections with an angle θ(DS) in the range 35-145° are selected for an optimized improvement, where θ(DS) is the angle between the initial phase φ(SAD) and a preliminary density-modification (DM) phase φ(DM)(NHL). The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  16. Improving the accuracy of protein secondary structure prediction using structural alignment

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2006-06-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

  17. Gas hydrate inhibition by perturbation of liquid water structure

    Science.gov (United States)

    Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Lee, Kun-Hong

    2015-06-01

    Natural gas hydrates are icy crystalline materials that contain hydrocarbons, which are the primary energy source for this civilization. The abundance of naturally occurring gas hydrates leads to a growing interest in exploitation. Despite their potential as energy resources and in industrial applications, there is insufficient understanding of hydrate kinetics, which hinders the utilization of these invaluable resources. Perturbation of liquid water structure by solutes has been proposed to be a key process in hydrate inhibition, but this hypothesis remains unproven. Here, we report the direct observation of the perturbation of the liquid water structure induced by amino acids using polarized Raman spectroscopy, and its influence on gas hydrate nucleation and growth kinetics. Amino acids with hydrophilic and/or electrically charged side chains disrupted the water structure and thus provided effective hydrate inhibition. The strong correlation between the extent of perturbation by amino acids and their inhibition performance constitutes convincing evidence for the perturbation inhibition mechanism. The present findings bring the practical applications of gas hydrates significantly closer, and provide a new perspective on the freezing and melting phenomena of naturally occurring gas hydrates.

  18. Structuring strategy and relationships in North American gas markets

    International Nuclear Information System (INIS)

    Fisher, J.

    1998-01-01

    Duke Energy's experience in strategy development and structuring relationships with other companies were described. Included was a description of their partnership with PanEnergy and Mobil and a merger between PanEnergy and Duke. In developing their growth strategy, Duke Energy was guided by the following considerations: (1) an assessment of the market, (2) the identification of opportunities, (3) a self-assessment, (4) the establishment of goals, and (5) determining strategic alternatives. The advantages and disadvantages of different structuring relationships were reviewed. Duke Energy's approach to Ontario's residential market and their agreement with Alliance Gas Management were also discussed. The goal of the Alliance Gas management agreement was to simplify Alliance's wholesale gas supply management needs and to allow Alliance access to diverse gas supplies. figs

  19. Mapping domain structures in silks from insects and spiders related to protein assembly.

    Science.gov (United States)

    Bini, Elisabetta; Knight, David P; Kaplan, David L

    2004-01-02

    The exceptional solubility in vivo (20-30%, w/v) of the silk proteins of insects and spiders is dictated by both the need to produce solid fibres with a high packing fraction and the high mesogen concentration required for lyotropic liquid crystalline spinning. A further design requirement for silk proteins is a strong predominance of hydrophobic amino acid residues to provide for the hydrophobic interactions, water exclusion, and beta-crystallite formation required to produce strong insoluble threads. Thus, the domain structure of silk proteins needs to enable nanoscale phase separation to achieve high solubility of hydrophobic proteins in aqueous solutions. Additionally, silk proteins need to avoid premature precipitation as beta-sheets during storage and processing. Here we use mapping of domain types, sizes and distributions in silks to identify consistent design features that have evolved to meet these requirements. We show that silk proteins consist of conspicuously hydrophilic terminal domains flanking a very long central portion constructed from hydrophobic blocks separated by hydrophilic ones, discussing the domain structure in detail. The general rules of construction for silk proteins based on our observations should give a useful guide to the way in which Nature has solved the problem of processing hydrophobic proteins in water and how this can be copied industrially. Following these rules may also help in obtaining adequate expression, soluble products and controllable conformational switches in the production of genetically engineered or chemically synthesized silk analogues. Thus these insights have implications for structural biology and relevance to fundamental and applied questions in material science and engineering.

  20. Revealing the hidden structural phases of FeRh

    Science.gov (United States)

    Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

    2016-11-01

    Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.