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Sample records for aggregated gas molecules

  1. Aggregated Gas Molecules: Toxic to Protein?

    PubMed Central

    Zhang, Meng; Zuo, Guanghong; Chen, Jixiu; Gao, Yi; Fang, Haiping

    2013-01-01

    The biological toxicity of high levels of breathing gases has been known for centuries, but the mechanism remains elusive. Earlier work mainly focused on the influences of dispersed gas molecules dissolved in water on biomolecules. However, recent studies confirmed the existence of aggregated gas molecules at the water-solid interface. In this paper, we have investigated the binding preference of aggregated gas molecules on proteins with molecular dynamics simulations, using nitrogen (N2) gas and the Src-homology 3 (SH3) domain as the model system. Aggregated N2 molecules were strongly bound by the active sites of the SH3 domain, which could impair the activity of the protein. In contrast, dispersed N2 molecules did not specifically interact with the SH3 domain. These observations extend our understanding of the possible toxicity of aggregates of gas molecules in the function of proteins. PMID:23588597

  2. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2007-05-22

    Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS.

  3. Oligomeric baroeffect and gas aggregation states

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1992-01-01

    The baroeffect is analyzed to include a gas that aggregates into higher-order polymers or oligomers. The resulting pressure change is found to vary independently of the molecular weight of the gas components and to depend only on the aggregation or oligomeric order of the gas. With increasing aggregation, diffusive slip velocities are found to increase. The calculations are extended to include general counterdiffusion of two distinct aggregation states (k-, j-mer) for the gas, and the pressure change is derived as a function that is independent of both molecular weight and the absolute aggregation. The only parameter that determines the baroeffect is the ratio of aggregated states, beta = k/j. For gases that reversibly aggregate, possible oscillatory behavior and complex dynamics for pressure are discussed. Gas aggregation may play a role for low-temperature crystal-growth conditions in which vapor concentrations of one (or more) species are high.

  4. Aggregation and folding phase transitions of RNA molecules

    NASA Astrophysics Data System (ADS)

    Bundschuh, Ralf

    2007-03-01

    RNA is a biomolecule that is involved in nearly all aspects of cellular functions. In order to perform many of these functions, RNA molecules have to fold into specific secondary structures. This folding is driven by the tendency of the bases to form Watson-Crick base pairs. Beyond the biological importance of RNA, the relatively simple rules for structure formation of RNA make it a very interesting system from the statistical physics point of view. We will present examples of phase transitions in RNA secondary structure formation that are amenable to analytical descriptions. A special focus will be on aggregation between several RNA molecules which is important for some regulatory circuits based on RNA structure, triplet repeat diseases like Huntington's, and as a model for prion diseases. We show that depending on the relative strength of the intramolecular and the intermolecular base pairing, RNA molecules undergo a transition into an aggregated phase and quantitatively characterize this transition.

  5. A quantum gas of polar molecules

    NASA Astrophysics Data System (ADS)

    Ni, Kang-Kuen

    Ultracold polar molecular gases promise new directions and exciting applications in precision measurements, ultracold chemistry, electric-field controlled collisions, dipolar quantum gases, and quantum information sciences. This thesis presents experimental realization of a near quantum degenerate gas of polar molecules, where the phase-space density of the gas achieved is more than 10 orders of magnitude higher than previous results. The near quantum degenerate gas of polar molecules is created using two coherent steps. First, atoms in an ultracold gas mixture are converted into extremely weakly bound molecules near a Fano-Feshbach resonance. Second, the weakly bound molecules are transferred to the ro-vibronic ground state using a coherent two-photon Raman technique. The fact that these ground-state molecules are polar is confirmed with a spectroscopic measurement of the permanent electric dipole moment. Finally, manipulation of the molecular hyperfine state is demonstrated; this allows molecules to be populated in a single quantum state, in particular, the lowest energy state. With an ultracold gas of molecules, full control of molecular internal state, and electric field as a new handle, ultracold molecular collisions, including ultracold chemical reactions and dipolar collisions, are studied.

  6. Long-range Rydberg molecules, Rydberg macrodimers and Rydberg aggregates in an ultracold Cs gas. Investigation of long-range interactions between atoms in electronically highly excited statesRydberg Few-Body Physics

    NASA Astrophysics Data System (ADS)

    Saßmannshausen, Heiner; Deiglmayr, Johannes; Merkt, Frédéric

    2016-12-01

    We present an overview of our recent investigations of long-range interactions in an ultracold Cs Rydberg gas. These interactions are studied by high-resolution photoassociation spectroscopy, using excitation close to one-photon transitions into np3/2 Rydberg states with pulsed and continuous-wave ultraviolet laser radiation, and lead to the formation of long-range Cs2 molecules. We observe two types of molecular resonances. The first type originates from the correlated excitation of two atoms into Rydberg-atom-pair states interacting at long range via multipole-multipole interactions. The second type results from the interaction of one atom excited to a Rydberg state with one atom in the electronic ground state. Which type of resonances is observed in the experiments depends on the laser intensity and frequency and on the pulse sequences used to prepare the Rydberg states. We obtain insights into both types of molecular resonances by modelling the interaction potentials, using a multipole expansion of the long-range interaction for the first type of resonances and a Fermi-contact pseudo-potential for the second type of resonances. We analyse the relation of these long-range molecular resonances to molecular Rydberg states and ion-pair states, and discuss their decay channels into atomic and molecular ions. In experiments carried out with a two-colour two-photon excitation scheme, we observe a large enhancement of Rydberg-excitation probability, which we interpret as a saturable autocatalytic antiblockade phenomenon.

  7. A Mechanofluorochromic Push-Pull Small Molecule with Aggregation-Controlled Linear and Nonlinear Optical Properties.

    PubMed

    Jiang, Yue; Gindre, Denis; Allain, Magali; Liu, Ping; Cabanetos, Clément; Roncali, Jean

    2015-08-05

    A small push-pull molecule involving a diphenylamine substituted by an oligo-oxyethylene chain is described. The compound exhibits aggregation-induced emission with solvent-dependent emission wavelength. Spin-cast deep-red amorphous films rapidly self-reorganize into colorless crystalline films which exhibit mechanofluorochromism and aggregation-induced second-harmonic generation.

  8. Single-Molecule Imaging of Individual Amyloid Protein Aggregates in Human Biofluids.

    PubMed

    Horrocks, Mathew H; Lee, Steven F; Gandhi, Sonia; Magdalinou, Nadia K; Chen, Serene W; Devine, Michael J; Tosatto, Laura; Kjaergaard, Magnus; Beckwith, Joseph S; Zetterberg, Henrik; Iljina, Marija; Cremades, Nunilo; Dobson, Christopher M; Wood, Nicholas W; Klenerman, David

    2016-03-16

    The misfolding and aggregation of proteins into amyloid fibrils characterizes many neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. We report here a method, termed SAVE (single aggregate visualization by enhancement) imaging, for the ultrasensitive detection of individual amyloid fibrils and oligomers using single-molecule fluorescence microscopy. We demonstrate that this method is able to detect the presence of amyloid aggregates of α-synuclein, tau, and amyloid-β. In addition, we show that aggregates can also be identified in human cerebrospinal fluid (CSF). Significantly, we see a twofold increase in the average aggregate concentration in CSF from Parkinson's disease patients compared to age-matched controls. Taken together, we conclude that this method provides an opportunity to characterize the structural nature of amyloid aggregates in a key biofluid, and therefore has the potential to study disease progression in both animal models and humans to enhance our understanding of neurodegenerative disorders.

  9. Single-Molecule Imaging of Individual Amyloid Protein Aggregates in Human Biofluids

    PubMed Central

    2016-01-01

    The misfolding and aggregation of proteins into amyloid fibrils characterizes many neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases. We report here a method, termed SAVE (single aggregate visualization by enhancement) imaging, for the ultrasensitive detection of individual amyloid fibrils and oligomers using single-molecule fluorescence microscopy. We demonstrate that this method is able to detect the presence of amyloid aggregates of α-synuclein, tau, and amyloid-β. In addition, we show that aggregates can also be identified in human cerebrospinal fluid (CSF). Significantly, we see a twofold increase in the average aggregate concentration in CSF from Parkinson’s disease patients compared to age-matched controls. Taken together, we conclude that this method provides an opportunity to characterize the structural nature of amyloid aggregates in a key biofluid, and therefore has the potential to study disease progression in both animal models and humans to enhance our understanding of neurodegenerative disorders. PMID:26800462

  10. Stability of Soil Carbon Fractions - from molecules to aggregates

    NASA Astrophysics Data System (ADS)

    Mueller, C. W.; Mueller, K. E.; Freeman, K. H.; Eissenstat, D.; Kögel-Knabner, I.

    2009-12-01

    The turnover of soil organic matter (SOM) is controlled both by its chemical composition, its spatial bioavailability and the association with the mineral phase. Separation by physical fractionation of bulk soils and subsequent chemical analysis of these fractions should give insights to how compositional differences in SOM drive turnover rates of different size-defined carbon pools. The main objective of the study was to elucidate the relative abundance and recalcitrance of lignin and plant lipids (e.g. cutin and suberin) in the course of SOM decomposition within aggregated bulk soils and SOM fractions. By the parallel incubation of physically-separated size fractions and bulk soils of the Ah horizon from a forested soil (Picea abies L.Karst) over a period of 400 days, a unique set of samples was created to study SOM dynamics. We used solid-state 13C-CPMAS NMR spectroscopy and GC-MS (after copper oxide oxidation and solvent extraction) to analyze the composition of the incubated samples. The abundance and isotopic composition (including 13C and 14C) of respired CO2 further enabled us to monitor the dynamics of SOM mineralization. This approach allowed for differentiating between C stabilization of soil fractions due to accessibility/aggregation and to recalcitrance at different scales of resolution (GC-MS, NMR). A relative enrichment of alkyl C and decreasing lignin contents in the order of sand < silt < clay were observed by 13C-NMR and GC-MS within soils and fractions before the incubation, resulting in increased lipid to lignin ratios with decreasing particle size. A relative enrichment of lignin in the incubated fractions compared to the incubated bulk soils clearly indicated the preferential mineralization of less recalcitrant C compounds that were spatially inaccessible in aggregates of the bulk soil. Differences in the abundance of various lignin, cutin, and suberin monomers measured by GC-MS before and after the incubation indicate selective degradation

  11. Single Molecule Characterization of α-Synuclein in Aggregation-Prone States

    PubMed Central

    Trexler, Adam J.; Rhoades, Elizabeth

    2010-01-01

    α-Synuclein (αS) is an intrinsically disordered protein whose aggregation into ordered, fibrillar structures underlies the pathogenesis of Parkinson's disease. A full understanding of the factors that cause its conversion from soluble protein to insoluble aggregate requires characterization of the conformations of the monomer protein under conditions that favor aggregation. Here we use single molecule Förster resonance energy transfer to probe the structure of several aggregation-prone states of αS. Both low pH and charged molecules have been shown to accelerate the aggregation of αS and induce conformational changes in the protein. We find that at low pH, the C-terminus of αS undergoes substantial collapse, with minimal effect on the N-terminus and central region. The proximity of the N- and C-termini and the global dimensions of the protein are relatively unaffected by the C-terminal collapse. Moreover, although compact at low pH, with restricted chain motion, the structure of the C-terminus appears to be random. Low pH has a dramatically different effect on αS structure than the molecular aggregation inducers spermine and heparin. Binding of these molecules gives rise to only minor conformational changes in αS, suggesting that their mechanism of aggregation enhancement is fundamentally different from that of low pH. PMID:21044603

  12. β-sheet interfering molecules acting against β-amyloid aggregation and fibrillogenesis.

    PubMed

    Francioso, Antonio; Punzi, Pasqualina; Boffi, Alberto; Lori, Clorinda; Martire, Sara; Giordano, Cesare; D'Erme, Maria; Mosca, Luciana

    2015-04-15

    β-Sheet aggregates and amyloid fibrils rising from conformational changes of proteins are observed in several pathological human conditions. These structures are organized in β-strands that can reciprocally interact by hydrophobic and π-π interactions. The amyloid aggregates can give rise to pathological conditions through complex biochemical mechanisms whose physico-chemical nature has been understood in recent times. This review focuses on the various classes of natural and synthetic small molecules able to act against β-amyloid fibrillogenesis and toxicity that may represent new pharmacological tools in Alzheimer's diseases. Some peptides, named 'β-sheet breaker peptides', are able to hamper amyloid aggregation and fibrillogenesis by interfering with and destabilizing the non native β-sheet structures. Other natural compounds, like polyphenols or indolic molecules such as melatonin, can interfere with β-amyloid peptide pathogenicity by inhibiting aggregation and counteracting oxidative stress that is a key hallmark in Alzheimer's disease.

  13. Changes in aggregation behavior of collagen molecules in solution with varying concentrations of acetic acid.

    PubMed

    Yang, Huan; Xu, Songcheng; Shen, Lirui; Liu, Wentao; Li, Guoying

    2016-11-01

    A critical aggregation concentration of 0.30-0.50mg/mL was previously obtained for type I collagen at 0.1M acetic acid (AA). In the present study, the aggregation behavior of collagen in solution (0.5mg/mL) in the presence of 0.1-2.0M AA was investigated. Circular dichroism showed that the three helix structure was maintained across the whole AA concentration range. However, the ratio of positive peak intensity over negative peak intensity varied depending on the conformational state of collagen aggregates. Ultra-sensitive differential scanning calorimetry revealed that transition temperatures Tm1 and Tm2 decreased by 8.35°C and 7.80°C, respectively, between 0.1M and 2.0M, indicating a possible relationship between the aggregation state and the thermal effect. The surrounding polarity of collagen molecules in solution containing pyrene was investigated by fluorescence spectroscopy, which demonstrated that disaggregation of collagen aggregates was enhanced with increasing AA concentration. This observation was correlated with changes in collagen fiber size observed by atomic force microscopy. Furthermore, collagen tyrosine residues were blue-shifted in an intrinsic fluorescence spectra, further indicating changes in aggregation behavior with increasing AA concentration. Finally, the dynamic response of collagen molecules to AA was analyzed by two-dimensional correlation fluorescence spectra.

  14. Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation

    PubMed Central

    Plate, Lars; Cooley, Christina B; Chen, John J; Paxman, Ryan J; Gallagher, Ciara M; Madoux, Franck; Genereux, Joseph C; Dobbs, Wesley; Garza, Dan; Spicer, Timothy P; Scampavia, Louis; Brown, Steven J; Rosen, Hugh; Powers, Evan T; Walter, Peter; Hodder, Peter; Wiseman, R Luke; Kelly, Jeffery W

    2016-01-01

    Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. The ER reprogramming afforded by our molecules requires activation of endogenous ATF6 and occurs independent of global ER stress. Furthermore, our molecules phenocopy the ability of genetic ATF6 activation to selectively reduce secretion and extracellular aggregation of amyloidogenic proteins. These results show that small molecule-dependent ER reprogramming, achieved through preferential activation of the ATF6 transcriptional program, is a promising strategy to ameliorate imbalances in ER function associated with degenerative protein aggregation diseases. DOI: http://dx.doi.org/10.7554/eLife.15550.001 PMID:27435961

  15. Comparative studies on the structure and aggregative properties of the myosin molecule. III. The in vitro aggregative properties of the lobster myosin molecule.

    PubMed

    Siemankowski, R F; Zobel, C R

    1976-02-20

    The solubility of rabbit skeletal and lobster abdominal muscle myosin has been studied in monovalent salt solutions as a function of pH (over the range 4.75 to 8.5) and ionic strength (50-500 mM). Rabbit skeletal muscle myosin was found to precipitate over a narrower pH range than the lobster abdominal muscle myosin but at equivalent pH values and ionic strengths the former exhibited greater solubility. Comparison of the solubility of rabbit myosin, per se with that of light meromyosin and lobster myosin with its equivalent proteolytically produced fragment (fraction B1) showed that both rod fragments were more soluble than their parent molecules. Under conditions of low solubility (low ionic strength and pH) the quantitiy of protein in solution remained essentially constant with increasing total protein, thus suggesting that the aggregation phenomenon is of a phase transition type. Examination of the aggregates by electron microscopy revealed that rabbit myosin formed classical, elongate, spindle-shaped filaments similar to those previously observed by others. In contrast lobster myosin only formed short, dumbbell-shaped filaments 0.2-0.3 mum long. Consideration of the pH ranges over which aggregation occurred suggests that protonation of histidine residues may be involved in rabbit myosin filament formation while for lobster myosin, aggregation may involve protonation of epsilon-amino or guanidino groups. The possible relationship between the distribution of these groups along the rod portion of the myosin molecule and the formation of elongate filaments has been explored.

  16. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    SciTech Connect

    Sazhin, O.

    2009-05-15

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  17. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    NASA Astrophysics Data System (ADS)

    Sazhin, O.

    2009-05-01

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  18. Kinetics of aggregation of an anisotropic model of self-assembling molecules.

    PubMed

    Khan, Siddique; Haaga, Jason; Gunton, J D

    2015-07-14

    We study the kinetics of aggregation of a two site model of interacting spherical molecules. A given site on one molecule can interact with one or more sites on other neighboring molecules. The sites represent the result of a simple coarse graining of putative amino acid residues or two specifically designed sites on a colloidal particle. We study the kinetics and equilibrium morphology for a fixed angle between the two sites, for several angles between 30° and 150°. In the model, the sites interact via an attractive Asakura-Oosawa potential and the molecules have the usual hard sphere repulsion interaction. We find a transition from a micelle-like morphology at small angles to a rod-like morphology at intermediate angles and to a gel-like structure at values of the angle greater than about ninety degrees. However, at 150 degrees, after a long induction time during which there is no aggregation, we observe a nucleation and growth process that leads to a final spherical-like aggregate. Our results show that this angle is a control parameter for the kinetics and equilibrium properties of the system.

  19. Novel Applications of Buffer-gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules

    NASA Astrophysics Data System (ADS)

    Drayna, Garrett Korda

    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In this thesis, I present novel applications of buffer-gas cooling to obtaining gases of trapped, ultracold atoms and diatomic molecules, as well as the study of the cooling of large organic molecules. In the first experiment of this thesis, a buffer-gas beam source of atoms is used to directly load a magneto-optical trap. Due to the versatility of the buffer-gas beam source, we obtain trapped, sub-milliKelvin gases of four different lanthanide species using the same experimental apparatus. In the second experiment of this thesis, a buffer-gas beam is used as the initial stage of an experiment to directly laser cool and magneto-optically trap the diatomic molecule CaF. In the third experiment of this thesis, buffer-gas cooling is used to study the cooling of the conformational state of large organic molecules. We directly observe conformational relaxation of gas-phase 1,2-propanediol due to cold collisions with helium gas. Lastly, I present preliminary results on a variety of novel applications of buffer-gas cooling, such as mixture analysis, separation of chiral mixtures, the measurement of parity-violation in chiral molecules, and the cooling and spectroscopy of highly unstable reaction intermediates.

  20. Tunneling properties of nonplanar molecules in a gas medium

    SciTech Connect

    Bahrami, Mohammad; Bassi, Angelo

    2011-12-15

    We propose a simple, general, and accurate formula for analyzing the tunneling between classical configurations of a nonplanar molecule in a gas medium, as a function of the thermodynamic parameters of the gas. We apply it to two interesting cases: (i) the shift to zero frequency of the inversion line of ammonia, upon an increase in the pressure of the gas; and (ii) the destruction of the coherent tunneling of D{sub 2}S{sub 2} molecules in a He gas. In both cases, we compare our analysis with previous theoretical and experimental results.

  1. Aggregation of dipolar molecules in SiO2 hybrid organic-inorganic films: use of silver nanoparticles as inhibitors of molecular aggregation

    NASA Astrophysics Data System (ADS)

    Franco, Alfredo; García-Macedo, Jorge; Brusatin, Giovanna; Guglielmi, Massimo

    2013-04-01

    The technological implementation of hybrid organic-inorganic materials in second order nonlinear optical photonic devices depends strongly on the ability of the host matrixes to contain high loads of dipolar molecules without aggregation. Some organic molecules are often used to diminish the attracting interactions between dipolar molecules in such kind of materials, but their efficiency as inhibitors of molecular aggregation is limited by their polarizability. In this work, we report the use of silver nanoparticles as inhibitors of molecular aggregation in hybrid organic-inorganic films doped with dipolar molecules. The large polarizability of the silver nanoparticles makes them ideal moieties for the inhibition of the electrostatic interactions between dipolar nonlinear optical molecules. The average size of the silver nanoparticles in this work was 70.5 nm in diameter, they were synthesized using silver nitrate (AgNO3) as precursor and aminoethylaminopropyltrimethoxysilane as reducing agent. These nanoparticles were immersed in SiO2 hybrid organic-inorganic sol-gel films doped with dipolar chromophores to study their effect as inhibitors of dipolar chromophores aggregation. The presence of the silver nanoparticles in the solid films was confirmed by transmission electronic microscopy and UV-Visible spectroscopy. UV-Visible spectroscopy was also used to monitor the dipolar chromophores aggregation in the SiO2 films. We found that, at room temperature, silver nanoparticles are good inhibiting chromophores aggregation in comparison with the performance of organic inhibitors.

  2. Heme binding site in apomyoglobin may be effectively targeted with small molecules to control aggregation.

    PubMed

    Azami-Movahed, Mehrnaz; Shariatizi, Sajad; Sabbaghian, Marjan; Ghasemi, Atiyeh; Ebrahim-Habibi, Azadeh; Nemat-Gorgani, Mohsen

    2013-02-01

    A number of ligands with affinities for the heme binding site of apomyoglobin were tested to control amorphous and fibrillar aggregation in the protein. Several techniques, including fluorescence, dynamic light scattering, transmission electron microscopy, dot blot analysis combined with viability studies were employed for structural characterization and cytotoxicity assessment of the intermediate and final protein structures formed during the aggregation process. Of the small molecules investigated, chrysin and Nile red with high structural similarities to heme were chosen for further studies. Only fibril formation was found to be prevented by Nile red, while chrysin, with a greater structural flexibility, was able to prevent both types of aggregate formation. The two ligands were found to influence aggregation at different stages of intermediate structure formation, an ability determined by their degrees of similarities with heme. Based on structural characterization and toxicity studies, it is concluded that ligands similar in structure to heme may be effective in influencing various stages of aggregate formation and toxicity potencies of the protein structures. Since metalloproteins constitute more than thirty percent of all known proteins, it is concluded that the present strategy may be of general significance.

  3. Ultraviolet absorption spectra of metalorganic molecules diluted in hydrogen gas

    NASA Astrophysics Data System (ADS)

    Itoh, Hideo; Watanabe, Masanobu; Mukai, Seiji; Yajima, Hiroyoshi

    1988-12-01

    Ultraviolet absorption spectra of trimethyl gallium, triethyl gallium, and trimethyl aluminum diluted in hydrogen gas were measured as a function of the wavelength (185-350 nm) and the concentration of the molecules (4.8×10 -6 -1.6×10 -4 mol/liter). Their absorbances changed linearly with the concentration of the molecules, which allowed us to calculate the molar absorption coefficients of the molecules on the basis of the Beer-Lambert law.

  4. Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease

    PubMed Central

    Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R.; Challa, Pavan Kumar; Cohen, Samuel I. A.; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

    2017-01-01

    The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer’s disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery. PMID:28011763

  5. Small stress molecules inhibit aggregation and neurotoxicity of prion peptide 106-126

    SciTech Connect

    Kanapathipillai, Mathumai; Ku, Sook Hee; Girigoswami, Koyeli; Park, Chan Beum

    2008-01-25

    In prion diseases, the posttranslational modification of host-encoded prion protein PrP{sup c} yields a high {beta}-sheet content modified protein PrP{sup sc}, which further polymerizes into amyloid fibrils. PrP106-126 initiates the conformational changes leading to the conversion of PrP{sup c} to PrP{sup sc}. Molecules that can defunctionalize such peptides can serve as a potential tool in combating prion diseases. In microorganisms during stressed conditions, small stress molecules (SSMs) are formed to prevent protein denaturation and maintain protein stability and function. The effect of such SSMs on PrP106-126 amyloid formation is explored in the present study using turbidity, atomic force microscopy (AFM), and cellular toxicity assay. Turbidity and AFM studies clearly depict that the SSMs-ectoine and mannosylglyceramide (MGA) inhibit the PrP106-126 aggregation. Our study also connotes that ectoine and MGA offer strong resistance to prion peptide-induced toxicity in human neuroblastoma cells, concluding that such molecules can be potential inhibitors of prion aggregation and toxicity.

  6. Small Molecule Catalysts for Harvesting Methane Gas

    SciTech Connect

    Baker, S. E.; Ceron-Hernandez, M.; Oakdale, J.; Lau, E. Y.

    2016-12-06

    As the average temperature of the earth increases the impact of these changes are becoming apparent. One of the most dramatic changes to the environment is the melting of arctic permafrost. The disappearance of the permafrost has resulted in release of streams of methane that was trapped in remote areas as gas hydrates in ice. Additionally, the use of fracking has also increased emission of methane. Currently, the methane is either lost to the atmosphere or flared. If these streams of methane could be brought to market, this would be an abundant source of revenue. A cheap conversion of gaseous methane to a more convenient form for transport would be necessary to economical. Conversion of methane is a difficult reaction since the C-H bond is very stable (104 kcal/mole). At the industrial scale, the Fischer-Tropsch reaction can be used to convert gaseous methane to liquid methanol but is this method is impractical for these streams that have low pressures and are located in remote areas. Additionally, the Fischer-Tropsch reaction results in over oxidation of the methane leading to many products that would need to be separated.

  7. Supramolecular aggregation of inorganic molecules at Au(111) electrodes under a strong ionic atmosphere.

    PubMed

    Fu, Yong-Chun; Su, Yu-Zhuan; Wu, De-Yin; Yan, Jia-Wei; Xie, Zhao-Xiong; Mao, Bing-Wei

    2009-10-21

    Neutral inorganic molecules are generally weak in surface adsorption and intermolecular interactions. Self-assembly of such types of molecule would provide valuable information about various interactions. At electrochemical interfaces, the relative strength of these interactions may be modified through control of electrode potential and electrolyte, which may lead to the discovery of new structures and new phenomena. However, studies of this nature are as yet lacking. In this work, we consider the covalent-bound semimetal compound molecules, XCl(3) (X = Sb, Bi), as model systems of neutral inorganic molecules to investigate their self-assembly at electrochemical interfaces under a high ionic atmosphere. To fulfill such investigations, in situ STM and cyclic voltammetry are employed, and comparative experiments are performed on Au(111) in ionic liquids as well as aqueous solutions with high ionic strength. In the room temperature ionic liquid of 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF(4)), potential-dependent partial charge transfer between the Au surface and XCl(3) molecules creates a molecule-surface interaction and provides the driving force for adsorption of the molecules. Supramolecular aggregations of adsorbed XCl(3) are promoted through chlorine-based short-range intermolecular correlation under crystallographic constraint, while repulsive Coulombic interactions created between the partially charged aggregations facilitate their long-range ordering. For SbCl(3) molecules, hexagonally arranged 6- or 7-member clusters are formed at 0.08 to -0.2 V (vs Pt), which assemble into a secondary ( radical31 x radical31)R8.9 degrees structure. For BiCl(3) molecules, both the 6-membered hexagonal and 3-membered trigonal clusters are formed in the narrow potential range -0.3 to -0.35 V, and are also arranged into an ordered secondary structure. Comparative studies were performed with SbCl(3) in concentrated aqueous solutions containing 2 M HCl to simulate the

  8. Fluorescence study on the aggregation of collagen molecules in acid solution influenced by hydroxypropyl methylcellulose.

    PubMed

    Ding, Cuicui; Zhang, Min; Li, Guoying

    2016-01-20

    The effect of hydroxypropyl methylcellulose (HPMC) on the aggregation of collagen molecules with collagen concentrations of 0.25, 0.5 and 1.0mg/mL was studied by fluorescence techniques. On one hand, both the synchronous fluorescence spectra and fluorescence emission spectra showed that there was no change in the fluorescence intensity of collagen intrinsic fluorescence when 30% HPMC was added, while it decreased obviously when HPMC content ≥ 50%. From the two-dimensional fluorescence correlation analysis, it was indicated that collagen molecules in 0.25 and 0.5mg/mL collagen solutions were more sensitive to HPMC than those in 1.0mg/mL collagen solution. On the other hand, the pyrene fluorescence and the fluorescence anisotropy measurements indicated that HPMC inhibited the collagen aggregation for 0.25 and 0.5mg/mL collagen, but promoted it for 1.0mg/mL collagen. The atomic force microscopy images further confirmed the effect of HPMC on collagen with different initial states.

  9. Dose response of surfactants to attenuate gas embolism related platelet aggregation

    NASA Astrophysics Data System (ADS)

    Eckmann, David M.; Eckmann, Yonaton Y.; Tomczyk, Nancy

    2014-03-01

    Intravascular gas embolism promotes blood clot formation, cellular activation, and adhesion events, particularly with platelets. Populating the interface with surfactants is a chemical-based intervention to reduce injury from gas embolism. We studied platelet activation and platelet aggregation, prominent adverse responses to blood contact with bubbles. We examined dose-response relationships for two chemically distinct surfactants to attenuate the rise in platelet function stimulated by exposure to microbubbles. Significant reduction in platelet aggregation and platelet activation occurred with increasing concentration of the surfactants, indicating presence of a saturable system. A population balance model for platelet aggregation in the presence of embolism bubbles and surfactants was developed. Monte Carlo simulations for platelet aggregation were performed. Results agree qualitatively with experimental findings. Surfactant dose-dependent reductions in platelet activation and aggregation indicate inhibition of the gas/liquid interface's ability to stimulate cellular activation mechanically.

  10. Interactions and aggregation of apoferritin molecules in solution: effects of added electrolytes.

    PubMed Central

    Petsev, D N; Thomas, B R; Yau, S; Vekilov, P G

    2000-01-01

    We have studied the structure of the protein species and the protein-protein interactions in solutions containing two apoferritin molecular forms, monomers and dimers, in the presence of Na(+) and Cd(2+) ions. We used chromatographic, and static and dynamic light scattering techniques, and atomic force microscopy (AFM). Size-exclusion chromatography was used to isolate these two protein fractions. The sizes and shapes of the monomers and dimers were determined by dynamic light scattering and AFM. Although the monomer is an apparent sphere with a diameter corresponding to previous x-ray crystallography determinations, the dimer shape corresponds to two, bound monomer spheres. Static light scattering was applied to characterize the interactions between solute molecules of monomers and dimers in terms of the second osmotic virial coefficients. The results for the monomers indicate that Na(+) ions cause strong intermolecular repulsion even at concentrations higher than 0.15 M, contrary to the predictions of the commonly applied Derjaguin-Landau-Verwey-Overbeek theory. We argue that the reason for such behavior is hydration force due to the formation of a water shell around the protein molecules with the help of the sodium ions. The addition of even small amounts of Cd(2+) changes the repulsive interactions to attractive but does not lead to oligomer formation, at least at the protein concentrations used. Thus, the two ions provide examples of strong specificity of their interactions with the protein molecules. In solutions of the apoferritin dimer, the molecules attract even in the presence of Na(+) only, indicating a change in the surface of the apoferritin molecule. In view of the strong repulsion between the monomers, this indicates that the dimers and higher oligomers form only after partial denaturation of some of the apoferritin monomers. These observations suggest that aggregation and self-assembly of protein molecules or molecular subunits may be driven by

  11. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  12. The prebiotic molecules observed in the interstellar gas

    PubMed Central

    Thaddeus, P

    2006-01-01

    Over 130 molecules have been identified in the interstellar gas and circumstellar shells, the largest among them is a carbon chain with 13 atoms and molecular weight of 147 (twice that of the simplest amino acid glycine). The high reliability of astronomical identifications, as well as the fairly accurate quantitative analysis which can often be achieved, is emphasized. Glycine itself has been claimed, but a recent analysis indicates that few, if any, of the astronomical radio lines attributed to glycine are actually from that molecule. Polycyclic aromatic hydrocarbons (PAHs) have long been proposed as the source of the unidentified infrared bands between 3 and 16 μm, but no single PAH has been identified in space, partly because PAHs generally have weak or non-existent radio spectra. A remarkable exception is the non-planar corannulene molecule (C20H10) that has a strong radio spectrum; in the rich molecular cloud TMC-1, it is found that less than 10−5 of the carbon is contained in this molecule, suggesting that PAHs are not the dominant large molecules in the interstellar gas, as has been claimed. Owing to inherent spectroscopic limitations, determining the structures of the large molecules in space may require capture of the dust grains, which are continually entering the outer Solar System. PMID:17008209

  13. Line broadening of confined CO gas: from molecule-wall to molecule-molecule collisions with pressure.

    PubMed

    Hartmann, J-M; Boulet, C; Auwera, J Vander; El Hamzaoui, H; Capoen, B; Bouazaoui, M

    2014-02-14

    The infrared absorption in the fundamental band of CO gas confined in porous silica xerogel has been recorded at room temperature for pressures between about 5 and 920 hPa using a high resolution Fourier transform spectrometer. The widths of individual lines are determined from fits of measured spectra and compared with ab initio predictions obtained from requantized classical molecular dynamics simulations. Good agreement is obtained from the low pressure regime where the line shapes are governed by molecule-wall collisions to high pressures where the influence of molecule-molecule interactions dominates. These results, together with those obtained with a simple analytical model, indicate that both mechanisms contribute in a practically additive way to the observed linewidths. They also confirm that a single collision of a molecule with a wall changes its rotational state. These results are of interest for the determination of some characteristics of the opened porosity of porous materials through optical soundings.

  14. PRODUCTION OF CONSTRUCTION AGGREGATES FROM FLUE GAS DESULFURIZATION SLUDGE

    SciTech Connect

    M.M. Wu; D.C. McCoy; R.O. Scandrol; M.L. Fenger; J.A. Withum; R.M. Statnick

    2000-05-01

    The three main conclusions of this report are: (1) The pilot plant successfully demonstrated the continuous, fully-integrated, long-term process operation, including the mixing, pelletizing, and curing steps for aggregate production. The curing vessel, which was designed for the pilot plant test, was operated in a mass flow mode and performed well during pilot plant operation. (2) The pilot plant test demonstrated process flexibility. The same equipment was used to produce lightweight, medium-weight, and road aggregates. The only change was the mix formulation. Aggregates were produced from a variety of mix designs and from FGD sludge with solids concentrations between 45.0% and 56.7% and moisture contents between 55.0% and 43.3%. (3) The pilot plant provided operating data and experience to design and cost a commercial plant, which was not part of the cooperative agreement.

  15. Production of manufactured aggregates from flue gas desulfurization by-products

    SciTech Connect

    Wu, M.M.; McCoy, D.C.; Fenger, M.L.; Scandrol, R.O.; Winschel, R.A.; Withum, J.A.; Statnick, R.M.

    1999-07-01

    CONSOL R and D has developed a disk pelletization process to produce manufactured aggregates from the by-products of various technologies designed to reduce sulfur emissions produced from coal utilization. Aggregates have been produced from the by-products of the Coolside and LIMB sorbent injection, the fluidized-bed combustion (FBC), spray dryer absorption (SDA), and lime and limestone wet flue gas desulfurization (FGD) processes. The aggregates produced meet the general specifications for use as road aggregate in road construction and for use as lightweight aggregate in concrete masonry units. Small field demonstrations with 1200 lb to 5000 lb of manufactured aggregates were conducted using aggregates produced from FBC ash and lime wet FGD sludge in road construction and using aggregates made from SDA ash and lime wet FGD sludge to manufacture concrete blocks. The aggregates for this work were produced with a bench-scale (200--400 lb batch) unit. In 1999, CONSOL R and D constructed and operated a 500 lb/hr integrated, continuous pilot plant. A variety of aggregate products were produced from lime wet FGD sludge. The pilot plant test successfully demonstrated the continuous, integrated operation of the process. The pilot plant demonstration was a major step toward commercialization of manufactured aggregate production from FGD by-products. In this paper, progress made in the production of aggregates from dry FGD (Coolside, LIMB, SDA) and FBC by-products, and lime wet FGD sludge is discussed. The discussion covers bench-scale and pilot plant aggregate production and aggregate field demonstrations.

  16. Detection of individual gas molecules adsorbed on graphene.

    PubMed

    Schedin, F; Geim, A K; Morozov, S V; Hill, E W; Blake, P; Katsnelson, M I; Novoselov, K S

    2007-09-01

    The ultimate aim of any detection method is to achieve such a level of sensitivity that individual quanta of a measured entity can be resolved. In the case of chemical sensors, the quantum is one atom or molecule. Such resolution has so far been beyond the reach of any detection technique, including solid-state gas sensors hailed for their exceptional sensitivity. The fundamental reason limiting the resolution of such sensors is fluctuations due to thermal motion of charges and defects, which lead to intrinsic noise exceeding the sought-after signal from individual molecules, usually by many orders of magnitude. Here, we show that micrometre-size sensors made from graphene are capable of detecting individual events when a gas molecule attaches to or detaches from graphene's surface. The adsorbed molecules change the local carrier concentration in graphene one by one electron, which leads to step-like changes in resistance. The achieved sensitivity is due to the fact that graphene is an exceptionally low-noise material electronically, which makes it a promising candidate not only for chemical detectors but also for other applications where local probes sensitive to external charge, magnetic field or mechanical strain are required.

  17. Aggregation induced enhanced and exclusively highly Stokes shifted emission from an excited state intramolecular proton transfer exhibiting molecule.

    PubMed

    Behera, Santosh Kumar; Murkherjee, Anwesha; Sadhuragiri, G; Elumalai, Palani; Sathiyendiran, M; Kumar, Manishekhar; Mandal, Biman B; Krishnamoorthy, G

    2017-02-01

    The inner filter effect due to self-quenching dominates the normal emission of dyes at higher concentrations, which would limit their applications. Since normal emission was also observed with aggregation induced emission enhancement (AIEE) active excited state intramolecular proton transfer (ESIPT) exhibiting molecules, two new molecules are synthesized and studied to obtain normal emission free AIEE. The molecules are 4-(3-(benzo[d]thiazol-2-yl)-5-tert-butyl-4-hydroxybenzyl)-2-(benzo[d]thiazol-2-yl)-6-tert-butyl phenol (bis-HPBT) and its oxazole analogue (bis-HPBO). Of these molecules, bis-HPBT, which is weakly fluorescent in tetrahydrofuran solution, shows a sudden high enhancement in fluorescence upon addition of 70% water due to the formation of aggregates. Though the normal emission is also observed in tetrahydrofuran, it is completely eliminated in the aggregates, and the aggregates display exclusive tautomer emission. However, bis-HPBO does not emit such an exclusive tautomer emission in the water/tetrahydrofuran mixture. The enhancement in the fluorescence quantum yield of bis-HPBT in 70% water is ∼300 times higher than that in tetrahydrofuran. The modulated molecular structure of bis-HPBT is the cause of this outstanding AIEE. The observation of almost exclusive tautomer emission is a new additional advantage of AIEE from bis-HPBT over other ESIPT molecules. Since the tautomer emission is highly Stokes shifted, no overlap with the absorption spectrum occurs and therefore, the inner filter effect is averted. The aggregated structure acts as a good fluorescence chemosensor for metal ions as well as anions. The aggregated structure is cell permeable and can be used for cell imaging.

  18. High-Resolution Single-Molecule Fluorescence Imaging of Zeolite Aggregates within Real-Life Fluid Catalytic Cracking Particles**

    PubMed Central

    Ristanović, Zoran; Kerssens, Marleen M; Kubarev, Alexey V; Hendriks, Frank C; Dedecker, Peter; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M

    2015-01-01

    Fluid catalytic cracking (FCC) is a major process in oil refineries to produce gasoline and base chemicals from crude oil fractions. The spatial distribution and acidity of zeolite aggregates embedded within the 50–150 μm-sized FCC spheres heavily influence their catalytic performance. Single-molecule fluorescence-based imaging methods, namely nanometer accuracy by stochastic chemical reactions (NASCA) and super-resolution optical fluctuation imaging (SOFI) were used to study the catalytic activity of sub-micrometer zeolite ZSM-5 domains within real-life FCC catalyst particles. The formation of fluorescent product molecules taking place at Brønsted acid sites was monitored with single turnover sensitivity and high spatiotemporal resolution, providing detailed insight in dispersion and catalytic activity of zeolite ZSM-5 aggregates. The results point towards substantial differences in turnover frequencies between the zeolite aggregates, revealing significant intraparticle heterogeneities in Brønsted reactivity. PMID:25504139

  19. Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease.

    PubMed

    Burra, Gunasekhar; Thakur, Ashwani Kumar

    2017-04-12

    The mutant huntingtin protein (mHtt) fragments with expanded polyglutamine sequence forms microscopically visible aggregates in neurons, a hallmark of Huntington's disease (HD). The aggregation process and aggregates are possible targets of therapeutic intervention in HD. Due to lack of treatment and cure, the patients die within 15-20 years after the disease onset. Therefore, discovering therapeutic molecules that may either inhibit the aggregation mechanism or downregulate the toxic effects of mhtt are highly needed. The present study demonstrates the design and use of peptide inhibitors based on the role played by the N-terminal seventeen amino acid sequence (NT17 ) of huntingtin fragment in its aggregation. Fug-NT17 (Fugu), Xen-NT17 (Xenopus), Dro-NT17 (Drosophila), Aib-NT17 , and Pro-NT17 sequences were tested for their ability to inhibit aggregation. Among them, the first three are the sequence variants of human NT17 from evolutionarily distant organisms and the latter two are the analogs of human NT17 containing aminoisobutyric acid (Aib) and proline (Pro). Four out of five inhibited the aggregation of huntingtin fragment, NT17 Q35 P10 K2 polypeptide. Data indicates that the physicochemical properties of the inhibitors play a crucial role in exhibiting the inhibitory effect. These inhibitors can be tested in cell and animal models for the preclinical evaluation in the treating of HD. This article is protected by copyright. All rights reserved.

  20. Bacteriochlorophyll aggregates self-assembled on functionalized gold nanorod cores as mimics of photosynthetic chlorosomal antennae: a single molecule study.

    PubMed

    Furumaki, Shu; Vacha, Frantisek; Hirata, Shuzo; Vacha, Martin

    2014-03-25

    We prepare artificial aggregates that mimic the structure and function of natural chlorosomal light harvesting complexes of green photosynthetic bacteria. Gold nanorods functionalized with hydroxyl groups and immobilized on a substrate serve as cores for the growth of bacteriochlorophyll (BChl) aggregates from a buffer solution. The BChl pigments form large self-assembled aggregate particles with sizes more than twice that of natural chlorosomes. The size is controllable by the aggregation time. The aggregates are characterized on a single-particle level by atomic force microscopy, electron microscopy, and single-molecule spectroscopy. The absorption and fluorescence spectral properties which reflect the molecular level arrangement of the BChl aggregates closely resemble those of the natural chlorosomes of the photosynthetic bacterium Chlorobaculum tepidum. On the other hand, the results of linear dichroism and circular dichroism are different from those of the chlorosomes and indicate a different mesoscopic structure for the artificial aggregates. These results emphasize the structural role played by the baseplate pigment-protein complex in natural chlorosomes.

  1. Smart-aggregation imaging for single molecule localisation with SPAD cameras

    PubMed Central

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A. W.; Duncan, Rory R.; Rickman, Colin; Henderson, Robert K.; Dalgarno, Paul A.

    2016-01-01

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics. PMID:27876857

  2. Smart-aggregation imaging for single molecule localisation with SPAD cameras

    NASA Astrophysics Data System (ADS)

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A. W.; Duncan, Rory R.; Rickman, Colin; Henderson, Robert K.; Dalgarno, Paul A.

    2016-11-01

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics.

  3. Smart-aggregation imaging for single molecule localisation with SPAD cameras.

    PubMed

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A W; Duncan, Rory R; Rickman, Colin; Henderson, Robert K; Dalgarno, Paul A

    2016-11-23

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics.

  4. Aggregation and sedimentation in gas-fluidized beds of cohesive powders.

    PubMed

    Castellanos, A; Valverde, J M; Quintanilla, M A

    2001-10-01

    We present measurements on the settling velocity of gas-fluidized beds of fine cohesive powders. In the solidlike regime (solid volume fraction straight phi>straight phi(c)) particles are static, sustained by enduring contacts. The settling is hindered by interparticle contacts and is a very slow process. In the fluidlike regime (straight phiaggregates, and for this reason the sedimentation velocity exceeds the predicted value by empirical or theoretical laws on the settling of individual particles. We use an extension of the Richardson-Zaki empirical law for the settling of aggregates in the fluidlike regime to fit the experimental data. Aggregates are characterized by the number of aggregated particles N and by an effective radius R. The trend followed by these parameters with particle size is confirmed by direct visualization of the aggregates, and shows that cohesive effects become important when the adhesion force between particles is above particle weight. Results show that aggregates form open structures with a fractal dimension close to the predicted one in the diffusion-limited-aggregation model (D=2.5).

  5. A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

    PubMed

    Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

    2016-03-14

    The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

  6. Thermodynamic properties of small aggregates of rare-gas atoms

    NASA Technical Reports Server (NTRS)

    Etters, R. D.; Kaelberer, J.

    1975-01-01

    The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

  7. Structure and Dynamics of Anaerobic Bacterial Aggregates in a Gas-Lift Reactor

    PubMed Central

    Beeftink, H. H.; Staugaard, P.

    1986-01-01

    Anaerobic mixed-culture aggregates, which converted glucose to acetic, propionic, butyric, and valeric acids, were formed under controlled conditions of substrate feed (carbon limitation) and hydraulic regimen. The continuous-flow system used (anaerobic gas-lift reactor) was designed to retain bacterial aggregates in a well-mixed reactor. Carrier availability (i.e., liquid-suspended sand grains) proved necessary for bacterial aggregate formation from individual cells during reactor start-up. Electron microscopic examination revealed that incipient colonization of sand grains by bacteria from the bulk liquid occurred in surface irregularities, conceivably reflecting local quiescence. Subsequent confluent biofilm formation on sand grains proved to be unstable, however. Substrate depletion in the bulk liquid is assumed to weaken deeper parts of the biofilm due to cellular lysis, after which production of gas bubbles and liquid shearing forces cause sloughing. The resulting fragments, although sand free, were nevertheless large enough to be retained in the reactor and gradually grew larger through bacterial growth and by clumping together with other fragments. In the final steady state, high cell densities were maintained in the form of aggregates, while sand had virtually disappeared due to sampling losses and wash-out. Numerical cell densities within aggregates ranged from 1012/ml at the periphery to very low values in the center. The cells were enmeshed in a polymer matrix containing polysaccharides; nevertheless, carbon sufficiency was not a prerequisite to sustain high hold-up ratios. Images PMID:16347213

  8. A Theoretical Study of some Rheological Properties of the Aggregation of the Molecules Deoxy- Hemoglobin S

    NASA Astrophysics Data System (ADS)

    Mensah, Francis; Grant, Julius; Thorpe, Arthur

    2010-02-01

    Sickle cell disease is a serious public health problem that affects many people worldwide. In this paper, the Langevin equation is used for hemoglobin's aggregation in sickle cell anemia. Several parameters are explored such as the time-dependent deformation of the aggregates whose plot gives a sigmoid, the time-dependent expressions obtained for the coefficient of viscosity and the elastic modulus which characterize the aggregation of the sickle hemoglobin. Other properties such as the viscoelastic and the elasto-thixotropic properties of the sickle hemoglobin polymer are also described. An attempt is made to approach the polymerization process in terms of a dynamical system. )

  9. Buffer Gas Cooled Molecule Source for Cpmmw Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhou, Yan; Grimes, David; Barnum, Timothy J.; Klein, Ethan; Field, Robert W.

    2014-06-01

    We have built a new molecular beam source that implements 20 K Neon buffer gas cooling for the study of the spectra of small molecules. In particular, laser ablation of BaF2 pellets has been optimized to produce a molecular beam of BaF with a number density more than 100 times greater than what we have previously obtained from a typical Smalley-type photoablation supersonic beam source. Moreover, the forward beam velocity of 150 m/s in our apparatus represents an approximate 10-fold reduction, improving spectroscopic resolution from 500 kHz to better than 50 kHz at 100 GHz in a chirped-pulse millimeter-wave experiment in which resolution is limited by Doppler broadening. Novel improvements in our buffer gas source and advantages for CPmmW spectroscopy studies will be discussed. We thank David Patterson, John Barry, John Doyle, and David DeMille for help in the design of our source.

  10. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules--specifically hydrogen, methane, or carbon dioxide.

  11. Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

    DOEpatents

    Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

    2015-06-23

    A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

  12. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence

    PubMed Central

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E.; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R.; Ross, Ian; Parton, Robert G.; Böcking, Till; Gambin, Yann

    2016-01-01

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer’s and Parkinson’s disease. Parkinson’s disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson’s disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils. PMID:27892477

  13. Tuning morphology and fluorescence of aggregated nanostructures of derived perylene diimide molecules.

    PubMed

    He, Xiaorong; Zhou, Weidong; Li, Yuliang; Liu, Xiaofeng; Li, Cuihong; Liu, Huibiao; Zhu, Daoben

    2008-04-01

    In this paper, we report on the self-assembly of water-soluble N,N'-di(N,N'-dimethyl-dodecane-1, 12-diamide)-perylene-3,4,9,10-tetracarboxylic diimide (PDDoAM) in formic acid and chloride salts for producing varied nano-aggregates with different optical properties. Interestingly, the self-assembly can lead to nanocubic, microsheet and "tower-like" nanostructures respectively, as demonstrated by Scanning Electron Microscopy (SEM) images. The optical properties of molecular aggregates were investigated by means of Confocal Raman Microscopy, indicating the morphologies and fluorescence of these nanomaterials are dependent on acids, acid concentrations and casting methods.

  14. Trehalose impairs aggregation of PrPSc molecules and protects prion-infected cells against oxidative damage.

    PubMed

    Béranger, Florence; Crozet, Carole; Goldsborough, Andrew; Lehmann, Sylvain

    2008-09-12

    Neurodegenerative disorders such as Alzheimer's, Huntington's, and prion diseases are characterized by abnormal protein deposits in the brain of affected patients. In prion diseases, a key event in the pathogenesis is the conversion of the normal prion protein (PrP(c)) into abnormal protease resistant PrP(Sc) deposits, a phenomenon associated with a higher sensitivity to oxidative stress in vitro. In cellular models of Alzheimer and Huntington diseases, the disaccharide trehalose has been shown to be effective in inhibiting huntingtin and Abeta peptide aggregates and reducing their associated toxicity. We show in this study that trehalose treatment of prion-infected cells decreases the size of de novo produced PrP(Sc) aggregates and modify their subcellular localization. Despite the fact that trehalose does not modify the protease resistance properties of PrP(Sc) molecules, it significantly protects prion-infected cells from induced oxidative damage, suggesting that this compound is of therapeutic interest.

  15. Investigation of the bistability in J aggregates upon resonant optical excitation with inclusion of pair correlations between molecules

    NASA Astrophysics Data System (ADS)

    Nesterov, L. A.; Rosanov, N. N.

    2016-09-01

    A theory of resonant interaction with radiation of J aggregates based on chains of two-level molecules coupled by the retarded dipole‒dipole interaction has been developed. The effect of pair correlations between the chain molecules on the bistable response of this system under the influence of external resonant radiation has been investigated within the homogeneous chain model. Traditionally, these systems have been described using single-particle density matrices corresponding to each molecule. In this description, twoparticle interactions are represented in the factorized form and do not include correlations between the interacting molecules. In this study, the correlation corrections have been estimated taking into account the influence of only the nearest neighbors, while their values have found to be of the same order of magnitude as the factorized two-particle expectation values for which these corrections have been calculated. As a result, the dipole‒dipole interaction of a particular molecule with the nearest neighbors is so strong that the description of this interaction in the factorized form becomes inappropriate and can be used only for a qualitative analysis of the response of the chain. In order to obtain correct quantitative characteristics, it is necessary to abandon the factorization of the two-particle expectation values, at least for nearest neighbors.

  16. Analysis of the Molecules Structure and Vertical Electron Affinity of Organic Gas Impact on Electric Strength

    NASA Astrophysics Data System (ADS)

    Jiao, Juntao; Xiao, Dengming; Zhao, Xiaoling; Deng, Yunkun

    2016-05-01

    It is necessary to find an efficient selection method to pre-analyze the gas electric strength from the perspective of molecule structure and the properties for finding the alternative gases to sulphur hexafluoride (SF6). As the properties of gas are determined by the gas molecule structure, the research on the relationship between the gas molecule structure and the electric strength can contribute to the gas pre-screening and new gas development. In this paper, we calculated the vertical electron affinity, molecule orbits distribution and orbits energy of gas molecules by the means of density functional theory (DFT) for the typical structures of organic gases and compared their electric strengths. By this method, we find part of the key properties of the molecule which are related to the electric strength, including the vertical electron affinity, the lowest unoccupied molecule orbit (LUMO) energy, molecule orbits distribution and negative-ion system energy. We also listed some molecule groups such as unsaturated carbons double bonds (C=C) and carbonitrile bonds (C≡N) which have high electric strength theoretically by this method. supported by National Natural Science Foundation of China (Nos. 51177101 and 51337006)

  17. Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules

    SciTech Connect

    Larriba-Andaluz, Carlos Hogan, Christopher J.

    2014-11-21

    Structural characterization of ions in the gas phase is facilitated by measurement of ion collision cross sections (CCS) using techniques such as ion mobility spectrometry. Further information is gained from CCS measurement when comparison is made between measurements and accurately predicted CCSs for model ion structures and the gas in which measurements are made. While diatomic gases, namely molecular nitrogen and air, are being used in CCS measurement with increasingly prevalency, the majority of studies in which measurements are compared to predictions use models in which gas molecules are spherical or non-rotating, which is not necessarily appropriate for diatomic gases. Here, we adapt a momentum transfer based CCS calculation approach to consider rotating, diatomic gas molecule collisions with polyatomic ions, and compare CCS predictions with a diatomic gas molecule to those made with a spherical gas molecular for model spherical ions, tetra-alkylammonium ions, and multiply charged polyethylene glycol ions. CCS calculations are performed using both specular-elastic and diffuse-inelastic collisions rules, which mimic negligible internal energy exchange and complete thermal accommodation, respectively, between gas molecule and ion. The influence of the long range ion-induced dipole potential on calculations is also examined with both gas molecule models. In large part we find that CCSs calculated with specular-elastic collision rules decrease, while they increase with diffuse-inelastic collision rules when using diatomic gas molecules. Results clearly show the structural model of both the ion and gas molecule, the potential energy field between ion and gas molecule, and finally the modeled degree of kinetic energy exchange between ion and gas molecule internal energy are coupled to one another in CCS calculations, and must be considered carefully to obtain results which agree with measurements.

  18. Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules.

    PubMed

    Larriba-Andaluz, Carlos; Hogan, Christopher J

    2014-11-21

    Structural characterization of ions in the gas phase is facilitated by measurement of ion collision cross sections (CCS) using techniques such as ion mobility spectrometry. Further information is gained from CCS measurement when comparison is made between measurements and accurately predicted CCSs for model ion structures and the gas in which measurements are made. While diatomic gases, namely molecular nitrogen and air, are being used in CCS measurement with increasingly prevalency, the majority of studies in which measurements are compared to predictions use models in which gas molecules are spherical or non-rotating, which is not necessarily appropriate for diatomic gases. Here, we adapt a momentum transfer based CCS calculation approach to consider rotating, diatomic gas molecule collisions with polyatomic ions, and compare CCS predictions with a diatomic gas molecule to those made with a spherical gas molecular for model spherical ions, tetra-alkylammonium ions, and multiply charged polyethylene glycol ions. CCS calculations are performed using both specular-elastic and diffuse-inelastic collisions rules, which mimic negligible internal energy exchange and complete thermal accommodation, respectively, between gas molecule and ion. The influence of the long range ion-induced dipole potential on calculations is also examined with both gas molecule models. In large part we find that CCSs calculated with specular-elastic collision rules decrease, while they increase with diffuse-inelastic collision rules when using diatomic gas molecules. Results clearly show the structural model of both the ion and gas molecule, the potential energy field between ion and gas molecule, and finally the modeled degree of kinetic energy exchange between ion and gas molecule internal energy are coupled to one another in CCS calculations, and must be considered carefully to obtain results which agree with measurements.

  19. Co-CoO nanoparticles prepared by reactive gas-phase aggregation

    NASA Astrophysics Data System (ADS)

    González, J. A.; Andrés, J. P.; De Toro, J. A.; Muñiz, P.; Muñoz, T.; Crisan, O.; Binns, C.; Riveiro, J. M.

    2009-11-01

    The technique of gas-phase aggregation has been used to prepare partially oxidized Co nanoparticles films by allowing a controlled flow of oxygen gas into the aggregation zone. This method differs from those previously reported, that is, the passivation of a beam of preformed particles in a secondary chamber and the conventional (low Ar pressure) reactive sputtering of Co to produce Co-CoO composite films. Transmission electron microscopy shows that the mean size of the particles is about 6 nm. For sufficiently high oxygen pressures, the nanoparticles films become super-paramagnetic at room temperature. X-ray diffraction patterns display reflections corresponding to fcc Co and fcc CoO phases, with an increasing dominance of the latter upon increasing the oxygen pressure in the aggregation zone, which is consistent with the observed reduction in saturation magnetization. The cluster films assembled with particles grown under oxygen in the condensation zone exhibit exchange-bias fields (about 8 kOe at 20 K) systematically higher than those measured for Co-CoO core-shell nanoparticles prepared by oxidizing preformed particles in the deposition chamber, which we attribute, in the light of results from annealing experiments, to a higher ferromagnetic-antiferromagnetic (Co-CoO) interface density.

  20. Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy

    PubMed Central

    Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K.; Sud, Sudha; Stringer, Kathleen A.; Rosania, Gus R.

    2017-01-01

    Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals. PMID:28270989

  1. Mn12 single-molecule magnet aggregates as magnetic resonance imaging contrast agents.

    PubMed

    Wang, Yinglin; Li, Wen; Zhou, Shengyan; Kong, Daliang; Yang, Haishan; Wu, Lixin

    2011-03-28

    Mn(12) single-molecule magnets have been dispersed in water through an emulsion-assisted self-assembly method with an improved stability in water, in order to investigate the use of Mn(12) as MRI contrast agents.

  2. High density flux of Co nanoparticles produced by a simple gas aggregation apparatus.

    PubMed

    Landi, G T; Romero, S A; Santos, A D

    2010-03-01

    Gas aggregation is a well known method used to produce clusters of different materials with good size control, reduced dispersion, and precise stoichiometry. The cost of these systems is relatively high and they are generally dedicated apparatuses. Furthermore, the usual sample production speed of these systems is not as fast as physical vapor deposition devices posing a problem when thick samples are needed. In this paper we describe the development of a multipurpose gas aggregation system constructed as an adaptation to a magnetron sputtering system. The cost of this adaptation is negligible and its installation and operation are both remarkably simple. The gas flow for flux in the range of 60-130 SCCM (SCCM denotes cubic centimeter per minute at STP) is able to completely collimate all the sputtered material, producing spherical nanoparticles. Co nanoparticles were produced and characterized using electron microscopy techniques and Rutherford back-scattering analysis. The size of the particles is around 10 nm with around 75 nm/min of deposition rate at the center of a Gaussian profile nanoparticle beam.

  3. High density flux of Co nanoparticles produced by a simple gas aggregation apparatus

    SciTech Connect

    Landi, G. T.; Romero, S. A.; Santos, A. D.

    2010-03-15

    Gas aggregation is a well known method used to produce clusters of different materials with good size control, reduced dispersion, and precise stoichiometry. The cost of these systems is relatively high and they are generally dedicated apparatuses. Furthermore, the usual sample production speed of these systems is not as fast as physical vapor deposition devices posing a problem when thick samples are needed. In this paper we describe the development of a multipurpose gas aggregation system constructed as an adaptation to a magnetron sputtering system. The cost of this adaptation is negligible and its installation and operation are both remarkably simple. The gas flow for flux in the range of 60-130 SCCM (SCCM denotes cubic centimeter per minute at STP) is able to completely collimate all the sputtered material, producing spherical nanoparticles. Co nanoparticles were produced and characterized using electron microscopy techniques and Rutherford back-scattering analysis. The size of the particles is around 10 nm with around 75 nm/min of deposition rate at the center of a Gaussian profile nanoparticle beam.

  4. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-11-21

    One strategy to markedly increase the gas storage capacity of metal–organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules—specifically hydrogen, methane, or carbon dioxide.

  5. Self-assembled aggregates of amphiphilic perylene diimide-based semiconductor molecules: effect of morphology on conductivity.

    PubMed

    Chen, Yanli; Feng, Yajuan; Gao, Jian; Bouvet, Marcel

    2012-02-15

    Two amphiphilic perylenetetracarboxylic diimide derivatives modified with different side chains at imide nitrogen, N-n-hexyl-N'-(2-hydroxyethyl)-1,7-di(4'-t-butyl)phenoxy-perylene-3,4:9,10-tetracarboxylic diimide (PDI 1) and N,N'-di(2-hydroxyethyl)-1,7-di(4'-t-butyl)phenoxy-perylene-3,4:9,10-tetracarboxylic diimide (PDI 2), were fabricated into organic nanostructures via solution-phase self-assembly. Their self-assembling properties in methanol and n-hexane have been comparatively studied by electronic absorption, fluorescence, and Fourier transform infrared spectroscopy (FT-IR). The morphologies and structures of the self-assemblies were examined by scanning electronic microscopy (SEM), atomic force microscopy (AFM), as well as X-ray diffraction (XRD) techniques. The conducting properties were evaluated by current-voltage (I-V) measurements. Due to the presence of different number of hydroxyethyl groups in the molecule of PDI 1 and PDI 2, the self-assembly of the two molecules in methanol and n-hexane results in nanostructures with distinctly different morphology as follows: nanobelts and nanoleaves for PDI 1 and nanobelt dendrites and nanosheets for PDI 2, respectively. Analysis of the spectral change for the aggregates relative to that of monomeric PDI in solution revealed that in polar and apolar solvents, both nanobelts and nanoleaves precipitated from PDI 1 adopt the H aggregation mode, whereas nanobelt dendrites and nanosheets from PDI 2 adopt H and J aggregation mode, respectively, implying the effect of both side-chain substituent and solvent on tuning the intermolecular stacking. Furthermore, the conductivity of the aggregates of either PDI 1 or PDI 2 from methanol is more than ca. 1 order of magnitude higher than those from n-hexane. In particular, the well-defined, one-dimensional (1D) nanobelts of PDI 1 show excellent semiconducting property with the electrical conductivity as high as 3.3×10(-3) S cm(-1), which might serve as promising candidates for

  6. Two-Photon Optical Properties of AIE-active D-TPE-A Molecules: Aggregation Enhancement and Structure-Property Relationships

    NASA Astrophysics Data System (ADS)

    Zhang, Yilin; Li, Jie; Tang, Ben Zhong; Wong, Kam Sing

    We present an aggregation enhancement in two-photon-excited fluorescence (TPEF) of about two orders of magnitude in a series of novel non-centrosymmetric D- π-A molecules. Aggregation-induced emission characteristics are introduced into these D- π-A molecules via tetraphenylethylene (TPE), which is used as their π-bridge. Detailed analysis shows that the TPEF of these molecules are enhanced in aggregation environment with both fluorescence quantum efficiency and two-photon absorptivity concomitantly. The two-photon absorption (TPA) transition bands of these branched- or butterfly-configured molecules are similar to those in their linear absorption. The molecular TPA cross sections in aggregation environment reach around 50-130 GM, and peak within the available wavelength ranges of a Ti:Sapphire femtosecond oscillator. We also observe that two-photon absorptivity increases progressively with the addition of donor/acceptor moieties on the TPE backbone. This phenomenon is presumably attributed to the improved conjugation length and enhanced intramolecular charge transfer, hence better delocalization of π-electrons. For each compound, the aggregation enhancement in TPA may also offers clues of aggregation effect on the molecular electronic structure.

  7. Coupled plasmon-exciton hybrid excitations in colloidal gold nanorods coated with J-aggregated dye molecules (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Simon, Thomas; Melnikau, Dimitry; Sanchez-Iglesia, Ana; Grzelczak, Marek; Liz-Marzán, Luis M.; Rakovich, Yury P.; Feldmann, Jochen; Urban, Alexander S.

    2016-09-01

    Strong coupling of plasmons and excitons can form hybrid states, the so called "plexcitons". Especially with molecular J-aggregated dye molecules strong interaction becomes observable even under ambient conditions. In our work we investigate the nature of plexcitonic states formed in gold nanorods coated with a cyanine dye by transient absorption spectroscopy. We demonstrate that plexcitons show tunable plasmonic and excitonic non-linear optical behaviour. Our experimental data can be explained on the basis of a simple Lorentz oscillator model. We find that both the quality factor and the coupling strength between plasmons and excitons can be optically manipulated on an ultrashort time scale. T. Simon, D. Melnikau, A. Sánchez-Iglesias, M. Grzelczak, L. Liz-Marzán, Y. Rakovich, J. Feldmann and A. Urban, Exploring the optical non-linearities of plasmon-exciton hybrid resonances in coupled colloidal nanostructures, submitted (2016)

  8. Characterization of Sizes of Aggregates of Insulin Analogs and the Conformations of the Constituent Protein Molecules: A Concomitant Dynamic Light Scattering and Raman Spectroscopy Study.

    PubMed

    Zhou, Chen; Qi, Wei; Lewis, E Neil; Carpenter, John F

    2016-02-01

    To generate aggregates, 3 insulin analogs, lispro, aspart, and glulisine, were incubated without phenolic preservatives for 30 days at 37 °C. As a function of incubation time, aggregation was quantified with size exclusion chromatography, and the sizes of aggregates and the conformations of the constituent molecules were characterized with concomitant dynamic light scattering and Raman spectroscopy. During incubation, lispro was progressively converted into soluble aggregates with hydrodynamic diameters of circa 15 nm, and 95% of the native protein had aggregated at day 30. Raman spectroscopy documented that aggregation resulted in conversion of a large fraction of native alpha helix into nonnative beta sheet structure and a distortion of disulfide bonds. In contrast, for aspart and glulisine only 20% of the native proteins aggregated after 30 days, and minimal structural perturbations were detected. In addition, consistent with the relative aggregation rates during isothermal incubation, Raman spectroscopy showed that during heating the onset temperature for secondary structural perturbations of lispro occurred 7 °C-10 °C lower than those for aspart or glulisine. Overall the results of this study demonstrated that-as in the case during formation of amyloid fibrils from insulin-formation of soluble aggregates of lispro resulted in a high level of conversion of alpha helix into beta sheet.

  9. Molecules, magic and forgetful fruit flies: the supernatural science of medical gas research.

    PubMed

    Mychaskiw, George

    2011-09-06

    Medical gas research often involves the study of molecules under extraphysiologic conditions, that is, conditions that do not exist in nature. This "supernatural" nature of medical gas research sometimes produces results that appear to be almost "magic" to those schooled in traditional physiology"Any sufficiently advanced technology is indistinguishable from magic".-Arthur C. Clarke.

  10. Control of water molecule aggregations in copper 1,4-cyclohexanedicarboxylate coordination polymers containing pyridyl-piperazine type ligands

    NASA Astrophysics Data System (ADS)

    Qiblawi, Sultan H.; LaDuca, Robert L.

    2014-01-01

    A series of layered divalent copper coordination polymers containing 1,4-cyclohexanedicarboxylate and long-spanning pyridyl-piperazine type ligands exhibits greatly different co-crystallized water molecule aggregations depending on the specific ligands used. Both [Cu(t-14cdc)(4-bpmp)]n (1, t-14cdc = trans-1,4-cyclohexanedicarboxylate, 4-bpmp = bis(4-pyridylmethyl)piperazine) and {[Cu(t-14cdc)(4-bpfp)(H2O)2]·6H2O}n (2, 4-bpfp = bis(4-pyridylformyl)piperazine) possess 2D (4,4) coordination polymer grids. However 1 lacks any co-crystallized water and has pinched grid apertures, while 2 manifests infinite water tapes with T6(2)4(2) classification and rectangular grid apertures. {[Cu2(c-14cdc)2(4-bpmp)]·2H2O}n (3, c-14cdc = cis-1,4-cyclohexanedicarboxylate) has [Cu2(c-14cdc)]2 ribbons with paddlewheel dimeric units linked into 2D slabs by 4-bpmp tethers, along with isolated water molecule pairs. In contrast, {[Cu2(c-14cdc)2(4-bpfp)]·10H2O}n (4) shows a very similar underlying coordination polymer topology but entrains unique decameric water molecule clusters. The minor product {[Cu2(c-14cdcH)2(t-1,4-cdc)(4-bpfp)2(H2O)2]·2H2O}n (5) was isolated along with 4; this compound underwent some in situ cis to trans cyclohexane-dicarboxylate ligand isomerization and exhibits a ladder polymer motif.

  11. Interactions of gas molecules with monolayer MoSe2: A first principle study

    NASA Astrophysics Data System (ADS)

    Sharma, Munish; Jamdagni, Pooja; Kumar, Ashok; Ahluwalia, P. K.

    2016-05-01

    We present a first principle study of interaction of toxic gas molecules (NO, NO2 and SO2) with monolayer MoSe2. The predicted order of sensitivity of gas molecule is NO2 > SO2 > NO. Adsorbed molecules strongly influence the electronic behaviour of monolayer MoSe2 by inducing impurity levels in the vicinity of Fermi energy. NO and SO2 is found to induce p-type doping effect while semiconductor to metallic transitions occur on NO2 adsorption. Our findings may guide the experimentalist for fabricating sensor devices based on MoSe2 monolayer.

  12. Gas-phase laser synthesis of aggregation-free, size-controlled hydroxyapatite nanoparticles

    NASA Astrophysics Data System (ADS)

    Bapat, Parimal V.; Kraft, Rebecca; Camata, Renato P.

    2012-10-01

    Nanophase hydroxyapatite (HA) is finding applications in many areas of biomedical research, including bone tissue engineering, drug delivery, and intracellular imaging. Details in chemical composition, crystal phase makeup, size, and shape of HA nanoparticles play important roles in achieving the favorable biological responses required in these applications. Most of the nanophase HA synthesis techniques involve solution-based methods that exhibit substantial aggregation of particles upon precipitation. Typically these methods also have limited control over the particle size and crystal phase composition. In this study, we describe the gas-phase synthesis of aggregation-free, size-controlled HA nanoparticles with mean size in the 20-70 nm range using laser ablation followed by aerosol electrical mobility classification. Nanoparticle deposits with adjustable number concentration were obtained on solid substrates. Particles were characterized by transmission electron microscopy, atomic force microscopy, and X-ray diffraction. Samples are well represented by log-normal size distributions with geometric standard deviation σ g ≈ 1.2. The most suitable conditions for HA nanoparticle formation at a laser fluence of 5 J/cm2 were found to be a temperature of 800 °C and a partial pressure of water of 160 mbar.

  13. Cooling, Collisions and non-Sticking of Polyatomic Molecules in a Cryogenic Buffer Gas Cell

    NASA Astrophysics Data System (ADS)

    Piskorski, Julia Hege

    We cool and study trans-Stilbene, Nile Red and Benzonitrile in a cryogenic (7K) cell filled with low density helium buffer gas. No molecule-helium cluster formation is observed, indicating limited atom-molecule sticking in this system. We place an upper limit of 5% on the population of clustered He-trans-Stilbene, consistent with a measured He-molecule collisional residence time of less than 1 mus. With several low energy torsional modes, trans-Stilbene is less rigid than any molecule previously buffer gas cooled into the Kelvin regime. We report cooling and gas phase visible spectroscopy of Nile Red, a much larger molecule. Our data suggest that buffer gas cooling will be feasible for a variety of small biological molecules. The same cell is also ideal for studying collisional relaxation cross sections. Measurements of Benzonitrile vibrational state decay results in determination of the vibrational relaxation cross sections of sigma22 = 8x10-15 cm2 and sigma 21 = 6x10-15 cm2 for the 22 (v=1) and 21 (v=1) states. For the first time, we directly observe formation of cold molecular dimers in a cryogenic buffer gas cell and determine the dimer formation cross section to be ˜10-13 cm2.

  14. Effects of gas molecules on an ultraviolet photodetector with a single-layer titania nanosheet

    NASA Astrophysics Data System (ADS)

    Matsuzaki, Koji; Taniguchi, Takaaki; Matsumoto, Yasumichi; Hara, Masahiro

    2015-01-01

    We have demonstrated an ultraviolet photodetector fabricated from a chemically exfoliated single-layer titania nanosheet. The photocurrent showed a clear on/off switching with a short time response under periodic pulsed illuminations. Suppressions of the photocurrent due to environmental gas molecules were observed under medium vacuum region (1.0-300 Pa). The observation even in inert nitrogen gas implies an enhancement of annihilations of photo-excited carriers due to collisions of inert gas molecules on the surface-sensitive titania nanosheet.

  15. Research on Sources of Gas Phase Metastable Atoms and Molecules

    DTIC Science & Technology

    1982-05-01

    PAGI(Whi DeE# WA..teod) -systems of interest to such diverse areas as gas discharge physics, chemical physics, flame chemistry and plasma physics. "A...second task involved a literature review of prior basic research meta- stable sources followed by the development and experimental testing of appro...appropriate for this phase of the program. The operation of this type of metastable source wab investigated and tested for the production of metastable argon

  16. Preferable binding site of gas molecules on graphene nanoribbon with Stone–Wales defect

    NASA Astrophysics Data System (ADS)

    Auzar, Zuriana; Johari, Zaharah; Sakina, S. H.; Alias, N. E.; Abidin, M. S. Z.

    2017-02-01

    The issue of sensitivity of sensing device has focused on the development of sensing devices by using new materials, such as graphene. The gas molecules in different positions such as on, near and far from the defect are placed in the same binding site in two graphene configurations for fair comparison. The interaction between two different graphene configurations such as (pristine armchair graphene nanoribbon (P-AGNR) and Stone–Wales defect on graphene surface (SW-AGNR)) with gas molecules (e.g. O2, N2 and NH3) have been investigated to observe the preferential position site of adsorbate gas molecules. The preferable position sites are investigated by using Extended-Huckel Theory. It is found that, the electronic properties of each configuration are strongly depends on the position of gas molecules and graphene system. Meanwhile, the binding site of the gas molecules on the defective site of graphene surface is a significant factor in determining the sensing behavior of graphene based gas defection device.

  17. Adsorption and Gas Separation of Molecules by Carbon Nanohorns.

    PubMed

    Gatica, Silvina M; Nekhai, Anton; Scrivener, Adam

    2016-05-19

    In this paper, we report the results of Monte Carlo simulations of the adsorption of neon, argon, methane and carbon dioxide in carbon nanohorns. We model the nanohorns as an array of carbon cones and obtained adsorption isotherms and isosteric heats. The main sites of adsorption are inside the cones and in the interstices between three cones. We also calculated the selectivity of carbon dioxide/methane, finding that nanohorns are a suitable substrate for gas separation. Our simulations are compared to available experimental data.

  18. Small Molecules Detected by Second-Harmonic Generation Modulate the Conformation of Monomeric α-Synuclein and Reduce Its Aggregation in Cells*

    PubMed Central

    Moree, Ben; Yin, Guowei; Lázaro, Diana F.; Munari, Francesca; Strohäker, Timo; Giller, Karin; Becker, Stefan; Outeiro, Tiago F.; Zweckstetter, Markus; Salafsky, Joshua

    2015-01-01

    Proteins are structurally dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. Here we applied a second-harmonic generation-based technique for studying protein conformation in solution and in real time to the intrinsically disordered, Parkinson disease related protein α-synuclein. From a fragment library, we identified small molecule modulators that bind to monomeric α-synuclein in vitro and significantly reduce α-synuclein aggregation in a neuronal cell culture model. Our results indicate that the conformation of α-synuclein is linked to the aggregation of protein in cells. They also provide support for a therapeutic strategy of targeting specific conformations of the protein to suppress or control its aggregation. PMID:26396193

  19. GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

    SciTech Connect

    MUCKERMAN,J.T.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

  20. Single target sputter deposition of alloy nanoparticles with adjustable composition via a gas aggregation cluster source.

    PubMed

    Vahl, Alexander; Strobel, Julian; Reichstein, Wiebke; Polonskyi, Oleksandr; Strunskus, Thomas; Kienle, Lorenz; Faupel, Franz

    2017-04-28

    Alloy nanoparticles with variable compositions add a new dimension to nanoscience and have many applications. Here we suggest a novel approach for the fabrication of variable composition alloy nanoparticles that is based on a Haberland type gas aggregation cluster source with a custom-made multicomponent target for magnetron sputtering. The approach, which was demonstrated here for gold-rich AgAu nanoparticles, combines a narrow nanoparticle size distribution with in operando variation of composition via the gas pressure as well as highly efficient usage of target material. The latter is particularly attractive for precious metals. Varying argon pressure during deposition, we achieved in operando changes of AgAu alloy nanoparticle composition of more than 13 at%. The alloy nanoparticles were characterized by x-ray photoelectron spectroscopy and energy dispersive x-ray spectroscopy. The characteristic plasmon resonances of multilayer nanoparticle composites were analyzed by UV-vis spectroscopy. Tuning of the number of particles per unit area (particle densities) within individual layers showed an additional degree of freedom to tailor the optical properties of multilayer nanocomposites. By extension of this technique to more complex systems, the presented results are expected to encourage and simplify further research based on plasmonic multi-element nanoparticles. The present method is by no means restricted to plasmonics or nanoparticle based applications, but is also highly relevant for conventional magnetron sputtering of alloys and can be extended to in operando control of alloy concentration by magnetic field.

  1. Small molecule inhibitors block Gas6-inducible TAM activation and tumorigenicity

    PubMed Central

    Kimani, Stanley G.; Kumar, Sushil; Bansal, Nitu; Singh, Kamalendra; Kholodovych, Vladyslav; Comollo, Thomas; Peng, Youyi; Kotenko, Sergei V.; Sarafianos, Stefan G.; Bertino, Joseph R.; Welsh, William J.; Birge, Raymond B.

    2017-01-01

    TAM receptors (Tyro-3, Axl, and Mertk) are a family of three homologous type I receptor tyrosine kinases that are implicated in several human malignancies. Overexpression of TAMs and their major ligand Growth arrest-specific factor 6 (Gas6) is associated with more aggressive staging of cancers, poorer predicted patient survival, acquired drug resistance and metastasis. Here we describe small molecule inhibitors (RU-301 and RU-302) that target the extracellular domain of Axl at the interface of the Ig-1 ectodomain of Axl and the Lg-1 of Gas6. These inhibitors effectively block Gas6-inducible Axl receptor activation with low micromolar IC50s in cell-based reporter assays, inhibit Gas6-inducible motility in Axl-expressing cell lines, and suppress H1299 lung cancer tumor growth in a mouse xenograft NOD-SCIDγ model. Furthermore, using homology models and biochemical verifications, we show that RU301 and 302 also inhibit Gas6 inducible activation of Mertk and Tyro3 suggesting they can act as pan-TAM inhibitors that block the interface between the TAM Ig1 ectodomain and the Gas6 Lg domain. Together, these observations establish that small molecules that bind to the interface between TAM Ig1 domain and Gas6 Lg1 domain can inhibit TAM activation, and support the further development of small molecule Gas6-TAM interaction inhibitors as a novel class of cancer therapeutics. PMID:28272423

  2. Understanding and controlling laser-matter interactions: From solvated dye molecules to polyatomic molecules in gas phase

    NASA Astrophysics Data System (ADS)

    Konar, Arkaprabha

    The goal of my research is to obtain a better understanding of the various processes that occur during and following laser-matter interactions from both the physical and chemical point of view. In particular I focused my research on understanding two very important aspects of laser-matter interaction; 1) Intense laser-matter interactions for polyatomic molecules in the gas phase in order to determine to what extent processes like excitation, ionization and fragmentation can be controlled by modifying the phase and amplitude of the laser field according to the timescales for electronic, vibrational and rotational energy transfer. 2) Developing pulse shaping based single beam methods aimed at studying solvated molecules in order to elucidate processes like inhomogeneous broadening, solvatochromic shift and to determine the electronic coherence lifetimes of solvated molecules. The effect of the chirped femtosecond pulses on fluorescence and stimulated emission from solvated dye molecules was studied and it was observed that the overall effect depends quadratically on pulse energy, even where excitation probabilities range from 0.02 to 5%, in the so-called "linear excitation regime". The shape of the chirp dependence is found to be independent of the energy of the pulse. It was found that the chirp dependence reveals dynamics related to solvent rearrangement following excitation and also depends on electronic relaxation of the chromophore. Furthermore, the chirped pulses were found to be extremely sensitive to solvent environment and that the complementary phases having the opposite sign provide information about the electronic coherence lifetimes. Similar to chirped pulses, the effects of a phase step on the excitation spectrum and the corresponding changes to the stimulated emission spectrum were also studied and it was found that the coherent feature on the spectrum is sensitive to the dephasing time of the system. Therefore a single phase scanning method can

  3. Positron Impact Ionization in Noble Gas Atoms and Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Marler, J. P.

    2005-05-01

    Results are presented for absolute positronium formation and direct ionization by positron impact on Ne, Ar, Kr, Xe, N2, CO and O2 at energies from threshold up to 90 eV. The experiments use a high-resolution, trap-based positron beam and exploit the properties of positron orbits in a magnetic field [1]. Results for the noble gases are compared with theoretical predictions and with measurements obtained using a significantly different method [2]. Results for diatomic molecules are compared to other available measurements and theoretical calculations where available. There is generally good agreement between the experimental measurements, providing an important benchmark for theoretical calculations. Intriguing features in Ar and O2 will be discussed. [1] J.P. Sullivan, S.J. Gilbert, J.P. Marler, R.G. Greaves, S.J. Buckman and C.M. Surko., Phys. Rev. A. 66, 042708 (2002) [2] J.P. Marler, J.P. Sullivan and C.M. Surko, Phys. Rev. A (2005), in press.

  4. Exploring the dynamic behaviors and transport properties of gas molecules in a transmembrane cyclic peptide nanotube.

    PubMed

    Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi

    2013-12-05

    The dynamic behaviors and transport properties of O2, CO2, and NH3 molecules through a transmembrane cyclic peptide nanotube (CPNT) of 8×cyclo-(WL)4/POPE have been investigated by steered molecular dynamics (SMD) simulations and adaptive biasing force (ABF) samplings. Different external forces are needed for three gas molecules to enter the channel. The periodic change of the pulling force curve for a gas traveling through the channel mainly arises from the regular and periodic arrangement of the composed CP subunits of the CPNT. Radial distribution functions (RDFs) between gas and water disclose the density decrease of channel water, which strongly aggravates the discontinuity of H-bond formation between a gas molecule and the neighboring water. Compared to hardly any H-bond formation between CO2 (or O2) and the framework of the CPNT, NH3 can form abundant H-bonds with the carbonyl/amide groups of the CPNT, leading to a fierce competition to NH3-water H-bonded interactions. In addition to direct H-bonded interactions, all three gases can form water bridges with the tube. The potential profile of mean force coincides with the occurring probability of a gas molecule along the tube axis. The energy barriers at two mouths of the CPNT elucidate the phenomenon that CO2 and O2 are thoroughly confined in the narrow lumen while NH3 can easily go outside the tube. Intermolecular interactions of each gas with channel water and the CPNT framework and the formation of H-bonds and water bridges illuminate the different gas translocation behaviors. The results uncover interesting and comprehensive mechanisms underlying the permeation characteristics of three gas molecules traveling through a transmembrane CPNT.

  5. Measurement of the orientation of buffer-gas-cooled, electrostatically-guided ammonia molecules

    NASA Astrophysics Data System (ADS)

    Steer, Edward W.; Petralia, Lorenzo S.; Western, Colin M.; Heazlewood, Brianna R.; Softley, Timothy P.

    2017-02-01

    The extent to which the spatial orientation of internally and translationally cold ammonia molecules can be controlled as molecules pass out of a quadrupole guide and through different electric field regions is examined. Ammonia molecules are collisionally cooled in a buffer gas cell, and are subsequently guided by a three-bend electrostatic quadrupole into a detection chamber. The orientation of ammonia molecules is probed using (2 + 1) resonance-enhanced multiphoton ionisation (REMPI), with the laser polarisation axis aligned both parallel and perpendicular to the time-of-flight axis. Even with the presence of a near-zero field region, the ammonia REMPI spectra indicate some retention of orientation. Monte Carlo simulations propagating the time-dependent Schrödinger equation in a full basis set including the hyperfine interaction enable the orientation of ammonia molecules to be calculated - with respect to both the local field direction and a space-fixed axis - as the molecules pass through different electric field regions. The simulations indicate that the orientation of ∼95% of ammonia molecules in JK =11 could be achieved with the application of a small bias voltage (17 V) to the mesh separating the quadrupole and detection regions. Following the recent combination of the buffer gas cell and quadrupole guide apparatus with a linear Paul ion trap, this result could enable one to examine the influence of molecular orientation on ion-molecule reaction dynamics and kinetics.

  6. Generation and orientation of organoxenon molecule H-Xe-CCH in the gas phase

    SciTech Connect

    Poterya, Viktoriya; Votava, Ondrej; Farnik, Michal; Oncak, Milan; Slavicek, Petr; Buck, Udo; Friedrich, Bretislav

    2008-03-14

    We report on the first observation of the organoxenon HXeCCH molecule in the gas phase. This molecule has been prepared in a molecular beam experiment by 193 nm photolysis of an acetylene molecule on Xe{sub n} clusters (n{approx_equal}390). Subsequently the molecule has been oriented via the pseudo-first-order Stark effect in a strong electric field of the polarized laser light combined with the weak electrostatic field in the extraction region of a time-of-flight spectrometer. The experimental evidence for the oriented molecule has been provided by measurements of its photodissociation. For comparison, photolysis of C{sub 2}H{sub 2} on Ar{sub n} clusters (n{approx_equal}280) has been measured. Here the analogous rare gas molecule HArCCH could not be generated. The interpretation of our experimental findings has been supported by ab initio calculations. In addition, the experiment together with the calculations reveals information on the photochemistry of the HXeCCH molecule. The 193 nm radiation excites the molecule predominantly into the 2 {sup 1}{sigma}{sup +} state, which cannot dissociate the Xe-H bond directly, but the system evolves along the Xe-C coordinate to a conical intersection of a slightly nonlinear configuration with the dissociative 1 {sup 1}{pi} state, which then dissociates the Xe-H bond.

  7. Generation and orientation of organoxenon molecule H-Xe-CCH in the gas phase

    NASA Astrophysics Data System (ADS)

    Poterya, Viktoriya; Votava, Ondřej; Fárník, Michal; Ončák, Milan; Slavíček, Petr; Buck, Udo; Friedrich, Břetislav

    2008-03-01

    We report on the first observation of the organoxenon HXeCCH molecule in the gas phase. This molecule has been prepared in a molecular beam experiment by 193nm photolysis of an acetylene molecule on Xen clusters (n¯≈390). Subsequently the molecule has been oriented via the pseudo-first-order Stark effect in a strong electric field of the polarized laser light combined with the weak electrostatic field in the extraction region of a time-of-flight spectrometer. The experimental evidence for the oriented molecule has been provided by measurements of its photodissociation. For comparison, photolysis of C2H2 on Arn clusters (n¯≈280) has been measured. Here the analogous rare gas molecule HArCCH could not be generated. The interpretation of our experimental findings has been supported by ab initio calculations. In addition, the experiment together with the calculations reveals information on the photochemistry of the HXeCCH molecule. The 193nm radiation excites the molecule predominantly into the 2Σ+1 state, which cannot dissociate the Xe-H bond directly, but the system evolves along the Xe-C coordinate to a conical intersection of a slightly nonlinear configuration with the dissociative 1Π1 state, which then dissociates the Xe-H bond.

  8. PAHs molecules and heating of the interstellar gas

    NASA Technical Reports Server (NTRS)

    Verstraete, Laurent; Leger, Alain; Dhendecourt, Louis B.; Dutuit, O.; Defourneau, D.

    1989-01-01

    Until now it has remained difficult to account for the rather high temperatures seen in many diffuse interstellar clouds. Various heating mechanisms have been considered: photoionization of minor species, ionization of H by cosmic rays, and photoelectric effect on small grains. Yet all these processes are either too weak or efficient under too restricting conditions to balance the observed cooling rates. A major heat source is thus still missing in the thermal balance of the diffuse gas. Using photoionization cross sections measured in the lab, it was shown that in order to balance the observed cooling rates in cold diffuse clouds (T approx. 80 K) the PAHs would have to contain 15 percent of the cosmic abundance of carbon. This value does not contradict the former estimation of 6 percent deduced from the IR emission bands since this latter is to be taken as a lower limit. Further, it was estimated that the contribution to the heating rate due to PAH's in a warm HI cloud, assuming the same PAH abundance as for a cold HI cloud, would represent a significant fraction of the value required to keep the medium in thermal balance. Thus, photoionization of PAHs might well be a major heat source for the cold and warm HI media.

  9. Effects of polymer coating on the adsorption of gas molecules on carbon nanotube networks

    SciTech Connect

    Kim, Sanghun; Lee, Hyeong Rag; Yun, Yong Ju; Ji, Seungmuk; Yoo, Kwonjae; Yun, Wan Soo; Koo, Ja-Yong; Ha, Dong Han

    2007-08-27

    Functionalization of carbon nanotubes (CNTs) with polymers such as polyethyleneimine or nafion was found to not change the adsorption properties of gas molecules on CNTs, although functionalization can remarkably enhance the sensitivity of gas sensors. Charge transfer between adsorbed molecules and single-walled carbon nanotubes (SWCNTs) at defect sites causes a steep and nonlinear conductance change at low gas concentrations, while molecules physically adsorbed on the pristine surfaces result in the linear electrical responses at higher concentrations. In addition, the molecular binding energies at defect sites of SWCNTs were measured to be 0.61 eV for NO{sub 2} and 0.53 eV for NH{sub 3}.

  10. Sensitivity and resolution in frequency comb spectroscopy of buffer gas cooled polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Changala, P. Bryan; Spaun, Ben; Patterson, David; Doyle, John M.; Ye, Jun

    2016-12-01

    We discuss the use of cavity-enhanced direct frequency comb spectroscopy in the mid-infrared region with buffer gas cooling of polyatomic molecules for high-precision rovibrational absorption spectroscopy. A frequency comb coupled to an optical enhancement cavity allows us to collect high-resolution, broad-bandwidth infrared spectra of translationally and rotationally cold (10-20 K) gas-phase molecules with high absorption sensitivity and fast acquisition times. The design and performance of the combined apparatus are discussed in detail. Recorded rovibrational spectra in the CH stretching region of several organic molecules, including vinyl bromide (CH_2CHBr), adamantane (C_{10}H_{16}), and diamantane (C_{14}H_{20}) demonstrate the resolution and sensitivity of this technique, as well as the intrinsic challenges faced in extending the frontier of high-resolution spectroscopy to large complex molecules.

  11. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    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 distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  12. From molecules to aggregates

    NASA Astrophysics Data System (ADS)

    Roesky, Herbert W.

    2001-11-01

    The preparation of organometallic oxides, imides and nitrides is described. The molecular structures of these compounds resemble those found in binary systems. However, due to the organic envelope of the molecular solids, they are soluble in organic solvents, easy to crystallize and unambiguously characterizable by single X-ray structural analysis and NMR investigations. Moreover, inorganic oxides can be incorporated in organometallic phosphonates or organoalumoxanes. Herein we describe the organometallic phosphonates as hosts with a hydrophobic exterior.

  13. Composite thermochemistry of gas phase U(VI)-containing molecules.

    PubMed

    Bross, David H; Peterson, Kirk A

    2014-12-28

    Reaction energies have been calculated for a series of reactions involving UF6, UO3, UO2(OH)2, and UO2F2 using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF6 to determine the enthalpies of formation of UO3, UO2(OH)2, and UO2F2. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO2F2 was in excellent agreement with experiment, while the two results obtained for UO3 were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO2(OH)2 is predicted from this work to be -288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of -292.7 ± 6 kcal/mol.

  14. Composite thermochemistry of gas phase U(VI)-containing molecules

    SciTech Connect

    Bross, David H.; Peterson, Kirk A.

    2014-12-28

    Reaction energies have been calculated for a series of reactions involving UF{sub 6}, UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2} using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF{sub 6} to determine the enthalpies of formation of UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2}. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO{sub 2}F{sub 2} was in excellent agreement with experiment, while the two results obtained for UO{sub 3} were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO{sub 2}(OH){sub 2} is predicted from this work to be −288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of −292.7 ± 6 kcal/mol.

  15. Composite thermochemistry of gas phase U(VI)-containing molecules

    NASA Astrophysics Data System (ADS)

    Bross, David H.; Peterson, Kirk A.

    2014-12-01

    Reaction energies have been calculated for a series of reactions involving UF6, UO3, UO2(OH)2, and UO2F2 using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF6 to determine the enthalpies of formation of UO3, UO2(OH)2, and UO2F2. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ˜1 kcal/mol of each other. The final composite heat of formation for UO2F2 was in excellent agreement with experiment, while the two results obtained for UO3 were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO2(OH)2 is predicted from this work to be -288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of -292.7 ± 6 kcal/mol.

  16. Exchange Bias Optimization by Controlled Oxidation of Cobalt Nanoparticle Films Prepared by Sputter Gas Aggregation.

    PubMed

    Antón, Ricardo López; González, Juan A; Andrés, Juan P; Normile, Peter S; Canales-Vázquez, Jesús; Muñiz, Pablo; Riveiro, José M; De Toro, José A

    2017-03-11

    Porous films of cobalt nanoparticles have been obtained by sputter gas aggregation and controllably oxidized by air annealing at 100 °C for progressively longer times (up to more than 1400 h). The magnetic properties of the samples were monitored during the process, with a focus on the exchange bias field. Air annealing proves to be a convenient way to control the Co/CoO ratio in the samples, allowing the optimization of the exchange bias field to a value above 6 kOe at 5 K. The occurrence of the maximum in the exchange bias field is understood in terms of the density of CoO uncompensated spins and their degree of pinning, with the former reducing and the latter increasing upon the growth of a progressively thicker CoO shell. Vertical shifts exhibited in the magnetization loops are found to correlate qualitatively with the peak in the exchange bias field, while an increase in vertical shift observed for longer oxidation times may be explained by a growing fraction of almost completely oxidized particles. The presence of a hummingbird-like form in magnetization loops can be understood in terms of a combination of hard (biased) and soft (unbiased) components; however, the precise origin of the soft phase is as yet unresolved.

  17. Exchange Bias Optimization by Controlled Oxidation of Cobalt Nanoparticle Films Prepared by Sputter Gas Aggregation

    PubMed Central

    Antón, Ricardo López; González, Juan A.; Andrés, Juan P.; Normile, Peter S.; Canales-Vázquez, Jesús; Muñiz, Pablo; Riveiro, José M.; De Toro, José A.

    2017-01-01

    Porous films of cobalt nanoparticles have been obtained by sputter gas aggregation and controllably oxidized by air annealing at 100 °C for progressively longer times (up to more than 1400 h). The magnetic properties of the samples were monitored during the process, with a focus on the exchange bias field. Air annealing proves to be a convenient way to control the Co/CoO ratio in the samples, allowing the optimization of the exchange bias field to a value above 6 kOe at 5 K. The occurrence of the maximum in the exchange bias field is understood in terms of the density of CoO uncompensated spins and their degree of pinning, with the former reducing and the latter increasing upon the growth of a progressively thicker CoO shell. Vertical shifts exhibited in the magnetization loops are found to correlate qualitatively with the peak in the exchange bias field, while an increase in vertical shift observed for longer oxidation times may be explained by a growing fraction of almost completely oxidized particles. The presence of a hummingbird-like form in magnetization loops can be understood in terms of a combination of hard (biased) and soft (unbiased) components; however, the precise origin of the soft phase is as yet unresolved. PMID:28336895

  18. Laboratory Studies of Stabilities of Heterocyclic Aromatic Molecules: Suggested Gas Phase Ion-Molecule Routes to Production in Interstellar Gas Clouds

    NASA Technical Reports Server (NTRS)

    Adams, Nigel G.; Fondren, L. Dalila; McLain, Jason L.; Jackson, Doug M.

    2006-01-01

    Several ring compounds have been detected in interstellar gas clouds, ISC, including the aromatic, benzene. Polycyclic aromatic hydrocarbons, PAHs, have been implicated as carriers of diffuse interstellar bands (DIBs) and unidentified infrared (UIR) bands. Heterocyclic aromatic rings of intermediate size containing nitrogen, possibly PreLife molecules, were included in early searches but were not detected and a recent search for Pyrimidine was unsuccessful. Our laboratory investigations of routes to such molecules could establish their existence in ISC and suggest conditions under which their concentrations would be maximized thus aiding the searches. The stability of such ring compounds (C5H5N, C4H4N2, C5H11N and C4H8O2) has been tested in the laboratory using charge transfer excitation in ion-molecule reactions. The fragmentation paths, including production of C4H4(+), C3H3N(+) and HCN, suggest reverse routes to the parent molecules, which are presently under laboratory investigation as production sources.

  19. Bombardment of gas molecules on single graphene layer at high temperature

    SciTech Connect

    Murugesan, Ramki; Park, Jae Hyun; Ha, Dong Sung

    2014-12-09

    Graphite is widely used as a material for rocket-nozzle inserts due to its excellent thermo-physical properties as well as low density. During the operation of rockets, the surface of the graphite nozzle is subjected to very high heat fluxes and the undesirable erosion of the surface occurs due to the bombardment of gas molecules with high kinetic energy, which causes a significant reduction of nozzle performance. However, the understanding and quantification of such bombardment is not satisfactory due to its complexity: The bond breaking-forming happens simultaneously for the carbon atoms of graphene, some gas molecules penetrate through the surface, some of them are reflected from the surface, etc. In the present study, we perform extensive molecular dynamics (MD) simulations to examine the bombardment phenomena in high temperature environment (several thousand Kelvin). Advanced from the previous studies that have focused on the bombardment by light molecules (e.g., H{sub 2}), we will concentrate on the impact by realistic molecules (e.g., CO{sub 2} and H{sub 2}O). LAMMPS is employed for the MD simulations with NVE ensemble and AIREBO potential for graphene. The molecular understanding of the interaction between graphene and highly energetic gas molecules will enable us to design an efficient thermo-mechanical protection system.

  20. Bombardment of gas molecules on single graphene layer at high temperature

    NASA Astrophysics Data System (ADS)

    Murugesan, Ramki; Park, Jae Hyun; Ha, Dong Sung

    2014-12-01

    Graphite is widely used as a material for rocket-nozzle inserts due to its excellent thermo-physical properties as well as low density. During the operation of rockets, the surface of the graphite nozzle is subjected to very high heat fluxes and the undesirable erosion of the surface occurs due to the bombardment of gas molecules with high kinetic energy, which causes a significant reduction of nozzle performance. However, the understanding and quantification of such bombardment is not satisfactory due to its complexity: The bond breaking-forming happens simultaneously for the carbon atoms of graphene, some gas molecules penetrate through the surface, some of them are reflected from the surface, etc. In the present study, we perform extensive molecular dynamics (MD) simulations to examine the bombardment phenomena in high temperature environment (several thousand Kelvin). Advanced from the previous studies that have focused on the bombardment by light molecules (e.g., H2), we will concentrate on the impact by realistic molecules (e.g., CO2 and H2O ). LAMMPS is employed for the MD simulations with NVE ensemble and AIREBO potential for graphene. The molecular understanding of the interaction between graphene and highly energetic gas molecules will enable us to design an efficient thermo-mechanical protection system.

  1. Probing Buffer-Gas Cooled Molecules with Direct Frequency Comb Spectroscopy in the Mid-Infrrared

    NASA Astrophysics Data System (ADS)

    Spaun, Ben; Changala, Bryan; Bjork, Bryce J.; Heckl, Oliver H.; Patterson, David; Doyle, John M.; Ye, Jun

    2015-06-01

    We present the first demonstration of cavity-enhanced direct frequency comb spectroscopy on buffer-gas cooled molecules.By coupling a mid-infrared frequency comb to a high-finesse cavity surrounding a helium buffer-gas chamber, we can gather rotationally resolved absorption spectra with high sensitivity over a broad wavelength region. The measured ˜10 K rotational and translational temperatures of buffer-gas cooled molecules drastically simplify the observed spectra, compared to those of room temperature molecules, and allow for high spectral resolution limited only by Doppler broadening (10-100 MHz). Our system allows for the extension of high-resolution spectroscopy to larger molecules, enabling detailed analysis of molecular structure and dynamics, while taking full advantage of the powerful optical properties of frequency combs. A. Foltynowicz et al. Cavity-enhanced optical frequency comb spectroscopy in the mid-infrared application to trace detection of hydrogen peroxide. Applied Physics B, vol. 110, pp. 163-175, 2013. {D. Patterson and J. M. Doyle. Cooling molecules in a cell for FTMW spectroscopy. Molecular Physics 110, 1757-1766, 2012

  2. A Gas Chromatography Experiment for Proving the Application of Quantum Symmetry Restrictions in Homonuclear Diatomic Molecules.

    ERIC Educational Resources Information Center

    Dosiere, M.

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment in which gas chromatography is used to prove the application of quantum symmetry restrictions in homonuclear diatomic molecules. Comparisons between experimental results and theoretical computed values show good agreement, within one to two…

  3. Guest Molecule Exchange Kinetics for the 2012 Ignik Sikumi Gas Hydrate Field Trial

    SciTech Connect

    White, Mark D.; Lee, Won Suk

    2014-05-14

    A commercially viable technology for producing methane from natural gas hydrate reservoirs remains elusive. Short-term depressurization field tests have demonstrated the potential for producing natural gas via dissociation of the clathrate structure, but the long-term performance of the depressurization technology ultimately requires a heat source to sustain the dissociation. A decade of laboratory experiments and theoretical studies have demonstrated the exchange of pure CO2 and N2-CO2 mixtures with CH4 in sI gas hydrates, yielding critical information about molecular mechanisms, recoveries, and exchange kinetics. Findings indicated the potential for producing natural gas with little to no production of water and rapid exchange kinetics, generating sufficient interest in the guest-molecule exchange technology for a field test. In 2012 the U.S. DOE/NETL, ConocoPhillips Company, and Japan Oil, Gas and Metals National Corporation jointly sponsored the first field trial of injecting a mixture of N2-CO2 into a CH4-hydrate bearing formation beneath the permafrost on the Alaska North Slope. Known as the Ignik Sikumi #1 Gas Hydrate Field Trial, this experiment involved three stages: 1) the injection of a N2-CO2 mixture into a targeted hydrate-bearing layer, 2) a 4-day pressurized soaking period, and 3) a sustained depressurization and fluid production period. Data collected during the three stages of the field trial were made available after an extensive quality check. These data included continuous temperature and pressure logs, injected and recovered fluid compositions and volumes. The Ignik Sikumi #1 data set is extensive, but contains no direct evidence of the guest-molecule exchange process. This investigation is directed at using numerical simulation to provide an interpretation of the collected data. A numerical simulator, STOMP-HYDT-KE, was recently completed that solves conservation equations for energy, water, mobile fluid guest molecules, and hydrate guest

  4. Ground state of a hydrogen ion molecule immersed in an inhomogeneous electron gas

    NASA Astrophysics Data System (ADS)

    Diaz-Valdes, J.; Gutierrez, F. A.; Matamala, A. R.; Denton, C. D.; Vargas, P.; Valdes, J. E.

    2007-01-01

    In this work we have calculated the ground state energy of the hydrogen molecule, H2+, immersed in the highly inhomogeneous electron gas around a metallic surface within the local density approximation. The molecule is perturbed by the electron density of a crystalline surface of Au <1 0 0> with the internuclear axis parallel to the surface. The surface spatial electron density is calculated through a linearized band structure method (LMTO-DFT). The ground state of the molecule-ion was calculated using the Born-Oppenheimer approximation for a fixed-ion while the screening effects of the inhomogeneous electron gas are depicted by a Thomas-Fermi like electrostatic potential. We found that within our model the molecular ion dissociates at the critical distance of 2.35 a.u. from the first atomic layer of the solid.

  5. Interface-Induced Ordering of Gas Molecules Confined in a Small Space

    PubMed Central

    Lu, Yi-Hsien; Yang, Chih-Wen; Fang, Chung-Kai; Ko, Hsien-Chen; Hwang, Ing-Shouh

    2014-01-01

    The thermodynamic properties of gases have been understood primarily through phase diagrams of bulk gases. However, observations of gases confined in a nanometer space have posed a challenge to the principles of classical thermodynamics. Here, we investigated interfacial structures comprising either O2 or N2 between water and a hydrophobic solid surface by using advanced atomic force microscopy techniques. Ordered epitaxial layers and cap-shaped nanostructures were observed. In addition, pancake-shaped disordered layers that had grown on top of the epitaxial base layers were observed in oxygen-supersaturated water. We propose that hydrophobic solid surfaces provide low-chemical-potential sites at which gas molecules dissolved in water can be adsorbed. The structures are further stabilized by interfacial water. Here we show that gas molecules can agglomerate into a condensed form when confined in a sufficiently small space under ambient conditions. The crystalline solid surface may even induce a solid-gas state when the gas-substrate interaction is significantly stronger than the gas-gas interaction. The ordering and thermodynamic properties of the confined gases are determined primarily according to interfacial interactions. PMID:25424443

  6. New structural types of Mn16 single-molecule magnets: W-shaped topology from reductive aggregation.

    PubMed

    Thuijs, Annaliese E; King, Philippa; Abboud, Khalil A; Christou, George

    2015-09-21

    Two new Mn16 clusters are reported: [Mn16O10(OH)3(OMe)8(O2CPhBut)17(MeOH)5] (2) and [Mn16O16(OMe)6(O2CPh)12(NO3)4(MeOH)2(H2O)4] (3). The complexes were obtained by reductive aggregation of MnO4– in CH2Cl2/MeOH, and oxidation of MnII and preformed (NnBu4)[Mn4IIIO2(O2CPh)9(H2O)] with CeIV, respectively. The core of 2 has a Mn16III core with an unusual 1:2:3:4:3:2:1 layer structure and a W-shaped pleated topology, whereas 3 contains a central 2 × 3 Mn6IV planar grid held within a nonplanar Mn10III loop and is a rare example of a complex with nitrate ions bridging like carboxylate ions. Variable-temperature, solid-state dc susceptibility, and ac susceptibility studies reveal that 2 and 3 possess S = 12 and S = 8 ground states, respectively. Fits of dc magnetization data collected over a temperature range of 1.8–4.0 K and a magnetization range of 0.1–4 T were fit to give S = 12, D = −0.16(2) cm–1, g = 1.98(3) for 2 and S = 8, D = −0.22(1) cm–1, g = 1.99(2) for 3, where D is the axial zero-field splitting parameter. The ac in-phase (χM′T) susceptibility below 15 K confirmed the ground-state spin values of 2 and 3, as determined from dc data, and the appearance of frequency-dependent out-of-phase (χM″) signals revealed that both complexes are new single-molecule magnets (SMMs). Fits of the ac data gave Ueff = 49.7(1) K and τ0 = 4.32 × 10–9 s for 2 and Ueff ≈ 14.0 ± 2 cm–1 and τ0 ≈ 3.2 ± 0.5 × 10–8 s for 3, where Ueff is the effective barrier to magnetization relaxation and τ0 is the pre-exponential factor. Thus, complexes 2 and 3 are two new members of a growing family of Mn16 clusters, and two new examples of high-nuclearity SMMs, with the Ueff for 2 approaching the value for the prototypical SMM family, [Mn12O12(O2CR)16(H2O)4].

  7. Size controlled deposition of Cu and Si nano-clusters by an ultra-high vacuum sputtering gas aggregation technique

    NASA Astrophysics Data System (ADS)

    Banerjee, A. N.; Krishna, R.; Das, B.

    2008-02-01

    In this paper we have reported the syntheses of copper and silicon nano-clusters by a sputtering-gas-aggregation type growth technique. The process involves typical magnetron sputtering vaporization of target materials followed by an inert gas condensation to form clusters of varying sizes. The size-distributions of the clusters typically follow a normal-distribution and the peak cluster sizes of the distributions depends on several factors, which include gas-flow rate, length of the growth region, deposition pressure etc. We have observed a variation in the peak cluster size with the variation of the gas (argon) flow rates. The experimental values are compared with the existing models and the results are found to be in good agreement. The results are significant since it demonstrates that proper optimization of operation conditions can lead to desired cluster sizes as well as desired cluster-size distributions.

  8. Enhancement of Sublimation of Single Graphene Layer by Interacting with Gas Molecules in Rarefied Environment

    NASA Astrophysics Data System (ADS)

    Murugesan, Ramki; Park, Jae Hyun

    2014-11-01

    Graphene has excellent mechanical properties. One of them is the resistance to high temperature environment. Since the sublimation temperature of graphene is over 4500 K, it has been used for diverse high temperature applications in order to protect the system. In this study, using extensive molecular dynamics simulations, we show that the sublimation of graphene could be enhanced (occurs at the lower temperature) by interacting with the gas molecules. With increase in temperature, the bonds in graphene becomes so sensitive to interact with the incoming gas molecules. When the temperature is low, the graphene is stable to the impingement of gas molecules: The light H2 gases are stick to the graphene surface and remains being attached while the heavy CO2 and H2O are bounced back from the surface. However, at high temperature H2 gases are absorbed on the graphene and destroy the C -C bonds by forming C -H bonds. The local breakage of bond at the impingement spot spreads the entire graphene soon, causing a complete sublimation. Even though the heavy CO2 and H2O molecules also break the C -C bonds at high temperature,but their impingement effect is localized and the breakage does not propagate over the entire surface. This research was supported by Agency for Defence Development (ADD).

  9. High Resolution Rovibrational Spectroscopy of Large Molecules Using Infrared Frequency Combs and Buffer Gas Cooling

    NASA Astrophysics Data System (ADS)

    Changala, Bryan; Spaun, Ben; Patterson, David; Bjork, Bryce J.; Heckl, Oliver H.; Doyle, John M.; Ye, Jun

    2016-06-01

    We have recently demonstrated the integration of cavity-enhanced direct frequency comb spectroscopy with buffer gas cooling to acquire high resolution infrared spectra of translationally and rotationally cold (˜10 K) gas-phase molecules. Here, we extend this method to significantly larger systems, including naphthalene (C10H_8), a prototypical polyaromatic hydrocarbon, and adamantane (C10H_{16}), the fundamental building block of diamonoids. To the authors' knowledge, the latter molecule represents the largest system for which rotationally resolved spectra in the CH stretch region (3 μm) have been obtained. In addition to the measured spectra, we present several details of our experimental methods. These include introducing non-volatile species into the cold buffer gas cell and obtaining broadband spectra with single comb mode resolution. We also discuss recent modifications to the apparatus to improve its absorption sensitivity and time resolution, which facilitate the study of both larger molecular systems and cold chemical dynamics. B. Spaun, et al. Probing buffer-gas cooled molecules with direct frequency comb spectroscopy in the mid-infrared, WF02, 70th International Symposium on Molecular Spectroscopy, Champaign-Urbana, IL, 2015.

  10. Prospect for the formation of a gas of ultracold polar NaRb molecules

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Vexiau, Romain; Wang, Gaoren; Lepers, Maxence; Luc, Eliane; Bouloufa-Maafa, Nadia; Dulieu, Olivier; Wang, Dajun

    2015-05-01

    We present a complete theoretical model for the formation of an ultracold gas of polar NaRb molecules, based on high-precision spectroscopic data completed with accurate quantum chemistry calculations. Weakly-bound molecules are first created via a Feshbach resonance with main triplet character. The population is transfered down to the lowest rovibrational level of the ground state by a coherent STIRAP process. The efficiency of various paths via different electronically-excited molecular states is discussed in relation of the ongoing experimental implementation. Supported by Agence Nationale de la Recherche (ANR), project COPOMOL (# ANR-13-IS04-0004-01).

  11. Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

    NASA Astrophysics Data System (ADS)

    Yatsyna, Vasyl; Bakker, Daniël J.; Salén, Peter; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, Vitali

    2016-09-01

    We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N -methylacetamide molecules in the mid-IR spectral range of 1000 - 1800 cm-1 , utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N -methylacetamide are measured in the full amide I-III range.

  12. Formation of complex organic molecules in cold objects: the role of gas-phase reactions

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

    While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.

  13. Responses of the Microalga Chlorophyta sp. to Bacterial Quorum Sensing Molecules (N-Acylhomoserine Lactones): Aromatic Protein-Induced Self-Aggregation.

    PubMed

    Zhou, Dandan; Zhang, Chaofan; Fu, Liang; Xu, Liang; Cui, Xiaochun; Li, Qingcheng; Crittenden, John C

    2017-03-21

    Bacteria and microalgae often coexist during the recycling of microalgal bioresources in wastewater treatment processes. Although the bacteria may compete with the microalgae for nutrients, they could also facilitate microalgal harvesting by forming algal-bacterial aggregates. However, very little is known about interspecies interactions between bacteria and microalgae. In this study, we investigated the responses of a model microalga, Chlorophyta sp., to the typical quorum sensing (QS) molecules N-acylhomoserine lactones (AHLs) extracted from activated sludge bacteria. Chlorophyta sp. self-aggregated in 200 μm bioflocs by secreting 460-1000 kDa aromatic proteins upon interacting with AHLs, and the settling efficiency of Chlorophyta sp. reached as high as 41%. However, Chlorophyta sp. cells were essentially in a free suspension in the absence of AHLs. Fluorescence intensity of the aromatic proteins had significant (P < 0.05) relationship with the Chlorophyta sp. settleability, and showed a positive correlation, indicating that aromatic proteins helped aggregate microalga. Transcriptome results further revealed up-regulation of synthesis pathways for aromatic proteins from tyrosine and phenylalanine that was assisted by anthranilate accumulation. To the best of our knowledge, this is the first study to confirm that eukaryotic microorganisms can sense and respond to prokaryotic QS molecules.

  14. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent.

  15. High-order-harmonic generation using gas-phase H{sub 2}O molecules

    SciTech Connect

    Zhao Songfeng; Jin, Cheng; Le, Anh-Thu; Lin, C. D.; Lucchese, R. R.

    2011-03-15

    We investigate high-order-harmonic generation of isotropically distributed gas-phase H{sub 2}O molecules exposed to an intense laser field. The induced dipole of each individual molecule by the laser field is first calculated using the recently developed quantitative rescattering theory. In a thin medium, harmonic spectra generated coherently from all the molecules are then calculated by solving Maxwell's equation of propagation. By using accurate transition dipoles of H{sub 2}O, we show that the harmonics in the lower plateau region are quite different from models that employ the simpler strong-field approximation. We also examine the magnitude and phase of the harmonics and their dependence on laser focusing conditions.

  16. Buffer Gas Modifiers Effect Resolution in Ion Mobility Spectrometry through Selective Ion-Molecule Clustering Reactions

    PubMed Central

    Fernández-Maestre, Roberto; Wu, Ching; Hill, Herbert H.

    2013-01-01

    RATIONALE When polar molecules (modifiers) are introduced into the buffer gas of an ion mobility spectrometer, most ion mobilities decrease due to the formation of ion-modifier clusters. METHODS We used ethyl lactate, nitrobenzene, 2-butanol, and tetrahydrofuran-2-carbonitrile as buffer gas modifiers and electrospray ionization ion mobility spectrometry (IMS) coupled to quadrupole mass spectrometry. Ethyl lactate, nitrobenzene, and tetrahydrofuran-2-carbonitrile had not been tested as buffer gas modifiers and 2-butanol had not been used with basic amino acids. RESULTS The ion mobilities of several diamines (arginine, histidine, lysine, and atenolol) were not affected or only slightly reduced when these modifiers were introduced into the buffer gas (3.4% average reduction in an analyte's mobility for the three modifiers). Intramolecular bridges caused limited change in the ion mobilities of diamines when modifiers were added to the buffer gas; these bridges hindered the attachment of modifier molecules to the positive charge of ions and delocalized the charge, which deterred clustering. There was also a tendency towards large changes in ion mobility when the mass of the analyte decreased; ethanolamine, the smallest compound tested, had the largest reduction in ion mobility with the introduction of modifiers into the buffer gas (61%). These differences in mobilities, together with the lack of shift in bridge-forming ions, were used to separate ions that overlapped in IMS, such as isoleucine and lysine, and arginine and phenylalanine, and made possible the prediction of separation or not of overlapping ions. CONCLUSIONS The introduction of modifiers into the buffer gas in IMS can selectively alter the mobilities of analytes to aid in compound identification and/or enable the separation of overlapping analyte peaks. PMID:22956312

  17. Enhanced fluorescence and aggregation of rhodamine molecules dispersed in a thin polymer film in the presence of plasmonic nanostructures

    NASA Astrophysics Data System (ADS)

    Kamalieva, Aisylu N.; Toropov, Nikita A.; Vartanyan, Tigran A.

    2016-04-01

    Optical properties of composite structures comprised of the island films of silver nanoparticles with a thin molecular layer of a dye rhodamine 6G were obtained and studied in this paper. In the near field of plasmonic nanoparticles enhancement and shifting of the maximums of the absorption and fluorescence spectra were observed. In the absorption and fluorescence spectra of thin molecular films with nanoparticles the new red-shifted band in comparison with spectra of thin films without nanoparticles was found. This band was associated with the formation of aggregates. Thus, the silver nanoparticles can contribute to fluorescence enhancement and formation of the aggregates in the rhodamine thin films.

  18. Numerical analysis on gas-surface interaction by molecular dynamics method. I - Simulation with Lennard-Jones molecules

    NASA Astrophysics Data System (ADS)

    Matsumoto, Yoichiro; Matsui, Jun; Ohashi, Hideo

    1992-07-01

    Rarefied gas flows in various situations are calculated successfully by the direct simulation Monte Carlo method. In the simulation, the Maxwell model, where a gas molecule reflects diffusely with the probability alpha and reflects specularly with the probability 1 - alpha, is widely used for boundary conditions on solid surfaces. However, the value of alpha is determined empirically and varies greatly with conditions such as degree of contamination and temperature of the surface. Rational prediction of the value and analysis of the interaction between gas and solid surface are required. In this paper, the behavior of a gas molecule with collides onto the solid surface is simulated by the molecular dynamics method. The numerical results reveal that the scattering behavior of the gas molecule is neither specular, diffuse, nor Maxwell-type reflection, and that the sticking probability is affected by the initial gas velocity and the potential well depth.

  19. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    SciTech Connect

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; Lu, Zhengliang; Chen, Banglin; Dai, Sheng; Yue, Yanfeng; Rabone, Jeremy A.; Liu, Hongjun; Wang, Jihang; Fang, Youxing

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, and CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.

  20. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    DOE PAGES

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; ...

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, andmore » CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.« less

  1. Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters.

    PubMed

    Baumfalk, R; Nahler, N H; Buck, U

    2001-01-01

    Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.

  2. Exobiological implications of dust aggregation in planetary atmospheres: An experiment for the gas-grain simulation facility

    NASA Technical Reports Server (NTRS)

    Huntington, J. L.; Schwartz, D. E.; Marshall, J. R.

    1991-01-01

    The Gas-Grain Simulation Facility (GGSF) will provide a microgravity environment where undesirable environmental effects are reduced, and thus, experiments involving interactions between small particles and grains can be more suitably performed. Slated for flight aboard the Shuttle in 1992, the ESA glovebox will serve as a scientific and technological testbed for GGSF exobiology experiments as well as generating some basic scientific data. Initial glovebox experiments will test a method of generating a stable, mono-dispersed cloud of fine particles using a vibrating sprinkler system. In the absence of gravity and atmospheric turbulence, it will be possible to determine the influence of interparticle forces in controlling the rate and mode of aggregation. The experimental chamber can be purged of suspended matter to enable multiple repetitions of the experiments. Of particular interest will be the number of particles per unit volume of the chamber, because it is suspected that aggregation will occur extremely rapidly if the number exceeds a critical value. All aggregation events will be recorded on high-resolution video film. Changes in the experimental procedure as a result of surprise events will be accompanied by real-time interaction with the mission specialist during the Shuttle flight.

  3. The double dark resonance in a cold gas of Cs atoms and molecules.

    PubMed

    Feng, ZhiFang; Li, WeiDong; Xiao, LianTuan; Jia, SuoTang

    2008-09-29

    We theoretically investigated the properties of the effective four-level stimulated Raman adiabatic passage scheme in a cold gas of Cs atoms and molecules, where exists the tunnelling coupling between two excited molecular states due to the 0(g)- (6S,6P(3/2)) double well structure. The double dark resonance is predicted in the absorption spectrum when the tunnelling coupling strength is large enough. The double dark resonance not only reveals the formation of the ultra-cold molecules, but also provides further evidence for the tunnelling as one effective coupling mechanism between the two excited molecular states. The effect of the various experimental conditions on this phenomena has been discussed.

  4. The Buffer-Gas Positron Accumulator and Resonances in Positron-Molecule Interactions

    NASA Technical Reports Server (NTRS)

    Surko, C.M.

    2007-01-01

    This is a personal account of the development of our buffer-gas positron trap and the new generation of cold beams that these traps enabled. Dick Drachman provided much appreciated advice to us from the time we started the project. The physics underlying trap operation is related to resonances (or apparent resonances) in positron-molecule interactions. Amusingly, experiments enabled by the trap allowed us to understand these processes. The positron-resonance "box score" to date is one resounding "yes," namely vibrational Feshbach resonances in positron annihilation on hydrocarbons; a "probably" for positron-impact electronic excitation of CO and NZ;an d a "maybe" for vibrational excitation of selected molecules. Two of these processes enabled the efficient operation of the trap, and one almost killed it in infancy. We conclude with a brief overview of further applications of the trapping technology discussed here, such as "massive" positron storage and beams with meV energy resolution.

  5. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

    PubMed Central

    Moser, Adam; Range, Kevin; York, Darrin M.

    2010-01-01

    Benchmark quantum calculations of proton affinities and gas phase basicities of molecules relevant to biochemical processes, particulsarly acid/base catalysis, are presented and compared for a variety of multi-level and density-functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states, and provides a benchmark database for development of next-generation semiempirical and approximate density-functional quantum models, and parameterization of methods to predict pKa values and relative solvation energies. PMID:20942500

  6. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  7. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent. Previously announced in STAR as N84-16955

  8. Probing the role of metal cations on the aggregation behavior of amyloid β-peptide at a single molecule level by AFM

    NASA Astrophysics Data System (ADS)

    Xie, Yang; Wang, Jianhua; Liu, Chundong

    2016-09-01

    With the development of nanotechnology, understanding of intermolecular interactions on a single molecule level by atomic force spectroscopy (AFM) has played an important role in molecular biology and biomedical science. In recent years, some research suggested that the presence of metal cations is an important regulator in the processes of misfolding and aggregation of the amyloid β-protein (Aβ), which may be an important etiological factor of Alzheimer's disease. However, the knowledge on the principle of interactions between Aβ and metal cations at the single molecule level is still poor understood. In this paper, the amyloid β-protein (Aβ) was fabricated on substrate of mixed thiol-modified gold nanoparticles using self-assembled monolayer method and the adhesion force in the longitudinal direction between metal cations and Aβ42 were investigated by AFM. The role of metal ions on Aβ aggregation is discussed from the perspective of single molecular force. The force results showed that the specific adhesion force F i and the nonspecific force F 0 between a single Aβ-Aβ pair in control experiment were calculated as 42 ± 3 and 80 pN, respectively. However, F i between a single Aβ-Aβ pair in the presence of Cu2+, Zn2+, Ca2+ and Al3+ increased dramatically to 84 ± 6, 89 ± 3, 73 ± 5, 95 ± 5 pN successively, which indicated that unbinding between Aβ proteins is accelerated in the presence of metal cations. What is more, the imaging results showed that substoichiometric copper cations accelerate the formation of fibrils within 3 days. The combined atomic force spectroscopy and imaging analysis indicate that metal cations play a role in promoting the aggregating behavior of Aβ42.

  9. Stereochemical determination of chlorophyll-d molecule from Acaryochloris marina and its modification to a self-aggregative chlorophyll as a model of green photosynthetic bacterial antennae.

    PubMed

    Mizoguchi, Tadashi; Shoji, Ayumi; Kunieda, Michio; Miyashita, Hideaki; Tsuchiya, Tohru; Mimuro, Mamoru; Tamiaki, Hitoshi

    2006-03-01

    Acaryochloris marina is a unique photosynthetic prokaryote containing chlorophyll(Chl)-d as a major photoactive pigment (over 95%). The molecular structure of Chl-d is proposed as the 3-formyl analog of Chl-a. However, the stereochemistry of Chl-d at the 13(2)-, 17- and 18-positions has not yet been established unambiguously. In the first part of this paper, we describe the determination of their stereochemistries to be 13(2)-(R)-, 17-(S)- and 18-(S)-configurations by using 1H-1H NOE correlations in 1H-NMR and circular dichroism spectra as well as chemical modification of Chl-a to produce stereochemically defined Chl derivatives. In the second part of the paper, we report a facile synthesis of a self-aggregative Chl by modifying isolated Chl-d. Since Chl-d was characterized by its reactive 3-formyl group, the formyl group was reduced with t-BuNH2BH3 to afford the desirable Chl, 3-deformyl-3-hydroxymethyl-pyrochlorophyll-d (3(1)-OH-pyroChl-d). The synthetic 3(1)-OH-pyroChl-d molecules spontaneously self-organized to form well-ordered aggregates in a non-polar organic solvent. The self-aggregates are a good model of major light-harvesting antenna systems of green photosynthetic bacteria, chlorosomes, in terms of the following three findings. (1) Both the red-shifted electronic absorption band above 750 nm and its induced reverse S-shape CD signal around 750 nm were observed in 0.5% (v/v) THF-cyclohexane. (2) The stretching mode of the 13-carbonyl group was downshifted by about 35 cm(-1) from the wavenumber of its free carbonyl. (3) The self-aggregates were quite stable on titration of pyridine to the suspension, in comparison with those of natural chlorosomal bacteriochlorophyll-d possessing the 3-(1-hydroxyethyl) group.

  10. Production efficiencies of U.S. electric generation plants: Effects of data aggregation and greenhouse gas and renewable energy policy

    NASA Astrophysics Data System (ADS)

    Lynes, Melissa Kate

    Over the last few decades there has been a shift in electricity production in the U.S. Renewable energy sources are becoming more widely used. In addition, electric generation plants that use coal inputs are more heavily regulated than a couple decades ago. This shift in electricity production was brought on by changes in federal policy -- a desire for electricity produced in the U.S. which led to policies being adopted that encourage the use of renewable energy. The change in production practices due to policies may have led to changes in the productivity of electric generation plants. Multiple studies have examined the most efficient electric generation plants using the data envelopment analysis (DEA) approach. This study builds on past research to answer three questions: 1) Does the level of aggregation of fuel input variables affect the plant efficiency scores and how does the efficiency of renewable energy input compare to nonrenewable energy inputs; 2) Are policies geared toward directly or indirectly reducing greenhouse gas emissions affecting the production efficiencies of greenhouse gas emitting electric generation plants; and 3) Do renewable energy policies and the use of intermittent energy sources (i.e. wind and solar) affect the productivity growth of electric generation plants. All three analysis, presented in three essays, use U.S. plant level data obtained from the Energy Information Administration to answer these questions. The first two essays use DEA to determine the pure technical, overall technical, and scale efficiencies of electric generation plants. The third essay uses DEA within the Malmquist index to assess the change in productivity over time. Results indicate that the level of aggregation does matter particularly for scale efficiency. This implies that valuable information is likely lost when fuel inputs are aggregated together. Policies directly focused on reducing greenhouse gas emissions may improve the production efficiencies of

  11. Relativistic ultrafast electron diffraction from molecules in the gas phase (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Guehr, Markus; Vecchione, Theodore; Robinson, Matthew S.; Li, Renkai; Hartmann, Nick; Shen, Xiaozhe; Centurion, Martin; Wang, Xijie

    2016-10-01

    Ultrafast electron diffraction (UED) is a powerful technique that can be used to resolve structural changes of gas molecules during a photochemical reaction. However, the temporal resolution in pump-probe experiments has been limited to the few-ps level by the space-charge effect that broadens the electron pulse duration and by velocity mismatch between the pump laser pulses and the probe electron pulses, making only long-lived intermediate states accessible. Taking advantage of relativistic effects, Mega-electron-volt (MeV) electrons can be used to suppress both the space-charge effect and the velocity mismatch, and hence to achieve a temporal resolution that is fast enough to follow coherent nuclear motion in the target molecules. In this presentation, we show the first MeV UED experiments on gas phase targets. These experiments not only demonstrate that femtosecond temporal resolution is achieved, but also show that the spatial resolution is not compromised. This unprecedented combination of spatiotemporal resolution is sufficient to image coherent nuclear motions, and opens the door to a new class of experiments where the structural changes can be followed simultaneously in both space and time.

  12. Monte Carlo calculations of diatomic molecule gas flows including rotational mode excitation

    NASA Technical Reports Server (NTRS)

    Yoshikawa, K. K.; Itikawa, Y.

    1976-01-01

    The direct simulation Monte Carlo method was used to solve the Boltzmann equation for flows of an internally excited nonequilibrium gas, namely, of rotationally excited homonuclear diatomic nitrogen. The semi-classical transition probability model of Itikawa was investigated for its ability to simulate flow fields far from equilibrium. The behavior of diatomic nitrogen was examined for several different nonequilibrium initial states that are subjected to uniform mean flow without boundary interactions. A sample of 1000 model molecules was observed as the gas relaxed to a steady state starting from three specified initial states. The initial states considered are: (1) complete equilibrium, (2) nonequilibrium, equipartition (all rotational energy states are assigned the mean energy level obtained at equilibrium with a Boltzmann distribution at the translational temperature), and (3) nonequipartition (the mean rotational energy is different from the equilibrium mean value with respect to the translational energy states). In all cases investigated the present model satisfactorily simulated the principal features of the relaxation effects in nonequilibrium flow of diatomic molecules.

  13. Dispersion and Functionalization of Nanoparticles Synthesized by Gas Aggregation Source: Opening New Routes Toward the Fabrication of Nanoparticles for Biomedicine.

    PubMed

    Oprea, B; Martínez, L; Román, E; Vanea, E; Simon, S; Huttel, Y

    2015-12-29

    The need to find new nanoparticles for biomedical applications is pushing the limits of the fabrication methods. New techniques with versatilities beyond the extended chemical routes can provide new insight in the field. In particular, gas aggregation sources offer the possibility to fabricate nanoparticles with controlled size, composition, and structure out of thermodynamics. In this context, the milestone is the optimization of the dispersion and functionalization processes of nanoparticles once fabricated by these routes as they are generated in the gas phase and deposited on substrates in vacuum or ultra-high vacuum conditions. In the present work we propose a fabrication route in ultra-high vacuum that is compatible with the subsequent dispersion and functionalization of nanoparticles in aqueous media and, which is more remarkable, in one single step. In particular, we will present the fabrication of nanoparticles with a sputter gas aggregation source using a Fe50B50 target and their further dispersion and functionalization with polyethyleneglycol (PEG). Characterization of these nanoparticles is carried out before and after PEG functionalization. During functionalization, significant boron dissolution occurs, which facilitates nanoparticle dispersion in the aqueous solution. The use of different complementary techniques allows us to prove the PEG attachment onto the surface of the nanoparticles, creating a shell to make them biocompatible. The result is the formation of nanoparticles with a structure mainly composed by a metallic Fe core and an iron oxide shell, surrounded by a second PEG shell dispersed in aqueous solution. Relaxivity measurements of these PEG-functionalized nanoparticles assessed their effectiveness as contrast agents for magnetic resonance imaging (MRI) analysis. Therefore, this new fabrication route is a reliable alternative for the synthesis of nanoparticles for biomedicine.

  14. Computational study of peptide bond formation in the gas phase through ion-molecule reactions.

    PubMed

    Redondo, Pilar; Martínez, Henar; Cimas, Alvaro; Barrientos, Carmen; Largo, Antonio

    2013-08-21

    A computational study of peptide bond formation from gas-phase ion-molecule reactions has been carried out. We have considered the reaction between protonated glycine and neutral glycine, as well as the reaction between two neutral glycine molecules for comparison purposes. Two different mechanisms, concerted and stepwise, were studied. Both mechanisms show significant energy barriers for the neutral reaction. The energy requirements for peptide bond formation are considerably reduced upon protonation of one of the glycine molecules. For the reaction between neutral glycine and N-protonated glycine the lowest energy barrier is observed for the concerted mechanism. For the reaction between neutral glycine and protonated glycine at carbonyl oxygen, the preferred mechanism is the stepwise one, with a relatively small energy barrier (23 kJ mol(-1) at 0 K) and leading to the lowest-lying protonated glycylglycine isomer. In the case that the reaction could be initiated by protonated glycine at hydroxyl oxygen the process would be barrier-free and clearly exothermic. In that case peptide bond formation could take place even under interstellar conditions if glycine is present in space.

  15. The study of excited oxygen molecule gas species production and quenching on thermal protection system materials

    NASA Technical Reports Server (NTRS)

    Nordine, Paul C.; Fujimoto, Gordon T.; Greene, Frank T.

    1987-01-01

    The detection of excited oxygen and ozone molecules formed by surface catalyzed oxygen atom recombination and reaction was investigated by laser induced fluorescence (LIF), molecular beam mass spectrometric (MBMS), and field ionization (FI) techniques. The experiment used partially dissociated oxygen flows from a microwave discharge at pressures in the range from 60 to 400 Pa or from an inductively coupled RF discharge at atmospheric pressure. The catalyst materials investigated were nickel and the reaction cured glass coating used for Space Shuttle reusable surface insulation tiles. Nonradiative loss processes for the laser excited states makes LIF detection of O2 difficult such that formation of excited oxygen molecules could not be detected in the flow from the microwave discharge or in the gaseous products of atom loss on nickel. MBMS experiments showed that ozone was a product of heterogeneous O atom loss on nickel and tile surfaces at low temperatures and that ozone is lost on these materials at elevated temperatures. FI was separately investigated as a method by which excited oxygen molecules may be conveniently detected. Partial O2 dissociation decreases the current produced by FI of the gas.

  16. A redox-active, compact molecule for cross-linking amyloidogenic peptides into nontoxic, off-pathway aggregates: In vitro and in vivo efficacy and molecular mechanisms

    SciTech Connect

    Derrick, Jeffrey S.; Kerr, Richard A.; Nam, Younwoo; Oh, Shin Bi; Lee, Hyuck Jin; Earnest, Kaylin G.; Suh, Nayoung; Peck, Kristy L.; Ozbil, Mehmet; Korshavn, Kyle J.; Ramamoorthy, Ayyalusamy; Prabhakar, Rajeev; Merino, Edward J.; Shearer, Jason; Lee, Joo -Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2015-11-17

    Chemical reagents targeting and controlling amyloidogenic peptides have received much attention for helping identify their roles in the pathogenesis of protein-misfolding disorders. In this paper, we report a novel strategy for redirecting amyloidogenic peptides into nontoxic, off-pathway aggregates, which utilizes redox properties of a small molecule (DMPD, N,N-dimethyl-p-phenylenediamine) to trigger covalent adduct formation with the peptide. In addition, for the first time, biochemical, biophysical, and molecular dynamics simulation studies have been performed to demonstrate a mechanistic understanding for such an interaction between a small molecule (DMPD) and amyloid-β (Aβ) and its subsequent anti-amyloidogenic activity, which, upon its transformation, generates ligand–peptide adducts via primary amine-dependent intramolecular cross-linking correlated with structural compaction. Furthermore, in vivo efficacy of DMPD toward amyloid pathology and cognitive impairment was evaluated employing 5xFAD mice of Alzheimer’s disease (AD). Such a small molecule (DMPD) is indicated to noticeably reduce the overall cerebral amyloid load of soluble Aβ forms and amyloid deposits as well as significantly improve cognitive defects in the AD mouse model. Altogether our in vitro and in vivo studies of DMPD toward Aβ with the first molecular-level mechanistic investigations present the feasibility of developing new, innovative approaches that employ redox-active compounds without the structural complexity as next-generation chemical tools for amyloid management.

  17. A redox-active, compact molecule for cross-linking amyloidogenic peptides into nontoxic, off-pathway aggregates: In vitro and in vivo efficacy and molecular mechanisms

    DOE PAGES

    Derrick, Jeffrey S.; Kerr, Richard A.; Nam, Younwoo; ...

    2015-11-17

    Chemical reagents targeting and controlling amyloidogenic peptides have received much attention for helping identify their roles in the pathogenesis of protein-misfolding disorders. In this paper, we report a novel strategy for redirecting amyloidogenic peptides into nontoxic, off-pathway aggregates, which utilizes redox properties of a small molecule (DMPD, N,N-dimethyl-p-phenylenediamine) to trigger covalent adduct formation with the peptide. In addition, for the first time, biochemical, biophysical, and molecular dynamics simulation studies have been performed to demonstrate a mechanistic understanding for such an interaction between a small molecule (DMPD) and amyloid-β (Aβ) and its subsequent anti-amyloidogenic activity, which, upon its transformation, generates ligand–peptidemore » adducts via primary amine-dependent intramolecular cross-linking correlated with structural compaction. Furthermore, in vivo efficacy of DMPD toward amyloid pathology and cognitive impairment was evaluated employing 5xFAD mice of Alzheimer’s disease (AD). Such a small molecule (DMPD) is indicated to noticeably reduce the overall cerebral amyloid load of soluble Aβ forms and amyloid deposits as well as significantly improve cognitive defects in the AD mouse model. Altogether our in vitro and in vivo studies of DMPD toward Aβ with the first molecular-level mechanistic investigations present the feasibility of developing new, innovative approaches that employ redox-active compounds without the structural complexity as next-generation chemical tools for amyloid management.« less

  18. Gas molecule scattering & ion mobility measurements for organic macro-ions in He versus N2 environments.

    PubMed

    Larriba-Andaluz, Carlos; Fernández-García, Juan; Ewing, Michael A; Hogan, Christopher J; Clemmer, David E

    2015-06-14

    A pending issue in linking ion mobility measurements to ion structures is that the collisional cross section (CCS, the measured structural parameter in ion mobility spectrometry) of an ion is strongly dependent upon the manner in which gas molecules effectively impinge on and are reemitted from ion surfaces (when modeling ions as fixed structures). To directly examine the gas molecule impingement and reemission processes and their influence, we measured the CCSs of positively charged ions of room temperature ionic liquids 1-ethyl-3-methylimidazolium dicyanamide (EMIM-N(CN)2) and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) in N2 using a differential mobility analyzer-mass spectrometer (DMA-MS) and in He using a drift tube mobility spectrometer-mass spectrometer (DT-MS). Cluster ions, generated via electrosprays, took the form (AB)N(A)z, spanning up to z = 20 and with masses greater than 100 kDa. As confirmed by molecular dynamics simulations, at the measurement temperature (∼300 K), such cluster ions took on globular conformations in the gas phase. Based upon their attained charge levels, in neither He nor N2 did the ion-induced dipole potential significantly influence gas molecule-ion collisions. Therefore, differences in the CCSs measured for ions in the two different gases could be primarily attributed to differences in gas molecule behavior upon collision with ions. Overwhelmingly, by comparison of predicted CCSs with selected input impingement-reemission laws to measurements, we find that in N2, gas molecules collide with ions diffusely--they are reemitted at random angles relative to the gas molecule incoming angle--and inelastically. Meanwhile, in He, gas molecules collide specularly and elastically and are emitted from ion surfaces at determined angles. The results can be rationalized on the basis of the momentum transferred per collision; in the case of He, individual gas molecule collisions minimally perturb the atoms within a cluster ion

  19. Salt bridge stabilization of charged zwitterionic arginine aggregates in the gas phase.

    PubMed

    Julian, R R; Hodyss, R; Beauchamp, J L

    2001-04-18

    The discovery of several new unusually stable aggregates of arginine that are intermolecularly bound by salt bridges is reported. Quadrupole ion-trap mass spectrometry provides evidence for the stability of arginine in the zwitterionic state, where the protonated guanidinium group of one arginine interacts strongly with the carboxylate of another to form stable noncovalent complexes, coordinated to either a cation or anion. Clusters of arginine with itself, sodium, potassium, lithium, magnesium, chloride, fluoride, bromide, iodide, and nitrate are observed. DFT calculations at the B3LYP/6-31G level are used to assess the structures and energetics of particularly prominent clusters. An examination of mixtures of D-arginine with isotopically labeled L-arginine indicates that the stability of these clusters does not depend on arginine enantiomeric purity. The cyclic trimers of arginine, capped with either Cl(-) or NO(3)(-), possess exceptional stability.

  20. J-aggregates of organic dye molecules complexed with iron oxide nanoparticles for imaging-guided photothermal therapy under 915-nm light.

    PubMed

    Song, Xuejiao; Gong, Hua; Liu, Teng; Cheng, Liang; Wang, Chao; Sun, Xiaoqi; Liang, Chao; Liu, Zhuang

    2014-11-12

    Recently, the development of nano-theranostic agents aiming at imaging guided therapy has received great attention. In this work, a near-infrared (NIR) heptamethine indocyanine dye, IR825, in the presence of cationic polymer, polyallylamine hydrochloride (PAH), forms J-aggregates with red-shifted and significantly enhanced absorbance. After further complexing with ultra-small iron oxide nanoparticles (IONPs) and the followed functionalization with polyethylene glycol (PEG), the obtained IR825@PAH-IONP-PEG composite nanoparticles are highly stable in different physiological media. With a sharp absorbance peak, IR825@PAH-IONP-PEG can serve as an effective photothermal agent under laser irradiation at 915 nm, which appears to be optimal in photothermal therapy application considering its improved tissue penetration compared with 808-nm light and much lower water heating in comparison to 980-nm light. As revealed by magnetic resonance (MR) imaging, those nanoparticles after intravenous injection exhibit high tumor accumulation, which is then harnessed for in vivo photothermal ablation of tumors, achieving excellent therapeutic efficacy in a mouse tumor model. This study demonstrates for the first time that J-aggregates of organic dye molecules are an interesting class of photothermal material, which when combined with other imageable nanoprobes could serve as a theranostic agent for imaging-guided photothermal therapy of cancer.

  1. Detecting the Formation and Transformation of Oligomers during Insulin Fibrillation by a Dendrimer Conjugated with Aggregation-Induced Emission Molecule.

    PubMed

    Huang, Qin; Xie, Jing; Liu, Yanpeng; Zhou, Anna; Li, Jianshu

    2017-02-08

    The fibrillation of protein is harmful and impedes the use of protein drugs. It also relates to various debilitating diseases such as Alzheimer's diseases. Thus, investigating the protein fibrillation process is necessary. In this study, poly(amido amine) dendrimers (PAMAM) of generation 3 (G3) and generation 4 (G4) were synthesized and conjugated with 4-aminobiphenyl, an aggregation-induced emission (AIE) moiety, at varied grafting ratios. Among them, one fluorescence probe named G3-biph-3 that was grafted average 3.25 4-aminobiphenyl to the G3, can detect the transformations both from native insulin to oligomers and from oligomers to fibrils. The size difference of native insulin, oligomers, and fibrils was proposed to be the main factor leading to the detection of the above transformations. Different molecular weights of sodium polyacrylate (PAAS) were also applied as a model to interact with G3-biph-3 to further reveal the mechanism. The results indicated that PAMAM with a certain generation and grafted with appropriate AIE groups can detect the oligomer formation and transformation during the insulin fibrillation process.

  2. NMR dynamics of quantum discord for spin-carrying gas molecules in a closed nanopore

    SciTech Connect

    Yurishchev, M. A.

    2014-11-15

    A local orthogonal transformation that transforms any centrosymmetric density matrix of a two-qubit system to the X form has been found. A piecewise-analytic-numerical formula Q = min(Q{sub π/2}, Q{sub θ}, Q{sub 0}), where Q{sub π/2} and Q{sub 0} are analytical expressions and the branch Q{sub 0θ} can be obtained only by numerically searching for the optimal measurement angle θ ∈ (0, π/2), is proposed to calculate the quantum discord Q of a general X state. The developed approaches have been applied for a quantitative description of the recently predicted flickering (periodic disappearance and reappearance) of the quantum-information pair correlation between nuclear 1/2 spins of atoms or molecules of a gas (for example, {sup 129}Xe) in a bounded volume in the presence of a strong magnetic field.

  3. Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin

    2017-03-01

    In the molecular Ammosov–Delone–Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen–Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  4. Relevance of the Pharmacokinetic and Pharmacodynamic Profiles of Puerariae lobatae Radix to Aggregation of Multi-Component Molecules in Aqueous Decoctions.

    PubMed

    Su, Bili; Kan, Yongjun; Xie, Jianwei; Hu, Juan; Pang, Wensheng

    2016-06-28

    The complexity of traditional Chinese medicines (TCMs) is related to their multi-component system. TCM aqueous decoction is a common clinical oral formulation. Between molecules in solution, there exist intermolecular strong interactions to form chemical bonds or weak non-bonding interactions such as hydrogen bonds and Van der Waals forces, which hold molecules together to form "molecular aggregates". Taking the TCM Puerariae lobatae Radix (Gegen) as an example, we explored four Gegen decoctions of different concentration of 0.019, 0.038, 0.075, and 0.30 g/mL, named G-1, G-2, G-3, and G-4. In order of molecular aggregate size (diameter) the four kinds of solution were ranked G-1 < G-2 < G-3 < G-4 by Flow Cell 200S IPAC image analysis. A rabbit vertebrobasilar artery insufficiency (VBI) model was set up and they were given Gegen decoction (GGD) at a clinical dosage of 0.82 g/kg (achieved by adjusting the gastric perfusion volume depending on the concentration). The HPLC fingerprint of rabbit plasma showed that the chemical component absorption into blood in order of peak area values was G-1 < G-2 > G-3 > G-4. Puerarin and daidzin are the major constituents of Gegen, and the pharmacokinetics of G-1 and G-2 puerarin conformed with the two compartment open model, while for G-3 and G-4, they conformed to a one compartment open model. For all four GGDs the pharmacokinetics of daidzin complied with a one compartment open model. FQ-PCR assays of rabbits' vertebrobasilar arterial tissue were performed to determine the pharmacodynamic profiles of the four GGDs. GGD markedly lowered the level of AT₁R mRNA, while the AT₂R mRNA level was increased significantly vs. the VBI model, and G-2 was the most effective. In theory the dosage was equal to the blood drug concentration and should be consistent; however, the formation of molecular aggregates affects drug absorption and metabolism, and therefore influences drugs' effects. Our data provided references for the rational use

  5. Markedly different adsorption behaviors of gas molecules on defective monolayer MoS2: a first-principles study.

    PubMed

    Li, Hongxing; Huang, Min; Cao, Gengyu

    2016-06-01

    Sulfur vacancy (SV) is one of the most typical defects in two-dimensional monolayer MoS2, leading to reactive sites. We presented a systematic study of the adsorption behaviors of gas molecules, CO2, N2, H2O, CO, NH3, NO, O2, H2 and NO2, on monolayer MoS2 with single SV by first-principles calculations. It was found that CO2, N2 and H2O molecules physisorbed at the proximity of single SV. Our adsorption energy calculations and charge transfer analysis showed that the interactions between CO2, N2 and H2O molecules and defective MoS2 are stronger than the cases of CO2, N2 and H2O molecules adsorbed on pristine MoS2, respectively. The defective MoS2 based gas sensors may be more sensitive to CO2, N2 and H2O molecules than pristine MoS2 based ones. CO, NO, O2 and NH3 molecules were found to chemisorb at the S vacancy site and thus modify the electronic properties of defective monolayer MoS2. Magnetism was induced upon adsorption of NO molecules and the defective states induced by S vacancy can be completely removed upon adsorption of O2 molecules, which may provide some helpful information for designing new MoS2 based nanoelectronic devices in future. The H2 and NO2 molecules were found to dissociate at S vacancy. The dissociation of NO2 molecules resulted in O atoms located at the S vacancy site and NO molecules physisorbed on O-doped MoS2. The calculated results showed that NO2 molecules can help heal the S vacancy of the MoS2 monolayer.

  6. Generation, Detection and characterization of Gas-Phase Transition Metal containing Molecules

    SciTech Connect

    Steimle, Timothy

    2015-12-15

    The objective of this project was to generate, detect, and characterize small, gas-phase, metal containing molecules. In addition to being relevant to high temperature chemical environments (e.g. plasmas and combustion), gas-phase experiments on metal containing molecules serve as the most direct link to a molecular-level theoretical model for catalysis. Catalysis (i.e. the addition of a small about of recoverable material to control the rate and direction of a chemical reaction) is critical to the petroleum and pharmaceutical industries as well as environmental remediation. Currently, the majority of catalytic materials are based on very expensive metals such as platinum (Pt), palladium (Pd), iridium (Ir,) rhenium (Re), and rhodium (Rh). For example, the catalyst used for converting linear hydrocarbon molecules (e.g. hexane) to cyclic molecules (e.g. cyclohexane) is a mixture of Pt and Re suspended on alumina. It enables straight chain alkanes to be converted into branched-chain alkanes, cyclohexanes and aromatic hydrocarbons which are used, amongst other things, to enhance the octane number of petrol. A second example is the heterogeneous catalysis used in automobile exhaust systems to: a) decrease nitrogen oxide; b) reduce carbon monoxide; and c) oxidize unburned hydrocarbons. The exhaust is vented through a high-surface area chamber lined with Pt, Pd, and Rh. For example, the carbon monoxide is catalytically converted to carbon dioxide by reaction with oxygen. The research results from this work have been published in readily accessible journals1-28. The ground and excited electronic state properties of small metal containing molecules that we determine were: a) electronic state distributions and lifetimes, b) vibrational frequencies, c) bond lengths and angles, d) hyperfine interactions, e) permanent electric dipole moments, mel, and f) magnetic dipoles, μm. In general terms, μel, gives insight into the charge distribution and mm into

  7. Dissociation Chemistry of Gas Molecules on Carbon Nanotubes - Applications to Chemical Sensing.

    SciTech Connect

    Govind, Niri; Andzelm, Jan; Maiti, Amitesh

    2008-06-01

    It is well known in the literature that carbon nanotubes (CNTs) interact weakly with many gas molecules like H2O, CO, NH3, H2, NO2 and so on. Exposure to NO2, O2, and NH3 significantly affects the electrical conductance of a single wall nanotube (SWNT). These can be explained using a simple charge transfer picture, which results in the observed changes in the hole conduction of the tubes. It is also known that pure SWNTs only weakly interact with these molecules. We have recently investigated [AGM2006] how common defects in CNTs (Stone-Wales (SW), monovacancy, and interstitial) influence the chemisorption of NH3. This paper is a continuation of our previous work. Here we further investigate, via Density Functional Theory (DFT) calculations, the effects of Stone-Wales (SW) defects on the adsorption/dissociation of O2 and H2O. We also study the diffusion of adsorbed oxygen atoms on the nanotube surface in the vicinity of the SW defect as well as the dissociation of NH3 in the presence of adsorbed oxygen atoms.

  8. Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Ochkin, V. N.

    2017-01-01

    A new approach is considered to detect the water leaks in inert plasma-forming gas present in the reactor chamber. It is made up of the intensity ratio of D α and H α spectral lines in combination with O, Ar and Xe lines intensity. The concentrations of H2O, O, H and D particles have been measured with high sensitivity. At the D2 admixture pressure {{p}{{\\text{D}\\text{2}}}}   =  0.025 mbar, we used the acquisition time of 10 s to measure the rate of water molecules injected from the outside, Γ0  =  1.4 · 10-9 mbar · m3 · s-1, and the incoming water molecules to plasma, Γ  =  5 ·10-11 mbar · m3 · s-1. The scaling proves that at small D2 admixtures (10-4 mbar), the leaks with the rates Γ0  ≈  6 · 10-12 mbar · m3 · s-1 and Γ  ≈  2 · 10-13 mbar · m3 · s-1 can be detected and measured. The difference between Γ0 and Γ values is due to the high degree of H2O dissociation, which can be up to 97-98%.

  9. Gas phase ion - molecule reactions studied by Fourier transform ion cyclotron resonance mass spectrometry

    SciTech Connect

    Ross, C.W. III.

    1993-01-01

    Intrinsic thermodynamic information of molecules can easily be determined in the low pressure FT/ICR mass spectrometer. The gas phase basicity of two carbenes were measured by isolating the protonated carbene ion and reacting it with neutral reference compounds by the bracketing method. A fundamentally new-dimensional FT/ICR/MS experiment, SWIM (stored waveform ion modulation) 2D-FT/ICR MS/MS, is described. Prior encodement of the second dimension by use of two identical excitation waveforms separated by a variable delay period is replaced by a new encodement in which each row of the two-dimensional data array is obtained by use of a single stored excitation waveform whose frequency-domain magnitude spectrum is a sinusoid whose frequency increases from one row to the next. In the two-dimensional mass spectrum, the conventional one-dimensional FT/ICR mass spectrum appears along the diagonal, and each off-diagonal peak corresponds to an ion-neutral reaction whose ionic components may be identified by horizontal and vertical projections to the diagonal spectrum. All ion-molecule reactions in a gaseous mixture may be identified from a single 2D-FT/ICR MS/MS experiment, without any prior knowledge of the system. In some endoergic reactions there is a minimum energy threshold that must overcome for a reaction to occur. Hence, a simple sinusoidal modulation of parent ion cyclotron radius leads to a clipped sinusoidal signal of the product ion abundance in the second dimension, which upon Fourier transformation produces signals with harmonic and combination ion cyclotron resonance frequencies. Moreover, ion-molecule reaction rates may vary directly within kinetic energy rather than cyclotron radius. With SWIM, it is possible to tailor the excitation profile so as to produce a sinusoidal modulation of ion kinetic energy as a function of cyclotron frequency.

  10. Complex Organic Molecules Formation in Space Through Gas Phase Reactions: A Theoretical Approach

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2017-02-01

    Chemistry in the interstellar medium (ISM) is capable of producing complex organic molecules (COMs) of great importance to astrobiology. Gas phase and grain surface chemistry almost certainly both contribute to COM formation. Amino acids as building blocks of proteins are some of the most interesting COMs. The simplest one, glycine, has been characterized in meteorites and comets and, its conclusive detection in the ISM seems to be highly plausible. In this work, we analyze the gas phase reaction of glycine and {{{CH}}5}+ to establish the role of this process in the formation of alanine or other COMs in the ISM. Formation of protonated α- and β-alanine in spite of being exothermic processes is not viable under interstellar conditions because the different paths leading to these isomers present net activation energies. Nevertheless, glycine can evolve to protonated 1-imide-2, 2-propanediol, protonated amino acetone, protonated hydroxyacetone, and protonated propionic acid. However, formation of acetic acid and protonated methylamine is also a favorable process and therefore will be a competitive channel with the evolution of glycine to COMs.

  11. Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

    PubMed

    Cohen, A; Niv, M Y; Gerber, R B

    2001-01-01

    Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to

  12. Inhalation of Whole Diesel Exhaust but not Gas-Phase Components Affects In Vitro Platelet Aggregation in Hypertensive Rats

    EPA Science Inventory

    Rationale: Intravascular thrombosis and platelet aggregation are enhanced following exposure to diesel exhaust (DE) and other respirable particulate matter; however, the roles of endothelial and circulating mediators on platelet aggregation remain unclear. We hypothesized that ad...

  13. Definitive Ideal-Gas Thermochemical Functions of the H216O Molecule

    NASA Astrophysics Data System (ADS)

    Furtenbacher, Tibor; Szidarovszky, Tamás; Hrubý, Jan; Kyuberis, Aleksandra A.; Zobov, Nikolai F.; Polyansky, Oleg L.; Tennyson, Jonathan; Császár, Attila G.

    2016-12-01

    A much improved temperature-dependent ideal-gas internal partition function, Qint(T), of the H216O molecule is reported for temperatures between 0 and 6000 K. Determination of Qint(T) is principally based on the direct summation technique involving all accurate experimental energy levels known for H216O (almost 20 000 rovibrational energies including an almost complete list up to a relative energy of 7500 cm-1), augmented with a less accurate but complete list of first-principles computed rovibrational energy levels up to the first dissociation limit, about 41 000 cm-1 (the latter list includes close to one million bound rovibrational energy levels up to J = 69, where J is the rotational quantum number). Partition functions are developed for ortho- and para-H216O as well as for their equilibrium mixture. Unbound rovibrational states of H216O above the first dissociation limit are considered using an approximate model treatment. The effect of the excited electronic states on the thermochemical functions is neglected, as their contribution to the thermochemical functions is negligible even at the highest temperatures considered. Based on the high-accuracy Qint(T) and its first two moments, definitive results, in 1 K increments, are obtained for the following thermochemical functions: Gibbs energy, enthalpy, entropy, and isobaric heat capacity. Reliable uncertainties (approximately two standard deviations) are estimated as a function of temperature for each quantity determined. These uncertainties emphasize that the present results are the most accurate ideal-gas thermochemical functions ever produced for H216O. It is recommended that the new value determined for the standard molar enthalpy increment at 298.15 K, 9.904 04 ± 0.000 01 kJ mol-1, should replace the old CODATA datum, 9.905 ± 0.005 kJ mol-1.

  14. Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

    NASA Astrophysics Data System (ADS)

    Theis, Riley A.; Fortenberry, Ryan C.

    2016-03-01

    The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

  15. Three new defined proton affinities for polybasic molecules in the gas-phase: Proton microaffinity, proton macroaffinity and proton overallaffinity

    NASA Astrophysics Data System (ADS)

    Salehzadeh, Sadegh; Bayat, Mehdi

    2006-08-01

    A theoretical study on complete protonation of a series of tetrabasic molecules with general formula N[(CH 2) nNH 2][(CH 2) mNH 2][(CH 2) pNH 2] (tren, pee, ppe, tpt, epb and ppb) is reported. For first time, three kinds of gas-phase proton affinities for each polybasic molecule are defined as: 'proton microaffinity (PA n, i)', 'proton macroaffinity (PA)' and 'proton overall affinity ( PA)'. The variations of calculated logPA in the series of these molecules is very similar to that of their measured log Kn. There is also a good correlation between the calculated gas-phase proton macroaffinities and proton overallaffinities with corresponding equilibrium macroconstants and overall protonation constants in solution.

  16. Excitation and dissociation of molecules by femtosecond IR laser radiation in the gas phase and on dielectric surfaces

    SciTech Connect

    Kompanets, V O; Laptev, Vladimir B; Makarov, Aleksandr A; Pigulskii, S V; Ryabov, Evgenii A; Chekalin, Sergei V

    2013-04-30

    This paper presents an overview of early studies and new experimental data on the effect of near-IR (0.8-1.8 {mu}m) and mid-IR (3.3-5.8 {mu}m) intense femtosecond (130-350 fs) laser pulses on polyatomic molecules in the gas phase and on the surface of substrates. We examine the vibrational dynamics of nine molecules containing a C=O chromophore group, which are initiated by resonance femtosecond IR laser radiation at a wavelength of {approx}5 {mu}m, and report measured characteristic times of intramolecular vibrational redistribution. The characteristic time of molecules containing a single C=O group lies in the range 2.4-20 ps and that of the Fe(CO){sub 5} and Cr(CO){sub 6} molecules lies in the nanosecond range ({approx}1.0 and {approx}1.5 ns, respectively). Carbon structures have been observed for the first time to result from the decomposition of (CF{sub 3}){sub 2}CCO molecules on the surface of metal fluorides under the effect of femtosecond IR laser radiation in the wavelength range 3.3-5.4 {mu}m with no gas-phase decomposition of the molecules. (extreme light fields and their applications)

  17. Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

    PubMed

    Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

    2017-01-21

    Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

  18. Comparative investigation of pure and mixed rare gas atoms on coronene molecules

    NASA Astrophysics Data System (ADS)

    Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

    2017-01-01

    Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

  19. C-C stretching Raman spectra and stabilities of hydrocarbon molecules in natural gas hydrates: a quantum chemical study.

    PubMed

    Liu, Yuan; Ojamäe, Lars

    2014-12-11

    The presence of specific hydrocarbon gas molecules in various types of water cavities in natural gas hydrates (NGHs) are governed by the relative stabilities of these encapsulated guest molecule-water cavity combinations. Using molecular quantum chemical dispersion-corrected hybrid density functional computations, the interaction (ΔE(host--guest)) and cohesive energies (ΔE(coh)), enthalpies, and Gibbs free energies for the complexes of host water cages and hydrocarbon guest molecules are calculated at the ωB97X-D/6-311++G(2d,2p) level of theory. The zero-point energy effect of ΔE(host-guest) and ΔE(coh) is found to be quite substantial. The energetically optimal host-guest combinations for seven hydrocarbon gas molecules (CH4, C2H6, C3H6, C3H8, C4H8, i-C4H10, and n-C4H10) and various water cavities (D, ID, T, P, H, and I) in NGHs are found to be CH4@D, C2H6@T, C3H6@T, C3H8@T, C4H8@T/P/H, i-C4H10@H, and n-C4H10@H, as the largest cohesive energy magnitudes will be obtained with these host-guest combinations. The stabilities of various water cavities enclosing hydrocarbon molecules are evaluated from the computed cohesive Gibbs free energies: CH4 prefers to be trapped in a ID cage; C2H6 prefer T cages; C3H6 and C3H8 prefer T and H cages; C4H8 and i-C4H10 prefer H cages; and n-C4H10 prefer I cages. The vibrational frequencies and Raman intensities of the C-C stretching vibrational modes for these seven hydrocarbon molecules enclosed in each water cavity are computed. A blue shift results after the guest molecule is trapped from gas phase into various water cages due to the host-guest interactions between the water cage and hydrocarbon molecule. The frequency shifts to the red as the radius of water cages increases. The model calculations support the view that C-C stretching vibrations of hydrocarbon molecules in the water cavities can be used as a tool to identify the types of crystal phases and guest molecules in NGHs.

  20. Xyloketal-derived small molecules show protective effect by decreasing mutant Huntingtin protein aggregates in Caenorhabditis elegans model of Huntington's disease.

    PubMed

    Zeng, Yixuan; Guo, Wenyuan; Xu, Guangqing; Wang, Qinmei; Feng, Luyang; Long, Simei; Liang, Fengyin; Huang, Yi; Lu, Xilin; Li, Shichang; Zhou, Jiebin; Burgunder, Jean-Marc; Pang, Jiyan; Pei, Zhong

    2016-01-01

    Huntington's disease is an autosomal-dominant neurodegenerative disorder, with chorea as the most prominent manifestation. The disease is caused by abnormal expansion of CAG codon repeats in the IT15 gene, which leads to the expression of a glutamine-rich protein named mutant Huntingtin (Htt). Because of its devastating disease burden and lack of valid treatment, development of more effective therapeutics for Huntington's disease is urgently required. Xyloketal B, a natural product from mangrove fungus, has shown protective effects against toxicity in other neurodegenerative disease models such as Parkinson's and Alzheimer's diseases. To identify potential neuroprotective molecules for Huntington's disease, six derivatives of xyloketal B were screened in a Caenorhabditis elegans Huntington's disease model; all six compounds showed a protective effect. Molecular docking studies indicated that compound 1 could bind to residues GLN369 and GLN393 of the mutant Htt protein, forming a stable trimeric complex that can prevent the formation of mutant Htt aggregates. Taken together, we conclude that xyloketal derivatives could be novel drug candidates for treating Huntington's disease. Molecular target analysis is a good method to simulate the interaction between proteins and drug compounds. Further, protective candidate drugs could be designed in future using the guidance of molecular docking results.

  1. Collision lifetimes of polyatomic molecules at low temperatures: Benzene–benzene vs benzene–rare gas atom collisions

    SciTech Connect

    Cui, Jie; Krems, Roman V.; Li, Zhiying

    2014-10-28

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom–molecule interaction. We then compare the results of the atom–benzene calculations with those for benzene–benzene collisions. The comparison illustrates that the mean lifetimes of the benzene–benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene–benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  2. Collision lifetimes of polyatomic molecules at low temperatures: Benzene-benzene vs benzene-rare gas atom collisions

    NASA Astrophysics Data System (ADS)

    Cui, Jie; Li, Zhiying; Krems, Roman V.

    2014-10-01

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom-molecule interaction. We then compare the results of the atom-benzene calculations with those for benzene-benzene collisions. The comparison illustrates that the mean lifetimes of the benzene-benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene-benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  3. Collision lifetimes of polyatomic molecules at low temperatures: benzene-benzene vs benzene-rare gas atom collisions.

    PubMed

    Cui, Jie; Li, Zhiying; Krems, Roman V

    2014-10-28

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom-molecule interaction. We then compare the results of the atom-benzene calculations with those for benzene-benzene collisions. The comparison illustrates that the mean lifetimes of the benzene-benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene-benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  4. Tracking all-vapor instant gas-hydrate formation and guest molecule populations: A possible probe for molecules trapped in water nanodroplets

    NASA Astrophysics Data System (ADS)

    Uras-Aytemiz, Nevin; Cwiklik, Lukasz; Paul Devlin, J.

    2012-11-01

    Quantitative Fourier-transform infrared spectra for low-temperature (160-200 K) aerosols of clathrate-hydrate nanoparticles that contain large-cage catalysts and small-cage nonpolar guests have been extended to a broad range of vapor compositions and sampling conditions. The data better reveal the stages by which room-temperature vapor mixtures, when cooled below ˜220 K, instantly generate aerosols with particles composed exclusively of the corresponding clathrate hydrates. In particular the quantitative data help relate the nature of the hydrates that form to the composition of the aqueous nanodroplets of the first stages of the rapid transition from the all-vapor mixture. The overall transition from an all-vapor mixture to "gas"-hydrate nanocrystals is a multistage one that has been characterized as homogeneous nucleation and growth of solution nanodroplets (˜240 K) followed by nucleation and growth of the gas-hydrate particles (˜220 K); all occurring within a subsecond that follows pulsing of the warm vapor into a sampling cold chamber. This may serve well as a general description of the instantaneous generation of the gas-hydrate aerosols, but closer consideration of the nature of the sampling method, in context with recent computation-based insights to (a) gas-hydrate nucleation stages/rates and (b) the lifetimes of trapped small nonpolar molecules in cold aqueous nanodroplets, suggests a more complex multistage transition. The simulated lifetimes and extensive new quantitative infrared data significantly broaden the knowledge base in which the instantaneous transition from vapor to crystalline hydrate particles is viewed. The apparent need for a high occupancy of large-cage catalytic guest molecules currently limits the practical value of the all-vapor method. Only through greater clarity in the molecular-level description of the transition will the ultimate limits be defined.

  5. Absolute configuration assignment of a chiral molecule in the gas phase using foil-induced Coulomb explosion imaging

    NASA Astrophysics Data System (ADS)

    Herwig, Philipp; Zawatzky, Kerstin; Schwalm, Dirk; Grieser, Manfred; Heber, Oded; Jordon-Thaden, Brandon; Krantz, Claude; Novotný, Oldřich; Repnow, Roland; Schurig, Volker; Vager, Zeev; Wolf, Andreas; Trapp, Oliver; Kreckel, Holger

    2014-11-01

    Chiral molecules exist in two configurations that are nonsuperposable mirror images of one another. The underlying molecular structure is referred to as the absolute configuration. In chiral environments, the handedness of molecules influences their chemical characteristics dramatically, and therefore the determination of absolute configurations is of fundamental interest in organic chemistry and biology. Commonly applied techniques to assign absolute configuration are anomalous single-crystal x-ray diffraction and vibrational circular dichroism. However, these techniques become increasingly more challenging when applied to molecules that are made out of light atoms exclusively. Furthermore, there is no established method to determine the absolute handedness of gas-phase molecules that are not optically active. In this work, we apply the foil-induced Coulomb explosion imaging technique to determine directly the absolute configuration of the chiral molecule trans-2,3-dideuterooxirane (C2OD2H2) in the gas phase. The experiment leads to the definitive assignment of the (R ,R ) configuration to an enantio-selected dideuterooxirane sample with a statistical confidence of 5 σ . As the handedness of trans-2,3-dideuterooxirane is unambiguously linked by chemical synthesis to the stereochemical key reference glyceraldehyde, our results provide an independent verification of the absolute configuration of the stereochemical reference standard.

  6. Photodissociation of HBr molecules in clusters: from rare gas clusters to water nanoparticles

    NASA Astrophysics Data System (ADS)

    Fárník, M.; Buck, Udo

    2007-09-01

    Experiments on the photodissociation of molecules in different cluster environments are described and illustrated based on the example of HBr molecules photolysed at 193 nm in various clusters. The photolysis of HBr molecules incorporated in the hydrogen bonded network of (HBr)n clusters exhibits pronounced direct exits of the H-fragments. On the other hand, the H-fragments from HBr molecules bound by much weaker van der Waals forces at the surface of large Arn clusters are trapped efficiently by the cluster cage. These observations are mainly explained by the geometry of the molecule bound to the cluster. The HBr molecules deposited on the large (H2O)n clusters behave quite differently. They undergo acid dissociation and the resulting zwitterionic form is excited by the radiation giving rise to the generation of the hydronium H3O molecule and its subsequent dissociation.

  7. Molecular orbital studies of gas-phase interactions between complex molecules.

    PubMed

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

  8. Ab initio potential energy surface for the carbon dioxide molecule pair and thermophysical properties of dilute carbon dioxide gas

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert

    2014-10-01

    A four-dimensional intermolecular potential energy surface (PES) for two rigid carbon dioxide molecules was determined from quantum-chemical ab initio calculations. Interaction energies for 1229 CO2-CO2 configurations were computed at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. An analytical site-site potential function with seven sites per CO2 molecule was fitted to the interaction energies. The PES was validated by calculating the second virial coefficient as well as viscosity and thermal conductivity in the dilute-gas limit.

  9. Thermodynamic properties of water in the lattice gas model with consideration of the vibrational motions of molecules

    NASA Astrophysics Data System (ADS)

    Titov, S. V.; Tovbin, Yu. K.

    2016-11-01

    A molecular model developed earlier for a polar fluid within the lattice gas model is supplemented by considering the vibrational motions of molecules using water as an example. A combination of point dipole and Lennard-Jones potentials from SPC parametrization is chosen as the force field model for the molecule. The main thermodynamic properties of liquid water (density, internal energy, and entropy) are studied as functions of temperature. There is qualitative agreement between the calculation results and the experimental data. Ways of refining the molecular theory are discussed.

  10. Calculation of Ground State Rotational Populations for Kinetic Gas Homonuclear Diatomic Molecules including Electron-Impact Excitation and Wall Collisions

    SciTech Connect

    David R. Farley

    2010-08-19

    A model has been developed to calculate the ground-state rotational populations of homonuclear diatomic molecules in kinetic gases, including the effects of electron-impact excitation, wall collisions, and gas feed rate. The equations are exact within the accuracy of the cross sections used and of the assumed equilibrating effect of wall collisions. It is found that the inflow of feed gas and equilibrating wall collisions can significantly affect the rotational distribution in competition with non-equilibrating electron-impact effects. The resulting steady-state rotational distributions are generally Boltzmann for N≥3, with a rotational temperature between the wall and feed gas temperatures. The N=0,1,2 rotational level populations depend sensitively on the relative rates of electron-impact excitation versus wall collision and gas feed rates.

  11. A Comparative High-Resolution Electron Microscope Study of Ag Clusters Produced by a Sputter-Gas Aggregation and Ion Cluster Beam Technique

    NASA Astrophysics Data System (ADS)

    Hohl, Georg-Friedrich; Hihara, Takehiko; Sakurai, Masaki; Oishi, Takashi; Wakoh, Kimio; Sumiyama, Kenji; Suzuki, Kenji

    1994-03-01

    Ag clusters were formed by a sputter-gas-aggregation process [H. Haberland et al..: J. Vac. Sci. Technol. A 10 (1992) 3266] and the ionized cluster beam (ICB) [T. Takagi: Ionized-Cluster Beam Deposition and Epitaxy (Noyes, Park Ridge, 1988)] technique. The Ag clusters deposited on collodion-coated microgrids were investigated by high-resolution transmission electron microscopy. The diameter of those clusters, d, ranges from 1 nm up to about 10 nm for specimens produced by the sputter-gas aggregation technique, depending on the sputter condition and the deposition time. Comparable times of the ICB deposition lead to a broader distribution up to d≈20 nm, suggesting the formation of islands with extremely flat shapes. High percentages of crystalline particles obtained by both techniques are either single crystals or multiple twins with clear lattice images.

  12. Spectral Luminescent Properties of the Glycine Molecule in a Gas Discharge

    NASA Astrophysics Data System (ADS)

    General, A. A.; Migovich, M. I.; Kelman, V. A.; Zhmenyak, Yu. V.; Zvenigorodsky, V. V.

    2016-01-01

    We have experimentally studied the luminescence spectra of glycine powder in the plasma of a repetitively pulsed longitudinal discharge in argon-glycine and helium-glycine mixtures. We have identified the main fragments of the glycine molecule emitting in the 200-1000 nm region. The emitting molecules due to fragmentation of glycine and dissociation of the carboxyl (-COOH) and amino (-NH2) groups are nitrogen, carbon monoxide, and cyanogen molecules.

  13. Cooperative Reformable Channel System with Unique Recognition of Small Gas Molecules in a two-dimensional ZIF-membrane

    NASA Astrophysics Data System (ADS)

    Motevalli, Benyamin; Taherifar, Neda; Liu, Zhe

    We report a cooperative reformable channel system in a coordination porous polymer, named as ZIF-L. Three types of local flexible ligands coexist in the crystal structure of this polymer, resulting in ultra-flexibility. The reformable channel is able to regulate permeation of a nonspherical guest molecule, such as N2 or CO2, based on its longer molecular dimension, which is in a striking contrast to conventional molecular sieves that regulate the shorter cross-sectional dimension of the guest molecules. Our density functional theory (DFT) calculations reveal that the guest molecule induces dynamic motion of the flexible ligands, leading to the channel reformation, and then the guest molecule reorientates itself to fit in the reformed channel. Such a unique ``induced fit-in'' mechanism causes the gas molecule to pass through 6 membered-ring windows in the c- crystal direction of ZIF-L with its longer axis parallel to the window plane. Our experimental permeance of N2 through the ZIF-L membranes is about three times greater than that of CO2, supporting the DFT simulation predictions.

  14. Co(II)-doped MOF-5 nano/microcrystals: Solvatochromic behaviour, sensing solvent molecules and gas sorption property

    SciTech Connect

    Yang, Ji-Min; Liu, Qing; Sun, Wei-Yin

    2014-10-15

    Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were successfully obtained by solvothermal method. The products were characterized by powder X-ray diffraction (PXRD), energy dispersive spectrometry (EDS), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA), inductively coupled plasma optical emission spectrometer (ICP-OES), elemental analysis, UV–vis and infrared (IR) spectroscopy. The factors influencing the crystal morphology and size were investigated. The gas sorption measurements reveal that highly crystalline particles have large Langmuir surface area. It was found that the Co(II)-doped MOF-5 shows enhanced hydrostability and the sorption profiles of the Co(II)-doped MOF-5 nano/microcrystals are dependent on the morphology and size of the particles. Porous Co(II)-doped MOF-5 is stable upon the removal of guest molecules and exhibits different colour with accommodating different solvent molecule, which means that it can act as solvatochromic sensing materials for recognition of solvent molecules. - Graphical abstract: Co(II)-doped MOF-5 nano/microcrystals with different shapes and sizes were synthesized by a facile hydrothermal method, which not only enhance gas sorption properties and structural stability of MOFs towards moisture, but also act as new sensing materials for sensing small molecules. - Highlights: • Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were obtained. • Co(II)-doped MOF-5 nano/microcrystals enhance the structural stability towards moisture. • Co(II)-doped MOF-5 can act as new sensing material for sensing small molecules.

  15. A quantum gas of polar KRb molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Covey, Jacob; Miecnikowski, Matthew; Moses, Steven; Fu, Zhengkun; Jin, Deborah; Ye, Jun

    2016-05-01

    Ultracold polar molecules provide new opportunities for investigation of strongly correlated many-body spin systems such as many-body localization and quantum magnetism. In an effort to access such phenomena, we load polar KRb molecules into a three-dimensional optical lattice. In this system, we observed many-body spin dynamics between molecules pinned in a deep lattice, even though the filling fraction of the molecules was only 5%. We have recently performed a thorough investigation of the molecule creation process in an optical lattice, and consequently improved our filling fraction to 30% by preparing and overlapping Mott and band insulators of the initial atomic gases. More recently, we switched to a second generation KRb apparatus that will allow application of large, stable electric fields as well as high-resolution addressing and detection of polar molecules in optical lattices. We plan to use these capabilities to study non-equilibrium spin dynamics in an optical lattice with nearly single site resolution. I will present the status and direction of the second generation apparatus.

  16. Investigating the nature of noble gas-copper bonds by the quantum theory of atoms in molecules.

    PubMed

    Rodrigues, Eduardo F F; de Sá, Eduardo L; Haiduke, Roberto L A

    2010-04-22

    We investigated noble gas-copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy of noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.

  17. Characterization of a DAPI-RIT-DAPI system for gas-phase ion/molecule and ion/ion reactions.

    PubMed

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10(-1) Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  18. Characterization of a DAPI-RIT-DAPI System for Gas-Phase Ion/Molecule and Ion/Ion Reactions

    NASA Astrophysics Data System (ADS)

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10-1 Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  19. An investigation of the interaction of intense laser radiation with molecules of sulfur hexafluoride through the buffer gas technique

    NASA Astrophysics Data System (ADS)

    Eletskii, A. V.; Klimov, V. D.; Udalova, T. A.

    1981-02-01

    Measurements of the coefficient of the absorption of intense (approximately 10 to the 7th W/sq cm) radiation from a CO2 laser by SF6 molecules in the presence of noble gases and at pressures up to 40 bars are presented. The dependence of the coefficient of absorption on the pressure and type of buffer gas, as well as on the wavelength and intensity of the incident radiation, makes it possible to follow the formation of the vibrational state distribution function of the molecules. The character of the distribution function depends on the competition between vibrational relaxation processes and laser radiation absorption. At high pressures, that is, at helium pressures greater than approximately 20-40 bars, a two-level scheme for the interaction of intense laser radiation with SF6 is implemented experimentally for the first time. Here, molecules excited by light to the v = 1 state relax instantaneously upon collision. The dependence of the rate constant for the destruction of SF6 molecular states on the number of the vibrational level v upon collision with helium atoms can be evaluated from the experimental data. Taken as a whole, the data confirm the assumption of the linear, single-photon nature of the interaction of laser radiation with SF6 molecules.

  20. The role of multiparticle correlations and Cooper pairing in the formation of molecules in an ultracold gas of Fermi atoms with a negative scattering length

    SciTech Connect

    Babichenko, V. S. Kagan, Yu.

    2012-11-15

    The influence of multiparticle correlation effects and Cooper pairing in an ultracold Fermi gas with a negative scattering length on the formation rate of molecules is investigated. Cooper pairing is shown to cause the formation rate of molecules to increase, as distinct from the influence of Bose-Einstein condensation in a Bose gas on this rate. This trend is retained in the entire range of temperatures below the critical one.

  1. Oxygen K-edge absorption spectra of small molecules in the gas phase

    SciTech Connect

    Yang, B.X.; Kirz, J.; Sham, T.K.

    1986-01-01

    The absorption spectra of O/sub 2/, CO, CO/sub 2/ and OCS have been recorded in a transmission mode in the energy region from 500 to 950 eV. Recent observation of EXAFS in these molecules is confirmed in this study. 7 refs., 3 figs.

  2. Creation of a strongly dipolar gas of ultracold ground-state 23 Na87 Rb molecules

    NASA Astrophysics Data System (ADS)

    Guo, Mingyang; Zhu, Bing; Lu, Bo; Ye, Xin; Wang, Fudong; Wang, Dajun; Vexiau, Romain; Bouloufa-Maafa, Nadia; Quéméner, Goulven; Dulieu, Olivier

    2016-05-01

    We report on successful creation of an ultracold sample of ground-state 23 Na87 Rb molecules with a large effective electric dipole moment. Through a carefully designed two-photon Raman process, we have successfully transferred the magneto-associated Feshbach molecules to the singlet ground state with high efficiency, obtaining up to 8000 23 Na87 Rb molecules with peak number density over 1011 cm-3 in their absolute ground-state level. With an external electric field, we have induced an effective dipole moment over 1 Debye, making 23 Na87 Rb the most dipolar ultracold particle ever achieved. Contrary to the expectation, we observed a rather fast population loss even for 23 Na87 Rb in the absolute ground state with the bi-molecular exchange reaction energetically forbidden. The origin for the short lifetime and possible ways of mitigating it are currently under investigation. Our achievements pave the way toward investigation of ultracold bosonic molecules with strong dipolar interactions. This work is supported by the Hong Kong RGC CUHK404712 and the ANR/RGC Joint Research Scheme ACUHK403/13.

  3. Drag force and transport property of a small cylinder in free molecule flow: A gas-kinetic theory analysis

    NASA Astrophysics Data System (ADS)

    Liu, Changran; Li, Zhigang; Wang, Hai

    2016-08-01

    Analytical expressions are derived for aerodynamic drag force on small cylinders in the free molecule flow using the gas-kinetic theory. The derivation considers the effect of intermolecular interactions between the cylinder and gas media. Two limiting collision models, specular and diffuse scattering, are investigated in two limiting cylinder orientations with respect to the drift velocity. The earlier solution of Dahneke [B. E. Dahneke, J. Aerosol Sci. 4, 147 (1973), 10.1016/0021-8502(73)90066-9] is shown to be a special case of the current expressions in the rigid-body limit of collision. Drag force expressions are obtained for cylinders that undergo Brownian rotation and for those that align with the drift velocity. The validity of the theoretical expressions is tested against experimental mobility data available for carbon nanotubes.

  4. Multispectral actinometry of water and water-derivative molecules in moist, inert gas discharge plasmas

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Ochkin, V. N.; Kochetov, I. V.

    2016-10-01

    A new version of optical actinometry (OA) is used to determine the concentrations of water molecules and their fragments in hollow cathode discharge plasma in moist inert gases. Use is made of two actinometer particles, namely, the atoms Xe and Ar, for concurrent measurements of the concentrations of the H2O molecule and its fragments O, H, and OH. A self-consistent method is suggested for the determination of particle concentrations with due regard for the quenching of the emitting states. The temporal behavior of particles during discharge glow is studied. Noted are fast variations (lasting from a few to a few tens of s) in the concentrations of all the particles, followed by their stabilization (within a few to a few tens of mins). The scheme of the processes responsible for the observed dynamics of the plasma composition is discussed.

  5. Radiation and Laser Potential of Homo and Heteronuclear Rare-Gas Diatomic Molecules.

    DTIC Science & Technology

    1982-12-01

    SUPPLEMENTARY NOTES " .. . . , 19 KEy WOODS (Continue on reverse side if necessary and identify by block number) Ll Vacuum Ultraviolet Spectroscopy Rare-Gas...absorption we used the same "C. H. Chen, P. E. Siska, and Y. T. Lee, J. Chem. Phys. terminology. See G. Herzberg, Spectrs of Diatomi Mole- 5, 601

  6. Strongly aligned gas-phase molecules at free-electron lasers

    DOE PAGES

    Kierspel, Thomas; Wiese, Joss; Mullins, Terry; ...

    2015-09-16

    Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment ofmore » $$\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.« less

  7. Strongly aligned gas-phase molecules at free-electron lasers

    SciTech Connect

    Kierspel, Thomas; Wiese, Joss; Mullins, Terry; Robinson, Joseph; Aquila, Andy; Barty, Anton; Bean, Richard; Boll, Rebecca; Boutet, Sebastien; Bucksbaum, Philip; Chapman, Henry N.; Christensen, Lauge; Fry, Alan; Hunter, Mark; Koglin, Jason E.; Liang, Mengning; Mariani, Valerio; Morgan, Andrew; Natan, Adi; Petrovic, Vladimir; Rolles, Daniel; Rudenko, Artem; Schnorr, Kirsten; Stapelfeldt, Henrik; Stern, Stephan; Thogersen, Jan; Yoon, Chun Hong; Wang, Fenglin; Trippel, Sebastian; Kupper, Jochen

    2015-09-16

    Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment of $\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.

  8. Beams of fast neutral atoms and molecules in low-pressure gas-discharge plasma

    SciTech Connect

    Metel, A. S.

    2012-03-15

    Fast neutral atom and molecule beams have been studied, the beams being produced in a vacuum chamber at nitrogen, argon, or helium pressure of 0.1-10 Pa due to charge-exchange collisions of ions accelerated in the sheath between the glow discharge plasma and a negative grid immersed therein. From a flat grid, two broad beams of molecules with continuous distribution of their energy from zero up to e(U + U{sub c}) (where U is voltage between the grid and the vacuum chamber and U{sub c} is cathode fall of the discharge) are propagating in opposite directions. The beam propagating from the concave surface of a 0.2-m-diameter grid is focused within a 10-mm-diameter spot on the target surface. When a 0.2-m-diameter 0.2-m-high cylindrical grid covered by end disks and composed of parallel 1.5-mm-diameter knitting needles spaced by 4.5 mm is immersed in the plasma, the accelerated ions pass through the gaps between the needles, turn inside the grid into fast atoms or molecules, and escape from the grid through the gaps on its opposite side. The Doppler shift of spectral lines allows for measuring the fast atom energy, which corresponds to the potential difference between the plasma inside the chamber and the plasma produced as a result of charge-exchange collisions inside the cylindrical grid.

  9. Dipolar Effects in an Ultracold Gas of LiCs Molecules

    NASA Astrophysics Data System (ADS)

    Weidemueller, Matthias

    2011-05-01

    Recently, there has been important progress in the investigation of ultracold polar molecules in the absolute ground state, thus opening intriguing perspectives for strongly correlated quantum systems under the influence of long-range dipolar forces. We have studied the formation of LiCs molecules via photoassociation (PA) in a double-species magneto-optical trap. The LiCs dimer is a particularly promising candidate for observing dipolar effects, as it possesses the largest dipole moment of all alkali dimers (5.5 Debye in the ground state). Ultracold LiCs molecules in the absolute rovibrational ground state are formed by a single photo-association step. The dipole moment of ground state levels is determined by Stark spectroscopy and was found to be in excellent agreement with the theoretical predictions. Vibrational redistribution due to spontaneous emission and blackbody radiation is observed and compared a rate-equation model.In collaboration with Johannes Deiglmayr, Marc Repp, University of Heidelberg; Roland Wester, University of Innsbruck; and Olivier Dulieu, Laboratoire Aime Cotton. Work was supported by DFG and ESF in the framework of the Eurocores EuroQUAM as well as the Heidelberg Center for Quantum Dynamics.

  10. Quantum Engineering of a Low-Entropy Gas of Heteronuclear Bosonic Molecules in an Optical Lattice

    NASA Astrophysics Data System (ADS)

    Reichsöllner, Lukas; Schindewolf, Andreas; Takekoshi, Tetsu; Grimm, Rudolf; Nägerl, Hanns-Christoph

    2017-02-01

    We demonstrate a generally applicable technique for mixing two-species quantum degenerate bosonic samples in the presence of an optical lattice, and we employ it to produce low-entropy samples of ultracold Rb 87 Cs 133 Feshbach molecules with a lattice filling fraction exceeding 30%. Starting from two spatially separated Bose-Einstein condensates of Rb and Cs atoms, Rb-Cs atom pairs are efficiently produced by using the superfluid-to-Mott insulator quantum phase transition twice, first for the Cs sample, then for the Rb sample, after nulling the Rb-Cs interaction at a Feshbach resonance's zero crossing. We form molecules out of atom pairs and characterize the mixing process in terms of sample overlap and mixing speed. The dense and ultracold sample of more than 5000 RbCs molecules is an ideal starting point for experiments in the context of quantum many-body physics with long-range dipolar interactions.

  11. Photophysics of sunscreen molecules in the gas phase: a stepwise approach towards understanding and developing next-generation sunscreens

    PubMed Central

    Rodrigues, Natércia D. N.; Staniforth, Michael

    2016-01-01

    The relationship between exposure to ultraviolet (UV) radiation and skin cancer urges the need for extra photoprotection, which is presently provided by widespread commercially available sunscreen lotions. Apart from having a large absorption cross section in the UVA and UVB regions of the electromagnetic spectrum, the chemical absorbers in these photoprotective products should also be able to dissipate the excess energy in a safe way, i.e. without releasing photoproducts or inducing any further, harmful, photochemistry. While sunscreens are tested for both their photoprotective capability and dermatological compatibility, phenomena occurring at the molecular level upon absorption of UV radiation are largely overlooked. To date, there is only a limited amount of information regarding the photochemistry and photophysics of these sunscreen molecules. However, a thorough understanding of the intrinsic mechanisms by which popular sunscreen molecular constituents dissipate excess energy has the potential to aid in the design of more efficient, safer sunscreens. In this review, we explore the potential of using gas-phase frequency- and time-resolved spectroscopies in an effort to better understand the photoinduced excited-state dynamics, or photodynamics, of sunscreen molecules. Complementary computational studies are also briefly discussed. Finally, the future outlook of expanding these gas-phase studies into the solution phase is considered. PMID:27956888

  12. Photophysics of sunscreen molecules in the gas phase: a stepwise approach towards understanding and developing next-generation sunscreens

    NASA Astrophysics Data System (ADS)

    Rodrigues, Natércia D. N.; Staniforth, Michael; Stavros, Vasilios G.

    2016-11-01

    The relationship between exposure to ultraviolet (UV) radiation and skin cancer urges the need for extra photoprotection, which is presently provided by widespread commercially available sunscreen lotions. Apart from having a large absorption cross section in the UVA and UVB regions of the electromagnetic spectrum, the chemical absorbers in these photoprotective products should also be able to dissipate the excess energy in a safe way, i.e. without releasing photoproducts or inducing any further, harmful, photochemistry. While sunscreens are tested for both their photoprotective capability and dermatological compatibility, phenomena occurring at the molecular level upon absorption of UV radiation are largely overlooked. To date, there is only a limited amount of information regarding the photochemistry and photophysics of these sunscreen molecules. However, a thorough understanding of the intrinsic mechanisms by which popular sunscreen molecular constituents dissipate excess energy has the potential to aid in the design of more efficient, safer sunscreens. In this review, we explore the potential of using gas-phase frequency- and time-resolved spectroscopies in an effort to better understand the photoinduced excited-state dynamics, or photodynamics, of sunscreen molecules. Complementary computational studies are also briefly discussed. Finally, the future outlook of expanding these gas-phase studies into the solution phase is considered.

  13. THE SINTERING REGION OF ICY DUST AGGREGATES IN A PROTOPLANETARY NEBULA

    SciTech Connect

    Sirono, Sin-iti

    2011-07-10

    Icy grain aggregates are formed in the outer region of a protoplanetary nebula. The infall of these aggregates to the central star is due to gas drag, and their temperature increases as the infall proceeds. The icy molecules on the grain move to the neck where the grains get connected through sublimation and condensation of the molecules. This process is called sintering. As the sintering proceeds, the mechanical strength of the neck changes considerably, strongly affecting the collisional evolution of the aggregates. The timescale required for sintering is determined in this study, based on which the region where the sintering proceeds within a prescribed timescale is obtained. It is found that the region covers a substantial fraction of the protoplanetary nebula, and the location of the region depends on the temperature distribution inside the nebula. If the aggregate is stirred up and the temperature of the aggregate increases temporally, the sintering region spreads to the whole nebula.

  14. Neutralization of solvated protons and formation of noble-gas hydride molecules: Matrix-isolation indications of tunneling mechanisms?

    SciTech Connect

    Khriachtchev, Leonid; Lignell, Antti; Raesaenen, Markku

    2005-08-08

    The (NgHNg){sup +} cations (Ng=Ar and Kr) produced via the photolysis of HF/Ar, HF/Kr, and HBr/Kr solid mixtures are studied, with emphasis on their decay mechanisms. The present experiments provide a large variety of parameters connected to this decay phenomenon, which allows us to reconsider various models for the decay of the (NgHNg){sup +} cations in noble-gas matrices. As a result, we propose that this phenomenon could be explained by the neutralization of the solvated protons by electrons. The mechanism of this neutralization reaction probably involves tunneling of an electron from an electronegative fragment or another trap to the (NgHNg){sup +} cation. The proposed electron-tunneling mechanism should be considered as a possible alternative to the literature models based on tunneling-assisted or radiation-induced diffusion of protons in noble-gas solids. As a novel experimental observation of this work, the efficient formation of HArF molecules occurs at 8 K in a photolyzed HF/Ar matrix. It is probable that the low-temperature formation of HArF involves local tunneling of the H atom to the Ar-F center, which in turn supports the locality of HF photolysis in solid Ar. In this model, the decay of (ArHAr){sup +} ions and the formation of HArF molecules observed at low temperatures are generally unconnected processes; however, the decaying (ArHAr){sup +} ions may contribute to some extent to the formation of HArF molecules.

  15. Gas phase chemical kinetics at high temperature of carbonaceous molecules: application to circumstellar envelopes

    NASA Astrophysics Data System (ADS)

    Biennier, L.; Gardez, A.; Saidani, G.; Georges, R.; Rowe, B.; Reddy, K. P. J.

    2011-05-01

    Circumstellar shells of evolved stars are a theater of extremely rich physical and chemical processes. More than seventy molecules of varied nature have been identified in the envelopes through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals and a significant number are unique to the circumstellar medium. However, observational data remain scarce and more than half of the detected species have been observed in only one object, the nearby carbon star IRC + 10216. Chemical kinetic models are needed to describe the formation of molecules in evolved circumstellar outflows. Upcoming terrestrial telescopes such as ALMA will increase the spatial resolution by several orders of magnitude and provide a wealth of data. The determination of relevant laboratory kinetics data is critical to keep up with the development of the observations and of the refinement of chemical models. Today, the majority of reactions studied in the laboratory are the ones involved in combustion and concerning light hydrocarbons. Our objective is to provide the scientific community with rate coefficients of reactions between abundant species in these warm environments. Cyanopolyynes from HC_2N to HC_9N have all been detected in carbon rich circumstellar envelopes in up to 10 sources for HC_3N. Neutral-neutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures. Our approach aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high enthalpy source (Moudens et al. 2011) with a flow tube and a pulsed laser photolysis and laser induced fluorescence system to probe the undergoing chemical reactions. The high enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane, propene

  16. Experimental and Numerical Investigation of Guest Molecule Exchange Kinetics based on the 2012 Ignik Sikumi Gas Hydrate Field Trial

    NASA Astrophysics Data System (ADS)

    Ruprecht Yonkofski, C. M.; Horner, J.; White, M. D.

    2015-12-01

    In 2012 the U.S. DOE/NETL, ConocoPhillips Company, and Japan Oil, Gas and Metals National Corporation jointly sponsored the first field trial of injecting a mixture of N2-CO2 into a CH4-hydrate bearing formation beneath the permafrost on the Alaska North Slope. Known as the Ignik Sikumi #1 Gas Hydrate Field Trial, this experiment involved three stages: 1) the injection of a N2-CO2 mixture into a targeted hydrate-bearing layer, 2) a 4-day pressurized soaking period, and 3) a sustained depressurization and fluid production period. Data collected during the three stages of the field trial were made available after a thorough quality check. The Ignik Sikumi #1 data set is extensive, but contains no direct evidence of the guest-molecule exchange process. This study uses numerical simulation to provide an interpretation of the CH4/CO2/N2 guest molecule exchange process that occurred at Ignik Sikumi #1. Simulations were further informed by experimental observations. The goal of the scoping experiments was to understand kinetic exchange rates and develop parameters for use in Iġnik Sikumi history match simulations. The experimental procedure involves two main stages: 1) the formation of CH4 hydrate in a consolidated sand column at 750 psi and 2°C and 2) flow-through of a 77.5/22.5 N2/CO2 molar ratio gas mixture across the column. Experiments were run both above and below the hydrate stability zone in order to observe exchange behavior across varying conditions. The numerical simulator, STOMP-HYDT-KE, was then used to match experimental results, specifically fitting kinetic behavior. Once this behavior is understood, it can be applied to field scale models based on Ignik Sikumi #1.

  17. Gas Separation Membranes Derived from High-Performance Immiscible Polymer Blends Compatibilized with Small Molecules.

    PubMed

    Panapitiya, Nimanka P; Wijenayake, Sumudu N; Nguyen, Do D; Huang, Yu; Musselman, Inga H; Balkus, Kenneth J; Ferraris, John P

    2015-08-26

    An immiscible polymer blend comprised of high-performance copolyimide 6FDA-DAM:DABA(3:2) (6FDD) and polybenzimidazole (PBI) was compatibilized using 2-methylimidazole (2-MI), a commercially available small molecule. Membranes were fabricated from blends of 6FDD:PBI (50:50) with and without 2-MI for H2/CO2 separations. The membranes demonstrated a matrix-droplet type microstructure as evident with scanning electron microscopy (SEM) imaging where 6FDD is the dispersed phase and PBI is the continuous phase. In addition, membranes with 2-MI demonstrated a uniform microstructure as observed by smaller and more uniformly dispersed 6FDD domains in contrast to 6FDD:PBI (50:50) blend membranes without 2-MI. This compatibilization effect of 2-MI was attributed to interfacial localization of 2-MI that lowers the interfacial energy similar to a surfactant. Upon the incorporation of 2-MI, the H2/CO2 selectivity improved remarkably, compared to the pure blend, and surpassed the Robeson's upper bound. To our knowledge, this is the first report of the use of a small molecule to compatibilize a high-performance immiscible polymer blend. This approach could afford a novel class of membranes in which immiscible polymer blends can be compatibilized in an economical and convenient fashion.

  18. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  19. In-situ Evaluation of Soil Organic Molecules: Functional Group Chemistry Aggregate Structures, Metal & Surface Complexation Using Soft X-Ray

    SciTech Connect

    Myneni, Satish, C

    2008-11-30

    Organic molecules are common in all Earth surface environments, and their composition and chemistry play an important role in a variety of biogeochemical reactions, such as mineral weathering, nutrient cycling and the solubility and transport of contaminants. However, most of what we know about the chemistry of these molecules comes from spectroscopy and microscopy studies of organic molecules extracted from different natural systems using either inorganic or organic solvents. Although all these methods gave us clues about the composition of these molecules, their composition and structure change with the extraction and the type of ex-situ analysis, their true behavior is less well understood. The goal of this project is to develop synchrotron instrumentation for studying natural organics, and to apply these recently developed synchrotron X-ray spectroscopy and microscopy techniques for understanding the: (1) functional group composition of naturally occurring organic molecules; (2) macromolecular structures of organic molecules; and (3) the nature of interactions of organic molecules with mineral surfaces in different environmental conditions.

  20. An index of the literature for bimolecular gas phase cation-molecule reaction kinetics

    NASA Technical Reports Server (NTRS)

    Anicich, V. G.

    2003-01-01

    This is an index to the literature for gas phase bimolecular positive ionmolecule reactions. Over 2300 references are cited. Reaction rate coefficients and product distributions of the reactions are abstracted out of the original citations where available. This index is intended to cover the literature from 1936 to 2003. This is a continuation of several surveys: the original (Huntress Astrophys. J. Suppl. Ser., 33, 495 (1977)), an expansion (Anicich and Huntress, Astrophys. J. Suppl. Ser. 62, 553 (1986)), a supplement (Anicich, Astrophys. J. Suppl. Ser. 84, 215 (1993)), and an evaluation (Anicich, V. G. J. Phys. Chem. Ref. Data 22,1469 (1993b). The Table of reactions is listed by reactant ion.

  1. Interactions of molecules with HCl in the gas and matrix phases

    NASA Astrophysics Data System (ADS)

    George, W. O.; Lewis, Rh.; Hussain, G.; Rees, G. J.

    1988-10-01

    The FT-IR spectra of mixtures of HCl and the following compounds have been recorded in the gaseous and matrix isolated phases: argon, ethene, ethyne, d 6-benzene, fluorobenzene, CO, CO 2, SO 2, CCl 4, CHCl 3, d 6-acetone, ethanal, HCN, acrylonitrile. The features which are measured are: firstly the changes in the integrated intensity of lines in the rotation—vibration spectrum of the fundamental HCl band as a function of non-specific interactions with other components of the mixture and secondly bands associated with specific interactions forming hydrogen bonded complexes in the gas and matrix isolated phases. The relationship between the two kinds of interactions is discussed.

  2. Dispersion and functionalization of nanoparticles synthesized by gas aggregation source: Opening new routes towards the fabrication of nanoparticles for bio-medicine

    PubMed Central

    Oprea, B.; Martínez, L.; Román, E.; Vanea, E.; Simon, S.; Huttel, Y.

    2015-01-01

    The need to find new nanoparticles for biomedical applications is pushing the limits of the fabrication methods. New techniques with versatilities beyond the extended chemical routes can provide new insight in the field. In particular gas aggregation sources offer the possibility to fabricate nanoparticles with controlled size, composition and structure out of thermodynamics. In this context, the milestone is the optimization of the dispersion and functionalization processes of nanoparticles once fabricated by these routes as they are generated in the gas phase and deposited on substrates in vacuum or ultra-high vacuum conditions. In the present work we propose a fabrication route in ultra-high vacuum that is compatible with the subsequent dispersion and functionalization of nanoparticles in aqueous media and, that is more remarkable, in one single step. In particular, we will present the fabrication of nanoparticles with a sputter gas aggregation source, using a Fe50B50 target, and their further dispersion and functionalization with polyethileneglycol (PEG). A characterization of these nanoparticles is carried out before and after PEG functionalization. During functionalization, significant boron dissolution occurs, which facilitates nanoparticle dispersion in the aqueous solution. The use of different complementary techniques allows us to prove the PEG attachment onto the surface of the nanoparticles creating a shell to make them biocompatible. The result is the formation of nanoparticles with a structure mainly composed by a metallic Fe core and an iron oxide shell, surrounded by a second PEG shell dispersed in aqueous solution. Relaxivitiy measurements of these PEG functionalized nanoparticles assessed their effectiveness as contrast agents for Magnetic Resonance Imaging (MRI) analysis. Therefore, this new fabrication route is a reliable alternative for the synthesis of nanoparticles for biomedicine. PMID:26640032

  3. Gas-phase Reactions of Polycyclic Aromatic Hydrocarbon Anions with Molecules of Interstellar Relevance

    NASA Astrophysics Data System (ADS)

    Demarais, Nicholas J.; Yang, Zhibo; Martinez, Oscar; Wehres, Nadine; Snow, Theodore P.; Bierbaum, Veronica M.

    2012-02-01

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C6H- 5), naphthalenide (C10H- 7), and anthracenide (C14H- 9) with atomic H, H2, and D2 using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O2, CO2, N2O, C2H2, CH3OH, CH3CN, (CH3)2CO, CH3CHO, CH3Cl, and (CH3CH2)2O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  4. Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

    NASA Astrophysics Data System (ADS)

    Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

    2017-02-01

    Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

  5. Charged Dust Aggregate Interactions

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin; Hyde, Truell

    2015-11-01

    A proper understanding of the behavior of dust particle aggregates immersed in a complex plasma first requires a knowledge of the basic properties of the system. Among the most important of these are the net electrostatic charge and higher multipole moments on the dust aggregate as well as the manner in which the aggregate interacts with the local electrostatic fields. The formation of elongated, fractal-like aggregates levitating in the sheath electric field of a weakly ionized RF generated plasma discharge has recently been observed experimentally. The resulting data has shown that as aggregates approach one another, they can both accelerate and rotate. At equilibrium, aggregates are observed to levitate with regular spacing, rotating about their long axis aligned parallel to the sheath electric field. Since gas drag tends to slow any such rotation, energy must be constantly fed into the system in order to sustain it. A numerical model designed to analyze this motion provides both the electrostatic charge and higher multipole moments of the aggregate while including the forces due to thermophoresis, neutral gas drag, and the ion wakefield. This model will be used to investigate the ambient conditions leading to the observed interactions. This research is funded by NSF Grant 1414523.

  6. Far-infrared permanent and induced dipole absorption of diatomic molecules in rare-gas fluids. I. Spectral theory

    NASA Astrophysics Data System (ADS)

    Roco, J. M. M.; Hernández, A. Calvo; Velasco, S.

    1995-12-01

    We present a spectral theory for the far-infrared absorption spectrum of a very diluted solution of diatomic molecules in a rare-gas fluid, that includes permanent and induced contributions. The absorption coefficient is given as the convolution of a translational spectrum and a rotational spectrum. The former is described in terms of time correlation functions associated to the induced dipole moment. The latter is discussed on the basis of a model consisting of a quantum rigid rotor interacting with a thermal bath, making use of time correlation functions associated to the different anisotropic orders of the solute-solvent intermolecular potential. Non-Markovian and line mixing effects are taken into account. Explicit expressions for the five leading contributions of the induced dipole moment are given.

  7. Dissociation degree of nitrogen molecule in low-pressure microwave-discharge nitrogen plasma with various rare-gas admixtures

    NASA Astrophysics Data System (ADS)

    Kuwano, Kei; Nezu, Atsushi; Matsuura, Haruaki; Akatsuka, Hiroshi

    2016-08-01

    The dissociation degree of nitrogen molecules is examined in a microwave discharge nitrogen-rare gas mixture plasma with a total discharge pressure of 1 Torr, by actinometry measurement. Although the spectral line from the excited nitrogen atoms is overlapped by the band spectrum of the N2 first positive system (1PS), the subtraction of the 1PS spectrum fitted theoretically can successfully extract the atomic nitrogen line, which enables actinometry measurement. The nitrogen dissociation degree decreases with increasing mixture ratio of Ar to Kr, whereas it increases with He, which is attributed to the variations in the electron temperature and density. When we dilute the nitrogen with neon, however, we find an anomalous increase in the nitrogen dissociation degree by several orders of magnitude even at a downstream region in the discharge tube. The reason for the dissociation enhancement upon adding neon is discussed in terms of atomic and molecular processes in the plasma.

  8. Nuclear dynamics and spectator effects in resonant inelastic soft x-ray scattering of gas-phase water molecules

    SciTech Connect

    Weinhardt, Lothar; Benkert, Andreas; Meyer, Frank; Blum, Monika; Wilks, Regan G.; Yang, Wanli; Baer, Marcus; Reinert, Friedrich; and others

    2012-04-14

    The electronic structure of gas-phase H{sub 2}O and D{sub 2}O molecules has been investigated using resonant inelastic soft x-ray scattering (RIXS). We observe spectator shifts for all valence orbitals when exciting into the lowest three absorption resonances. Strong changes of the relative valence orbital emission intensities are found when exciting into the different absorption resonances, which can be related to the angular anisotropy of the RIXS process. Furthermore, excitation into the 4a{sub 1} resonance leads to nuclear dynamics on the time scale of the RIXS process; we find evidence for vibrational coupling and molecular dissociation in both, the spectator and the participant emission.

  9. Use of inverse gas chromatography to characterize cotton fabrics and their interactions with fragrance molecules at controlled relative humidity.

    PubMed

    Cantergiani, Ennio; Benczédi, Daniel

    2002-09-06

    The present work focused on the surface characterization and fragrance interactions of a common cotton towel at different relative humidities (RHs) using inverse gas chromatography (IGC) and dynamic vapour sorption. The sigmoidal water sorption isotherms showed a maximum of 16% (w/w) water uptake with limited swelling at 100% RH. This means that water interacts strongly with cotton and might change its initial physico-chemical properties. The same cotton towel was then packed in a glass column and characterized by IGC at different relative humidities, calculating the dispersive and specific surface energy components. The dispersive component of the surface energy decreases slightly as a function of relative humidity (42 mJ/m2 at 0% RH to 36 mJ/m2 at 80% RH) which would be expected from swelling of the humidified cotton. The Gutmann's donor constant Kd increased from 0.28 kJ/mol at 0% RH to 0.42 kJ/mol at 80% RH, indicating that a greater hydrophilic surface exists at 80% RH, which is also as expected. Water, undecane and four fragrance molecules (dimetol, benzyl acetate, decanal and phenylethanol) were used to investigate cotton-fragrance interactions between 0 and 80% RH. The adsorption enthalpies and the Henry's constants were calculated and are discussed. The higher values for the adsorption enthalpies of polar molecules such as dimetol and phenylethanol suggest the presence of hydrogen bonds as the main adsorption mechanism. The Henry's constant of dimetol was also determined by headspace gas chromatography measurements at 20% RH, giving a similar value (230 nmol/Pa g by IGC and 130 nmol/Pa g by headspace GC), supporting the usefulness of IGC for such determinations. This work confirms the usefulness of chromatographic methods to investigate biopolymers such as textiles, starches and hairs.

  10. Fabrication of zeolitic imidazolate framework-8-methacrylate monolith composite capillary columns for fast gas chromatographic separation of small molecules.

    PubMed

    Yusuf, Kareem; Badjah-Hadj-Ahmed, Ahmed Yacine; Aqel, Ahmad; ALOthman, Zeid Abdullah

    2015-08-07

    A composite zeolitic imidazolate framework-8 (ZIF-8) with a butyl methacrylate-co-ethylene dimethacrylate (BuMA-co-EDMA) monolithic capillary column (33.5cm long×250μm i.d.) was fabricated to enhance the separation efficiency of methacrylate monoliths toward small molecules using conventional low-pressure gas chromatography in comparison with a neat butyl methacrylate-co-ethylene dimethacrylate (BuMA-co-EDMA) monolithic capillary column (33.5cm long×250μm i.d.). The addition of 10mgmL(-1) ZIF-8 micro-particles increased the BET surface area of BuMA-co-EDMA by 3.4-fold. A fast separation of five linear alkanes in 36s with high resolution (Rs≥1.3) was performed using temperature program. Isothermal separation of the same sample also showed a high efficiency (3315platesm(-1) for octane) at 0.89min. Moreover, the column was able to separate skeletal isomers, such as iso-octane/octane and 2-methyl octane/nonane. In addition, an iso-butane/iso-butylene gas mixture was separated at ambient temperature. Comparison with an open tubular TR-5MS column (30m long×250μm i.d.) revealed the superiority of the composite column in separating the five-membered linear alkane mixture with 4-5 times increase in efficiency and a total separation time of 0.89min instead of 4.67min. A paint thinner sample was fully separated using the composite column in 2.43min with a good resolution (Rs≥0.89). The perfect combination between the polymeric monolith, with its high permeability, and ZIF-8, with its high surface area and flexible 0.34nm pore openings, led to the fast separation of small molecules with high efficiency and opened a new horizon in GC applications.

  11. GAS-PHASE REACTIONS OF POLYCYCLIC AROMATIC HYDROCARBON ANIONS WITH MOLECULES OF INTERSTELLAR RELEVANCE

    SciTech Connect

    Demarais, Nicholas J.; Yang Zhibo; Martinez, Oscar; Wehres, Nadine; Bierbaum, Veronica M.; Snow, Theodore P. E-mail: Zhibo.Yang@Colorado.edu E-mail: Nadine.Wehres@Colorado.edu E-mail: Theodore.Snow@Colorado.edu

    2012-02-10

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C{sub 6}H{sup -}{sub 5}), naphthalenide (C{sub 10}H{sup -}{sub 7}), and anthracenide (C{sub 14}H{sup -}{sub 9}) with atomic H, H{sub 2}, and D{sub 2} using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O{sub 2}, CO{sub 2}, N{sub 2}O, C{sub 2}H{sub 2}, CH{sub 3}OH, CH{sub 3}CN, (CH{sub 3}){sub 2}CO, CH{sub 3}CHO, CH{sub 3}Cl, and (CH{sub 3}CH{sub 2}){sub 2}O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  12. On the effect of spatial aggregation of source regions on the stability of greenhouse gas emission estimates calculated by an inverse Lagrangian box model

    NASA Astrophysics Data System (ADS)

    Pieterse, G.; Vermeulen, A.

    2005-12-01

    Estimation of emission rates from atmospheric concentration observations has proven to remain a big challenge. In this paper, a new approach is chosen for the source strength estimation algorithm based on Source Receptor Matrices (SRM's) as derived for the COMET trajectory model for methane (Vermeulen et al., 2001). In the new approach, source regions are identified automatically by calculation of the Potential Source Region Contribution (PSRC) to measurements performed at multiple sites and spatial aggregation of these regions to achieve uniform PSRC in the aggregated Source-Receptor Matrix (aSRM). The emission strengths are then estimated using Singular Value Decomposition (SVD) of the aSRM. The SVD procedure also yields a Covariance Matrix (CM), which describes the statistical accuracies and mutual dependencies of the solutions. A recursive algorithm is implemented to further accumulate source regions in order to improve covariance and accuracy for the source strength estimates. The aSRM of Europe was constructed using the influence functions for the year 2002 for the locations of the CHIOTTO Tall Tower sites. Measurement data was not available for all sites. The results indicate that the new approach will enable accurate and stable methane budget calculations for the monitored region. As expected, the spatial distribution of the aggregated source regions will not be uniform, because the individual sources are not represented uniformly in the measured signals. Currently, the method is also evaluated for estimation of other greenhouse gas budgets of Europe, like CO2, SF6 and N2O. In principle, the aSRM method can be applied to SRM's of any transport model and component, provided that the forward performance of the model is adequate and that matching observations exist.

  13. Molecular aggregation of humic substances

    USGS Publications Warehouse

    Wershaw, R. L.

    1999-01-01

    Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

  14. Absorption into fluorescence. A method to sense biologically relevant gas molecules

    NASA Astrophysics Data System (ADS)

    Strianese, Maria; Varriale, Antonio; Staiano, Maria; Pellecchia, Claudio; D'Auria, Sabato

    2011-01-01

    In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection ofanalytes related to climate change. In particular, we focused our attention on the detection ofnitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.

  15. Absorption into fluorescence. A method to sense biologically relevant gas molecules.

    PubMed

    Strianese, Maria; Varriale, Antonio; Staiano, Maria; Pellecchia, Claudio; D'Auria, Sabato

    2011-01-01

    In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection of analytes related to climate change. In particular, we focused our attention on the detection of nitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.

  16. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy

    PubMed Central

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-01-01

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction. PMID:26690165

  17. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy.

    PubMed

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-12-04

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.

  18. Interaction energy and itinerant ferromagnetism in a strongly interacting Fermi gas in the absence of molecule formation

    SciTech Connect

    He, Lianyi

    2014-11-26

    In this study, we investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase-space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interaction energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.

  19. Interaction energy and itinerant ferromagnetism in a strongly interacting Fermi gas in the absence of molecule formation

    DOE PAGES

    He, Lianyi

    2014-11-26

    In this study, we investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase-space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interactionmore » energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.« less

  20. Four molecules of the 33 kDa haemagglutinin component of the Clostridium botulinum serotype C and D toxin complexes are required to aggregate erythrocytes.

    PubMed

    Mutoh, Shingo; Suzuki, Tomonori; Hasegawa, Kimiko; Nakazawa, Yozo; Kouguchi, Hirokazu; Sagane, Yoshimasa; Niwa, Koichi; Watanabe, Toshihiro; Ohyama, Tohru

    2005-12-01

    Normally, large-sized botulinum toxin complexes (L-TC) of serotype C and D are composed of a single neurotoxin, a single non-toxic non-haemagglutinin, two HA-70 molecules, four HA-33 molecules and four HA-17 molecules that assemble to form a 650 kDa L-TC. The 540 and 610 kDa TC species (designated here as L-TC2 and L-TC3, respectively) were purified in addition to the 650 kDa L-TC from the culture supernatants of serotype D strains (D-4947 and D-CB16) and serotype C strains (C-6814 and C-Yoichi). The 650 kDa L-TC from D-4947, D-CB16 and C-6814 showed haemagglutination and erythrocyte-binding activity, but their L-TC2 and L-TC3 species had only binding activity. In contrast, every TC species from C-Yoichi having the C-terminally truncated variant of HA-33 exhibited neither haemagglutination activity nor erythrocyte-binding activity. Four strain-specific HA-33/HA-17 complexes were isolated from the 650 kDa L-TC of each strain. The 650 kDa HA-hybrid L-TCs were reconstituted by various combinations of isolated HA-33/HA-17 complexes and haemagglutination-negative L-TC2 or L-TC3 from each strain. HA-hybrid 650 kDa L-TC, including at least one HA-33/HA-17 complex derived from C-Yoichi, lost haemagglutination activity, leading to the conclusion that the binding of four HA-33 molecules is required for haemagglutination activity of botulinum L-TC. The results of the modelling approach indicated that the structure of a variant C-Yoichi HA-33 molecule reveals clear deformation of the beta-trefoil domain responsible for the carbohydrate recognition site.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

    Part of the 1994 Industrial Minerals Review. The production, consumption, and applications of construction aggregates are reviewed. In 1994, the production of construction aggregates, which includes crushed stone and construction sand and gravel combined, increased 7.7 percent to 2.14 Gt compared with the previous year. These record production levels are mostly a result of funding for highway construction work provided by the Intermodal Surface Transportation Efficiency Act of 1991. Demand is expected to increase for construction aggregates in 1995.

  2. Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase.

    PubMed

    Grimme, Stefan; Steinmetz, Marc

    2013-10-14

    A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.

  3. Effect of Solvent Molecule in Pore for Flexible Porous Coordination Polymer upon Gas Adsorption and Iodine Encapsulation.

    PubMed

    Arıcı, Mürsel; Yeşilel, Okan Zafer; Taş, Murat; Demiral, Hakan

    2015-12-07

    Four new Zn(II)-coordination polymers, namely, [Zn2(μ6-ao2btc)(μ-obix)2]n (1), [Zn2(μ4-ao2btc)(μ-obix)2]n (2), [Zn2(μ4-ao2btc)(μ-mbix)2]n (3), and {[Zn2(μ4-ao2btc)(μ-pbix)2] · 2DMF · 8H2O}n (4), where ao2btc = dioxygenated form of 3,3',5,5'-azobenzenetetracarboxylate and obix, mbix, and pbix = 1,2-, 1,3-, and 1,4-bis(imidazol-1-ylmethyl)benzene, have been synthesized with azobenzenetetracarboxylic acid and isomeric bis(imidazole) ligands and characterized by elemental analyses, IR spectra, single-crystal X-ray diffraction, powder X-ray diffraction, and thermal analyses. X-ray results showed that 1, 2, and 4 had two-dimensional structures with 3,4L13 topology, while 3 was a three-dimensional coordination polymer with bbf topology. For 4, two types of activation strategies, solvent exchange + heating (which produced 4a) and direct heating (which produced 4b), were used to investigate the effect of a guest molecule in a flexible framework. Gas adsorption and iodine encapsulation properties of activated complexes were studied. The CO2 uptake capacities for 4a and 4b were 3.62% and 9.50%, respectively, and Langmuir surface areas calculated from CO2 isotherms were 167.4 and 350.7 m(2)/g, respectively. Moreover, 4b exhibited 19.65% and 15.27% iodine uptake in vapor phase and cyclohexane solution, respectively, which corresponded to 1.47 and 0.97 molecules of iodine/formula unit, respectively. Moreover, photoluminescence properties of the complexes were studied.

  4. Hemoglobin: a gas transport molecule that is hormonally regulated in the ovarian follicle in mice and humans.

    PubMed

    Brown, Hannah M; Anastasi, Marie R; Frank, Laura A; Kind, Karen L; Richani, Dulama; Robker, Rebecca L; Russell, Darryl L; Gilchrist, Robert B; Thompson, Jeremy G

    2015-01-01

    An increasing number of nonerythroid tissues are found to express hemoglobin mRNA and protein. Hemoglobin is a well-described gas transport molecule, especially for O2, but also for NO, CO2, and CO, and also acts as a reactive oxygen species scavenger. We previously found Hba-a1 and Hbb mRNA and protein at high levels within mouse periovulatory cumulus cells, but not in cumulus following in vitro maturation. This led us to investigate the temporal and spatial regulation in follicular cells during the periovulatory period. Cumulus-oocyte complexes were collected from equine chorionic gonadotropin/human chorionic gonadotropin-treated peripubertal SV129 female mice and collected and analyzed for gene expression and protein localization at a variety of time points over the periovulatory period. A further cohort matured in vitro with different forms of hemoglobin (ferro- and ferrihemoglobin) under different O2 atmospheric conditions (2%, 5%, and 20% O2) were subsequently fertilized in vitro and cultured to the blastocyst stage. Murine mRNA transcripts for hemoglobin were regulated by stimulation of the ovulatory cascade, in both granulosa and cumulus cells, and expression of HBA1 and HBB was highly significant in human granulosa and cumulus, but erythrocyte cell marker genes were not. Several other genes involved in hemoglobin function were similarly luteinizing hormone-regulated, including genes for heme biosynthesis. Immunohistochemistry revealed a changing localization pattern of HBA-A1 protein in murine cumulus cells and oocytes following the ovulatory signal. Significantly, no positive staining for HBA-A1 protein was observed within in vitro-matured oocytes, but, if coincubated with ferro- or ferrihemoglobin, cytoplasmic HBA-A1 was observed, similar to in vivo-derived oocytes. Addition of ferro-, but not ferrihemoglobin, had a small, positive effect on blastocyst yield, but only under either 2% or 20% O2 gas atmosphere. The identification of hemoglobin within

  5. Structures and aggregation states of fluoromethyllithium and chloromethyllithium carbenoids in the gas phase and in ethereal solvent.

    PubMed

    Pratt, Lawrence M; Ramachandran, Bala; Xidos, James D; Cramer, Christopher J; Truhlar, Donald G

    2002-11-01

    Using high-level quantum mechanical calculations and various models to account for solvation effects, monomers and dimers of fluoromethyllithium and chloromethyllithium carbenoids are studied in the gas phase and in dimethyl ether solvent. A combination of explicit microsolvation and a continuum reaction field is required to account fully for the structural and energetic effects of solvation. One important effect of solvent is the stabilization of charge-separated structures in which the lithium-halogen distance is much greater than in the gas-phase structures. At the most complete level of theory the 173 K standard-state free energy of dimerization of fluoromethyllithium in dimethyl ether is predicted to be -0.9 kcal mol(-)(1), while that for chloromethyllithium in the same solvent is predicted to be 3.7 kcal mol(-)(1). This suggests that, under typical experimental conditions, dimers of chloroalkyllithiums will not be observed, while dimers of fluoroalkyllithiums may contribute to the equilibrium population at a detectable level.

  6. Infrared Spectroscopy of Gas-Phase M(+)(CO2)n (M = Co, Rh, Ir) Ion-Molecule Complexes.

    PubMed

    Iskra, Andreas; Gentleman, Alexander S; Kartouzian, Aras; Kent, Michael J; Sharp, Alastair P; Mackenzie, Stuart R

    2017-01-12

    The structures of gas-phase M(+)(CO2)n (M = Co, Rh, Ir; n = 2-15) ion-molecule complexes have been investigated using a combination of infrared resonance-enhanced photodissociation (IR-REPD) spectroscopy and density functional theory. The results provide insight into fundamental metal ion-CO2 interactions, highlighting the trends with increasing ligand number and with different group 9 ions. Spectra have been recorded in the region of the CO2 asymmetric stretch around 2350 cm(-1) using the inert messenger technique and their interpretation has been aided by comparison with simulated infrared spectra of calculated low-energy isomeric structures. All vibrational bands in the smaller complexes are blue-shifted relative to the asymmetric stretch in free CO2, consistent with direct binding to the metal center dominated by charge-quadrupole interactions. For all three metal ions, a core [M(+)(CO2)2] structure is identified to which subsequent ligands are less strongly bound. No evidence is observed in this size regime for complete activation or insertion reactions.

  7. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy.

    PubMed

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-06-15

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident.

  8. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy

    PubMed Central

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-01-01

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident. PMID:27301319

  9. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-06-01

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident.

  10. Nanoarchitectonics of Molecular Aggregates: Science and Technology

    SciTech Connect

    Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin; Hill, Dr. Jonathan P; Ariga, Katsuhiko; Yusuke, Yonamine

    2014-01-01

    The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

  11. Luminescence characteristics of Xe{sub 2}Cl excimer molecules under pumping the dense Xe-CCl{sub 4} gas mixtures with a pulsed electron beam

    SciTech Connect

    Mis'kevich, A I; Jinbo, Guo

    2013-05-31

    Temporal and spectral characteristics of the luminescence of dense Xe-CCl{sub 4} gas mixtures of different composition, excited by a 5-ns pulsed electron beam, were measured. The energy of the electrons amounted to 150 keV and the electron beam current pulse amplitude was 5 A. The gas mixtures were used containing Xe (38-700 Torr) and CCl{sub 4} (0.03-0.3 Torr). The studies were performed within the wavelength range 200-1200 nm using a MAYA-2000Pro diffraction grating spectrometer and a RIGOL DS 5022 ME fast digital oscilloscope. The luminescence lifetimes of the excimer molecules XeCl* (band with {lambda}{sub max} = 308 nm) and Xe{sub 2}Cl* (band with {lambda}{sub max} = 486 nm) were measured, as well as the constants of quenching by the components of the gas mixture for Xe{sub 2}Cl* molecules. A model of plasma-chemical processes for dense Xe-CCl{sub 4} gas mixtures with a very low content of the CCl{sub 4} donor is proposed. It is shown that in such 'poor' mixtures Xe{sub 2}Cl* molecules are mainly produced as a result of recombination of the Xe{sub 2}{sup +} and Cl{sup -} ions. (active media)

  12. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  13. Gas-phase infrared and ab initio study of the unstable CF3CNO molecule and its stable furoxan ring dimer.

    PubMed

    Havasi, Balázs; Pasinszki, Tibor; Westwood, Nicholas P C

    2005-05-05

    The unstable trifluoroacetonitrile N-oxide molecule, CF3CNO, has been generated in high yield in the gas phase from CF3BrC=NOH and studied for the first time by gas-phase mid-infrared spectroscopy. Cold trapping of this molecule followed by slow warming forms the stable ring dimer, bis(trifluoromethyl)furoxan, also investigated by gas-phase infrared spectroscopy. The spectroscopy provides an investigation into the vibrational character of the two molecules, the assignments supported by calculations of the harmonic vibrational frequencies using in the case of CF3CNO both ab initio (CCSD(T)) and density functional theory (B3LYP) and B3LYP for the ring dimer. The ground-state structures of both molecules were investigated at the B3LYP level of theory, with CF3CNO further investigated using coupled-cluster. The CCSD(T) method suggests a slightly bent (C(s)) structure for CF3CNO, while the B3LYP method (with basis sets ranging from 6-311G(d) to cc-pVTZ) suggests a close-to-linear or linear CCNO chain. The CCN bending potential in CF3CNO was explored at the CCSD(T)(fc)/cc-pVTZ level, with the results suggesting that CF3CNO exhibits strong quasi-symmetric top behavior with a barrier to linearity of 174 cm(-1). Since both isomerization and dimerization are feasible loss processes for this unstable molecule, the relative stability of CF3CNO with respect to the known cyanate (CF3OCN), isocyanate (CF3NCO), and fulminate (CF3ONC) isomers and the mechanism of the dimerization process to the ring furoxan and other isomers were studied with density functional theory.

  14. Determination of local concentration of H2O molecules and gas temperature in the process of hydrogen - oxygen gas mixture heating by means of linear and nonlinear laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Kozlov, D. N.; Kobtsev, V. D.; Stel'makh, O. M.; Smirnov, Valery V.; Stepanov, E. V.

    2013-01-01

    Employing the methods of linear absorption spectroscopy and nonlinear four-wave mixing spectroscopy using laserinduced gratings we have simultaneously measured the local concentrations of H2O molecules and the gas temperature in the process of the H2 - O2 mixture heating. During the measurements of the deactivation rates of pulsed-laser excited singlet oxygen O2 (b 1Σ+g) in collisions with H2 in the range 294 - 850 K, the joint use of the two methods made it possible to determine the degree of hydrogen oxidation at a given temperature. As the mixture is heated, H2O molecules are formed by 'dark' reactions of H2 with O2 in the ground state. The experiments have shown that the measurements of tunable diode laser radiation absorption along an optical path through the inhomogeneously heated gas mixture in a cell allows high-accuracy determination of the local H2O concentration in the O2 laser excitation volume, if the gas temperature in this volume is known. When studying the collisional deactivation of O2 (b 1Σ+g) molecules, the necessary measurements of the local temperature can be implemented using laser-induced gratings, arising due to spatially periodic excitation of O2 (X3Σ-g) molecules to the b 1Σ+g state by radiation of the pump laser of the four-wave mixing spectrometer.

  15. Synthesis of Pure and N-substituted Cyclic Hydrocarbons (e.g. Pyrimidine) via Gas-Phase Ion-Molecule Reactions

    NASA Astrophysics Data System (ADS)

    Bera, Partha P.; Peverati, Roberto; Head-Gordon, Martin; Lee, Timothy J.

    2015-08-01

    Large polyatomic carbonaceous molecules, known as polycyclic aromatic hydrocarbons, are known to exist in the outflows of carbon stars. How these large polyatomic molecules are synthesized in such exotic conditions is, thus far, unknown. Molecular ions, including positive and negative ions, are in relative abundance in the high radiation fields present under such conditions. Hence, barrierless ion-molecule interactions may play a major role in guiding molecules towards each other and initiating reactions. We study these condensation pathways to determine whether they are a viable means of forming large pure hydrocarbon molecules, and nitrogen-containing carbonaceous chains, stacks, and even cyclic compounds. By employing accurate quantum chemical methods we have investigated the processes of growth, structures, nature of bonding, mechanisms, and spectroscopic properties of the ensuing ionic products after pairing small carbon, hydrogen, and nitrogen-containing molecules. We have also studied the ion-neutral association pathways involving pure-carbon molecules e.g. acetylene, ethylene and other hydrocarbons, and their dissociation fragments in a plasma discharge as well as how nitrogen atoms are incorporated into the carbon ring during growth. Specifically, we explored the mechanisms by which the synthesis of pyrimidine will be feasible in the gas phase in conjunction with ion-mobility experiments. We have used accurate ab initio coupled cluster theory, Møller-Plesset and Z-averaged perturbation theories, density functional theory, and coupled cluster theory quantum chemical methods together with large correlation consistent basis sets in these investigations. We found that a series of hydrocarbons with a specific stoichiometric composition prefers cyclic molecule formation rather than chains. Some of the association products we investigated have large oscillator strengths for charge-transfer type electronic excitations in the near infrared and visible regions of

  16. Stoichiometry and Physical Chemistry of Promiscuous Aggregate-Based Inhibitors

    PubMed Central

    Coan, Kristin E. D.

    2009-01-01

    Many false positives in early drug discovery owe to nonspecific inhibition by colloid-like aggregates of organic molecules. Despite their prevalence, little is known about aggregate concentration, structure, or dynamic equilibrium; the binding mechanism, stoichiometry with, and affinity for enzymes remain uncertain. To investigate the elementary question of concentration, we counted aggregate particles using flow cytometry. For seven aggregate-forming molecules, aggregates were not observed until the concentration of monomer crossed a threshold, indicating a “critical aggregation concentration” (CAC). Above the CAC, aggregate count increased linearly with added organic material, while the particles dispersed when diluted below the CAC. The concentration of monomeric organic molecule is constant above the CAC, as is the size of the aggregate particles. For two compounds that form large aggregates, nicardipine and miconazole, we measured particle numbers directly by flow cytometry, determining that the aggregate concentration just above the CAC ranged from 5 to 30 fM. By correlating inhibition of an enzyme with aggregate count for these two drugs, we determined that the stoichiometry of binding is about 10 000 enzyme molecules per aggregate particle. Using measured volumes for nicardipine and miconazole aggregate particles (2.1 × 1011 and 4.7 × 1010 Å3, respectively), computed monomer volumes, and the observation that past the CAC all additional monomer forms aggregate particles, we find that aggregates are densely packed particles. Finally, given their size and enzyme stoichiometry, all sequestered enzyme can be comfortably accommodated on the surface of the aggregate. PMID:18588298

  17. Neutral gas temperature measurements of high-power-density fluorocarbon plasmas by fitting swan bands of C{sub 2} molecules

    SciTech Connect

    Bai Bo; Sawin, Herbert H.; Cruden, Brett A.

    2006-01-01

    The neutral gas temperature of fluorocarbon plasmas in a remote toroidal transformer-coupled source was measured to be greater than 5000 K, under the conditions of a power density greater than 15 W/cm{sup 3} and pressures above 2 torr. The rovibrational bands of C{sub 2} molecules (swan bands, d {sup 3}{pi}{sub g}{yields}a {sup 3}{pi}{sub u}) were fitted to obtain the rotational temperature that was assumed to equal the translational temperature. This rotational-translational temperature equilibrium assumption was supported by the comparison with the rotational temperature of second positive system of added N{sub 2}. For the same gas mixture, the neutral gas temperature is nearly a linear function of plasma power, since the conduction to chamber wall and convection are the major energy-loss processes, and they are both proportional to neutral gas temperature. The dependence of the neutral gas temperature on O{sub 2} flow rate and pressure can be well represented through the power dependence, under the condition of constant current operation. An Arrhenius type of dependence between the etching rate of oxide film and the neutral gas temperature is observed, maybe indicating the importance of the pyrolytic dissociation in the plasma formation process when the temperature is above 5000 K.

  18. Kronecker-product periodic systems of small gas-phase molecules and the search for order in atomic ensembles of any phase.

    PubMed

    Hefferlin, Ray

    2008-11-01

    The periodic law, manifested in the chart of the elements, is so fundamental in chemistry and related areas of physics that the question arises "Might periodicity among molecules also be embodied in a periodic system?" This review paper details how a particular periodic system of gas-phase diatomic molecules, allowing for the forecasting of thousands of new data, was developed. It can include ionized and even quarked-nuclei molecules and it coincides with locality (averaging) and the additivity found in some data; it has interesting vector properties, and it may be related in challenging ways to partial order. The review then explains how periodic systems for triatomic and four-atomic species are evolving along a similar path. The systems rest largely upon exhaustive comparisons of tabulated data, relate to some extent to the octet rule, and include reducible representations of the dynamic group SO(4) in higher spaces. Finally, the paper shows how periodicity can be quantified in data for larger molecules. Data for properties of homologous or substituted molecules, in any phase, are quantified with a vector index, and the index for one set can be transformed into that for another set.

  19. Ab-initio investigation of adsorption of CO and CO2 molecules on graphene: Role of intrinsic defects on gas sensing

    NASA Astrophysics Data System (ADS)

    Tit, Nacir; Said, Khadija; Mahmoud, Nadin M.; Kouser, Summayya; Yamani, Zain H.

    2017-02-01

    We determine the chemical activity of (a) carbon site of pristine graphene (pG), (b) Stone-Wales (SW) defect site, and (c) Single-vacancy of graphene (vG) site towards the adsorption of CO and CO2 molecules, through comparative analysis based on first-principles density-functional calculations incorporating van der Waals (vdW) interactions, but excluding the heat effects (i.e., at T = 0 °K). The results show that the chemisorption of both latter molecules to possibly occur only on vG. The response (sensitivity) of vG towards detecting CO molecule was confirmed by the rise of conductance with the increasing CO gas dose. The selectivity was investigated by testing the response of vG towards detecting eight different gases (i.e., CO, CO2, N2, O2, H2O, H2S, H2, and NH3). Three gases are found to exhibit physisorption (namely: N2, H2O, and H2S) and the other five gases alter chemisorption (namely: CO, CO2, O2, H2, and NH3). The chemisorption of CO molecule is distinct by being direct and not involving dissociation. This fact made defected graphene have the highest sensitivity and selectivity towards the detection of CO molecules.

  20. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

    PubMed Central

    Staniforth, Michael; Stavros, Vasilios G.

    2013-01-01

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach. PMID:24204191

  1. Construction aggregates

    USGS Publications Warehouse

    Nelson, T.I.; Bolen, W.P.

    2007-01-01

    Construction aggregates, primarily stone, sand and gravel, are recovered from widespread naturally occurring mineral deposits and processed for use primarily in the construction industry. They are mined, crushed, sorted by size and sold loose or combined with portland cement or asphaltic cement to make concrete products to build roads, houses, buildings, and other structures. Much smaller quantities are used in agriculture, cement manufacture, chemical and metallurgical processes, glass production and many other products.

  2. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

    Part of the Annual Commodities Review 1995. Production of construction aggregates such as crushed stone and construction sand and gravel showed a marginal increase in 1995. Most of the 1995 increases were due to funding for highway construction work. The major areas of concern to the industry included issues relating to wetlands classification and the classification of crystalline silica as a probable human carcinogen. Despite this, an increase in demand is anticipated for 1996.

  3. Effect of hydration on the organo-noble gas molecule HKrCCH: role of krypton in the stabilization of hydrated HKrCCH complexes.

    PubMed

    Biswas, Biswajit; Singh, Prashant Chandra

    2015-11-11

    The effect of hydration on the fluorine free organo-noble gas compound HKrCCH and the role of krypton in the stabilization of the hydrated HKrCCH complexes have been investigated using the quantum chemical calculations on the HKrCCH-(H2O)n=1-6 clusters. Structure and energetics calculations show that water stabilizes HKrCCH through the π hydrogen bond in which the OH group of water interacts with the C[triple bond, length as m-dash]C group of HKrCCH. A maximum of four water molecules can directly interact with the C[triple bond, length as m-dash]C of HKrCCH and after that only inter-hydrogen bonding takes place between the water molecules indicating that the primary hydration shell contains four water molecules. Atom in molecule analysis depicts that π hydrogen bonded complexes of the hydrated HKrCCH are cyclic structures in which the OKr interaction cooperates in the formation of strong O-HC[triple bond, length as m-dash]C interaction. Structure, energetics and charge analysis clearly established that krypton plays an important role in the stabilization as well as the formation of the primary hydration shell of hydrated HKrCCH complexes.

  4. Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution.

    PubMed

    Santoro, Fabrizio; Lami, Alessandro; Improta, Roberto; Barone, Vincenzo

    2007-05-14

    The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky rotation of the normal modes and the effect of thermal excitation. The method automatically selects the relevant vibronic contributions to the spectrum, independently of their frequency, and it is able to provide fully converged spectra with moderate computational times, both in vacuo and in solution. By describing the electronic states in the frame of the density functional theory and its time-dependent extension, they computed the room temperature absorption spectra of coumarin C153 and trans-stilbene in cyclohexane and the phosphorescence spectrum of porphyrazine in gas phase, showing that the method is fast and efficient. The comparison with experiment for trans-stilbene and coumarin C153 is very satisfactory, confirming the progress made toward a reliable method for the computation and interpretation for the optical spectra of large molecules.

  5. Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

    PubMed

    Poully, Jean-Christophe; Vizcaino, Violaine; Schwob, Lucas; Delaunay, Rudy; Kocisek, Jaroslav; Eden, Samuel; Chesnel, Jean-Yves; Méry, Alain; Rangama, Jimmy; Adoui, Lamri; Huber, Bernd

    2015-08-03

    Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.

  6. Laboratory Studies on the Formation of Carbon-Bearing Molecules in Extraterrestrial Environments: From the Gas Phase to the Solid State

    NASA Technical Reports Server (NTRS)

    Jamieson, C. S.; Guo, Y.; Gu, X.; Zhang, F.; Bennett, C. J.; Kaiser, R. I.

    2006-01-01

    A detailed knowledge of the formation of carbon-bearing molecules in interstellar ices and in the gas phase of the interstellar medium is of paramount interest to understand the astrochemical evolution of extraterrestrial environments (1). This research also holds strong implications to comprehend the chemical processing of Solar System environments such as icy planets and their moons together with the atmospheres of planets and their satellites (2). Since the present composition of each interstellar and Solar System environment reflects the matter from which it was formed and the processes which have changed the chemical nature since the origin (solar wind, planetary magnetospheres, cosmic ray exposure, photolysis, chemical reactions), a detailed investigation of the physicochemical mechanisms altering the pristine environment is of paramount importance to grasp the contemporary composition. Once these underlying processes have been unraveled, we can identify those molecules, which belonged to the nascent setting, distinguish molecular species synthesized in a later stage, and predict the imminent chemical evolution of, for instance, molecular clouds. Laboratory experiments under controlled physicochemical conditions (temperature, pressure, chemical composition, high energy components) present ideal tools for simulating the chemical evolution of interstellar and Solar System environments. Here, laboratory experiments can predict where and how (reaction mechanisms; chemicals necessary) in extraterrestrial environments and in the interstellar medium complex, carbon bearing molecules can be formed on interstellar grains and in the gas phase. This paper overviews the experimental setups utilized in our laboratory to mimic the chemical processing of gas phase and solid state (ices) environments. These are a crossed molecular beams machine (3) and a surface scattering setup (4). We also present typical results of each setup (formation of amino acids, aldehydes, epoxides

  7. Towards reliable modelling of large clusters: on the overall accuracy of the diatomics-in-molecule method for rare gas cluster ions

    NASA Astrophysics Data System (ADS)

    Naumkin, Fedor Yu.; Knowles, Peter J.; Murrell, John N.

    1995-04-01

    The accuracy of the diatomics-in-molecules (DIM) method is examined for the case of rare gas ionic clusters through a series of careful calibration calculations. Ab initio potential energy functions for Rg 3+ and Rg 4+ (RgHe, Ne, Ar) are compared with the DIM model, taking diatomic potentials computed at exactly the same level of ab initio theory as input. For Ne n+, agreement is satisfactory (in most important regions within 0.05 eV), whereas for He n+, large deviations occur.

  8. Towards reliable modelling of large clusters: On the overall accuracy of the diatomics-in-molecule method for rare gas cluster ions

    NASA Astrophysics Data System (ADS)

    Naumkin, Fedor Yu.; Knowles, Peter J.; Murrell, John N.

    1995-04-01

    The accuracy of the diatomics-in-molecules (DIM) method is examined for the case of rare gas ionic clusters through a series of careful calibration calculations. Ab initio potential energy functions for Rg3(+) and Rg4(+) (Rg=He, Ne, Ar) are compared with the DIM model, taking diatomic potentials computed at exactly the same level of ab initio theory as input. For Ne(n)(+) and Ar(n)(+), agreement is satisfactory (in most important regions within 0.05 eV), whereas for He(n)(+), large deviations occur.

  9. Gas-phase dissociation of ionic liquid aggregates studied by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation.

    PubMed

    Fernandes, Ana M; Coutinho, João A P; Marrucho, Isabel M

    2009-01-01

    Positive singly charged ionic liquid aggregates [(C(n)mim)(m+1)(BF(4))(m)](+) (mim = 3-methylimidazolium; n = 2, 4, 8 and 10) and [(C(4)mim)(m+1)(A)(m)](+) (A = Cl(-), BF(4) (-), PF(6) (-), CF(3)SO(3) (-) and (CF(3)SO(2))(2)N(-)) were investigated by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation. The electrospray ionisation mass spectra (ESI-MS) showed the formation of an aggregate with extra stability for m = 4 for all the ionic liquids with the exception of [C(4)mim][CF(3)SO(3)]. ESI-MS-MS and breakdown curves of aggregate ions showed that their dissociation occurred by loss of neutral species ([C(n)mim][A])(a) with a >or= 1. Variable-energy collision induced dissociation of each aggregate from m = 1 to m = 8 for all the ionic liquids studied enabled the determination of E(cm, 1/2) values, whose variation with m showed that the monomers were always kinetically much more stable than the larger aggregates, independently of the nature of cation and anion. The centre-of-mass energy values correlate well with literature data on ionic volumes and interaction and hydrogen bond energies.

  10. Calculation of the Standard Molal Thermodynamic Properties of Crystalline, Liquid, and Gas Organic Molecules at High Temperatures and Pressures

    NASA Astrophysics Data System (ADS)

    Helgeson, Harold C.; Owens, Christine E.; Knox, Annette M.; Richard, Laurent

    1998-03-01

    Calculation of the thermodynamic properties of organic solids, liquids, and gases at high temperatures and pressures is a requisite for characterizing hydrothermal metastable equilibrium states involving these species and quantifying the chemical affinities of irreversible reactions of organic molecules in natural gas, crude oil, kerogen, and coal with minerals and organic, inorganic, and biomolecular aqueous species in interstitial waters in sedimentary basins. To facilitate calculations of this kind, coefficients for the Parameters From Group Contributions (PFGC) equation of state have been compiled for a variety of groups in organic liquids and gases. In addition, molecular weights, critical temperatures and pressures, densities at 25°C and 1 bar, transition, melting, and boiling temperatures ( Tt,Pr, Tm,Pr, and Tv,Pr, respectively) and standard molal enthalpies of transition (Δ H° t,Pr), melting (Δ H° m,Pr), and vaporization (Δ H° v,Pr) of organic species at 1 bar ( Pr) have been tabulated, together with an internally consistent and comprehensive set of standard molal Gibbs free energies and enthalpies of formation from the elements in their stable state at 298.15 K ( Tr) and Pr (Δ G° f and Δ H° f, respectively). The critical compilation also includes standard molal entropies ( S°) and volumes ( V°) at Tr and Pr, and standard molal heat capacity power function coefficients to compute the standard molal thermodynamic properties of organic solids, liquids, and gases as a function of temperature at 1 bar. These properties and coefficients have been tabulated for more than 500 crystalline solids, liquids, and gases, and those for many more can be computed from the equations of state group additivity algorithms. The crystalline species correspond to normal alkanes (C nH 2( n+1) ) with carbon numbers ( n, which is equal to the number of moles of carbon atoms in one mole of the species) ranging from 5 to 100, and 23 amino acids including glycine (C 2H 5NO

  11. Tuning the composition of guest molecules in clathrate hydrates: NMR identification and its significance to gas storage.

    PubMed

    Seo, Yutaek; Lee, Jong-Won; Kumar, Rajnish; Moudrakovski, Igor L; Lee, Huen; Ripmeester, John A

    2009-08-03

    Gas hydrates represent an attractive way of storing large quantities of gas such as methane and carbon dioxide, although to date there has been little effort to optimize the storage capacity and to understand the trade-offs between storage conditions and storage capacity. In this work, we present estimates for gas storage based on the ideal structures, and show how these must be modified given the little data available on hydrate composition. We then examine the hypothesis based on solid-solution theory for clathrate hydrates as to how storage capacity may be improved for structure II hydrates, and test the hypothesis for a structure II hydrate of THF and methane, paying special attention to the synthetic approach used. Phase equilibrium data are used to map the region of stability of the double hydrate in P-T space as a function of the concentration of THF. In situ high-pressure NMR experiments were used to measure the kinetics of reaction between frozen THF solutions and methane gas, and (13)C MAS NMR experiments were used to measure the distribution of the guests over the cage sites. As known from previous work, at high concentrations of THF, methane only occupies the small cages in structure II hydrate, and in accordance with the hypothesis posed, we confirm that methane can be introduced into the large cage of structure II hydrate by lowering the concentration of THF to below 1.0 mol %. We note that in some preparations the cage occupancies appear to fluctuate with time and are not necessarily homogeneous over the sample. Although the tuning mechanism is generally valid, the composition and homogeneity of the product vary with the details of the synthetic procedure. The best results, those obtained from the gas-liquid reaction, are in good agreement with thermodynamic predictions; those obtained for the gas-solid reaction do not agree nearly as well.

  12. Production of hyperpolarized H_{2} molecules from H[over →] atoms in gas-storage cells.

    PubMed

    Engels, R; Gaißer, M; Gorski, R; Grigoryev, K; Mikirtychyants, M; Nass, A; Rathmann, F; Seyfarth, H; Ströher, H; Weiss, P; Kochenda, L; Kravtsov, P; Trofimov, V; Tschernov, N; Vasilyev, A; Vznuzdaev, M; Schieck, H Paetz Gen

    2015-09-11

    The preservation of the nuclear polarization of hydrogen atoms during the recombination to molecules was observed on different surface materials in the temperature range from 45 to 100 K and for magnetic fields up to 1 T. On a gold and a fused quartz surface, the expected molecular polarization of about 50% or lower of the atomic polarization was measured, while a surface layer of perfluoropolyether (Fomblin) shows a nearly complete preservation (at least 97%) of the atomic polarization during the recombination process. Further experiments have the possibility of storing polarized deuterium molecules and to use them in nuclear-fusion installations. Another application might be the production of polarized substances for enhanced NMR techniques.

  13. A Robust Highly Interpenetrated Metal−Organic Framework Constructed from Pentanuclear Clusters for Selective Sorption of Gas Molecules

    SciTech Connect

    Zhang, Zhangjing; Xiang, Shengchang; Chen, Yu-Sheng; Ma, Shengqian; Lee, Yongwoo; Phely-Bobin, Thomas; Chen, Banglin

    2010-10-22

    A three-dimensional microporous metal-organic framework, Zn{sub 5}(BTA){sub 6}(TDA){sub 2} {center_dot} 15DMF {center_dot} 8H{sub 2}O (1; HBTA = 1,2,3-benzenetriazole; H{sub 2}TDA = thiophene-2,5-dicarboxylic acid), comprising pentanuclear [Zn{sub 5}] cluster units, was obtained through an one-pot solvothermal reaction of Zn(NO{sub 3}){sub 2}, 1,2,3-benzenetriazole, and thiophene-2,5-dicarboxylate. The activated 1 displays type-I N{sub 2} gas sorption behavior with a Langmuir surface area of 607 m{sup 2} g{sup -1} and exhibits interesting selective gas adsorption for C{sub 2}H{sub 2}/CH{sub 4} and CO{sub 2}/CH{sub 4}.

  14. Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

    PubMed

    Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

    2012-08-02

    The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

  15. Effects of non-local exchange on core level shifts for gas-phase and adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Van den Bossche, M.; Martin, N. M.; Gustafson, J.; Hakanoglu, C.; Weaver, J. F.; Lundgren, E.; Grönbeck, H.

    2014-07-01

    Density functional theory calculations are often used to interpret experimental shifts in core level binding energies. Calculations based on gradient-corrected (GC) exchange-correlation functionals are known to reproduce measured core level shifts (CLS) of isolated molecules and metal surfaces with reasonable accuracy. In the present study, we discuss a series of examples where the shifts calculated within a GC-functional significantly deviate from the experimental values, namely the CLS of C 1s in ethyl trifluoroacetate, Pd 3d in PdO and the O 1s shift for CO adsorbed on PdO(101). The deviations are traced to effects of the electronic self-interaction error with GC-functionals and substantially better agreements between calculated and measured CLS are obtained when a fraction of exact exchange is used in the exchange-correlation functional.

  16. Controlled growth of conical nickel oxide nanocrystals and their high performance gas sensing devices for ammonia molecule detection.

    PubMed

    Wang, Jian; Yang, Fan; Wei, Xiaowei; Zhang, Yafei; Wei, Liangming; Zhang, Jianjun; Tang, Qifeng; Guo, Biao; Xu, Lei

    2014-08-21

    NiO nanocones with good symmetry and highly ordered structure on NiO foil substrate have been successfully fabricated via a facile wet chemical approach combined with subsequent high temperature oxidation. These organized conical superstructures grow only along a certain direction and be controlled via the self-assembly and oriented attachment of a nucleus, which mainly rely on the similar surface energies and the extent of lattice matching of the oriented attached surfaces. During high temperature oxidation, the electric field created via the Ni(2+) and O(2-) facilitates Ni(2+) diffusion outward along the grain boundaries and O(2-) diffusion inward toward to meet the Ni(2+) ions, forming NiO. The as-grown NiO nanocones are 50-350 nm in diameter and 50-400 nm in height. The tip diameter of the nanocone is about 30 nm and the apex angle of the nanocone is about 40°. Meanwhile, we systematically investigated the gas sensing properties of the sensors based on the as-fabricated NiO foil covered with nanocone arrays for ammonia detection at room temperature. The results show that the gas sensing devices have outstanding sensitivity, reproducibility and selectivity, which are mainly because of the excellent connection between the NiO sensing materials and the Au electrodes, the strong electron donating ability of ammonia and the large active surface of selective physisorption for ammonia.

  17. Coherent Rayleigh-Brillouin scattering for in situ detection of nanoparticles and large molecules in gas and plasma

    NASA Astrophysics Data System (ADS)

    Gerakis, A.; Shneider, M. N.; Stratton, B. C.; Santra, B.; Car, R.; Raitses, Y.

    2016-09-01

    Laser-based diagnostics methods, such as Spontaneous and Coherent Rayleigh and Rayleigh-Brillouin scattering (SRBS and CRBS), can be used for in-situ detection and characterization of nanoparticle shape and size as well as their concentration in an inert gas atmosphere. We recently developed and tested this advanced diagnostic at PPPL. It was shown that the signal intensity of the CRBS signal depends on the gas-nanoparticle mixture composition, density and the polarizabilities of the mixture components. The measured results agree well with theoretical predictions of Refs. In this work, we report the application of this diagnostic to monitor nucleation and growth of nanoparticles in a carbon arc discharge. In support of these measurements, A time-dependent density functional theory was used to compute the frequency-dependent polarizabilities of various nanostructures in order to predict the corresponding Rayleigh scattering intensities as well as light depolarization. Preliminary results of measurements demonstrate that CRBS is capable to detect nanoparticles in volume. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

  18. The IRAM-30 m line survey of the Horsehead PDR. III. High abundance of complex (iso-)nitrile molecules in UV-illuminated gas

    NASA Astrophysics Data System (ADS)

    Gratier, P.; Pety, J.; Guzmán, V.; Gerin, M.; Goicoechea, J. R.; Roueff, E.; Faure, A.

    2013-09-01

    Context. Complex (iso-)nitrile molecules, such as CH3CN and HC3N, are relatively easily detected in our Galaxy and in other galaxies. Aims: We aim at constraining their chemistry through observations of two positions in the Horsehead edge: the photo-dissociation region (PDR) and the dense, cold, and UV-shielded core just behind it. Methods: We systematically searched for lines of CH3CN, HC3N, C3N, and some of their isomers in our sensitive unbiased line survey at 3, 2, and 1 mm. We stacked the lines of C3N to improve the detectability of this species. We derived column densities and abundances through Bayesian analysis using a large velocity gradient radiative transfer model. Results: We report the first clear detection of CH3NC at millimeter wavelength. We detected 17 lines of CH3CN at the PDR and 6 at the dense core position, and we resolved its hyperfine structure for 3 lines. We detected 4 lines of HC3N, and C3N is clearly detected at the PDR position. We computed new electron collisional rate coefficients for CH3CN, andwe found that including electron excitation reduces the derived column density by 40% at the PDR position, where the electron density is 1-5 cm-3. While CH3CN is 30 times more abundant in the PDR (2.5 × 10-10) than in the dense core (8 × 10-12), HC3N has similar abundance at both positions (8 × 10-12). The isomeric ratio CH3NC/CH3CN is 0.15 ± 0.02. Conclusions: The significant amount of complex (iso-)nitrile molecule in the UV illuminated gas is puzzling as the photodissociation is expected to be efficient. This is all the more surprising in the case of CH3CN, which is 30 times more abundant in the PDR than in the dense core. In this case, pure gas phase chemistry cannot reproduce the amount of CH3CN observed in the UV-illuminated gas. We propose that CH3CN gas phase abundance is enhanced when ice mantles of grains are destroyed through photo-desorption or thermal-evaporation in PDRs, and through sputtering in shocks. Based on observations

  19. Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules

    SciTech Connect

    Alvarado, Fresia; Bari, Sadia; Hoekstra, Ronnie; Schlathoelter, Thomas

    2007-07-21

    KeV atomic particles traversing biological matter are subject to charge exchange and screening effects which dynamically change this particle's effective charge. The understanding of the collision cascade along the track thus requires a detailed knowledge of the interaction dynamics of radiobiologically relevant molecules, such as DNA building blocks or water, not only with ionic but also with neutral species. We have studied collisions of keV H{sup +}, He{sup +}, and C{sup +} ions and H{sup 0}, He{sup 0}, and C{sup 0} atoms with the DNA base adenine by means of high resolution time-of-flight spectrometry. For H{sup 0} and H{sup +} we find qualitatively very similar fragmentation patterns, while for carbon, strong differences are observed when comparing C{sup 0} and C{sup +} impact. For collisions with He{sup 0} and He{sup +} projectiles, a pronounced delayed fragmentation channel is observed, which has not been reported before.

  20. Hydrogen gas acts as a novel bioactive molecule in enhancing plant tolerance to paraquat-induced oxidative stress via the modulation of heme oxygenase-1 signalling system.

    PubMed

    Jin, Qijiang; Zhu, Kaikai; Cui, Weiti; Xie, Yanjie; Han, Bin; Shen, Wenbiao

    2013-05-01

    Hydrogen gas (H2) was recently proposed as a novel antioxidant and signalling molecule in animals. However, the physiological roles of H2 in plants are less clear. Here, we showed that exposure of alfalfa seedlings to paraquat stress increased endogenous H2 production. When supplied with exogenous H2 or the heme oxygenase-1 (HO-1)-inducer hemin, alfalfa plants displayed enhanced tolerance to oxidative stress induced by paraquat. This was evidenced by alleviation of the inhibition of root growth, reduced lipid peroxidation and the decreased hydrogen peroxide and superoxide anion radical levels. The activities and transcripts of representative antioxidant enzymes were induced after exposure to either H2 or hemin. Further results showed that H2 pretreatment could dramatically increase levels of the MsHO-1 transcript, levels of the protein it encodes and HO-1 activity. The previously mentioned H2-mediated responses were specific for HO-1, given that the potent HO-1-inhibitor counteracted the effects of H2. The effects of H2 were reversed after the addition of an aqueous solution of 50% carbon monoxide (CO). We also discovered enhanced tolerance of multiple environmental stresses after plants were pretreated with H2 . Together, these results suggested that H2 might function as an important gaseous molecule that alleviates oxidative stress via HO-1 signalling.

  1. Mechanism for the atomic layer deposition of copper using diethylzinc as the reducing agent: a density functional theory study using gas-phase molecules as a model.

    PubMed

    Dey, Gangotri; Elliott, Simon D

    2012-09-06

    We present theoretical studies based on first-principles density functional theory calculations for the possible gas-phase mechanism of the atomic layer deposition (ALD) of copper by transmetalation from common precursors such as Cu(acac)(2), Cu(hfac)(2), Cu(PyrIm(R))(2) with R = (i)Pr and Et, Cu(dmap)(2), and CuCl(2) where diethylzinc acts as the reducing agent. An effect on the geometry and reactivity of the precursors due to differences in electronegativity, steric hindrance, and conjugation present in the ligands was observed. Three reaction types, namely, disproportionation, ligand exchange, and reductive elimination, were considered that together comprise the mechanism for the formation of copper in its metallic state starting from the precursors. A parallel pathway for the formation of zinc in its metallic form was also considered. The model Cu(I) molecule Cu(2)L(2) was studied, as Cu(I) intermediates at the surface play an important role in copper deposition. Through our study, we found that accumulation of an LZnEt intermediate results in zinc contamination by the formation of either Zn(2)L(2) or metallic zinc. Ligand exchange between Cu(II) and Zn(II) should proceed through a Cu(I) intermediate, as otherwise, it would lead to a stable copper molecule rather than copper metal. Volatile ZnL(2) favors the ALD reaction, as it carries the reaction forward.

  2. A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface.

    PubMed

    Gao, You Kun; Traeger, Franziska; Kotsis, Konstantinos; Staemmler, Volker

    2011-06-14

    The adsorption of alanine on the mixed-terminated ZnO(10 ̅10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ̅10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ̅10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ̅10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.

  3. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  4. The effect of H2O gas on volatilities of planet-forming major elements. I - Experimental determination of thermodynamic properties of Ca-, Al-, and Si-hydroxide gas molecules and its application to the solar nebula

    NASA Technical Reports Server (NTRS)

    Hashimoto, Akihiko

    1992-01-01

    The vapor pressures of Ca(OH)2(g), Al(OH)3(g), and Si(OH)4(g) molecules in equilibrium with solid calcium-, aluminum, and silicon-oxides, respectively, were determined, and were used to derive the heats of formation and entropies of these species, which are expected to be abundant under the currently postulated physical conditions in the primordial solar nebula. These data, in conjunction with thermodynamic data from literature, were used to calculate the relative abundances of M, MO(x), and M(OH)n gas species and relative volatilities of Fe, Mg, Si, Ca, and Al for ranges of temperature, total pressure, and H/O abundance ratio corresponding to the plausible ranges of physical conditions in the solar nebula. The results are used to explain how Ca and Al could have evaporated from Ca,Al-rich inclusions in carbonaceous chondrites, while Si, Mg, and Fe condensed onto them during the preaccretion alteration of CAIs.

  5. Intraspecific Signals Inducing Aggregation in Periplaneta americana (Insecta: Dictyoptera).

    PubMed

    Imen, Saïd; Christian, Malosse; Virginie, Durier; Colette, Rivault

    2015-06-01

    Chemical communication is necessary to induce aggregation and to maintain the cohesion of aggregates in Periplaneta americana (L.) cockroaches. We aimed to identify the chemical message inducing aggregation in this species. Two types of bioassays were used-binary choice tests in Petri dishes and tests in Y-olfactometer. Papers conditioned by direct contact of conspecifics induce aggregation when proposed in binary choice tests and were attractive in a Y-olfactometer. The identification of the molecules present on these conditioned papers indicated that dichloromethane extracts contained mainly cuticular hydrocarbons whereas methanol extracts contained more volatile molecules. Only a mixture of extracts in both solvents induced aggregation. High concentrations of cuticular hydrocarbons are necessary to induce aggregation when presented alone. When presented with volatile molecules present in methanol extracts, low concentrations of cuticular hydrocarbons are sufficient to induce aggregation if they are presented in contact. Among volatile molecules collected on filter paper, a mixture of three compounds-hexadecanoic acid, pentadecanoic acid, and pentaethylene glycol-induced aggregation. Our results provide evidence that aggregation processes in P. americana relies on a dual mechanism: attraction over long distances by three volatile molecules and maintenance on site by contact with cuticular hydrocarbons.

  6. Detergent-mediated protein aggregation.

    PubMed

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E; Privé, Gilbert G; Pomès, Régis

    2013-04-01

    Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.

  7. Classification and Characterization of Therapeutic Antibody Aggregates

    PubMed Central

    Joubert, Marisa K.; Luo, Quanzhou; Nashed-Samuel, Yasser; Wypych, Jette; Narhi, Linda O.

    2011-01-01

    A host of diverse stress techniques was applied to a monoclonal antibody (IgG2) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134–25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG1 and IgG2 subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced. PMID:21454532

  8. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    NASA Astrophysics Data System (ADS)

    Makarov, G. N.; Petin, A. N.

    2016-03-01

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF6 and CF3I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF6 molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation.

  9. Oxygen limitation within a bacterial aggregate.

    PubMed

    Wessel, Aimee K; Arshad, Talha A; Fitzpatrick, Mignon; Connell, Jodi L; Bonnecaze, Roger T; Shear, Jason B; Whiteley, Marvin

    2014-04-15

    ABSTRACT Cells within biofilms exhibit physiological heterogeneity, in part because of chemical gradients existing within these spatially structured communities. Previous work has examined how chemical gradients develop in large biofilms containing >10(8) cells. However, many bacterial communities in nature are composed of small, densely packed aggregates of cells (≤ 10(5) bacteria). Using a gelatin-based three-dimensional (3D) printing strategy, we confined the bacterium Pseudomonas aeruginosa within picoliter-sized 3D "microtraps" that are permeable to nutrients, waste products, and other bioactive small molecules. We show that as a single bacterium grows into a maximally dense (10(12) cells ml(-1)) clonal population, a localized depletion of oxygen develops when it reaches a critical aggregate size of ~55 pl. Collectively, these data demonstrate that chemical and phenotypic heterogeneity exists on the micrometer scale within small aggregate populations. IMPORTANCE Before developing into large, complex communities, microbes initially cluster into aggregates, and it is unclear if chemical heterogeneity exists in these ubiquitous micrometer-scale aggregates. We chose to examine oxygen availability within an aggregate since oxygen concentration impacts a number of important bacterial processes, including metabolism, social behaviors, virulence, and antibiotic resistance. By determining that oxygen availability can vary within aggregates containing ≤ 10(5) bacteria, we establish that physiological heterogeneity exists within P. aeruginosa aggregates, suggesting that such heterogeneity frequently exists in many naturally occurring small populations.

  10. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  11. Intercomparison of stratospheric water vapor observed by satellite experiments: Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

    SciTech Connect

    Chiou, E.W.; Larsen, J.C. ); McCormick, M.P.; McMaster, L.R.; Chu, W.P. ); Rind, D. ); Oltmans, S. )

    1993-03-20

    This paper presents a comparison of the stratospheric water vapor measurements made by the satellite-borne sensors the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS), and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. LIMS obtained data for 7 months between November 1978 and May 1979; ATMOS was carried on Shuttle and observed eight profiles from April 30 to May 6, 1985 at approximately 30[degrees]N and 50[degrees]S; and, SAGE II continues to make measurements since its launch in October 1984. For both 30[degrees]N and 50[degrees]S in May, the comparisons between SAGE II and ATMOS show agreement within the estimated combined uncertainty of the two experiments. Several important features identified by LIMS observations have been confirmed by SAGE II: a well-developed hygropause in the lower stratosphere at low- to mid-latitudes, a poleward latitudinal gradient, increasing water vapor mixing ratios with altitude in the tropics, and the transport of dry lower stratospheric water vapor upward and southward in May, and upward and northward in November. A detailed comparative study also indicates that the two previously suggested corrections for LIMS, a correction in tropical lower stratosphere due to a positive temperature bias and the correction above 28 km based on improved emissivities will bring LIMS measurements much closer to those of SAGE II. The only significant difference occurs at high southern latitudes in May below 18 km, where LIMS measurements are 2-3 ppmv greater. It should be noted that LIMS observations are from 16 to 50 km, ATMOS from 14 to 86 km, and SAGE II from mid-troposphere to 40 km. With multiyear coverage, SAGE II observations should be useful for studying tropospheric-stratospheric exchange, for stratospheric transport, and for preparing water vapor climatologies for the stratosphere and the upper troposphere. 32 refs., 14 figs., 2 tabs.

  12. Intercomparison of stratospheric water vapor observed by satellite experiments: Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

    NASA Astrophysics Data System (ADS)

    Chiou, E. W.; McCormick, M. P.; McMaster, L. R.; Chu, W. P.; Larsen, J. C.; Rind, D.; Oltmans, S.

    1993-03-01

    This paper presents a comparison of the stratospheric water vapor measurements made by the satellite-borne sensors the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS), and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. LIMS obtained data for 7 months between November 1978 and May 1979; ATMOS was carried on Shuttle and observed eight profiles from April 30 to May 6, 1985 at approximately 30°N and 50°S; and, SAGE II continues to make measurements since its launch in October 1984. For both 30°N and 50°S in May, the comparisons between SAGE II and ATMOS show agreement within the estimated combined uncertainty of the two experiments. Several important features identified by LIMS observations have been confirmed by SAGE II: a well-developed hygropause in the lower stratosphere at low- to mid-latitudes, a poleward latitudinal gradient, increasing water vapor mixing ratios with altitude in the tropics, and the transport of dry lower stratospheric water vapor upward and southward in May, and upward and northward in November. A detailed comparative study also indicates that the two previously suggested corrections for LIMS, a correction in tropical lower stratosphere due to a positive temperature bias and the correction above 28 km based on improved emissivities will bring LIMS measurements much closer to those of SAGE II. The only significant difference occurs at high southern latitudes in May below 18 km, where LIMS measurements are 2-3 ppmv greater. It should be noted that LIMS observations are from 16 to 50 km, ATMOS from 14 to 86 km, and SAGE II from mid-troposphere to 40 km. With multiyear coverage, SAGE II observations should be useful for studying tropospheric-stratospheric exchange, for stratospheric transport, and for preparing water vapor climatologies for the stratosphere and the upper troposphere.

  13. Heme and iron induce protein aggregation.

    PubMed

    Travassos, Leonardo H; Vasconcellos, Luiz R C; Bozza, Marcelo T; Carneiro, Leticia A M

    2017-03-04

    Heme is an essential molecule expressed in many tissues where it plays key roles as the prosthetic group of several proteins involved in vital physiological and metabolic processes such as gas and electron transport. Structurally, heme is a tetrapyrrole ring containing an atom of iron (Fe) in its center. When released into the extracellular milieu, heme exerts several deleterious effects, which make it an important player in infectious and noninfectious hemolytic diseases where large amounts of free heme are observed such as malaria, dengue fever, β-thalassemia, sickle cell disease and ischemia-reperfusion. Our recent work has uncovered an unappreciated cellular response triggered by heme or Fe, one of its degradation products, on macrophages, which is the formation of protein aggregates known as aggresome-like induced structres (ALIS). This response was shown to be fully dependent on ROS production and the activation of the transcription factor NFE2L2/NRF2. In addition, we have demonstrated that heme degradation by HMOX1/HO-1 (heme oxygenase 1) is required and that Fe is essential for the formation of ALIS, as heme analogs lacking the central atom of Fe are not able to induce these structures. ALIS formation is also observed in vivo, in a model of phenylhydrazine (PHZ)-induced hemolysis, indicating that it is an integral part of the host response to excessive free heme and that it may play a role in cellular homeostasis.

  14. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  15. On mean type aggregation.

    PubMed

    Yager, R R

    1996-01-01

    We introduce and define the concept of mean aggregation of a collection of n numbers. We point out that the lack of associativity of this operation compounds the problem of the extending mean of n numbers to n+1 numbers. The closely related concepts of self identity and the centering property are introduced as one imperative for extending mean aggregation operators. The problem of weighted mean aggregation is studied. A new concept of prioritized mean aggregation is then introduced. We next show that the technique of selecting an element based upon the performance of a random experiment can be considered as a mean aggregation operation.

  16. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  17. Protein aggregation in a membrane environment.

    PubMed

    Gorbenko, Galyna; Trusova, Valeriya

    2011-01-01

    Biological membranes are featured by a remarkable ability to modulate a wide range of physiological and pathological processes. Of these, protein aggregation is currently receiving the greatest attention, as one type of the ordered protein aggregates, amyloid fibrils, proved to be involved in molecular etiology of a number of fatal diseases. It has been hypothesized that nucleation of amyloid fibrils and toxic action of their precursors is mediated by lipid-protein interactions. Lipid bilayer provides a variety of environments in which aggregated state of polypeptide chain appears to be more thermodynamically favorable than its monomeric form. The major factors responsible for the enhanced self-association propensity of membrane-bound proteins include (i) structural transition of polypeptide chain into aggregation-prone conformation; (ii) protein crowding in a lipid phase; (iii) particular aggregation-favoring orientation and bilayer embedment of the protein molecules. All these factors are considered in the present review with an emphasis being put on the role of electrostatic, hydrophobic, and hydrogen-bonding phenomena in initiating and modulating the protein aggregation on a membrane template. Likewise, we survey the advanced experimental techniques employed for detection and structural characterization of the aggregated species in membrane systems.

  18. Mass spectrometry study of multiply negatively charged, gas-phase NaAOT micelles: how does charge state affect micellar structure and encapsulation?

    PubMed

    Fang, Yigang; Liu, Fangwei; Liu, Jianbo

    2013-01-01

    We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na(n-z)AOT(n)](z-) (n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Na(n-1)AOT(n)H(2)O](-) of n = 3-9. Incorporation of glycine and tryptophan into [Na(n-z)AOT(n)](z-) aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na(n-z)AOT(n)](z-) of n ≥ 7, and at most two glycine molecules could be hosted in that of n ≥ 13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n ≥ 6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na(n+z)AOT(n)](z+) aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.

  19. STAND: Surface Tension for Aggregation Number Determination.

    PubMed

    Garrido, Pablo F; Brocos, Pilar; Amigo, Alfredo; García-Río, Luis; Gracia-Fadrique, Jesús; Piñeiro, Ángel

    2016-04-26

    Taking advantage of the extremely high dependence of surface tension on the concentration of amphiphilic molecules in aqueous solution, a new model based on the double equilibrium between free and aggregated molecules in the liquid phase and between free molecules in the liquid phase and those adsorbed at the air/liquid interface is presented and validated using literature data and fluorescence measurements. A key point of the model is the use of both the Langmuir isotherm and the Gibbs adsorption equation in terms of free molecules instead of the nominal concentration of the solute. The application of the model should be limited to non ionic compounds since it does not consider the presence of counterions. It requires several coupled nonlinear fittings for which we developed a software that is publicly available in our server as a web application. Using this tool, it is straightforward to get the average aggregation number of an amphiphile, the micellization free energy, the adsorption constant, the maximum surface excess (and so the minimum area per molecule), the distribution of solute in the liquid phase between free and aggregate species, and the surface coverage in only a couple of seconds, just by uploading a text file with surface tension vs concentration data and the corresponding uncertainties.

  20. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

    Described is a school project to investigate aggregations in flatworms which may be influenced by light intensity, temperature, and some form of chemical stimulus released by already aggregating flatworms. Such investigations could be adopted to suit many educational levels of science laboratory activities. (DS)

  1. Unbonded Aggregate Surface Roads

    DTIC Science & Technology

    2006-12-01

    are sufficiently angular and rough in texture, thus ensuring mixture stability. A popular asphalt mixture design method called Superpave Level 1...would not pass either of the Superpave aggregate requirements. Table 18 Additional Characteristics for the Fine Fraction Abbreviated Common Name...CBR values when compacted wet of optimum. This is likely attributable to their relatively high permeabilities . For soaked CBR tests, the aggregates

  2. Erosion of dust aggregates

    NASA Astrophysics Data System (ADS)

    Seizinger, A.; Krijt, S.; Kley, W.

    2013-12-01

    Aims: The aim of this work is to gain a deeper insight into how much different aggregate types are affected by erosion. Especially, it is important to study the influence of the velocity of the impacting projectiles. We also want to provide models for dust growth in protoplanetary disks with simple recipes to account for erosion effects. Methods: To study the erosion of dust aggregates we employed a molecular dynamics approach that features a detailed micro-physical model of the interaction of spherical grains. For the first time, the model has been extended by introducing a new visco-elastic damping force, which requires a proper calibration. Afterwards, different sample generation methods were used to cover a wide range of aggregate types. Results: The visco-elastic damping force introduced in this work turns out to be crucial to reproduce results obtained from laboratory experiments. After proper calibration, we find that erosion occurs for impact velocities of 5 ms-1 and above. Though fractal aggregates as formed during the first growth phase are most susceptible to erosion, we observe erosion of aggregates with rather compact surfaces as well. Conclusions: We find that bombarding a larger target aggregate with small projectiles results in erosion for impact velocities as low as a few ms-1. More compact aggregates suffer less from erosion. With increasing projectile size the transition from accretion to erosion is shifted to higher velocities. This allows larger bodies to grow through high velocity collisions with smaller aggregates.

  3. Cell and Particle Interactions and Aggregation During Electrophoretic Motion

    NASA Technical Reports Server (NTRS)

    Davis, Robert H.

    2000-01-01

    The objectives of this research were (i) to perform experiments for observing and quantifying electrophoretic aggregation, (ii) to develop a theoretical description to appropriately analyze and compare with the experimental results, (iii) to study the combined effects of electrophoretic and gravitational aggregation of large particles, and the combined effects of electrophoretic and Brownian aggregation of small particles, and (iv) to perform a preliminary design of a potential future flight experiment involving electrophoretic aggregation. Electrophoresis refers to the motion of charged particles, droplets or molecules in response to an applied electric field. Electrophoresis is commonly used for analysis and separation of biological particles or molecules. When particles have different surface charge densities or potentials, they will migrate at different velocities in an electric field. This differential migration leads to the possibility that they will collide and aggregate, thereby preventing separation.

  4. Influence of Phenylalanine on Carotenoid Aggregation

    NASA Astrophysics Data System (ADS)

    Lu, L.; Ni, X.; Luo, X.

    2015-01-01

    The carotenoids lutein and β-carotene form, in 1:1 ethanol-water mixtures H-aggregates, of different strengths. The effects of phenylalanine on these aggregates were recorded by UV-Vis absorption, steady-state fluorescence, and Raman spectra. The H-aggregate of lutein was characterized by a large 78 nm blue shift in the absorption spectra, confirming the strong coupling between hydroxyl groups of adjacent molecules. The 15 nm blue shift in the β-carotene mixture also indicates that it was assembled by weak coupling between polyenes. After adding phenylalanine, the reducing absorption strength of the aggregates of lutein and reappearance of vibrational substructure indicate that the hydroxyl and amino groups of phenylalanine may coordinate to lutein and disaggregate the H-aggregates. However, phenylalanine had no effect on aggregates of β-carotene. The Raman spectra show three bands of carotenoids whose intensities decreased with increasing phenylalanine concentration. The frequency of ν1 corresponding to the length of the conjugated region was more sensitive to the solution of lutein. This coordination of phenylalanine to lutein could increase the length of the conjugated region. In addition, phenylalanine significantly affected the excited electronic states of carotenoids, which were crucial in the energy transfer from carotenoids to chlorophyll a in vivo.

  5. H- and J-aggregation of fluorene-based chromophores.

    PubMed

    Deng, Yonghong; Yuan, Wen; Jia, Zhe; Liu, Gao

    2014-12-11

    Understanding of H- and J-aggregation behaviors in fluorene-based polymers is significant both for determining the origin of various red-shifted emissions occurring in blue-emitting polyfluorenes and for developing polyfluorene-based device performance. In this contribution, we demonstrate a new theory of the H- and J-aggregation of polyfluorenes and oligofluorenes, and understand the influence of chromosphere aggregation on their photoluminescent properties. H- and J-aggregates are induced by a continuous increasing concentration of the oligofluorene or polyfluorene solution. A relaxed molecular configuration is simulated to illustrate the spatial arrangement of the bonding of fluorenes. It is indicated that the relaxed state adopts a 21 helical backbone conformation with a torsion angle of 18° between two connected repeat units. This configuration makes the formation of H- and J-aggregates through the strong π-π interaction between the backbone rings. A critical aggregation concentration is observed to form H- and J-aggregates for both polyfluorenes and oligofluorenes. These aggregates show large spectral shifts and distinct shape changes in photoluminescent excitation (PLE) and emission (PL) spectroscopy. Compared with "isolated" chromophores, H-aggregates induce absorption spectral blue-shift and fluorescence spectral red-shift but largely reduce fluorescence efficiency. "Isolated" chromophores not only refer to "isolated molecules" but also include those associated molecules if their conjugated backbones are not compact enough to exhibit perturbed absorption and emission. J-aggregates induce absorption spectral red-shift and fluorescence spectral red-shift but largely enhance fluorescence efficiency. The PLE and PL spectra also show that J-aggregates dominate in concentrated solutions. Different from the excimers, the H- and J-aggregate formation changes the ground-state absorption of fluorene-based chromophores. H- and J-aggregates show changeable

  6. Dynamics of Activated Molecules

    SciTech Connect

    Mullin, Amy S.

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  7. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  8. Sans study of asphaltene aggregation

    SciTech Connect

    Overfield, R.E.; Sheu, E.Y.; Sinha, S.K.; Liang, K.S. )

    1988-06-01

    The colloidal properties of asphaltenes have long been recognized from peculiarities in their solubility and colligative properties. A layered micellar model or asphaltenes was proposed by others in which a highly condensed alkyl aromatic formed the central part, and molecules of decreasingly aromatic character (resins) clustered around them. Numerous studies, based on a variety of techniques such as ultracentrifugation and electron microscopy indicated a particulate nature for asphaltenes with size 20-40 A diameter. Others have proposed a refined model based on x-ray diffraction and small angle scattering. In this model, interactions between flat sheets of condensed aromatic rings form the central ''crystallite'' part of a spherical particle with the outer part being comprised of the aliphatic positions of the same molecules. These particles are bunched together with some degree of entanglement into ''micelles''. Concentration and solvent dependent radii of gyration, ranging from 30-50 A were reported. The aggregation creates a good deal of uncertainty as to the true molecular size or weight of asphaltenes. Neutron scattering offers novel contrast relative to light scattering (refractive index) and x-ray scattering (electron density). This is because the scattering length of proton is negative, whereas that from deuterium and other nuclei such as C, S, O, and N are positive. Thus by replacing hydrogen with deuterium in either the solvent or the scatterer the contrast can be varied, and different parts of the molecule can be highlighted.

  9. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    SciTech Connect

    Makarov, G N; Petin, A N

    2016-03-31

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF{sub 6} and CF{sub 3}I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF{sub 6} molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation. (laser separation of isotopes)

  10. Aggregate and the environment

    USGS Publications Warehouse

    Langer, William H.; Drew, Lawrence J.; Sachs, J.S.

    2004-01-01

    This book is designed to help you understand our aggregate resources-their importance, where they come from, how they are processed for our use, the environmental concerns related to their mining and processing, how those concerns are addressed, and the policies and regulations designed to safeguard workers, neighbors, and the environment from the negative impacts of aggregate mining. We hope this understanding will help prepare you to be involved in decisions that need to be made-individually and as a society-to be good stewards of our aggregate resources and our living planet.

  11. Global optimization of cholic acid aggregates

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Viskolcz, Béla; Poša, Mihalj; Fejer, Szilard N.

    2014-04-01

    In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.

  12. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  13. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  14. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  15. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  16. Marine aggregate dynamics

    NASA Astrophysics Data System (ADS)

    The direction and scope of the Office of Naval Research's Marine Aggregate Dynamics Accelerated Research Initiative will be the topic of an open-house style meeting February 14, 7:30-10:00 P.M. in Ballroom D of the Hyatt Regency New Orleans at the Louisiana Superdome. This meeting is scheduled during the AGU/American Society of Limnology and Oceanography Ocean Sciences Meeting February 12-16 in New Orleans.The critical focus of the ARI is the measurement and modeling of the dynamics of the biological, physical, chemical and molecular processes that drive aggregation and produce aggregates. This new ARI will provide funding in Fiscal Years 1991-1995 to identify and quantify mechanisms that determine the distribution, abundance and size spectrum of aggregated particulate matter in the ocean.

  17. Protein Colloidal Aggregation Project

    NASA Technical Reports Server (NTRS)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  18. Aggregation and Averaging.

    ERIC Educational Resources Information Center

    Siegel, Irving H.

    The arithmetic processes of aggregation and averaging are basic to quantitative investigations of employment, unemployment, and related concepts. In explaining these concepts, this report stresses need for accuracy and consistency in measurements, and describes tools for analyzing alternative measures. (BH)

  19. The mechanism of oxidation-induced low-density lipoprotein aggregation: an analogy to colloidal aggregation and beyond?

    PubMed Central

    Xu, S; Lin, B

    2001-01-01

    Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein molecules aggregate and form nucleation units. The nucleation units chain together and form linear aggregates. The linear aggregates branch and interact with one another, forming fractals. In the fusion stage, spatially adjacent nucleation units in the fractal fuse into curved membrane surfaces, which, in turn, fuse into multilamellar or unilamellar vesicles. Alternatively, some adjacent nucleation units in the fractals assemble in a straight line and form rods. Subsequently, the rods flatten out into rough and then into smooth ribbons. Occasionally, tubular membrane vesicles are formed from the fractals. The aggregation stage seems to be analogous to colloidal aggregation and amyloid fiber formation. The fusion stage seems to be characteristic of the lipid-rich lipoproteins and is beyond colloidal aggregation and amyloid fiber formation. PMID:11566810

  20. High resolution UV resonance enhanced two-photon ionization spectroscopy with mass selection of biologically relevant molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Chervenkov, S.; Wang, P. Q.; Karaminkov, R.; Chakraborty, T.; Braun, Juergen E.; Neusser, Hans J.

    2005-04-01

    The high resolution Doppler-free resonance-enhanced two-photon ionization (R2PI) spectroscopy with mass selection of jet-cooled (2-12 K) molecular species is a powerful experimental method providing comprehensive information on both isolated molecules and molecular clusters. We have demonstrated for the first time that this technique can be applied to large molecules and provides detailed information on their conformational structure. It allows rotationally resolved (FWHM = 70 MHz) spectra of the vibronic bands of the S1<--S0 electronic transition of the studied molecular systems to be measured. A specially designed computer-assisted fitting routine based on genetic algorithms is used to determine their rotational constants in the ground and excited electronic states, respectively, and the transition moment ratio. To interpret the experimental information and to discriminate and unambiguously assign the observed approach to the study of the neurotransmitter molecule, ephedrine. The results elucidate the role of the intramolecular hydrogen bonds stabilizing the respective conformations and affecting their intrinsic properties.

  1. Characterization of Ovine Dermal Papilla Cell Aggregation

    PubMed Central

    Sari, Agnes Rosarina Prita; Rufaut, Nicholas Wolfgang; Jones, Leslie Norman; Sinclair, Rodney Daniel

    2016-01-01

    Context: The dermal papilla (DP) is a condensation of mesenchymal cells at the proximal end of the hair follicle, which determines hair shaft size and regulates matrix cell proliferation and differentiation. DP cells have the ability to regenerate new hair follicles. These cells tend to aggregate both in vitro and in vivo. This tendency is associated with the ability of papilla cells to induce hair growth. However, human papilla cells lose their hair-inducing activity in later passage number. Ovine DP cells are different from human DP cells since they do not lose their aggregative behavior or hair-inducing activity in culture. Nonetheless, our understanding of ovine DP cells is still limited. Aim: The aim of this study was to observe the expression of established DP markers in ovine cells and their association with aggregation. Subjects and Methods: Ovine DP cells from three different sheep were compared. Histochemistry, immunoflourescence, and polymerase chain reaction experiments were done to analyze the DP markers. Results: We found that ovine DP aggregates expressed all the 16 markers evaluated, including alkaline phosphatase and versican. Expression of the versican V0 and V3 isoforms, neural cell adhesion molecule, and corin was increased significantly with aggregation, while hey-1 expression was significantly decreased. Conclusions: Overall, the stable expression of numerous markers suggests that aggregating ovine DP cells have a similar phenotype to papillae in vivo. The stability of their molecular phenotype is consistent with their robust aggregative behavior and retained follicle-inducing activity after prolonged culture. Their phenotypic stability in culture contrasts with DP cells from other species, and suggests that a better understanding of ovine DP cells might provide opportunities to improve the hair-inducing activity and therapeutic potential of human cells. PMID:27625564

  2. Fibronectin Aggregation and Assembly

    PubMed Central

    Ohashi, Tomoo; Erickson, Harold P.

    2011-01-01

    The mechanism of fibronectin (FN) assembly and the self-association sites are still unclear and contradictory, although the N-terminal 70-kDa region (I1–9) is commonly accepted as one of the assembly sites. We previously found that I1–9 binds to superfibronectin, which is an artificial FN aggregate induced by anastellin. In the present study, we found that I1–9 bound to the aggregate formed by anastellin and a small FN fragment, III1–2. An engineered disulfide bond in III2, which stabilizes folding, inhibited aggregation, but a disulfide bond in III1 did not. A gelatin precipitation assay showed that I1–9 did not interact with anastellin, III1, III2, III1–2, or several III1–2 mutants including III1–2KADA. (In contrast to previous studies, we found that the III1–2KADA mutant was identical in conformation to wild-type III1–2.) Because I1–9 only bound to the aggregate and the unfolding of III2 played a role in aggregation, we generated a III2 domain that was destabilized by deletion of the G strand. This mutant bound I1–9 as shown by the gelatin precipitation assay and fluorescence resonance energy transfer analysis, and it inhibited FN matrix assembly when added to cell culture. Next, we introduced disulfide mutations into full-length FN. Three disulfide locks in III2, III3, and III11 were required to dramatically reduce anastellin-induced aggregation. When we tested the disulfide mutants in cell culture, only the disulfide bond in III2 reduced the FN matrix. These results suggest that the unfolding of III2 is one of the key factors for FN aggregation and assembly. PMID:21949131

  3. Critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point using the combination of the Tompa model and the van der Waals equation.

    PubMed

    Gençaslan, Mustafa; Keskin, Mustafa

    2012-02-14

    We combine the modified Tompa model with the van der Waals equation to study critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point. The van Laar point is coined by Meijer and it is the only point at which the mathematical double point curve is stable. It is the intersection of the tricritical point and the double critical end point. We calculate the critical lines as a function of χ(1) and χ(2), the density of type I molecules and the density of type II molecules for various values of the system parameters; hence the global phase diagrams are presented and discussed in the density-density plane. We also investigate the connectivity of critical lines at the van Laar point and its vicinity and discuss these connections according to the Scott and van Konynenburg classifications. It is also found that the critical lines and phase behavior are extremely sensitive to small modifications in the system parameters.

  4. Collisional Aggregation Due to Turbulence

    NASA Astrophysics Data System (ADS)

    Pumir, Alain; Wilkinson, Michael

    2016-03-01

    Collisions between particles suspended in a fluid play an important role in many physical processes. As an example, collisions of microscopic water droplets in clouds are a necessary step in the production of macroscopic raindrops. Collisions of dust grains are also conjectured to be important for planet formation in the gas surrounding young stars and to play a role in the dynamics of sand storms. In these processes, collisions are favored by fast turbulent motions. Here we review recent advances in the understanding of collisional aggregation due to turbulence. We discuss the role of fractal clustering of particles and caustic singularities of their velocities. We also discuss limitations of the Smoluchowski equation for modeling such processes. These advances lead to a semiquantitative understanding on the influence of turbulence on collision rates and point to deficiencies in the current understanding of rainfall and planet formation.

  5. Gas sensing at the nanoscale: engineering SWCNT-ITO nano-heterojunctions for the selective detection of NH3 and NO2 target molecules

    NASA Astrophysics Data System (ADS)

    Rigoni, F.; Drera, G.; Pagliara, S.; Perghem, E.; Pintossi, C.; Goldoni, A.; Sangaletti, L.

    2017-01-01

    The gas response of single-wall carbon nanotubes (SWCNT) functionalized with indium tin oxide (ITO) nanoparticles (NP) has been studied at room temperature and an enhanced sensitivity to ammonia and nitrogen dioxide is demonstrated. The higher sensitivity in the functionalized sample is related to the creation of nano-heterojunctions at the interface between SWCNT bundles and ITO NP. Furthermore, the different response of the two devices upon NO2 exposure provides a way to enhance also the selectivity. This behavior is rationalized by considering a gas sensing mechanism based on the build-up of space-charge layers at the junctions. Finally, full recovery of the signal after exposure to NO2 is achieved by UV irradiation for the functionalized sample, where the ITO NP can play a role to hinder the poisoning effects on SWCNT due to NO2 chemisorption.

  6. Gas sensing at the nanoscale: engineering SWCNT-ITO nano-heterojunctions for the selective detection of NH3 and NO2 target molecules.

    PubMed

    Rigoni, F; Drera, G; Pagliara, S; Perghem, E; Pintossi, C; Goldoni, A; Sangaletti, L

    2017-01-20

    The gas response of single-wall carbon nanotubes (SWCNT) functionalized with indium tin oxide (ITO) nanoparticles (NP) has been studied at room temperature and an enhanced sensitivity to ammonia and nitrogen dioxide is demonstrated. The higher sensitivity in the functionalized sample is related to the creation of nano-heterojunctions at the interface between SWCNT bundles and ITO NP. Furthermore, the different response of the two devices upon NO2 exposure provides a way to enhance also the selectivity. This behavior is rationalized by considering a gas sensing mechanism based on the build-up of space-charge layers at the junctions. Finally, full recovery of the signal after exposure to NO2 is achieved by UV irradiation for the functionalized sample, where the ITO NP can play a role to hinder the poisoning effects on SWCNT due to NO2 chemisorption.

  7. Search for evidence of life in space: analysis of enantiomeric organic molecules by N,N-dimethylformamide dimethylacetal derivative dependant Gas Chromatography-Mass Spectrometry.

    PubMed

    Freissinet, C; Buch, A; Sternberg, R; Szopa, C; Geffroy-Rodier, C; Jelinek, C; Stambouli, M

    2010-01-29

    Within the context of the future space missions to Mars (MSL 2011 and Exomars 2016), which aim at searching for traces of life at the surface, the detection and quantitation of enantiomeric organic molecules is of major importance. In this work, we have developed and optimized a method to derivatize and analyze chiral organic molecules suitable for space experiments, using N,N-dimethylformamide dimethylacetal (DMF-DMA) as the derivatization agent. The temperature, duration of the derivatization reaction, and chromatographic separation parameters have been optimized to meet instrument design constraints imposed upon space experiment devices. This work demonstrates that, in addition to its intrinsic qualities, such as production of light-weight derivatives and a great resistance to drastic operating conditions, DMF-DMA facilitates simple and fast derivatization of organic compounds (three minutes at 140 degrees C in a single-step) that is suitable for an in situ analysis in space. By using DMF-DMA as the derivatization agent, we have successfully identified 19 of the 20 proteinic amino acids and been able to enantiomerically separate ten of the potential 19 (glycine being non-chiral). Additionally, we have minimized the percentage of racemized amino acid compounds produced by optimizing the conditions of the derivatization reaction itself. Quantitative linearity studies and the determination of the limit of detection show that the proposed method is also suitable for the quantitative determination of both enantiomeric forms of most of the tested amino acids, as limits of detection obtained are lower than the ppb level of organic molecules already detected in Martian meteorites.

  8. Structure and mechanism of action of tau aggregation inhibitors

    PubMed Central

    Cisek, Katryna; Cooper, Grace L.; Huseby, Carol J.; Kuret, Jeff

    2015-01-01

    Since the discovery of phenothiazines as tau protein aggregation inhibitors, many additional small molecule inhibitors of diverse chemotype have been discovered and characterized in biological model systems. Although direct inhibition of tau aggregation has shown promise as a potential treatment strategy for depressing neurofibrillary lesion formation in Alzheimer’s disease, the mechanism of action of these compounds has been unclear. However, recent studies have found that tau aggregation antagonists exert their effects through both covalent and non-covalent means, and have identified associated potency and selectivity driving features. Here we review small-molecule tau aggregation inhibitors with a focus on compound structure and inhibitory mechanism. The elucidation of inhibitory mechanism has implications for maximizing on-target efficacy while minimizing off-target side effects. PMID:25387336

  9. Controlled Assembly of Biocompatible Metallic Nanoaggregates Using a Small Molecule Crosslinker

    PubMed Central

    Van Haute, Desiree; Longmate, Julia M.; Berlin, Jacob M.

    2015-01-01

    By introducing a capping step and controlling reaction parameters, the assembly of metallic nanoparticle aggregates can be achieved using a small molecule crosslinker. Aggregates can be assembled from particles of varied size and composition and the size of the aggregates can be systematically adjusted. Following cell uptake of 60 nm aggregates, the aggregates are stable and non-toxic to macrophage cells up to 55mM Au. PMID:26208123

  10. Aggregation kinetics of human mesenchymal stem cells under wave motion.

    PubMed

    Tsai, Ang-Chen; Liu, Yijun; Yuan, Xuegang; Chella, Ravindran; Ma, Teng

    2016-12-20

    Human mesenchymal stem cells (hMSCs) are primary candidates in cell therapy and regenerative medicine but preserving their therapeutic potency following culture expansion is a significant challenge. hMSCs can spontaneously assemble into three-dimensional (3D) aggregates that enhance their regenerative properties. The present study investigated the impact of hydrodynamics conditions on hMSC aggregation kinetics under controlled rocking motion. While various laboratory methods have been developed for hMSC aggregate production, the rocking platform provides gentle mixing and can be scaled up using large bags as in wave motion bioreactors. The results show that the hMSC aggregation is mediated by cell adhesion molecules and that aggregate size distribution is influenced by seeding density, culture time, and hydrodynamic conditions. The analysis of fluid shear stress by COMSOL indicated that aggregate size distribution is inversely correlated with shear stress and that the rocking angle had a more pronounced effect on aggregate size distribution than the rocking speed due to its impact on shear stress. hMSC aggregates obtained from the bioreactor exhibit increased stemness, migratory properties, and expression of angiogenic factors. The results demonstrate the potential of the rocking platform to produce hMSC aggregates with controlled size distribution for therapeutic application.

  11. Conformational stability as a design target to control protein aggregation.

    PubMed

    Costanzo, Joseph A; O'Brien, Christopher J; Tiller, Kathryn; Tamargo, Erin; Robinson, Anne Skaja; Roberts, Christopher J; Fernandez, Erik J

    2014-05-01

    Non-native protein aggregation is a prevalent problem occurring in many biotechnological manufacturing processes and can compromise the biological activity of the target molecule or induce an undesired immune response. Additionally, some non-native aggregation mechanisms lead to amyloid fibril formation, which can be associated with debilitating diseases. For natively folded proteins, partial or complete unfolding is often required to populate aggregation-prone conformational states, and therefore one proposed strategy to mitigate aggregation is to increase the free energy for unfolding (ΔGunf) prior to aggregation. A computational design approach was tested using human γD crystallin (γD-crys) as a model multi-domain protein. Two mutational strategies were tested for their ability to reduce/increase aggregation rates by increasing/decreasing ΔGunf: stabilizing the less stable domain and stabilizing the domain-domain interface. The computational protein design algorithm, RosettaDesign, was implemented to identify point variants. The results showed that although the predicted free energies were only weakly correlated with the experimental ΔGunf values, increased/decreased aggregation rates for γD-crys correlated reasonably well with decreases/increases in experimental ΔGunf, illustrating improved conformational stability as a possible design target to mitigate aggregation. However, the results also illustrate that conformational stability is not the sole design factor controlling aggregation rates of natively folded proteins.

  12. Binodal Colloidal Aggregation Test - 4: Polydispersion

    NASA Technical Reports Server (NTRS)

    Chaikin, Paul M.

    2008-01-01

    Binodal Colloidal Aggregation Test - 4: Polydispersion (BCAT-4-Poly) will use model hard-spheres to explore seeded colloidal crystal nucleation and the effects of polydispersity, providing insight into how nature brings order out of disorder. Crewmembers photograph samples of polymer and colloidal particles (tiny nanoscale spheres suspended in liquid) that model liquid/gas phase changes. Results will help scientists develop fundamental physics concepts previously cloaked by the effects of gravity.

  13. Technology meets aggregate

    SciTech Connect

    Wilson, C.; Swan, C.

    2007-07-01

    New technology carried out at Tufts University and the University of Massachusetts on synthetic lightweight aggregate has created material from various qualities of fly ash from coal-fired power plants for use in different engineered applications. In pilot scale manufacturing tests an 'SLA' containing 80% fly ash and 20% mixed plastic waste from packaging was produced by 'dry blending' mixed plastic with high carbon fly ash. A trial run was completed to produce concrete masonry unit (CMU) blocks at a full-scale facility. It has been shown that SLA can be used as a partial substitution of a traditional stone aggregate in hot asphalt mix. 1 fig., 2 photos.

  14. Different Strategies for Aggregation in Social Amoeba Colonies

    NASA Astrophysics Data System (ADS)

    Franck, Carl; Monaghan, Ryan; Bae, Albert; Loh, Duane; Bodenschatz, Eberhard

    2007-03-01

    When confronted by starvation, collections of the amoeba Dictyostelium discoideum seek to aggregate in order to form genome-preserving stalk and spore structures. We have been interested in the means by which individual cells unite for this purpose. It has long been recognized that communication by means of diffusion of small molecules affords one such strategy: periodic chemical wave signaling can direct individual cells to an aggregation site. By employing thin layer substrates that presumably alter the propagation characteristics of such waves, we have shifted the colonial aggregation strategies to modes that rely on adhesive interactions for initial stages of multicellular assembly. Besides relentless aggregation of individual cells into large scale streams, these substrates reveal remarkable structures composed of only a few cells which we call ``squads'' that search for each other in order to achieve sufficient aggregation mass in sparse populations.

  15. H- and J-aggregate behavior in polymeric semiconductors.

    PubMed

    Spano, Frank C; Silva, Carlos

    2014-01-01

    Aggregates of conjugated polymers exhibit two classes of fundamental electronic interactions: those occurring within a given chain and those occurring between chains. The impact of such excitonic interactions on the photophysics of polymer films can be understood using concepts of J- and H-aggregation originally developed by Kasha and coworkers to treat aggregates of small molecules. In polymer assemblies, intrachain through-bond interactions lead to J-aggregate behavior, whereas interchain Coulombic interactions lead to H-aggregate behavior. The photophysics of common emissive conjugated polymer films are determined by a competition between intrachain, J-favoring interactions and interchain, H-favoring interactions. We review formalisms describing absorption and photoluminescence lineshapes, based on intra- and intermolecular excitonic coupling, electron-vibrational coupling, and correlated energetic disorder. Examples include regioregular polythiophenes, pheneylene-vinylenes, and polydiacetylene.

  16. Development of tau aggregation inhibitors for Alzheimer's disease.

    PubMed

    Bulic, Bruno; Pickhardt, Marcus; Schmidt, Boris; Mandelkow, Eva-Maria; Waldmann, Herbert; Mandelkow, Eckhard

    2009-01-01

    A variety of human diseases are suspected to be directly linked to protein misfolding. Highly organized protein aggregates, called amyloid fibrils, and aggregation intermediates are observed; these are considered to be mediators of cellular toxicity and thus attract a great deal of attention from investigators. Neurodegenerative pathologies such as Alzheimer's disease account for a major part of these protein misfolding diseases. The last decade has witnessed a renaissance of interest in inhibitors of tau aggregation as potential disease-modifying drugs for Alzheimer's disease and other "tauopathies". The recent report of a phase II clinical trial with the tau aggregation inhibitor MTC could hold promise for the validation of the concept. This Review summarizes the available data concerning small-molecule inhibitors of tau aggregation from a medicinal chemistry point of view.

  17. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented.

  18. Rapid Coagulation of Porous Dust Aggregates outside the Snow Line: A Pathway to Successful Icy Planetesimal Formation

    NASA Astrophysics Data System (ADS)

    Okuzumi, Satoshi; Tanaka, Hidekazu; Kobayashi, Hiroshi; Wada, Koji

    2012-06-01

    Rapid orbital drift of macroscopic dust particles is one of the major obstacles to planetesimal formation in protoplanetary disks. We re-examine this problem by considering the porosity evolution of dust aggregates. We apply a porosity model based on recent N-body simulations of aggregate collisions, which allows us to study the porosity change upon collision for a wide range of impact energies. As a first step, we neglect collisional fragmentation and instead focus on dust evolution outside the snow line, where the fragmentation has been suggested to be less significant than inside the snow line because of the high sticking efficiency of icy particles. We show that dust particles can evolve into highly porous aggregates (with internal densities of much less than 0.1 g cm-3) even if collisional compression is taken into account. We also show that the high porosity triggers significant acceleration in collisional growth. This acceleration is a natural consequence of the particles' aerodynamical properties at low Knudsen numbers, i.e., at particle radii larger than the mean free path of the gas molecules. Thanks to this rapid growth, the highly porous aggregates are found to overcome the radial drift barrier at orbital radii less than 10 AU (assuming the minimum-mass solar nebula model). This suggests that, if collisional fragmentation is truly insignificant, formation of icy planetesimals is possible via direct collisional growth of submicron-sized icy particles.

  19. RAPID COAGULATION OF POROUS DUST AGGREGATES OUTSIDE THE SNOW LINE: A PATHWAY TO SUCCESSFUL ICY PLANETESIMAL FORMATION

    SciTech Connect

    Okuzumi, Satoshi; Kobayashi, Hiroshi; Tanaka, Hidekazu; Wada, Koji

    2012-06-20

    Rapid orbital drift of macroscopic dust particles is one of the major obstacles to planetesimal formation in protoplanetary disks. We re-examine this problem by considering the porosity evolution of dust aggregates. We apply a porosity model based on recent N-body simulations of aggregate collisions, which allows us to study the porosity change upon collision for a wide range of impact energies. As a first step, we neglect collisional fragmentation and instead focus on dust evolution outside the snow line, where the fragmentation has been suggested to be less significant than inside the snow line because of the high sticking efficiency of icy particles. We show that dust particles can evolve into highly porous aggregates (with internal densities of much less than 0.1 g cm{sup -3}) even if collisional compression is taken into account. We also show that the high porosity triggers significant acceleration in collisional growth. This acceleration is a natural consequence of the particles' aerodynamical properties at low Knudsen numbers, i.e., at particle radii larger than the mean free path of the gas molecules. Thanks to this rapid growth, the highly porous aggregates are found to overcome the radial drift barrier at orbital radii less than 10 AU (assuming the minimum-mass solar nebula model). This suggests that, if collisional fragmentation is truly insignificant, formation of icy planetesimals is possible via direct collisional growth of submicron-sized icy particles.

  20. Broadband Microwave Spectroscopy as a Tool to Study the Structures of Odorant Molecules and Weakly Bound Complexes in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-01

    The rotational spectrum of trans-cinnamaldehyde ((2E)-3-phenylprop-2-enal) has been obtained with chirped-pulse microwave spectroscopy in the frequency range of 2 - 8.5 GHz. The odorant molecule is the essential component in cinnamon oil and causes the characteristic smell. In the measured high-resolution spectrum, we were able to assign the rotational spectra of two conformers of trans-cinnamaldehyde as well as all singly 13C-substituted species of the lowest-energy conformer in natural abundance. Two different methods were used to determine the structure from the rotational constants, which will be compared within this contribution. In addition, the current progress of studying ether-alcohol complexes, aiming at an improved understanding of the interplay between hydrogen bonding and dispersion interaction, will be reported. Here, a special focus is placed on the complexes of diphenylether with small aliphatic alcohols.

  1. Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level

    NASA Astrophysics Data System (ADS)

    Keller, Adrian; Kopyra, Janina; Gothelf, Kurt V.; Bald, Ilko

    2013-08-01

    Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)-, (M-O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm2. To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm2 at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.

  2. Low symmetry in molecules with heavy peripheral atoms. The gas-phase structure of perfluoro(methylcyclohexane), C6F11CF3.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Wann, Derek A; Robertson, Heather E; Rankin, David W H

    2010-10-21

    When refining structures using gas electron diffraction (GED) data, assumptions are often made in order to reduce the number of required geometrical parameters. Where these relate to light, peripheral atoms there is little effect on the refined heavy-atom structure, which is well defined by the GED data. However, this is not the case when heavier atoms are involved. We have determined the gas-phase structure of perfluoro(methylcyclohexane), C(6)F(11)CF(3), using three different refinement methods and have shown that our new method, which makes use of both MP2 and molecular mechanics (MM) calculations to restrain the peripheral-atom geometry, gives a realistic structure without the need for damaging constraints. Only the conformer with the CF(3) group in an equatorial position was considered, as ab initio calculations showed this to be 25 kJ mol(-1) lower in energy than the axial conformer. Refinements combining both high-level and low-level calculations to give constraints were superior both to those based only on molecular mechanics and to those in which assumptions about the geometry were imposed.

  3. Aggregates, broccoli and cauliflower

    NASA Astrophysics Data System (ADS)

    Grey, Francois; Kjems, Jørgen K.

    1989-09-01

    Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

  4. Asphaltene aggregation and impact of alkylphenols.

    PubMed

    Goual, Lamia; Sedghi, Mohammad; Wang, Xiaoxiao; Zhu, Ziming

    2014-05-20

    The main objective of this study was to provide novel insights into the mechanism of asphaltene aggregation in toluene/heptane (Heptol) solutions and the effect of alkylphenols on asphaltene dispersion through the integration of advanced experimental and modeling methods. High-resolution transmission electron microscope (HRTEM) images revealed that the onset of asphaltene flocculation occurs near a toluene/heptane volume ratio of 70:30 and that flocculates are well below 1 μm in size. To assess the impact of alkylphenols on asphaltene aggregation, octylphenol (OP) and dodecylphenol (DP) were evaluated by impedance analysis based on their ability to delay the precipitation onset and to reduce the size of nonflocculated asphaltene aggregates in 80:20 toluene/heptane solutions. Although a longer dispersant chain length did not affect the precipitation onset, it reduced the size of the aggregates. Molecular dynamics simulations were then performed to understand the mechanism of interaction between a model asphaltene and OP in heptane. OP molecules saturated the H-bonding sites of asphaltenes and prevented them from interacting laterally between themselves. This explained why OP favored the formation of flocculates with filamentary rather than globular structures, which were clearly observed by HRTEM. Although OP proved to be an effective dispersant, its effectiveness was hindered by its self-association and the fact that it interacted at the periphery of asphaltenes, leaving their aromatic cores uncovered.

  5. Aggregation of MBP in chronic demyelination

    PubMed Central

    Frid, Kati; Einstein, Ofira; Friedman-Levi, Yael; Binyamin, Orli; Ben-Hur, Tamir; Gabizon, Ruth

    2015-01-01

    Objectives Misfolding of key disease proteins to an insoluble state is associated with most neurodegenerative conditions, such as prion, Parkinson, and Alzheimer’s diseases. In this work, and by studying animal models of multiple sclerosis, we asked whether this is also the case for myelin basic protein (MBP) in the late and neurodegenerative phases of demyelinating diseases. Methods To this effect, we tested whether MBP, an essential myelin component, present prion-like properties in animal models of MS, as is the case for Cuprizone-induced chronic demyelination or chronic phases of Experimental Autoimmune Encephalomyelitis (EAE). Results We show here that while total levels of MBP were not reduced following extensive demyelination, part of these molecules accumulated thereafter as aggregates inside oligodendrocytes or around neuronal cells. In chronic EAE, MBP precipitated concomitantly with Tau, a marker of diverse neurodegenerative conditions, including MS. Most important, analysis of fractions from Triton X-100 floatation gradients suggest that the lipid composition of brain membranes in chronic EAE differs significantly from that of naïve mice, an effect which may relate to oxidative insults and subsequently prevent the appropriate insertion and compaction of new MBP in the myelin sheath, thereby causing its misfolding and aggregation. Interpretation Prion-like aggregation of MBP following chronic demyelination may result from an aberrant lipid composition accompanying this pathological status. Such aggregation of MBP may contribute to neuronal damage that occurs in the progressive phase of MS. PMID:26273684

  6. In situ analysis of martian regolith with the SAM experiment during the first mars year of the MSL mission: Identification of organic molecules by gas chromatography from laboratory measurements

    NASA Astrophysics Data System (ADS)

    Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; François, P.; Coscia, D.; Bonnet, J. Y.; Teinturier, S.; Cabane, M.; Mahaffy, P. R.

    2016-09-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

  7. Unequilibrated, equilibrated, and reduced aggregates in anhydrous interplanetary dust particles

    NASA Astrophysics Data System (ADS)

    Bradley, J. P.

    1993-03-01

    Track-rich anhydrous IDP's are probably the most primitive IDP's because they have escaped significant post-accretional alteration; they exhibit evidence of (nebular) gas phase reactions; their mineralogy is similar to comet Halley's dust; and some of them exhibit comet-like IR spectral characteristics. However, basic questions about the mineralogy and petrography of anhydrous IDP's remain unanswered, because they contain aggregated components that can be heterogeneous on a scale of nanometers. In some IDP's, aggregates account for greater than 75 percent of the volume of the particle. The aggregates have been systematically examined using an analytical electron microscope (AEM), which provides probe-forming optics and (x-ray and electron) spectrometers necessary to analyze individual nanometer-sized grains. The AEM results reveal at least three mineralogically distinct classes of aggregates in an hydrous IDP's, with mineralogies reflecting significantly different formation/aggregation environments.

  8. Strain-dependent profile of misfolded prion protein aggregates

    PubMed Central

    Morales, Rodrigo; Hu, Ping Ping; Duran-Aniotz, Claudia; Moda, Fabio; Diaz-Espinoza, Rodrigo; Chen, Baian; Bravo-Alegria, Javiera; Makarava, Natallia; Baskakov, Ilia V.; Soto, Claudio

    2016-01-01

    Prions are composed of the misfolded prion protein (PrPSc) organized in a variety of aggregates. An important question in the prion field has been to determine the identity of functional PrPSc aggregates. In this study, we used equilibrium sedimentation in sucrose density gradients to separate PrPSc aggregates from three hamster prion strains (Hyper, Drowsy, SSLOW) subjected to minimal manipulations. We show that PrPSc aggregates distribute in a wide range of arrangements and the relative proportion of each species depends on the prion strain. We observed a direct correlation between the density of the predominant PrPSc aggregates and the incubation periods for the strains studied. The relative presence of PrPSc in fractions of different sucrose densities was indicative of the protein deposits present in the brain as analyzed by histology. Interestingly, no association was found between sensitivity to proteolytic degradation and aggregation profiles. Therefore, the organization of PrP molecules in terms of the density of aggregates generated may determine some of the particular strain properties, whereas others are independent from it. Our findings may contribute to understand the mechanisms of strain variation and the role of PrPSc aggregates in prion-induced neurodegeneration. PMID:26877167

  9. Strain-dependent profile of misfolded prion protein aggregates.

    PubMed

    Morales, Rodrigo; Hu, Ping Ping; Duran-Aniotz, Claudia; Moda, Fabio; Diaz-Espinoza, Rodrigo; Chen, Baian; Bravo-Alegria, Javiera; Makarava, Natallia; Baskakov, Ilia V; Soto, Claudio

    2016-02-15

    Prions are composed of the misfolded prion protein (PrP(Sc)) organized in a variety of aggregates. An important question in the prion field has been to determine the identity of functional PrP(Sc) aggregates. In this study, we used equilibrium sedimentation in sucrose density gradients to separate PrP(Sc) aggregates from three hamster prion strains (Hyper, Drowsy, SSLOW) subjected to minimal manipulations. We show that PrP(Sc) aggregates distribute in a wide range of arrangements and the relative proportion of each species depends on the prion strain. We observed a direct correlation between the density of the predominant PrP(Sc) aggregates and the incubation periods for the strains studied. The relative presence of PrP(Sc) in fractions of different sucrose densities was indicative of the protein deposits present in the brain as analyzed by histology. Interestingly, no association was found between sensitivity to proteolytic degradation and aggregation profiles. Therefore, the organization of PrP molecules in terms of the density of aggregates generated may determine some of the particular strain properties, whereas others are independent from it. Our findings may contribute to understand the mechanisms of strain variation and the role of PrP(Sc) aggregates in prion-induced neurodegeneration.

  10. Spatial control of chirality in supramolecular aggregates.

    PubMed

    Castriciano, Maria A; Gentili, Denis; Romeo, Andrea; Cavallini, Massimiliano; Scolaro, Luigi Monsù

    2017-03-09

    Chirality is one of the most intriguing properties of matter related to a molecule's lack of mirror symmetry. The transmission of chirality from the molecular level up to the macroscopic scale has major implications in life sciences but it is also relevant for many chemical applications ranging from catalysis to spintronic. These technological applications require an accurate control of morphology, homogeneity and chiral handedness of thin films and nanostructures. We demonstrate a simple approach to specifically transfer chirality to the model supramolecular system of J aggregates of the protonated form of tetrakis(4-sulfonatophenyl)-porphyrin by utilizing a soft lithography technique. This approach successfully allows the fabrication of an ordered distribution of sub-micrometric structures in precise and controllable positions with programmed chirality, providing a fundamental breakthrough toward the exploitation of chiral supramolecular aggregates in technological applications, such as sensors, non-linear optics and spintronic.

  11. Tau protein and tau aggregation inhibitors.

    PubMed

    Bulic, Bruno; Pickhardt, Marcus; Mandelkow, Eva-Maria; Mandelkow, Eckhard

    2010-01-01

    Alzheimer disease is characterized by pathological aggregation of two proteins, tau and Abeta-amyloid, both of which are considered to be toxic to neurons. In this review we summarize recent advances on small molecule inhibitors of protein aggregation with emphasis on tau, with activities mediated by the direct interference of self-assembly. The inhibitors can be clustered in several compound classes according to their chemical structure, with subsequent description of the structure-activity relationships, showing that hydrophobic interactions are prevailing. The description is extended to the pharmacological profile of the compounds in order to evaluate their drug-likeness, with special attention to toxicity and bioavailability. The collected data indicate that following the improvements of the in vitro inhibitory potencies, the consideration of the in vivo pharmacokinetics is an absolute prerequisite for the development of compounds suitable for a transfer from bench to bedside.

  12. Aggregation of phospholipid vesicles by water-soluble polymers.

    PubMed Central

    Meyuhas, D; Nir, S; Lichtenberg, D

    1996-01-01

    Water-soluble polymers such as dextran and polyethylene glycol are known to induce aggregation and size growth of phospholipid vesicles. The present study addresses the dependence of these processes on vesicle size and concentration, polymer molecular weight, temperature, and compartmentalization of the vesicles and polymers, using static and dynamic light scattering. Increasing the molecular weight of the polymers resulted in a reduction of the concentration of polymer needed for induction of aggregation of small unilamellar vesicles. The aggregation was fully reversible (by dilution), within a few seconds, up to a polymer concentration of at least 20 wt %. At relatively low phosphatidylcholine (PC) concentrations (up to approximately 1 mM), increasing the PC concentration resulted in faster kinetics of aggregation and reduced the threshold concentration of polymer required for rapid aggregation (CA). At higher PC concentrations, CA was only slightly dependent on the concentration of PC and was approximately equal to the overlapping concentration of the polymer (C*). The extent of aggregation was similar at 37 and 4 degrees C. Aggregation of large unilamellar vesicles required a lower polymer concentration, probably because aggregation occurs in a secondary minimum (without surface contact). In contrast to experiments in which the polymers were added directly to the vesicles, dialysis of the vesicles against polymer-containing solutions did not induce aggregation. Based on this result, it appears that exclusion of polymer from the hydration sphere of vesicles and the consequent depletion of polymer molecules from clusters of aggregated vesicles play the central role in the induction of reversible vesicle aggregation. The results of all the other experiments are consistent with this conclusion. PMID:8913598

  13. A selected ion flow tube study of the reactions of NO + and O + 2 ions with some organic molecules: The potential for trace gas analysis of air

    NASA Astrophysics Data System (ADS)

    Španěl, Patrik; Smith, David

    1996-02-01

    A study has been carried out using our selected ion flow tube apparatus of the reactions of NO+ and O+2 ions in their vibronic ground states with ten organic species: the hydrocarbons, benzene, toluene, isoprene, cyclopropane, and n-pentane; the oxygen-containing organics, methanol, ethanol, acetaldehyde, acetone, and diethyl ether. The major objectives of this work are, on the one hand, to fully understand the processes involved in these reactions and, on the other hand, to explore the potential of NO+ and O+2 as chemical ionization agents for the analysis of trace gases in air and on human breath. Amongst the NO+ reactions, charge transfer, hydride-ion transfer, and termolecular association occur, and the measured rate coefficients, k, for the reactions vary from immeasurably small to the maximum value, collisional rate coefficient, kc. The O+2 reactions are all fast, in each case the k being equal to or an appreciable fraction of kc, and charge transfer producing the parent organic ion or dissociative charge transfer resulting in two or three fragments of the parent ion are the reaction processes that occur. We conclude from these studies, and from previous studies, that NO+ ions and O+2 ions can be used to great effect as chemical ionization agents for trace gas analysis, especially in combination with H3O+ ions which we now routinely use for this purpose.

  14. Gas-Sensing Devices Based on Zn-Doped NiO Two-Dimensional Grainy Films with Fast Response and Recovery for Ammonia Molecule Detection.

    PubMed

    Wang, Jian; Wei, Xiaowei; Wangyang, Peihua

    2015-12-01

    Zn-doped NiO two-dimensional grainy films on glass substrates are shown to be an ammonia-sensing material with excellent comprehensive performance, which could real-time detect and monitor ammonia (NH3) in the surrounding environment. The morphology and structure analysis indicated that the as-fabricated semiconductor films were composed of particles with diameters ranging from 80 to 160 nm, and each particle was composed of small crystalline grain with a narrow size about 20 nm, which was the face-centered cubic single crystal structure. X-ray diffraction peaks shifted toward lower angle, and the size of the lattice increased compared with undoped NiO, which demonstrated that zinc ions have been successfully doped into the NiO host structure. Simultaneously, we systematically investigated the gas-sensing properties of the Zn-doped NiO sensors for NH3 detection at room temperature. The sensor based on doped NiO sensing films gave four to nine times faster response and four to six times faster recovery speeds than those of sensor with undoped NiO films, which is important for the NiO sensor practical applications. Moreover, we found that the doped NiO sensors owned outstanding selectivity toward ammonia.

  15. First application of mass spectrometry and gas chromatography in investigation of α-cellulose hydrolysates: the influence of climate changes on glucose molecules in pine tree-rings.

    PubMed

    Sensuła, Barbara M; Pazdur, Anna; Marais, Marie-France

    2011-02-28

    We present the first results of the quantitative and qualitative gas chromatographic and isotope ratio mass spectrometric analysis of monosaccharides derived from acid hydrolysis of α-cellulose extracted from annual pine tree-rings. The conifers investigated in this study grew in the Niepolomice Forest in Poland, and the annual rings covered the time span from 1940 to 2000 AD. The main components of the α-cellulose samples were two saccharides: glucose and mannose. The amount of glucose in the annual rings varied between 17 and 44%. The δ(13)C of glucose was found to be less negative than that of α-cellulose and the δ(18)O values in glucose were less positive than those in α-cellulose. The content of monosaccharides in the α-cellulose samples has an influence on the isotope fractionation factors. The values of the carbon isotope fractionation factor increase with an increase in the monosaccharides concentration in α-cellulose, while the values of the oxygen isotope fractionation factor decrease with an increase in monosaccharides concentration in α-cellulose. The challenge is to establish, with respect to climate changes and environmental conditions, the significance of the interannual variations in the observed monosaccharide concentration.

  16. Aggregation methodology for the circum-arctic resource appraisal

    USGS Publications Warehouse

    Schuenemeyer, John H.; Gautier, Donald L.

    2009-01-01

    This paper presents a methodology that intends to aggregate the results of a recent assessment of undiscovered conventional oil and gas resources of the Arctic by the U.S. Geological Survey. The assessment occurred in 48 geologically defined regions called assessment units. The methodology includes using assessor specified pair-wise correlations as the basis to construct a correlation matrix. Sampling from this matrix generates more realistic uncertainty estimates of aggregated resources than if assumptions of total independence or total dependence are made. The latter two assumptions result in overly narrow or overly broad estimates. Aggregation results for resources in regions north of the Arctic Circle are presented.

  17. Tracking protein aggregate interactions

    PubMed Central

    Bartz, Jason C; Nilsson, K Peter R

    2011-01-01

    Amyloid fibrils share a structural motif consisting of highly ordered β-sheets aligned perpendicular to the fibril axis.1, 2 At each fibril end, β-sheets provide a template for recruiting and converting monomers.3 Different amyloid fibrils often co-occur in the same individual, yet whether a protein aggregate aids or inhibits the assembly of a heterologous protein is unclear. In prion disease, diverse prion aggregate structures, known as strains, are thought to be the basis of disparate disease phenotypes in the same species expressing identical prion protein sequences.4–7 Here we explore the interactions reported to occur when two distinct prion strains occur together in the central nervous system. PMID:21597336

  18. Platelet aggregation Inhibitors from Hametophagous Animals

    PubMed Central

    Francischetti, Ivo M. B.

    2010-01-01

    Salivary glands from blood-sucking animals (e.g., mosquitoes, bugs, sandflies, fleas, ticks, leeches, hookworms, bats) are a rich source of bioactive molecules that counteract hemostasis in a redundant and synergistic manner. This review discusses recent progress in the identification of salivary inhibitors of platelet aggregation, their molecular characterization, and detailed mechanism of action. Diversity of inhibitors is remarkable, with distinct families of proteins characterized as apyrases that enzymatically degrade ADP or as collagen-binding proteins that prevent its interaction with vWF, or platelet integrin α2β1 or GPVI. Molecules that bind ADP, TXA2, epinephrine, or serotonin with high affinity have also been cloned, expressed, and their structure determined. In addition, a repertoire of antithrombins and an increasingly number of RGD and non-RGD disintegrins targeting platelet αIIbβ3 have been reported. Moreover, metalloproteases with fibrinogen(olytic) activity and PAF phosphorylcholine hydrolase are enzymes that have been recruited to the salivary gland to block platelet aggregation. Platelet inhibitory prostaglandins, lysophosphatydilcholine, adenosine, and nitric oxide (NO)-carrying proteins are other notable examples of molecules from hematophagous salivary secretions (herein named sialogenins) with antihemostatic properties. Sialogenins have been employed as tools in biochemistry and cell biology and also display potential therapeutic applications. PMID:20035779

  19. Zooplankton Aggregations Near Sills

    DTIC Science & Technology

    2003-09-30

    frequency echo-sounder system. This data were supplemented with multi-net (BIONESS) trawls, bongo nets, and otter trawls (operated by D. Mackas and group...side. The general composition of the zooplankton aggregations can be deduced from the relative levels of the three echo-sounder frequencies; krill ...Nov. 20th, 2002. Krill layer is evident at 66 – 90 m, coincident with BIONESS trawl through the region. 3 Figure 2 shows a comparison between

  20. Proteins aggregation and human diseases

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  1. SDS-assisted hydrothermal synthesis of NiO flake-flower architectures with enhanced gas-sensing properties

    NASA Astrophysics Data System (ADS)

    Miao, Ruiyang; Zeng, Wen; Gao, Qi

    2016-10-01

    A facile hydrothermal route was developed for the preparation of well-aligned hierarchical flower-like NiO nanostructure with the assistance of SDS that served as a structure-directing agent as well as a capping agent in the process of aggregation and assembly. Notably, the NiO sensors exhibit enhanced gas-sensing performance towards ethanol, which could be explained in association with the ultrathin nanosheets that are close to Debye length (LD) scale and thus get the majority carriers fully depleted due to the ionization of adsorbed oxygen, abundant effective gas diffusion paths as well as high surface-to-volume ratio to promote sufficient contact and reaction between the NiO sample and ethanol molecules, and numerous miniature reaction rooms assembled with nanosheets to make the test gas molecules stay long enough for completed gas-sensing reactions. Besides, a novel growth mechanism with the passage of reaction time was also proposed in detail.

  2. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions.

    PubMed

    Guerard, Jennifer J; Tentscher, Peter R; Seijo, Marianne; Samuel Arey, J

    2015-06-14

    First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

  3. Vibrational wave packets: Molecular state reconstruction in the gas phase and mixed quantum/semiclassical descriptions of small-molecule dynamics in low-temperature solid media

    NASA Astrophysics Data System (ADS)

    Chapman, Craig Thomas

    We explore the reconstruction of B-state vibrational wave packets in I2 from simulated two-color nonlinear wave packet interferometry data. As a simplification of earlier proposals, we make use of different vibrational energy ranges in the B-state---rather than different electronic potential surfaces---for the short-pulse preparation and propagation of both target and reference wave packets. Numerical results from noisy interferograms indicate that experimental reconstruction should be possible with high fidelity (>0.99). Time-resolved coherent nonlinear optical experiments on small molecules in low-temperature host crystals are exposing valuable information on quantum mechanical dynamics in condensed media. We make use of generic features of these systems to frame two simple, comprehensive theories that will enable the efficient calculation of their ultrafast spectroscopic signals and support their interpretation in terms of the underlying chemical dynamics. Both treatments rely on the identification of normal coordinates to unambiguously partition the well-structured guest-host complex into a system and a bath and expand the overall wave function as a sum of product states between fully anharmonic vibrational basis states for the system and approximate Gaussian wave packets for the bath degrees of freedom. The theories exploit the fact that ultrafast experiments typically drive large-amplitude motion in a few intramolecular degrees of freedom of higher frequency than the crystal phonons, while these intramolecular vibrations indirectly induce smaller-amplitude---but still perhaps coherent---motion among the lattice modes. The equations of motion for the time-dependent parameters of the bath wave packets are fairly compact in a fixed vibrational basis/Gaussian bath (FVB/GB) approach. An alternative adiabatic vibrational basis/Gaussian bath (AVB/GB) treatment leads to more complicated equations of motion involving adiabatic and nonadiabatic vector potentials

  4. An in vivo platform for identifying inhibitors of protein aggregation

    PubMed Central

    Mahood, Rachel A.; Jackson, Matthew P.; Revill, Charlotte H.; Foster, Richard J.; Smith, D. Alastair; Ashcroft, Alison E.; Brockwell, David J.; Radford, Sheena E.

    2015-01-01

    Protein aggregation underlies an array of human diseases, yet only one small molecule therapeutic has been successfully developed to date. Here, we introduce an in vivo system, based on a β-lactamase tripartite fusion construct, capable of identifying aggregation-prone sequences in the periplasm of Escherichia coli and inhibitors that prevent their aberrant self-assembly. We demonstrate the power of the system using a range of proteins, from small unstructured peptides (islet amyloid polypeptide and amyloid β) to larger, folded immunoglobulin domains. Configured in a 48-well format, the split β-lactamase sensor readily differentiates between aggregation-prone and soluble sequences. Performing the assay in the presence of 109 compounds enabled a rank ordering of inhibition and revealed a new inhibitor of IAPP aggregation. This platform can be applied to both amyloidogenic and other aggregation-prone systems, independent of sequence or size, and can identify small molecules or other factors able to ameliorate or inhibit protein aggregation. PMID:26656088

  5. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

    2013-12-01

    The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute

  6. Size and number density of precrystalline aggregates in lysozyme crystallization process

    NASA Astrophysics Data System (ADS)

    Tanaka, Shinpei; Ito, Kohzo; Hayakawa, Reinosuke; Ataka, Mitsuo

    1999-12-01

    Using dynamic light scattering, we investigated supersaturated aqueous solutions of hen egg white lysozyme. We could observe the formation of aggregates only in solutions, from which crystals grew within a few days. The aggregates were grouped into smaller "units" and larger "clusters." The units consisted of a few molecules, whereas the clusters grew from about 100 nm to 1 μm. At the beginning of aggregation, the number density of the units decreased, while that of the clusters increased. At this stage, unit-cluster aggregation proceeded. At the next stage, the number density of the units became constant, while that of the clusters began to decrease, which means that the units stopped aggregating and cluster-cluster aggregation started. The aggregation mechanism for the clusters fit well with the diffusion limited cluster aggregation model, but this model alone could not explain that the aggregates separated into two groups, corresponding to units and clusters, and that the units stopped aggregating during the aggregation process. We find that the observed aggregation process has several similarities to the liquid-liquid phase separation process, which occurs metastably in protein solution. Furthermore, using both models for diffusion limited aggregation and the liquid-liquid phase separation together, we could naturally explain the process of the cluster formation.

  7. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  8. Phase Transitions in a Model of Y-Molecules Abstract

    NASA Astrophysics Data System (ADS)

    Holz, Danielle; Ruth, Donovan; Toral, Raul; Gunton, James

    Immunoglobulin is a Y-shaped molecule that functions as an antibody to neutralize pathogens. In special cases where there is a high concentration of immunoglobulin molecules, self-aggregation can occur and the molecules undergo phase transitions. This prevents the molecules from completing their function. We used a simplified model of 2-Dimensional Y-molecules with three identical arms on a triangular lattice with 2-dimensional Grand Canonical Ensemble. The molecules were permitted to be placed, removed, rotated or moved on the lattice. Once phase coexistence was found, we used histogram reweighting and multicanonical sampling to calculate our phase diagram.

  9. The influence of erythrocyte aggregation on induced platelet aggregation.

    PubMed

    Ott, C; Lardi, E; Schulzki, T; Reinhart, W H

    2010-01-01

    Red blood cells (RBCs) affect platelet aggregation in flowing blood (primary hemostasis). We tested the hypothesis that RBC aggregation could influence platelet aggregation. RBC aggregation was altered in vitro by: (i) changing plasma aggregatory properties with 3.7 g% dextran 40 (D40), 3.0 g% dextran 70 (D70) or 1.55 g% dextran 500 (D500); (ii) changing RBC aggregatory properties by incubating RBCs in 50 mU/ml neuraminidase for 60 min (reduction of the surface sialic acid content, thus reducing electrostatic repulsion) and subsequent RBC resuspension in platelet rich plasma (PRP) containing 1 g% dextran 70. RBC aggregation was assessed with the sedimentation rate (ESR). Platelet aggregation was measured: (i) in flowing whole blood with a platelet function analyzer PFA-100(R), which simulates in vivo conditions with RBCs flowing in the center and platelets along the wall, where they adhere to collagen and aggregate; and (ii) in a Chrono-log 700 Aggregometer, which measures changes of impedance by platelet aggregation in whole blood or changes in light transmission in PRP. We found that RBC aggregation increased with increasing molecular weight of dextran (ESR: 4 +/- 3 mm/h, 34 +/- 14 mm/h and 89 +/- 23 mm/hfor D40, D70 and D500, respectively, p < 0.0001) and with neuraminidase-treated RBCs (76 +/- 27 mm/h vs 27 +/- 8 mm/h, respectively, p < 0.0001). Platelet aggregation measured in whole blood under flow conditions (PFA-100) and without flow (Chronolog Aggregometer) was not affected by RBC aggregation. Our data suggest that RBC aggregation does not affect platelet aggregation in vitro and plays no role in primary hemostasis.

  10. Asphaltene nanoparticle aggregation in mixtures of incompatible crude oils.

    PubMed

    Mason, T G; Lin, M Y

    2003-05-01

    We study the structure and phase behavior of asphaltenes comprised of large polyaromatic molecules in blends of naturally occurring crude oils using small angle neutron scattering (SANS). When two compatible oils are blended together, the asphaltenes remain dispersed as colloidal nanoparticles; however, when two incompatible oils are blended together, these asphaltene nanoparticles can aggregate to form microscale structures. We show that SANS directly probes asphaltene aggregation in unmodified (i.e., nondeuterated) crude oil mixtures due to a significant neutron scattering length density difference between the hydrogen-poor asphaltenes and the surrounding oil. Moreover, the small length scales probed by SANS are ideally suited for studying asphaltene aggregation: SANS simultaneously provides the average size and concentration of nanoscale asphaltene particles and also the volume fraction of microscale asphaltene aggregates. These discoveries yield a practical means for directly assessing the compatibility of crude oils and for diagnosing refinery fouling problems resulting from blending incompatible oils.

  11. Structure of Viral Aggregates

    NASA Astrophysics Data System (ADS)

    Barr, Stephen; Luijten, Erik

    2010-03-01

    The aggregation of virus particles is a particular form of colloidal self-assembly, since viruses of a give type are monodisperse and have identical, anisotropic surface charge distributions. In small-angle X-ray scattering experiments, the Qbeta virus was found to organize in different crystal structures in the presence of divalent salt and non-adsorbing polymer. Since a simple isotropic potential cannot explain the occurrence of all observed phases, we employ computer simulations to investigate how the surface charge distribution affects the virus interactions. Using a detailed model of the virus particle, we find an asymmetric ion distribution around the virus which gives rise to the different phases observed.

  12. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  13. Structure of amphotericin B aggregates based on calculations of optical spectra

    SciTech Connect

    Hemenger, R.P.; Kaplan, T.; Gray, L.J.

    1983-01-01

    The degenerate ground state approximation was used to calculate the optical absorption and CD spectra for helical polymer models of amphotericin B aggregates in aqueous solution. Comparisons with experimental spectra indicate that a two-molecule/unit cell helical polymer model is a possible structure for aggregates of amphotericin B.

  14. Activation of alpha chymotrypsin by three phase partitioning is accompanied by aggregation.

    PubMed

    Rather, Gulam Mohmad; Mukherjee, Joyeeta; Halling, Peter James; Gupta, Munishwar Nath

    2012-01-01

    Precipitation of alpha chymotrypsin in the simultaneous presence of ammonium sulphate and t-butanol (three phase partitioning) resulted in preparations which showed self aggregation of the enzyme molecules. Precipitation with increasing amounts of ammonium sulphate led to increasing size of aggregates. While light scattering estimated the hydrodynamic diameter of these aggregates in the range of 242-1124 nm; Nanoparticle tracking analysis (NTA) gave the value as 130-462 nm. Scanning electron microscopy and gel filtration on Sephadex G-200 showed extensive aggregation in these preparations. Transmission electron microscopy showed that the aggregates had irregular shapes. All the aggregates had about 3× higher catalytic activity than the native enzyme. These aggregates did not differ in λ(max) of fluorescence emission which was around 340 nm. However, all the aggregates showed higher fluorescence emission intensity. Far-UV and near-UV circular dichroism also showed no significant structural changes as compared to the native molecule. Interestingly, HPLC gel filtration (on a hydroxylated silica column) gave 14 nm as the diameter for all preparations. Light scattering of preparations in the presence of 10% ethylene glycol also dissociated the aggregates to monomers of 14 nm. Both these results indicated that hydrophobic interactions were the driving force behind this aggregation. These results indicate: (1) Even without any major structural change, three phase partitioning led to protein molecules becoming highly prone to aggregation. (2) Different methods gave widely different estimates of sizes of aggregates. It was however possible to reconcile the data obtained with various approaches. (3) The nature of the gel filtration column is crucial and use of this technique for refolding and studying aggregation needs a rethink.

  15. From Aggregate Availability to Sustainability in California

    NASA Astrophysics Data System (ADS)

    Testa, S. M.; Parrish, J. G.

    2012-12-01

    was to compare projected aggregate demand for the next 50 years with currently permitted aggregate resources in 31 "production-consumption" regions of the state, and flag regions where there were less than 10 years of permitted aggregate supply remaining. The 31 P-C aggregate study areas covered about 25 percent of the State's geography, but about 90 percent of California's population. It was shown that in the next 50 years, California was projected to need approximately 13.5 billion tons of aggregate, excluding needs associated with accelerated construction programs or from reconstruction following a major, damaging earthquake. Map 52 demonstrated the need for more permitting of mineral resources, but did not address the overall effectiveness of the state's efforts to protect aggregate resources, or aggregate sustainability. To address the effectiveness of the state's overall efforts to conserve and address aggregate sustainability, new maps are being considered. Such maps may incorporate other factors to reflect the pace of urbanization, quality of the mineral resource, and environmental factors (i.e., sensitive habitat, wildlife refuge, etc.), material haul distances, infrastructure (suitability of roads and bridges) condition, and greenhouse gas emissions.

  16. Aggregation-fragmentation model of robust concentration gradient formation

    NASA Astrophysics Data System (ADS)

    Saunders, Timothy E.

    2015-02-01

    Concentration gradients of signaling molecules are essential for patterning during development and they have been observed in both unicellular and multicellular systems. In subcellular systems, clustering of the signaling molecule has been observed. We develop a theoretical model of cluster-mediated concentration gradient formation based on the Becker-Döring equations of aggregation-fragmentation processes. We show that such a mechanism produces robust concentration gradients on realistic time and spatial scales so long as the process of clustering does not significantly stabilize the signaling molecule. Finally, we demonstrate that such a model is applicable to the pom1p subcellular gradient in fission yeast.

  17. Spherical and hyperspherical harmonics representation of van der Waals aggregates

    NASA Astrophysics Data System (ADS)

    Lombardi, Andrea; Palazzetti, Federico; Aquilanti, Vincenzo; Grossi, Gaia; Albernaz, Alessandra F.; Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.

    2016-12-01

    The representation of the potential energy surfaces of atom-molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic-molecule-diatomic-molecule interactions are shown.

  18. A new approach to quantification of mAb aggregates using peptide affinity probes

    PubMed Central

    Cheung, Crystal S. F.; Anderson, Kyle W.; Patel, Pooja M.; Cade, Keale L.; Phinney, Karen W.; Turko, Illarion V.

    2017-01-01

    Using mAbs as therapeutic molecules is complicated by the propensity of mAbs to aggregate at elevated concentrations, which can lead to a variety of adverse events in treatment. Here, we describe a proof-of-concept for new methodology to detect and quantify mAb aggregation. Assay development included using an aggregated mAb as bait for screening of phage display peptide library and identifying those peptides with random sequence which can recognize mAb aggregates. Once identified, the selected peptides can be used for developing quantitative methods to assess mAb aggregation. Results indicate that a peptide binding method coupled with mass spectrometric detection of bound peptide can quantify mAb aggregation and potentially be useful for monitoring aggregation propensity of therapeutic protein candidates. PMID:28186164

  19. Dye-sensitized solar cell employing zinc oxide aggregates grown in the presence of lithium

    DOEpatents

    Zhang, Qifeng; Cao, Guozhong

    2013-10-15

    Provided are a novel ZnO dye-sensitized solar cell and method of fabricating the same. In one embodiment, deliberately added lithium ions are used to mediate the growth of ZnO aggregates. The use of lithium provides ZnO aggregates that have advantageous microstructure, morphology, crystallinity, and operational characteristics. Employing lithium during aggregate synthesis results in a polydisperse collection of ZnO aggregates favorable for porosity and light scattering. The resulting nanocrystallites forming the aggregates have improved crystallinity and more favorable facets for dye molecule absorption. The lithium synthesis improves the surface stability of ZnO in acidic dyes. The procedures developed and disclosed herein also help ensure the formation of an aggregate film that has a high homogeneity of thickness, a high packing density, a high specific surface area, and good electrical contact between the film and the fluorine-doped tin oxide electrode and among the aggregate particles.

  20. A new approach to quantification of mAb aggregates using peptide affinity probes.

    PubMed

    Cheung, Crystal S F; Anderson, Kyle W; Patel, Pooja M; Cade, Keale L; Phinney, Karen W; Turko, Illarion V

    2017-02-10

    Using mAbs as therapeutic molecules is complicated by the propensity of mAbs to aggregate at elevated concentrations, which can lead to a variety of adverse events in treatment. Here, we describe a proof-of-concept for new methodology to detect and quantify mAb aggregation. Assay development included using an aggregated mAb as bait for screening of phage display peptide library and identifying those peptides with random sequence which can recognize mAb aggregates. Once identified, the selected peptides can be used for developing quantitative methods to assess mAb aggregation. Results indicate that a peptide binding method coupled with mass spectrometric detection of bound peptide can quantify mAb aggregation and potentially be useful for monitoring aggregation propensity of therapeutic protein candidates.

  1. Perturbing Streaming in Dictyostelium discoidium Aggregation

    NASA Astrophysics Data System (ADS)

    Rericha, Erin; Garcia, Gene; Parent, Carole; Losert, Wolfgang

    2009-03-01

    The ability of cells to move towards environmental cues is a critical process allowing the destruction of intruders by the immune system, the formation of the vascular system and the whole scale remodeling of tissues during embryo development. We examine the initial transition from single cell to group migration in the social amoeba Dictyostelium discoidium. Upon starvation, D. discoidium cells enter into a developmental program that triggers solitary cells to aggregate into a multicellular structure. The aggregation is mediated by the small molecule, cyclic-AMP, that cells sense, synthesize, secrete and migrate towards often in a head-to-tail fashion called a stream. Using experiment and numerical simulation, we study the sensitivity of streams to perturbations in the cyclic-AMP concentration field. We find the stability of the streams requires cells to shape the cyclic-AMP field through localized secretion and degradation. In addition, we find the streaming phenotype is sensitive to changes in the substrate properties, with slicker surfaces leading to longer more branched streams that yield large initial aggregates.

  2. Isothermal evaporation of ethanol in a dynamic gas atmosphere.

    PubMed

    Milev, Adriyan S; Wilson, Michael A; Kannangara, G S Kamali; Feng, Hai; Newman, Phillip A

    2012-01-12

    Optimization of evaporation and pyrolysis conditions for ethanol are important in carbon nanotube (CNT) synthesis. The activation enthalpy (ΔH(‡)), the activation entropy (ΔS(‡)), and the free energy barrier (ΔG(‡)) to evaporation have been determined by measuring the molar coefficient of evaporation, k(evap), at nine different temperatures (30-70 °C) and four gas flow rates (25-200 mL/min) using nitrogen and argon as carrier gases. At 70 °C in argon, the effect of the gas flow rate on k(evap) and ΔG(‡) is small. However, this is not true at temperatures as low as 30 °C, where the increase of the gas flow rate from 25 to 200 mL/min results in a nearly 6 times increase of k(evap) and decrease of ΔG(‡) by ~5 kJ/mol. Therefore, at 30 °C, the effect of the gas flow rate on the ethanol evaporation rate is attributed to interactions of ethanol with argon molecules. This is supported by simultaneous infrared spectroscopic analysis of the evolved vapors, which demonstrates the presence of different amounts of linear and cyclic hydrogen bonded ethanol aggregates. While the amount of these aggregates at 30 °C depends upon the gas flow rate, no such dependence was observed during evaporation at 70 °C. When the evaporation was carried out in nitrogen, ΔG(‡) was almost independent of the evaporation temperature (30-70 °C) and the gas flow rate (25-200 mL/min). Thus the evaporation of ethanol in a dynamic gas atmosphere at different temperatures may go via different mechanisms depending on the nature of the carrier gas.

  3. Holographic characterization of protein aggregates

    NASA Astrophysics Data System (ADS)

    Wang, Chen; Zhong, Xiao; Ruffner, David; Stutt, Alexandra; Philips, Laura; Ward, Michael; Grier, David

    Holographic characterization directly measures the size distribution of subvisible protein aggregates in suspension and offers insights into their morphology. Based on holographic video microscopy, this analytical technique records and interprets holograms of individual aggregates in protein solutions as they flow down a microfluidic channel, without requiring labeling or other exceptional sample preparation. The hologram of an individual protein aggregate is analyzed in real time with the Lorenz-Mie theory of light scattering to measure that aggregate's size and optical properties. Detecting, counting and characterizing subvisible aggregates proceeds fast enough for time-resolved studies, and lends itself to tracking trends in protein aggregation arising from changing environmental factors. No other analytical technique provides such a wealth of particle-resolved characterization data in situ. Holographic characterization promises accelerated development of therapeutic protein formulations, improved process control during manufacturing, and streamlined quality assurance during storage and at the point of use. Mrsec and MRI program of the NSF, Spheryx Inc.

  4. Fractal structure of asphaltene aggregates.

    PubMed

    Rahmani, Nazmul H G; Dabros, Tadeusz; Masliyah, Jacob H

    2005-05-15

    A photographic technique coupled with image analysis was used to measure the size and fractal dimension of asphaltene aggregates formed in toluene-heptane solvent mixtures. First, asphaltene aggregates were examined in a Couette device and the fractal-like aggregate structures were quantified using boundary fractal dimension. The evolution of the floc structure with time was monitored. The relative rates of shear-induced aggregation and fragmentation/restructuring determine the steady-state floc structure. The average floc structure became more compact or more organized as the floc size distribution attained steady state. Moreover, the higher the shear rate is, the more compact the floc structure is at steady state. Second, the fractal dimensions of asphaltene aggregates were also determined in a free-settling test. The experimentally determined terminal settling velocities and characteristic lengths of the aggregates were utilized to estimate the 2D and 3D fractal dimensions. The size-density fractal dimension (D(3)) of the asphaltene aggregates was estimated to be in the range from 1.06 to 1.41. This relatively low fractal dimension suggests that the asphaltene aggregates are highly porous and very tenuous. The aggregates have a structure with extremely low space-filling capacity.

  5. Aggregation dynamics of rigid polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Tom, Anvy Moly; Rajesh, R.; Vemparala, Satyavani

    2016-01-01

    Similarly charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of such rigid polyelectrolytes are studied using large scale molecular dynamics simulations. We find that the morphology of the aggregates depends on the value of the charge density of the polymers. For values close to the critical value, the shape of the aggregates is cylindrical with height equal to the length of a single polyelectrolyte chain. However, for larger values of charge, the linear extent of the aggregates increases as more and more polymers aggregate. In both the cases, we show that the number of aggregates decrease with time as power laws with exponents that are not numerically distinguishable from each other and are independent of charge density of the polymers, valency of the counterions, density, and length of the polyelectrolyte chain. We model the aggregation dynamics using the Smoluchowski coagulation equation with kernels determined from the molecular dynamics simulations and justify the numerically obtained value of the exponent. Our results suggest that once counterions condense, effective interactions between polyelectrolyte chains short-ranged and the aggregation of polyelectrolytes are diffusion-limited.

  6. Formation of large micellar aggregates before equilibrium in diluted solutions

    NASA Astrophysics Data System (ADS)

    de Moraes, J. N. B.; Figueiredo, W.

    2013-06-01

    We study the formation of premicelles for different values of the concentration of amphiphile molecules in water. Our model consists of a square lattice with water molecules occupying one cell of the lattice while the amphiphilic molecules, represented by chains of five interconnected sites, occupy five cells of the lattice. We perform Monte Carlo simulations in the NVT ensemble, for a fixed temperature and different concentration of amphiphiles, ranging from below to above the critical micelle concentration. We start our simulations from a monomeric state and follow in time all the aggregates sizes until the equilibrium state is reached. We pay particular attention to two aggregate sizes, one related to the minimum and the other to the maximum of the aggregate-size distribution curve obtained at equilibrium. We show that these aggregates evolve in time exhibiting a maximum concentration well before the equilibrium state, revealing the formation of premicelles. The times to reach these maximum concentrations decrease exponentially with the total concentration of the system.

  7. Aggregation of hsp70 and hsc70 in vivo is distinct and temperature-dependent and their chaperone function is directly related to non-aggregated forms.

    PubMed

    Angelidis, C E; Lazaridis, I; Pagoulatos, G N

    1999-01-01

    We used non-denaturing gradient analysis of cell extracts before and after heat treatment of the cells and showed that hsp70 and hsc70 aggregate in vivo in a temperature-dependent fashion. Their aggregation profiles were found to be clearly distinguishable and sensitive to ATP depletion. Pore exclusion limit electrophoresis showed that these two proteins are mainly found in autoaggregated forms including dimers, trimers and oligomers. The addition of denatured luciferase to the cell extracts reversed the aggregation of both proteins towards their non-aggregated forms. Immunoprecipitation and Western-blot analysis showed that the non-aggregated form is the only one bound to denatured luciferase. Our results suggest that aggregated hsp70 and hsc70 represent predominantly self-associated molecules unable to exert chaperone activity. The cochaperone hsp40 was also found to be aggregated and, on addition of denatured luciferase, its aggregation was reversed to a non-aggregated state. Immunoprecipitation analysis indicated that hsp40 forms a complex with the non-aggregated form of hsc70 and denatured luciferase. These results confirm previous in vitro studies and support the suggestion that in vivo cytosolic hsp70 and hsc70 exist mainly in an oligomer-monomer equilibrium which is dependent on the environmental temperature, the levels of ATP and the presence of denatured proteins.

  8. Free-surface microfluidic control of surface-enhanced Raman spectroscopy for the optimized detection of airborne molecules

    PubMed Central

    Piorek, Brian D.; Lee, Seung Joon; Santiago, Juan G.; Moskovits, Martin; Banerjee, Sanjoy; Meinhart, Carl D.

    2007-01-01

    We present a microfluidic technique for sensitive, real-time, optimized detection of airborne water-soluble molecules by surface-enhanced Raman spectroscopy (SERS). The method is based on a free-surface fluidic device in which a pressure-driven liquid microchannel flow is constrained by surface tension. A colloidal suspension of silver nanoparticles flowing through the microchannel that is open to the atmosphere absorbs gas-phase 4-aminobenzenethiol (4-ABT) from the surrounding environment. As surface ions adsorbed on the colloid nanoparticles are substituted by 4-ABT, the colloid aggregates, forming SERS “hot spots” whose concentrations vary predictably along the microchannel flow. 4-ABT confined in these hot spots produces SERS spectra of very great intensity. An aggregation model is used to account quantitatively for the extent of colloid aggregation as determined from the variation of the SERS intensity measured as a function of the streamwise position along the microchannel, which also corresponds to nanoparticle exposure time. This allows us to monitor simultaneously the nanoparticle aggregation process and to determine the location at which the SERS signal is optimized. PMID:18025462

  9. MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

    NASA Astrophysics Data System (ADS)

    Xu, Yuanwei; Rodger, P. Mark

    2017-03-01

    We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

  10. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  11. Topics in Probabilistic Judgment Aggregation

    ERIC Educational Resources Information Center

    Wang, Guanchun

    2011-01-01

    This dissertation is a compilation of several studies that are united by their relevance to probabilistic judgment aggregation. In the face of complex and uncertain events, panels of judges are frequently consulted to provide probabilistic forecasts, and aggregation of such estimates in groups often yield better results than could have been made…

  12. Mineral of the month: aggregates

    USGS Publications Warehouse

    Tepordei, Valentin V.

    2005-01-01

    Natural aggregates, consisting of crushed stone, and sand and gravel, are a major contributor to economic health, and have an amazing variety of uses. Aggregates are among the most abundant mineral resources and are major basic raw materials used by construction, agriculture and other industries that employ complex chemical and metallurgical processes.

  13. Optical dynamics of exciton and polaron formation in molecular aggregates

    NASA Astrophysics Data System (ADS)

    de Boer, Steven; Wiersma, Douwe A.

    1989-03-01

    Results of femtosecond accumulated photon echo, picosecond pump-probe and fluorescence lifetime measurements are reported on aggregates of the dyes pseudoisocyanine (PIC) and substituted thiapyrylium (TPY), embedded in a polycarbonate matrix. It is concluded that in the PIC aggregate, delocalized excitations (excitons) are formed, which are weakly coupled to the aggregate's nuclear frame. In the TPY aggregate, excitons are also initially formed, but through strong local electron-phonon coupling these excitons are not stable and decay into polarons, which become trapped. It is suggested that the nature of the excitations in aggregates crucially depends on the change of electron density distribution upon optical excitation. When this change is large, as revealed by a large change of dipole moment, polarons will be formed. In the other limit of a small change of dipole moment on optical excitation, excitons with an enhanced radiative lifetime are formed, which coherently propagate over that part of the aggregate where the molecules are electronically strongly coupled. The relevance of these findings towards energy transport in photo-biological systems is also discussed.

  14. Flow-cytometric screening of aggregation-inhibitors using a fluorescence-assisted intracellular method.

    PubMed

    Lindberg, Hanna; Sandersjöö, Lisa; Meister, Sebastian W; Uhlén, Mathias; Löfblom, John; Ståhl, Stefan

    2017-01-01

    Aggregation of misfolded peptides and proteins is a key event in several neurodegenerative diseases. Suggested treatments of such disorders aim to inhibit the initial aggregation process. Here, we have developed an intracellular, function-based screening method, intended for isolation of aggregation-inhibitors from combinatorial protein libraries by flow-cytometric cell sorting. The method is based on fusion of aggregation-prone peptides to a fluorescent protein, functioning as a solubility reporter. Co-expression of a protein-based aggregation-inhibitor should prevent aggregation and thus increase the whole-cell fluorescence. We evaluated the method using the aggregation-prone Alzheimer's-related amyloid-β (Aβ) peptide in fusion to green-fluorescent protein (GFP), and an Aβ aggregation-inhibiting Affibody molecule. To adapt the method for library applications, the inhibitor was linked to an mCherry reporter for normalization of protein expression levels. We found that aggregation propensity correlates with fluorescence intensity, as co-expression of the Affibody-inhibitor increased the whole-cell fluorescence relative to a non-inhibitor. Employing improved cultivation parameters, we furthermore demonstrated efficient rescue from aggregation of an α-synuclein-derived protein using a different type of aggregation-inhibitor. Importantly, we also showed that the Aβ aggregation-inhibiting Affibody molecule could be isolated from a 1:10,000 background of non-inhibitors, with around 3,500-fold enrichment, in one cycle of fluorescence-based cell sorting. In conclusion, our new method represents a promising approach for generation of novel protein-based aggregation-inhibitors.

  15. Effect of terbium(III) on the binding of aromatic guests with sodium taurocholate aggregates.

    PubMed

    Pace, Tamara C S; Souza, Sergio P; Zhang, Hui Ting; Bohne, Cornelia

    2011-10-01

    The effect of binding Tb(3+) to sodium taurocholate aggregates containing polyaromatic hydrocarbon guests was examined using pyrene and 1-ethylnaphthalene as guests that bind to the primary aggregate, and 1-naphthyl-1-ethanol as a secondary aggregate guest. Time-resolved fluorescence quenching studies were used to study the binding site properties, while laser flash photolysis quenching studies provided information on the dynamics of the guest-aggregate system. Both the primary and secondary aggregate binding sites became more compact in the presence of bound Tb(3+), while only the primary aggregate became more accessible to anionic molecules. The binding dynamics for the guest-primary aggregate system became faster when Tb(3+) was bound to the aggregate. In contrast, for the guest-secondary aggregate the presence of Tb(3+) resulted in a small decrease in the dissociation rate constant. The influence of bound Tb(3+) on the primary and secondary bile salt aggregates is significantly different, which affects how these aggregates can be used as supramolecular host systems to modify guest reactivity.

  16. Spreading and spontaneous motility of multicellular aggregates on soft substrates

    NASA Astrophysics Data System (ADS)

    Brochard-Wyart, Françoise

    2013-03-01

    We first describe the biomechanics of multicellular aggregates, a model system for tissues and tumors. We first characterize the tissue mechanical properties (surface tension, elasticity, viscosity) by a new pipette aspiration technique. The aggregate exhibits a viscoelastic response but, unlike an inert fluid, we observe aggregate reinforcement with pressure, which for a narrow range of pressures results in pulsed contractions or shivering. We interpret this reinforcement as a mechanosensitive active response of the acto-myosin cortex. Such an active behavior has previously been found to cause tissue pulsation during dorsal closure of Drosophila embryo. We then describe the spreading of aggregates on rigid glass substrates, varying both intercellular and substrate adhesion. We find both partial and complete wetting regimes. For the dynamics, we find a universal spreading law at short time, analogous to that of a viscoelastic drop. At long time, we observe, for strong substrate adhesion, a precursor film spreading around the aggregate. Depending on aggregate cohesion, this precursor film can be a dense cellular monolayer (liquid state) or consist of individual cells escaping from the aggregate body (gas state). The transition from liquid to gas state appears also to be present in the progression of a tumor from noninvasive to metastatic, known as the epithelial-mesenchymal transition. Finally, we describe the effect of the substrate rigidity on the phase diagram of wetting. On soft gels decorated with fibronectin and strongly cohesive aggregates, we have observed a wetting transition induced by the substrate rigidity: on ultra soft gels, below an elastic modulus Ec the aggregates do not spread, whereas above Ec we observe a precursor film expending with a diffusive law. The diffusion coefficient D(E) present a maximum for E =Em. A maximum of mobility versus the substrate rigidity had also been observed for single cells. Near Em, we observe a new phenomenon: a cell

  17. Premature red blood cells have decreased aggregation and enhanced aggregability.

    PubMed

    Arbell, D; Orkin, B; Bar-Oz, B; Barshtein, G; Yedgar, S

    2008-06-01

    Preterm infants are highly susceptible to ischemic damage. This damage is most obvious in the brain, retina, and gastrointestinal tract. Studies focusing on the rheological properties of premature red blood cells (pRBCs) have consistently shown minimal or no RBC aggregation. Previously, measurements of pRBC aggregation kinetics indicated that specific plasma properties are responsible for the decreased RBC aggregation observed in the neonates, but that their specific RBC properties do not affect it. However, the strength of interaction in the pRBC aggregates as a function of medium composition has not been tested. In our previous research, we described clinically relevant parameters, that is, the aggregate resistance to disaggregation by flow. With the help of a cell flow property analyzer (CFA), we can monitor RBC aggregation by direct visualization of its dynamics during flow. We used the CFA to examine pRBC (from 9 premature babies) in the natural plasma and in PBS buffer supplemented with dextran (500 kDa) to distinguish between RBC intrinsic-cellular and plasma factors. pRBCs suspended in the native plasma showed minimal or no aggregation in comparison to normal adult RBC. When we transferred pRBCs from the same sample to the dextran solution, enhanced resistance to disaggregation by flow was apparent.

  18. Orthogonal flexible Rydberg aggregates

    NASA Astrophysics Data System (ADS)

    Leonhardt, K.; Wüster, S.; Rost, J. M.

    2016-02-01

    We study the link between atomic motion and exciton transport in flexible Rydberg aggregates, assemblies of highly excited light alkali-metal atoms, for which motion due to dipole-dipole interaction becomes relevant. In two one-dimensional atom chains crossing at a right angle adiabatic exciton transport is affected by a conical intersection of excitonic energy surfaces, which induces controllable nonadiabatic effects. A joint exciton-motion pulse that is initially governed by a single energy surface is coherently split into two modes after crossing the intersection. The modes induce strongly different atomic motion, leading to clear signatures of nonadiabatic effects in atomic density profiles. We have shown how this scenario can be exploited as an exciton switch, controlling direction and coherence properties of the joint pulse on the second of the chains [K. Leonhardt et al., Phys. Rev. Lett. 113, 223001 (2014), 10.1103/PhysRevLett.113.223001]. In this article we discuss the underlying complex dynamics in detail, characterize the switch, and derive our isotropic interaction model from a realistic anisotropic one with the addition of a magnetic bias field.

  19. Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

    SciTech Connect

    Fasolato, C.; Domenici, F.; Brasili, F.; Mazzi, E.; Postorino, P.; Mura, F.; Sennato, S.; De Angelis, L.; Bordi, F.

    2015-06-23

    The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we report on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements

  20. Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

    NASA Astrophysics Data System (ADS)

    Fasolato, C.; Domenici, F.; Brasili, F.; Mura, F.; Sennato, S.; De Angelis, L.; Mazzi, E.; Bordi, F.; Postorino, P.

    2015-06-01

    The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we report on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 109) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements confirmed

  1. Ultracold Molecules: Physics in the Quantum Regime

    SciTech Connect

    Doyle, John

    2014-11-17

    Our research encompasses approaches to the trapping of diatomic molecules at low temperature plus the cooling and detection of polyatomic molecules in the kelvin temperature regime. We have cooled and trapped CaF and/or CaH molecules, loaded directly from a molecular beam. As part of this work, we are continuing to develop an important trapping technique, optical loading from a buffer-gas beam. This method was invented in our lab. We are also studying cold polyatomic molecules and their interactions with cold atoms.

  2. Kinetics of Aggregation with Choice

    DOE PAGES

    Ben-Naim, Eli; Krapivsky, Paul

    2016-12-01

    Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less

  3. Kinetics of Aggregation with Choice

    SciTech Connect

    Ben-Naim, Eli; Krapivsky, Paul

    2016-12-01

    Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tails of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.

  4. Fractal aggregates in Titan's atmosphere

    NASA Astrophysics Data System (ADS)

    Cabane, M.; Rannou, P.; Chassefiere, E.; Israel, G.

    1993-04-01

    The cluster structure of Titan's atmosphere was modeled by using an Eulerian microphysical model with the specific formulation of microphysical laws applying to fractal particles. The growth of aggregates in the settling phase was treated by introducing the fractal dimension as a parameter of the model. The model was used to obtain a vertical distribution of size and number density of the aggregates for different production altitudes. Results confirm previous estimates of the formation altitude of photochemical aerosols. The vertical profile of the effective radius of aggregates was calculated as a function of the visible optical depth.

  5. Salt-induced aggregation of lysozyme: Implications for crystal growth

    NASA Astrophysics Data System (ADS)

    Wilson, Lori J.

    1994-10-01

    Crystallization of proteins is a prerequisite for structural analysis by x-ray crystallography. While improvements in protein crystals have been obtained in microgravity onboard the U.S. Space Shuttle, attempts to improve the crystal growth process both on the ground and in space have been limited by our lack of understanding of the mechanisms involved. Almost all proteins are crystallized with the aid of a precipitating agent. Many of the common precipitating agents are inorganic salts. An understanding of the role of salts on the aggregation of protein monomers is the key to the elucidation of the mechanisms involved in protein crystallization. In order for crystallization to occur individual molecules must self-associate into aggregates. Detection and characterization of aggregates in supersaturated protein solutions is the first step in understanding salt-induced crystallization.

  6. Salt-induced aggregation of lysozyme: Implications for crystal growth

    NASA Technical Reports Server (NTRS)

    Wilson, Lori J.

    1994-01-01

    Crystallization of proteins is a prerequisite for structural analysis by x-ray crystallography. While improvements in protein crystals have been obtained in microgravity onboard the U.S. Space Shuttle, attempts to improve the crystal growth process both on the ground and in space have been limited by our lack of understanding of the mechanisms involved. Almost all proteins are crystallized with the aid of a precipitating agent. Many of the common precipitating agents are inorganic salts. An understanding of the role of salts on the aggregation of protein monomers is the key to the elucidation of the mechanisms involved in protein crystallization. In order for crystallization to occur individual molecules must self-associate into aggregates. Detection and characterization of aggregates in supersaturated protein solutions is the first step in understanding salt-induced crystallization.

  7. Surface fractals in liposome aggregation.

    PubMed

    Roldán-Vargas, Sándalo; Barnadas-Rodríguez, Ramon; Quesada-Pérez, Manuel; Estelrich, Joan; Callejas-Fernández, José

    2009-01-01

    In this work, the aggregation of charged liposomes induced by magnesium is investigated. Static and dynamic light scattering, Fourier-transform infrared spectroscopy, and cryotransmission electron microscopy are used as experimental techniques. In particular, multiple intracluster scattering is reduced to a negligible amount using a cross-correlation light scattering scheme. The analysis of the cluster structure, probed by means of static light scattering, reveals an evolution from surface fractals to mass fractals with increasing magnesium concentration. Cryotransmission electron microscopy micrographs of the aggregates are consistent with this interpretation. In addition, a comparative analysis of these results with those previously reported in the presence of calcium suggests that the different hydration energy between lipid vesicles when these divalent cations are present plays a fundamental role in the cluster morphology. This suggestion is also supported by infrared spectroscopy data. The kinetics of the aggregation processes is also analyzed through the time evolution of the mean diffusion coefficient of the aggregates.

  8. Cell aggregation: Packing soft grains

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Karttunen, M.

    2006-06-01

    Cellular aggregates may be considered as collections of membrane enclosed units with a pressure difference between the internal and external liquid phases. Cells are kept together by membrane adhesion and/or confined space compression. Pattern formation and, in particular, intercellular spacing have important roles in controlling solvent diffusion within such aggregates. A physical approach is used to study generic aspects of cellular packings in a confined space. Average material properties are derived from the free energy. The appearance of penetrating intercellular void channels is found to be critically governed by the cell wall adhesion mechanisms during the formation of dense aggregates. A fully relaxed aggregate efficiently hinders solvent diffusion at high hydrostatic pressures, while a small fraction (˜0.1) of adhesion related packing frustration is sufficient for breaking such a blockage even at high a pressure.

  9. Folding, Binding, Misfolding and Aggregation with AWSEM

    NASA Astrophysics Data System (ADS)

    Schafer, Nicholas P.

    This thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold, bind, and predict the misfolding behavior of proteins. AWSEM is capable of performing de novo structure prediction on small alpha-helical protein domains and predict the binding interfaces of homo- and hetero-dimers. More recent work demonstrates how the misfolding behavior of tandem constructs in AWSEM is consistent with crucial aspects of ensemble and single molecule experiments on the aggregation and misfolding of these constructs. The first chapter is a review of the energy landscape theory of protein folding as it applies to the problem of protein structure prediction, and more specifically how energy landscape theory and the principle of minimal frustration can be used to optimize parameters of coarse-grained protein folding simulation models. The subsequent four chapters are reports of novel research performed with one such model.

  10. Aggregate breakdown of nanoparticulate titania

    NASA Astrophysics Data System (ADS)

    Venugopal, Navin

    Six nanosized titanium dioxide powders synthesized from a sulfate process were investigated. The targeted end-use of this powder was for a de-NOx catalyst honeycomb monolith. Alteration of synthesis parameters had resulted principally in differences in soluble ion level and specific surface area of the powders. The goal of this investigation was to understand the role of synthesis parameters in the aggregation behavior of these powders. Investigation via scanning electron microscopy of the powders revealed three different aggregation iterations at specific length scales. Secondary and higher order aggregate strength was investigated via oscillatory stress rheometry as a means of simulating shear conditions encountered during extrusion. G' and G'' were measured as a function of the applied oscillatory stress. Oscillatory rheometry indicated a strong variation as a function of the sulfate level of the particles in the viscoelastic yield strengths. Powder yield stresses ranged from 3.0 Pa to 24.0 Pa of oscillatory stress. Compaction curves to 750 MPa found strong similarities in extrapolated yield point of stage I and II compaction for each of the powders (at approximately 500 MPa) suggesting that the variation in sulfate was greatest above the primary aggregate level. Scanning electron microscopy of samples at different states of shear in oscillatory rheometry confirmed the variation in the linear elastic region and the viscous flow regime. A technique of this investigation was to approach aggregation via a novel perspective: aggregates are distinguished as being loose open structures that are highly disordered and stochastic in nature. The methodology used was to investigate the shear stresses required to rupture the various aggregation stages encountered and investigate the attempt to realign the now free-flowing constituents comprising the aggregate into a denser configuration. Mercury porosimetry was utilized to measure the pore size of the compact resulting from

  11. Beam-induced graphitic carbon cage transformation from sumanene aggregates

    SciTech Connect

    Fujita, Jun-ichi Tachi, Masashi; Murakami, Katsuhisa; Sakurai, Hidehiro; Morita, Yuki; Higashibayashi, Shuhei; Takeguchi, Masaki

    2014-01-27

    We found that electron-beam irradiation of sumanene aggregates strongly enhanced their transformation into a graphitic carbon cage, having a diameter of about 20 nm. The threshold electron dose was about 32 mC/cm{sup 2} at 200 keV, but the transformation is still induced at 20 keV. The transformation sequence suggested that the cage was constructed accompanied by the dynamical movement of the transiently linked sumanene molecules in order to pile up inside the shell. Thus, bond excitation in the sumanene molecules rather than a knock-on of carbon atoms seems to be the main cause of the cage transformation.

  12. Mucin aggregation from a rod-like meso-scale model

    NASA Astrophysics Data System (ADS)

    Moreno, Nicolas; Perilla, Jairo E.; Colina, Coray M.; Lísal, Martin

    2015-05-01

    Dissipative particle dynamics, a meso-scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin-water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin-water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models.

  13. Glycation precedes lens crystallin aggregation

    SciTech Connect

    Swamy, M.S.; Perry, R.E.; Abraham, E.C.

    1987-05-01

    Non-enzymatic glycosylation (glycation) seems to have the potential to alter the structure of crystallins and make them susceptible to thiol oxidation leading to disulfide-linked high molecular weight (HMW) aggregate formation. They used streptozotocin diabetic rats during precataract and cataract stages and long-term cell-free glycation of bovine lens crystallins to study the relationship between glycation and lens crystallin aggregation. HMW aggregates and other protein components of the water-soluble (WS) and urea-soluble (US) fractions were separated by molecular sieve high performance liquid chromatography. Glycation was estimated by both (/sup 3/H)NaBH/sub 4/ reduction and phenylboronate agarose affinity chromatography. Levels of total glycated protein (GP) in the US fractions were about 2-fold higher than in the WS fractions and there was a linear increase in GP in both WS and US fractions. This increase was parallelled by a corresponding increase in HMW aggregates. Total GP extracted by the affinity method from the US fraction showed a predominance of HMW aggregates and vice versa. Cell-free glycation studies with bovine crystallins confirmed the results of the animals studies. Increasing glycation caused a corresponding increase in protein insolubilization and the insoluble fraction thus formed also contained more glycated protein. It appears that lens protein glycation, HMW aggregate formation, and protein insolubilization are interrelated.

  14. Model for amorphous aggregation processes

    NASA Astrophysics Data System (ADS)

    Stranks, Samuel D.; Ecroyd, Heath; van Sluyter, Steven; Waters, Elizabeth J.; Carver, John A.; von Smekal, Lorenz

    2009-11-01

    The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing models for linear protein aggregation, such as amyloid fibril formation, there are few reports of models which address amorphous aggregation. Here, we propose a model to describe the amorphous aggregation of proteins which is also more widely applicable to other situations where a similar process occurs, such as in the formation of colloids and nanoclusters. As first applications of the model, we have tested it against experimental turbidimetry data of three proteins relevant to the wine industry and biochemistry, namely, thaumatin, a thaumatinlike protein, and α -lactalbumin. The model is very robust and describes amorphous experimental data to a high degree of accuracy. Details about the aggregation process, such as shape parameters of the aggregates and rate constants, can also be extracted.

  15. Dis-aggregation of an insoluble porphyrin in a calixarene matrix: characterization of aggregate modes by extended dipole model.

    PubMed

    de Miguel, Gustavo; Martín-Romero, María T; Pedrosa, José M; Muñoz, Eulogia; Pérez-Morales, Marta; Richardson, Tim H; Camacho, Luis

    2008-03-21

    In this paper, the different aggregation modes of a water-insoluble porphyrin (EHO) mixed with an amphiphilic calix[8]arene (C8A), at the air-water interface and in Langmuir-Blodgett (LB) film form, are analyzed as a function of the mixed composition. The strategy used to control the EHO aggregation has consisted of preparing mixed thin films containing EHO and C8A, in different ratios, at the air-water interface. Therefore, the increase of the C8A molar ratio in the mixed film diminishes the aggregation of the EHO molecules, although such an effect must be exclusively related to the dilution of the porphyrin. The reflection spectra of the mixed C8A-EHO films registered at the air-water interface, show a complex Soret band exhibiting splitting, hypochromicity and broadening features. Also, during the transfer process at high surface pressure, it has been shown that the EHO molecules are ejected from the C8A monolayer and only a fraction of porphyrin is transferred to the solid support, in spite of a complete transfer for the C8A matrix. The complex structure of the reflection spectra at the air-water interface, as well as the polarization dependence of the absorption spectra for the mixed LB films, indicate the existence of four different arrangements for the EHO hosted in the C8A matrix. The aggregate formation is governed by two factors: the attraction between the porphyrin rings which minimizes their separation, and the alkyl chain interactions, that is, hydrophobic effect and/or steric hindrance which determine and restrict the possible aggregation structures. By using the extended dipole model, the assignment of the spectral peaks observed to different EHO aggregates is shown.

  16. Ash Aggregates in Proximal Settings

    NASA Astrophysics Data System (ADS)

    Porritt, L. A.; Russell, K.

    2012-12-01

    Ash aggregates are thought to have formed within and been deposited by the eruption column and plume and dilute density currents and their associated ash clouds. Moist, turbulent ash clouds are considered critical to ash aggregate formation by facilitating both collision and adhesion of particles. Consequently, they are most commonly found in distal deposits. Proximal deposits containing ash aggregates are less commonly observed but do occur. Here we describe two occurrences of vent proximal ash aggregate-rich deposits; the first within a kimberlite pipe where coated ash pellets and accretionary lapilli are found within the intra-vent sequence; and the second in a glaciovolcanic setting where cored pellets (armoured lapilli) occur within <1 km of the vent. The deposits within the A418 pipe, Diavik Diamond Mine, Canada, are the residual deposits within the conduit and vent of the volcano and are characterised by an abundance of ash aggregates. Coated ash pellets are dominant but are followed in abundance by ash pellets, accretionary lapilli and rare cored pellets. The coated ash pellets typically range from 1 - 5 mm in diameter and have core to rim ratios of approximately 10:1. The formation and preservation of these aggregates elucidates the style and nature of the explosive phase of kimberlite eruption at A418 (and other pipes?). First, these pyroclasts dictate the intensity of the kimberlite eruption; it must be energetic enough to cause intense fragmentation of the kimberlite to produce a substantial volume of very fine ash (<62 μm). Secondly, the ash aggregates indicate the involvement of moisture coupled with the presence of dilute expanded eruption clouds. The structure and distribution of these deposits throughout the kimberlite conduit demand that aggregation and deposition operate entirely within the confines of the vent; this indicates that aggregation is a rapid process. Ash aggregates within glaciovolcanic sequences are also rarely documented. The

  17. Characterization Techniques for Aggregated Nanomaterials in Biological and Environmental Systems

    NASA Astrophysics Data System (ADS)

    Jeon, Seongho

    colloidal systems. Aggregation mechanism and behavior of nanoparticles in surrounding were examined as a function of their quantified aggregate morphologies. The first three studies (Chapters 2, 3, and 4) introduced a new gas-phase particle size measurement system, a liquid nebulization-ion mobility spectrometry (LN-IMS) technique, to characterize nanomaterials (down to 5 nm in characteristic size) and nanoparticle-protein conjugates. In other two studies (Chapters 5 and 6), three dimensional structures of homo-aggregates were quantified with the fractal aggregate model, and resulted fractal structures of aggregates were correlated to their transport properties in surroundings.

  18. Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

    PubMed

    Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

    2014-03-01

    Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules.

  19. Aggregation of model asphaltenes: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Costa, J. L. L. F. S.; Simionesie, D.; Zhang, Z. J.; Mulheran, P. A.

    2016-10-01

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

  20. Aggregation of model asphaltenes: a molecular dynamics study.

    PubMed

    Costa, J L L F S; Simionesie, D; Zhang, Z J; Mulheran, P A

    2016-10-05

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

  1. Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates.

    PubMed

    Castello, Fabio; Paredes, Jose M; Ruedas-Rama, Maria J; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

    2017-01-09

    The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer's and Parkinson's. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation.

  2. Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates

    PubMed Central

    Castello, Fabio; Paredes, Jose M.; Ruedas-Rama, Maria J.; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

    2017-01-01

    The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation. PMID:28067252

  3. Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates

    NASA Astrophysics Data System (ADS)

    Castello, Fabio; Paredes, Jose M.; Ruedas-Rama, Maria J.; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

    2017-01-01

    The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation.

  4. Nonlinear Absorption Spectroscopy of Porphyrin J-aggregates in Aqueous Solution: Evidence for Control of Degree of Association by Light-Induced Force

    NASA Astrophysics Data System (ADS)

    Shirakawa, Masayuki; Nakata, Kazuaki; Suzuki, Masaya; Kobayashi, Takayoshi; Tokunaga, Eiji

    2017-04-01

    Spectroscopic evidence was obtained for molecular aggregation states to be controlled by the irradiation of light, which is off-resonant below the peak absorption energies of both monomers and well-grown J-aggregates. In low (undersaturated)-concentration aqueous solutions of porphyrin molecules (tetraphenyl porphyrin tetrasulfonic acid; TPPS) where the monomer absorbance dominates, irradiation with a 532 nm laser induces a decrease in the monomer absorbance and an increase in the aggregate absorbance. The increase in the absorbance of J-aggregates occurs in a broad spectral range associated with the increase in the number of not only variously sized oligomer aggregates but also aggregates structurally different from well-grown stable J-aggregates. In high-concentration solutions where the J-aggregate absorbance dominates, a blue shift of the absorption peak of J-aggregates is induced at the same 532 nm irradiation, corresponding to a decrease in the aggregation number or in the association energy. By contrast, for spin-coated polymer films of monomers and J-aggregates where molecules are immobile, these features are not observed. It is remarkable that the gradient force potential is smaller by more than seven orders of magnitude than the kinetic energy of the thermal motion of the molecule at room temperature, but the absorption change in solution indicating the increase in the number of aggregates is as large as ΔA ˜ 10-3 in magnitude.

  5. Kinetic analysis of the multistep aggregation mechanism of monoclonal antibodies.

    PubMed

    Nicoud, Lucrèce; Arosio, Paolo; Sozo, Margaux; Yates, Andrew; Norrant, Edith; Morbidelli, Massimo

    2014-09-11

    We investigate by kinetic analysis the aggregation mechanism of two monoclonal antibodies belonging to the IgG1 and IgG2 subclass under thermal stress. For each IgG, we apply a combination of size exclusion chromatography and light scattering techniques to resolve the time evolution of the monomer, dimer, and trimer concentrations, as well as the average molecular weight and the average hydrodynamic radius of the aggregate distribution. By combining the detailed experimental characterization with a theoretical kinetic model based on population balance equations, we extract relevant information on the contribution of the individual elementary steps on the global aggregation process. The analysis shows that the two molecules follow different aggregation pathways under the same operating conditions. In particular, while the monomer depletion of the IgG1 is found to be rate-limited by monomeric conformational changes, bimolecular collision is identified as the rate-limiting step in the IgG2 aggregation process. The measurement of the microscopic rate constants by kinetic analysis allows the quantification of the protein-protein interaction potentials expressed in terms of the Fuchs stability ratio (W). It is found that the antibody solutions exhibit large W values, which are several orders of magnitude larger than the values computed in the frame of the DLVO theory. This indicates that, besides net electrostatic repulsion, additional effects delay the aggregation kinetics of the antibody solutions with respect to diffusion-limited conditions. These effects likely include the limited efficiency of the collision events due to the presence of a limited number of specific aggregation-prone patches on the heterogeneous protein surface, and the contribution of additional repulsive non-DLVO forces to the protein-protein interaction potential, such as hydration forces.

  6. Labile aggregation stimulating substance, free fatty acids, and platelet aggregation.

    PubMed

    Gerrard, J M; White, J G; Krivit, W

    1976-01-01

    Labile aggregation stimulating substance (LASS), an intermediate produced during platelet biosynthesis of PGE2 and PGF2alpha, acts as a physiologic intercellular messenger to promote platelet aggregation and the release reaction. The activity is formed by intact cells after physiologic stimulation or can be generated from platelet membrane fractions after combination with arachidonate. In the present investigation, small amounts of polyunsaturated fatty acids added to an incubation mixture of platelet microsomes and arachidonate were found to significantly inhibit subsequent platelet aggregation. Saturated and mono-unsaturated fatty acids in the same concentrations were without effect. However, in higher concentrations mono-unsaturated fatty acids were found to be inhibitory and stearic acid was found to enhance subsequent platelet aggregation. The inhibition caused by the polyunsaturated fatty acid, linoleate, was shown to be the result of an effect on the production of LASS through an interaction with the platelet enzyme responsible for conversion of arachidonate to LASS. In contrast, stearic acid was found to enhance platelet aggregation by acting on the platelets and not directly on LASS production. The results suggest that small changes in the fatty acid composition of platelet phospholipids could significantly influence platelet reactivity.

  7. Electrokinetic concentration of charged molecules

    DOEpatents

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  8. Special Issue: "Molecules against Alzheimer".

    PubMed

    Decker, Michael; Muñoz-Torrero, Diego

    2016-12-16

    This Special Issue, entitled "Molecules against Alzheimer", gathers a number of original articles, short communications, and review articles on recent research efforts toward the development of novel drug candidates, diagnostic agents and therapeutic approaches for Alzheimer's disease (AD), the most prevalent neurodegenerative disorder and a leading cause of death worldwide. This Special Issue contains many interesting examples describing the design, synthesis, and pharmacological profiling of novel compounds that hit one or several key biological targets, such as cholinesterases, β-amyloid formation or aggregation, monoamine oxidase B, oxidative stress, biometal dyshomeostasis, mitochondrial dysfunction, serotonin and/or melatonin systems, the Wnt/β-catenin pathway, sigma receptors, nicotinamide phosphoribosyltransferase, or nuclear erythroid 2-related factor. The development of novel AD diagnostic agents based on tau protein imaging and the use of lithium or intranasal insulin for the prevention or the symptomatic treatment of AD is also covered in some articles of the Special Issue.

  9. Red-light-emitting system based on aggregation of donor-acceptor derivatives in polar aqueous media.

    PubMed

    Ishi-i, Tsutomu; Ikeda, Kei; Kichise, Yuki; Ogawa, Michiaki

    2012-06-01

    Glowing together: An efficient red-light-emitting system has been created in polar water media based on the aggregation of donor-acceptor molecules. In the THF/water mixture, the emission was quenched when a small volume of water was used, whereas it was recovered and enhanced upon aggregate formation with a large water volume.

  10. Effect of erythrocyte aggregation at pathological levels on NO/O2 transport in small arterioles.

    PubMed

    Cho, Seungkwan; Namgung, Bumseok; Kim, Han Sung; Leo, Hwa Liang; Kim, Sangho

    2015-01-01

    This study examined the effects of red blood cell (RBC) aggregation at pathological levels on NO/O2 transport in small arterioles. Transient gas diffusion simulations were performed with in vivo cell-free layer (CFL) widths data obtained from arteriolar flows in the rat cremaster muscle. The CFL data were measured at physiological and pathological levels of aggregation under reduced flow conditions (pseudoshear rate = 31.4 ± 10.5 s-1). Our results showed that the mean peak NO concentration significantly decreased with increasing the aggregation level from non-aggregating to normal-aggregating (P < 0.05) and to hyper-aggregating (P < 0.01) conditions. In contrast, the partial O2 pressure (PO2) in pathological aggregating conditions significantly increased from those under non-aggregating (P < 0.001) and normal-aggregating (P < 0.05) conditions. Although the NO scavenging by RBCs could be impaired with a thicker CFL at higher levels of aggregation, the overall decrease in NO production due to reduction of wall shear stress with the thicker CFL dominantly limited the NO availability in tissue. On the other hand, the O2 availability in tissue increased due to the relatively high core hematocrit in the blood lumen with the thicker CFL.

  11. Experimental aggregation of volcanic ash: the role of liquid bonding

    NASA Astrophysics Data System (ADS)

    Mueller, S.; Kueppers, U.; Jacob, M.; Ayris, P. M.; Dingwell, D. B.

    2015-12-01

    Explosive volcanic eruptions may release vast quantities of ash. Because of its size, it has the greatest dispersal potential and can be distributed globally. Ash may pose severe risks for 1) air traffic, 2) human and animal health, 3) agriculture and 4) infrastructure. Such ash particles can however cluster and form ash aggregates that range in size from millimeters to centimeters. During their growth, weight and aerodynamic properties change. This leads to significantly changed transport and settling behavior. The physico-chemical processes involved in aggregation are quantitatively poorly constrained. We have performed laboratory ash aggregation experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. Solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (e.g., air flow rate, gas temperature, humidity, liquid composition). In this manner we simulate the variable gas-particle flow conditions expected in eruption plumes and pyroclastic density currents. We have used 1) soda-lime glass beads as an analogue material and 2) natural volcanic ash from Laacher See Volcano (Germany). In order to influence form, size, stability and the production rate of aggregates, a range of experimental conditions (e.g., particle concentration, degree of turbulence, temperature and moisture in the process chamber and the composition of the liquid phase) have been employed. We have successfully reproduced several features of natural ash aggregates, including round, internally structured ash pellets up to 3 mm in diameter. These experimental results help to constrain the boundary conditions required for the generation of spherical, internally-structured ash aggregates that survive deposition and are preserved in the volcanological record. These results should also serve as input parameters for models of ash transport and ash mass distribution.

  12. Fractal Aggregates in Tennis Ball Systems

    ERIC Educational Resources Information Center

    Sabin, J.; Bandin, M.; Prieto, G.; Sarmiento, F.

    2009-01-01

    We present a new practical exercise to explain the mechanisms of aggregation of some colloids which are otherwise not easy to understand. We have used tennis balls to simulate, in a visual way, the aggregation of colloids under reaction-limited colloid aggregation (RLCA) and diffusion-limited colloid aggregation (DLCA) regimes. We have used the…

  13. Superdiffusive gas recovery from nanopores

    NASA Astrophysics Data System (ADS)

    Wu, Haiyi; He, Yadong; Qiao, Rui

    2016-11-01

    Understanding the recovery of gas from reservoirs featuring pervasive nanopores is essential for effective shale gas extraction. Classical theories cannot accurately predict such gas recovery and many experimental observations are not well understood. Here we report molecular simulations of the recovery of gas from single nanopores, explicitly taking into account molecular gas-wall interactions. We show that, in very narrow pores, the strong gas-wall interactions are essential in determining the gas recovery behavior both quantitatively and qualitatively. These interactions cause the total diffusion coefficients of the gas molecules in nanopores to be smaller than those predicted by kinetic theories, hence slowing down the rate of gas recovery. These interactions also lead to significant adsorption of gas molecules on the pore walls. Because of the desorption of these gas molecules during gas recovery, the gas recovery from the nanopore does not exhibit the usual diffusive scaling law (i.e., the accumulative recovery scales as R ˜t1 /2 ) but follows a superdiffusive scaling law R ˜tn (n >0.5 ), which is similar to that observed in some field experiments. For the system studied here, the superdiffusive gas recovery scaling law can be captured well by continuum models in which the gas adsorption and desorption from pore walls are taken into account using the Langmuir model.

  14. Thermodynamic modeling of asphaltene aggregation.

    PubMed

    Rogel, E

    2004-02-03

    A new molecular thermodynamic model for the description of the aggregation behavior of asphaltenes in different solvents is presented. This new model is relatively simple and strictly predictive and does not use any experimental information from asphaltene solutions. In this model, asphaltene aggregates are described as composed of an aromatic core formed by stacked aromatic sheets surrounded by aliphatic chains. The proposed model qualitatively predicts the asphaltene aggregation behavior in a series of different solvents. In particular, the experimental trends observed for the variation of aggregate size with (1) asphaltene molecular characteristics (condensation index, aromaticity, and chain length), (2) asphaltene concentration, (3) solvent characteristics, and (4) temperature have been successfully reproduced by the proposed model. The model also provides a plausible explanation for the existence or absence of a critical micelle concentration (cmc) for asphaltene solutions. Specifically, the model predicted that the asphaltenes with low aromaticities and low aromatic condensations do not exhibit cmc behavior. Finally, the obtained results clearly support the classical model for asphaltene aggregates.

  15. Spatial aggregation: Language and applications

    SciTech Connect

    Bailey-Kellogg, C.; Zhao, F.; Yip, K.

    1996-12-31

    Spatial aggregation is a framework for organizing computations around image-like, analogue representations of physical processes in data interpretation and control tasks. It conceptualizes common computational structures in a class of implemented problem solvers for difficult scientific and engineering problems. It comprises a mechanism, a language, and a programming style. The spatial aggregation mechanism transforms a numerical input field to successively higher-level descriptions by applying a small, identical set of operators to each layer given a metric, neighborhood relation and equivalence relation. This paper describes the spatial aggregation language and its applications. The spatial aggregation language provides two abstract data types - neighborhood graph and field - and a set of interface operators for constructing the transformations of the field, together with a library of component implementations from which a user can mix-and-match and specialize for a particular application. The language allows users to isolate and express important computational ideas in different problem domains while hiding low-level details. We illustrate the use of the language with examples ranging from trajectory grouping in dynamics interpretation to region growing in image analysis. Programs for these different task domains can be written in a modular, concise fashion in the spatial aggregation language.

  16. Leaching behaviour of synthetic aggregates.

    PubMed

    van der Sloot, H A; Hoede, D; Cresswell, D J; Barton, J R

    2001-01-01

    In the framework of EU project "Utilising innovative kiln technology to recycle waste into synthetic aggregate" (BRST-CT98-5234), the leaching behaviour of synthetic aggregates has been studied to assess its environmental compatibility in the various stages of its use. Since the conditions are very different for the different uses, the assessment calls for a variety of different leaching conditions. The pH dependence test is used to cover important differences in pH environment to which the materials are exposed to as well as for an assessment of the buffering capacity of the material. Synthetic aggregate features a low buffer capacity, which makes it sensitive to externally imposed pH conditions. Utilisation and storage exposed to acidic conditions needs to be avoided. The results of the pH dependence test and column leaching test are mutually consistent. The CEN TC 154 method appears to provide systematically low values due to the arbitrary selection of test conditions. Synthetic aggregate studied to date will not adversely affect the concrete in its service life. The main issue for aggregate use is the recycling and the "end of life" condition, when the material becomes construction debris. Not metals, but oxyanions, such as Cr VI and Mo are most relevant under these conditions. A concise test has been applied to assess crucial aspects of leaching for different production mixes.

  17. Novel insights into amylin aggregation

    PubMed Central

    Pillay, Karen; Govender, Patrick

    2014-01-01

    Amylin is a peptide that aggregates into species that are toxic to pancreatic beta cells, leading to type II diabetes. This study has for the first time quantified amylin association and dissociation kinetics (association constant (ka) = 28.7 ± 5.1 L mol−1 s−1 and dissociation constant (kd) = 2.8 ± 0.6 ×10−4 s−1) using surface plasmon resonance (SPR). Thus far, techniques used for the sizing of amylin aggregates do not cater for the real-time monitoring of unconstrained amylin in solution. In this regard we evaluated recently innovated nanoparticle tracking analysis (NTA). In addition, both SPR and NTA were used to study the effect of previously synthesized amylin derivatives on amylin aggregation and to evaluate their potential as a cell-free system for screening potential inhibitors of amylin-mediated cytotoxicity. Results obtained from NTA highlighted a predominance of 100–300 nm amylin aggregates and correlation to previously published cytotoxicity results suggests the toxic species of amylin to be 200–300 nm in size. The results seem to indicate that NTA has potential as a new technique to monitor the aggregation potential of amyloid peptides in solution and also to screen potential inhibitors of amylin-mediated cytotoxicity. PMID:26019498

  18. Aggregated Recommendation through Random Forests

    PubMed Central

    2014-01-01

    Aggregated recommendation refers to the process of suggesting one kind of items to a group of users. Compared to user-oriented or item-oriented approaches, it is more general and, therefore, more appropriate for cold-start recommendation. In this paper, we propose a random forest approach to create aggregated recommender systems. The approach is used to predict the rating of a group of users to a kind of items. In the preprocessing stage, we merge user, item, and rating information to construct an aggregated decision table, where rating information serves as the decision attribute. We also model the data conversion process corresponding to the new user, new item, and both new problems. In the training stage, a forest is built for the aggregated training set, where each leaf is assigned a distribution of discrete rating. In the testing stage, we present four predicting approaches to compute evaluation values based on the distribution of each tree. Experiments results on the well-known MovieLens dataset show that the aggregated approach maintains an acceptable level of accuracy. PMID:25180204

  19. Relaxation times and modes of disturbed aggregate distribution in micellar solutions with fusion and fission of micelles

    SciTech Connect

    Zakharov, Anatoly I.; Adzhemyan, Loran Ts.; Shchekin, Alexander K.

    2015-09-28

    We have performed direct numerical calculations of the kinetics of relaxation in the system of surfactant spherical micelles under joint action of the molecular mechanism with capture and emission of individual surfactant molecules by molecular aggregates and the mechanism of fusion and fission of the aggregates. As a basis, we have taken the difference equations of aggregation and fragmentation in the form of the generalized kinetic Smoluchowski equations for aggregate concentrations. The calculations have been made with using the droplet model of molecular surfactant aggregates and two modified Smoluchowski models for the coefficients of aggregate-monomer and aggregate-aggregate fusions which take into account the effects of the aggregate size and presence of hydrophobic spots on the aggregate surface. A full set of relaxation times and corresponding relaxation modes for nonequilibrium aggregate distribution in the aggregation number has been found. The dependencies of these relaxation times and modes on the total concentration of surfactant in the solution and the special parameter controlling the probability of fusion in collisions of micelles with other micelles have been studied.

  20. High-Throughput Multiplexed Quantitation of Protein Aggregation and Cytotoxicity in a Huntington’s Disease Model

    PubMed Central

    Titus, Steven A; Southall, Noel; Marugan, Juan; Austin, Christopher P; Zheng, Wei

    2012-01-01

    A hallmark of Huntington’s disease is the presence of a large polyglutamine expansion in the first exon of the Huntingtin protein and the propensity of protein aggregation by the mutant proteins. Aberrant protein aggregation also occurs in other polyglutamine expansion disorders, as well as in other neurodegenerative diseases including Parkinson’s, Alzheimer’s, and prion diseases. However, the pathophysiological role of these aggregates in the cell death that characterizes the diseases remains unclear. Identification of small molecule probes that modulate protein aggregation and cytotoxicity caused by aggregated proteins may greatly facilitate the studies on pathogenesis of these diseases and potentially lead to development of new therapies. Based on a detergent insoluble property of the Huntingtin protein aggregates, we have developed a homogenous assay to rapidly quantitate the levels of protein aggregates in a cellular model of Huntington’s disease. The protein aggregation assay has also been multiplexed with a protease release assay for the measurement of cytotoxicity resulting from aggregated proteins in the same cells. Through a testing screen of a compound library, we have demonstrated that this multiplexed cytotoxicity and protein aggregation assay has ability to identify active compounds that prevent cell death and/or modulate protein aggregation in cells of the Huntington’s disease model. Therefore, this multiplexed screening approach is also useful for development of high-throughput screening assays for other neurodegenerative diseases involving protein aggregation. PMID:23346268

  1. Phase behavior of a binary fluid mixture of quadrupolar molecules

    NASA Astrophysics Data System (ADS)

    Toda, Masatoshi; Kajimoto, Shinji; Toyouchi, Shuichi; Kawakatsu, Toshihiro; Akama, Yohji; Kotani, Motoko; Fukumura, Hiroshi

    2016-11-01

    We propose a model molecule to investigate microscopic properties of a binary mixture with a closed-loop coexistence region. The molecule is comprised of a Lennard-Jones particle and a uniaxial quadrupole. Gibbs ensemble Monte Carlo simulations demonstrate that the high-density binary fluid of the molecules with the quadrupoles of the same magnitude but of the opposite signs can show closed-loop immiscibility. We find that an increase in the magnitude of the quadrupoles causes a shrinkage of the coexistence region. Molecular dynamics simulations also reveal that aggregates with two types of molecules arranged alternatively are formed in the stable one-phase region both above and below the coexistence region. String structures are dominant below the lower critical solution temperature, while branched aggregates are observed above the upper critical solution temperature. We conclude that the anisotropic interaction between the quadrupoles of the opposite signs plays a crucial role in controlling these properties of the phase behavior.

  2. Rigidification or interaction-induced phosphorescence of organic molecules.

    PubMed

    Baroncini, Massimo; Bergamini, Giacomo; Ceroni, Paola

    2017-02-09

    Phosphorescent materials are mostly based on metal complexes. Metal-free organic molecules usually display phosphorescence only in a rigid matrix at 77 K. In the last few years, there has been increasing interest in the design of organic molecules displaying long-lived and highly intense room-temperature phosphorescence, an extremely difficult task since these two properties are generally conflicting. This review reports the most recent and tutorial examples of molecules that are weakly or non-phosphorescent in deaerated fluid solution and whose room temperature phosphorescence is switched on upon aggregation. The examples are divided into two classes according to the mechanism responsible for switching on phosphorescence: (i) rigidification by crystallization or by encapsulation in a polymeric matrix and (ii) interaction with other molecules of the same type (self-aggregation) or a different type by taking advantage of heavy-atom effects.

  3. Customer Aggregation: An Opportunity for Green Power?

    SciTech Connect

    Holt, E.; Bird, L.

    2001-02-26

    We undertook research into the experience of aggregation groups to determine whether customer aggregation offers an opportunity to bring green power choices to more customers. The objectives of this report, therefore, are to (1) identify the different types of aggregation that are occurring today, (2) learn whether aggregation offers an opportunity to advance sales of green power, and (3) share these concepts and approaches with potential aggregators and green power advocates.

  4. Equilibrium structure of ferrofluid aggregates.

    PubMed

    Yoon, Mina; Tománek, David

    2010-11-17

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  5. Equilibrium structure of ferrofluid aggregates

    SciTech Connect

    Yoon, Mina; Tomanek, David

    2010-01-01

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  6. Techniques for Monitoring Protein Misfolding and Aggregation in Vitro and in Living Cells

    PubMed Central

    Gregoire, Simpson; Irwin, Jacob; Kwon, Inchan

    2012-01-01

    Protein misfolding and aggregation have been considered important in understanding many neurodegenerative diseases and recombinant biopharmaceutical production. Therefore, various traditional and modern techniques have been utilized to monitor protein aggregation in vitro and in living cells. Fibril formation, morphology and secondary structure content of amyloidogenic proteins in vitro have been monitored by molecular probes, TEM/AFM, and CD/FTIR analyses, respectively. Protein aggregation in living cells has been qualitatively or quantitatively monitored by numerous molecular folding reporters based on either fluorescent protein or enzyme. Aggregation of a target protein is directly correlated to the changes in fluorescence or enzyme activity of the folding reporter fused to the target protein, which allows non-invasive monitoring aggregation of the target protein in living cells. Advances in the techniques used to monitor protein aggregation in vitro and in living cells have greatly facilitated the understanding of the molecular mechanism of amyloidogenic protein aggregation associated with neurodegenerative diseases, optimizing culture conditions to reduce aggregation of biopharmaceuticals expressed in living cells, and screening of small molecule libraries in the search for protein aggregation inhibitors. PMID:23565019

  7. The Effects of Latrepirdine on Amyloid-β Aggregation and Toxicity

    PubMed Central

    Porter, Tenielle; Bharadwaj, Prashant; Groth, David; Paxman, Adrian; Laws, Simon M.; Martins, Ralph N.; Verdile, Giuseppe

    2016-01-01

    Latrepirdine (Dimebon™) has been demonstrated to be a neuroprotective and cognition improving agent in neurodegenerative diseases that feature protein aggregation and deposition, such as Alzheimer’s disease (AD). The accumulation of amyloid-β (Aβ) protein aggregates is a key event in the neurodegenerative process in AD. This study explores if latrepirdine modulation of protein aggregation contributes to its neuroprotective mechanism of action. Assessment of neuronal cell death showed that there was a significant reduction in lactate dehydrogenase release at an equimolar ratio of Aβ:latrepirdine and with lower concentrations of latrepirdine. The ability of latrepirdine to alter the formation of Aβ42 aggregates was assessed by thioflavin-T fluorescence, western immunoblotting and atomic force microscopy (AFM). Despite showing a reduction in thioflavin-T fluorescence with latrepirdine treatment, indicating a decrease in aggregation, immunoblotting and AFM showed a modest increase in both the formation and size of Aβ aggregates. The discrepancies between thioflavin-T and the other assays are consistent with previous evidence that cyclic molecules can interfere with thioflavin-T binding of amyloid protein preparations. The ability of latrepirdine to modulate Aβ aggregation appears to be independent of its neuroprotective effects, and is unlikely to be a mechanism by which latrepirdine offers protection. This study investigates the effect of latrepirdine on Aβ aggregation, and presents evidence suggesting that caution should be applied in the use of thioflavin-T fluorescence based assays as a method for screening compounds for protein aggregation altering properties. PMID:26836170

  8. Aggregation of gramicidin A in phospholipid Langmuir-Blodgett monolayers.

    PubMed Central

    Diociaiuti, Marco; Bordi, Federico; Motta, Annelisa; Carosi, Alessandra; Molinari, Agnese; Arancia, Giuseppe; Coluzza, Carlo

    2002-01-01

    The aggregation of Gramicidin A (gA) in dipalmitoylphosphatidylcoline (DPPC) monolayers is investigated by both thermodynamic and structural methods. Compression isotherm analysis and atomic force microscopy (AFM) observations are performed. Our experimental results indicate that gA aggregation does occur in DPPC monolayers even at very low gA concentration (about 8 x 10(-4) mol%). At the low gA concentration limit, the aggregation process seems to be mainly horizontal (i.e., side-by-side, into the monolayer plane), following a fractal pattern growth producing the formation of typical, flat (0.5 nm height) "doughnut" structures, with a diameter of approximately 150 nm. These structures appear to be composed of smaller subunits (about 70 nm diameter) showing the same doughnut structure. At a molar fraction of approximately 3.8 mol%, the big doughnuts start to disaggregate and only small doughnuts appear. Above a gA concentration of approximately 4.4 mol%, all doughnuts (large and small) disappear, and the morphology assumes the appearance of a patchwork of two distinct phases: one that, being very flat, can be associated with a gA-free or gA-poor DPPC phase, and a second one, characterized by a more corrugated surface, associated with a gA-rich DPPC phase. At gA concentration of approximately 5 mol%, a percolation transition in the gA-rich DPPC phase occurs. Thermodynamic data indicate that the maximum of miscibility between gA and DPPC molecules occurs at approximately 28 mol%, suggesting that gA could aggregate in hexamers that are, on average, bound to 16 DPPC molecules. At the same concentration, AFM images show a network of small gA aggregation units of a size compatible with gA hexamers. PMID:12023244

  9. A specialist's audit of aggregated occurrence records: An 'aggregator's' perspective.

    PubMed

    Belbin, Lee; Daly, Joanne; Hirsch, Tim; Hobern, Donald; Salle, John La

    2013-01-01

    A recent ZooKeys' paper (Mesibov, 2013: http://www.pensoft.net/journal_home_page.php?journal_id=1&page=article&SESID=df7bcb35b02603283dcb83ee0e0af0c9&type=show&article_id=5111) has highlighted data quality issues in aggregated data sets, but did not provide a realistic way to address these issues. This paper provides an aggregator's perspective including ways that the whole community can help to address data quality issues. The establishment of GBIF and national nodes (national aggregators) such as the Atlas of Living Australia (ALA) have integrated and exposed a huge diversity of biological observations along with many associated issues. Much of the admirable work by Mesibov (2013) was enabled by having the data exposed. Data quality, one of the highest priorities for GBIF, the national nodes and other aggregators, depends on both automatic methods and community experts to detect and correct data issues. Not all issues can however be automatically detected or corrected, so community assistance is needed to help improve the quality of exposed biological data. We do need to improve the infrastructure and associated processes to more easily identify data issues and document all changes to ensure a full record is permanently and publicly available.

  10. Environmentalism and natural aggregate mining

    USGS Publications Warehouse

    Drew, L.J.; Langer, W.H.; Sachs, J.S.

    2002-01-01

    Sustaining a developed economy and expanding a developing one require the use of large volumes of natural aggregate. Almost all human activity (commercial, recreational, or leisure) is transacted in or on facilities constructed from natural aggregate. In our urban and suburban worlds, we are almost totally dependent on supplies of water collected behind dams and transported through aqueducts made from concrete. Natural aggregate is essential to the facilities that produce energy-hydroelectric dams and coal-fired powerplants. Ironically, the utility created for mankind by the use of natural aggregate is rarely compared favorably with the environmental impacts of mining it. Instead, the empty quarries and pits are seen as large negative environmental consequences. At the root of this disassociation is the philosophy of environmentalism, which flavors our perceptions of the excavation, processing, and distribution of natural aggregate. The two end-member ideas in this philosophy are ecocentrism and anthropocentrism. Ecocentrism takes the position that the natural world is a organism whose arteries are the rivers-their flow must not be altered. The soil is another vital organ and must not be covered with concrete and asphalt. The motto of the ecocentrist is "man must live more lightly on the land." The anthropocentrist wants clean water and air and an uncluttered landscape for human use. Mining is allowed and even encouraged, but dust and noise from quarry and pit operations must be minimized. The large volume of truck traffic is viewed as a real menace to human life and should be regulated and isolated. The environmental problems that the producers of natural aggregate (crushed stone and sand and gravel) face today are mostly difficult social and political concerns associated with the large holes dug in the ground and the large volume of heavy truck traffic associated with quarry and pit operations. These concerns have increased in recent years as society's demand for

  11. Hydrodynamic behavior of fractal aggregates

    NASA Astrophysics Data System (ADS)

    Wiltzius, Pierre

    1987-02-01

    Measurements of the radius of gyration RG and the hydrodynamic radius RH of colloidal silica aggregates are reported. These aggregates have fractal geometry and RH is proportional to RG for 500 Å<=RH<=7000 Å, with a ratio RH/RG=0.72+/-0.02. The results are compared with predictions for macromolecules of various shapes. The proportionality of the two radii can be understood with use of the pair correlation function of fractal objects and hydrodynamic interactions on the Oseen level. The value of the ratio remains to be explained.

  12. Measuring the optical chirality of molecular aggregates at liquid-liquid interfaces.

    PubMed

    Watarai, Hitoshi; Adachi, Kenta

    2009-10-01

    Some new experimental methods for measuring the optical chirality of molecular aggregates formed at liquid-liquid interfaces have been reviewed. Chirality measurements of interfacial aggregates are highly important not only in analytical spectroscopy but also in biochemistry and surface nanochemistry. Among these methods, a centrifugal liquid membrane method was shown to be a highly versatile method for measuring the optical chirality of the liquid-liquid interface when used in combination with a commercially available circular dichroism (CD) spectropolarimeter, provided that the interfacial aggregate exhibited a large molar absorptivity. Therefore, porphyrin and phthalocyanine were used as chromophoric probes of the chirality of itself or guest molecules at the interface. A microscopic CD method was also demonstrated for the measurement of a small region of a film or a sheet sample. In addition, second-harmonic generation and Raman scattering methods were reviewed as promising methods for detecting interfacial optical molecules and measuring bond distortions of chiral molecules, respectively.

  13. Tunneling electron induced molecular electroluminescence from individual porphyrin J-aggregates

    SciTech Connect

    Meng, Qiushi; Zhang, Chao; Zhang, Yang E-mail: zcdong@ustc.edu.cn; Zhang, Yao; Liao, Yuan; Dong, Zhenchao E-mail: zcdong@ustc.edu.cn

    2015-07-27

    We investigate molecular electroluminescence from individual tubular porphyrin J-aggregates on Au(111) by tunneling electron excitations in an ultrahigh-vacuum scanning tunneling microscope (STM). High-resolution STM images suggest a spiral tubular structure for the porphyrin J-aggregate with highly ordered “brickwork”-like arrangements. Such aggregated nanotube is found to behave like a self-decoupled molecular architecture and shows red-shifted electroluminescence characteristics of J-aggregates originated from the delocalized excitons. The positions of the emission peaks are found to shift slightly depending on the excitation sites, which, together with the changes in the observed spectral profiles with vibronic progressions, suggest a limited exciton coherence number within several molecules. The J-aggregate electroluminescence is also found unipolar, occurring only at negative sample voltages, which is presumably related to the junction asymmetry in the context of molecular excitations via the carrier injection mechanism.

  14. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    PubMed

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation.

  15. Rational design of aggregation-resistant bioactive peptides: reengineering human calcitonin.

    PubMed

    Fowler, Susan B; Poon, Stephen; Muff, Roman; Chiti, Fabrizio; Dobson, Christopher M; Zurdo, Jesús

    2005-07-19

    A high propensity to aggregate into intractable deposits is a common problem limiting the production and use of many peptides and proteins in a wide range of biotechnological and pharmaceutical applications. Many therapeutic polypeptides are frequently abandoned at an early stage in their development because of problems with stability and aggregation. It has been shown recently that parameters describing the physicochemical properties of polypeptides can be used as predictors of protein aggregation. Here we demonstrate that these and similar tools can be applied to the rational redesign of bioactive molecules with a significantly reduced aggregation propensity without loss of physiological activity. This strategy has been exemplified by designing variants of the hormone calcitonin that show a significantly reduced aggregation propensity, yet maintain, or even increase, their potency when compared to the current therapeutic forms. The results suggest that this approach could be used successfully to enhance the solubility and efficacy of a wide range of other peptide and protein therapeutics.

  16. A mechanistic model of tau amyloid aggregation based on direct observation of oligomers

    NASA Astrophysics Data System (ADS)

    Shammas, Sarah L.; Garcia, Gonzalo A.; Kumar, Satish; Kjaergaard, Magnus; Horrocks, Mathew H.; Shivji, Nadia; Mandelkow, Eva; Knowles, Tuomas P. J.; Mandelkow, Eckhard; Klenerman, David

    2015-04-01

    Protein aggregation plays a key role in neurodegenerative disease, giving rise to small oligomers that may become cytotoxic to cells. The fundamental microscopic reactions taking place during aggregation, and their rate constants, have been difficult to determine due to lack of suitable methods to identify and follow the low concentration of oligomers over time. Here we use single-molecule fluorescence to study the aggregation of the repeat domain of tau (K18), and two mutant forms linked with familial frontotemporal dementia, the deletion mutant ΔK280 and the point mutant P301L. Our kinetic analysis reveals that aggregation proceeds via monomeric assembly into small oligomers, and a subsequent slow structural conversion step before fibril formation. Using this approach, we have been able to quantitatively determine how these mutations alter the aggregation energy landscape.

  17. Inhibition of neuronal cell-cell adhesion measured by the microscopic aggregation assay and impedance sensing

    NASA Astrophysics Data System (ADS)

    Wiertz, R. W. F.; Marani, E.; Rutten, W. L. C.

    2010-10-01

    Microscopic aggregation assay and impedance sensing (IS) were used to monitor a change in in vitro neuron-neuron adhesion in response to blocking of cell adhesion molecules. By blocking neuron-neuron adhesion, migration and aggregation of neuronal cells can be inhibited. This leads to better control of spatial arrangement of cells in culture. In the literature N-CAM, L1 and N-cadherin proteins are pointed out as main regulators of neuronal adhesion. In this study, these three main cell adhesion molecules were used to inhibit neuron-to-neuron adhesion and aggregation. Both soluble extracellular domains and antigen antibodies were added to these adhesion molecules. They were investigated for their blocking ability in neuronal cultures. First, in a 96 h aggregation assay on a low-adhesive substrate, the effect of inhibition of the three proteins on aggregation of cortical neurons was investigated optically. Both L1 antibody and L1 protein had no effect on the degree of aggregation. An N-cadherin antibody however was shown to be effective in aggregation inhibition at concentrations of 1 and 3 µg ml-1. Up to 96 h no aggregation occurred. A similar effect was achieved by the N-cadherin protein, although less distinct. N-CAM blocking revealed no inhibition of aggregation. Second, results from IS corresponded to those of the aggregation assays. In these experiments neuron-neuron adhesion was also inhibited by blocking N-CAM L1 and N-cadherin. Cortical neurons were cultured in small wells containing circular 100 µm diameter gold electrodes, so small changes in cell-cell interactions in monolayers of neurons could be monitored by IS. Impedances of neuron-covered electrodes were significantly lower in the presence of the N-cadherin antibody and protein at concentrations of 1, 3 and 10 µg ml-1, indicating a less profound binding between adjacent neurons. Results from the aggregation assays and impedance measurements demonstrate the applicability of blocking cell adhesion

  18. Interaction and Aggregation of Colloidal Biological Particles and Droplets in Electrically-Driven Flows

    NASA Technical Reports Server (NTRS)

    Davis, Robert H.; Loewenberg, Michael

    1997-01-01

    The primary objective of this research was to develop a fundamental understanding of aggregation and coalescence processes during electrically-driven migration of cells, particles and droplets. The process by which charged cells, particles, molecules, or drops migrate in a weak electric field is known as electrophoresis. If the migrating species have different charges or surface potentials, they will migrate at different speeds and thus may collide and aggregate or coalesce. Aggregation and coalescence are undesirable, if the goal is to separate the different species on the basis of their different electrophoretic mobilities.

  19. Whispering gallery modes microcavities with J-aggregates and plasmonic hot spots

    NASA Astrophysics Data System (ADS)

    Rakovich, Yury P.; Melnikau, Dzmitry; Savateeva, Diana; Chuvilin, Andrey; Hillenbrand, Rainer

    2012-06-01

    We have studied the optical properties of a hybrid system consisting of cyanine dye J-aggregates (both PIC and TDBC) attached to a spherical microcavity. Instead of the commonly accepted chemical bonding of dye molecules to the surface of microspheres or deposition of dye-doped sol-gel film, in our experiments microspheres were coated with J-aggregate shell utilizing the layer-by-layer assembly of the ultrathin films. In this approach we aimed to take advantage of light confinement in the Whispering Gallery Modes (WGMs) microcavity by placing the emitter (shell of J-aggregates) just at the rim of the microsphere, where the resonant electromagnetic field reaches its maximum. A periodic structure of narrow peaks was observed in the photoluminescence spectrum of the J-aggregates, arising from the coupling between the emission of J-aggregates and the WGMs of the microcavity. The most striking result of our study is the observation of polarization sensitive mode damping caused by re-absorption of J-aggregate emission. This effect manifests itself in dominating emission from the transverse magnetic modes in the spectral region of J-aggregates absorption band where the transverse electric (TE) modes are strongly suppressed. Strong suppression of TE modes reflects preferential tangential orientation of transition dipole moment of J-aggregates in deposited microcavity shell. Observed polarization sensitive mode damping observed in the spectral region of high J-aggregate absorption can be used for suppression of unwanted modes in high Q optical resonators. We also demonstrate that the emission intensity can be further enhanced by depositing a hybrid layer of J-aggregates and Ag nanoparticles onto the spherical microcavity. Owing to the concerted action of WGMs and plasmonic hot spots in the Ag aggregates, we observe strongly enhanced Raman signal from the Jaggregates. Microcavities covered by J-aggregates and plasmonic nanoparticles could be thus useful for a variety of

  20. Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations.

    PubMed

    Vogt, Natalja; Khaikin, Leonid S; Grikina, Olga E; Rykov, Anatolii N; Vogt, Jürgen

    2008-08-21

    Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1

  1. Sulfate Anion Delays the Self-Assembly of Human Insulin by Modifying the Aggregation Pathway

    PubMed Central

    Owczarz, Marta; Arosio, Paolo

    2014-01-01

    The understanding of the molecular mechanisms underlying protein self-assembly and of their dependence on solvent composition has implications in a large number of biological and biotechnological systems. In this work, we characterize the aggregation process of human insulin at acidic pH in the presence of sulfate ions using a combination of Thioflavin T fluorescence, dynamic light scattering, size exclusion chromatography, Fourier transform infrared spectroscopy, and transmission electron microscopy. It is found that the increase of sulfate concentration inhibits the conversion of insulin molecules into aggregates by modifying the aggregation pathway. At low sulfate concentrations (0–5 mM) insulin forms amyloid fibrils following the nucleated polymerization mechanism commonly observed under acidic conditions in the presence of monovalent anions. When the sulfate concentration is increased above 5 mM, the sulfate anion induces the salting-out of ∼18–20% of insulin molecules into reversible amorphous aggregates, which retain a large content of α-helix structures. During time these aggregates undergo structure rearrangements into β-sheet structures, which are able to recruit monomers and bind to the Thioflavin T dye. The alternative aggregation mechanism observed at large sulfate concentrations is characterized by a larger activation energy and leads to more polymorphic structures with respect to the self-assembly in the presence of chloride ions. The system shown in this work represents a case where amorphous aggregates on pathway to the formation of structures with amyloid features could be detected and analyzed. PMID:24988354

  2. Effect of water on deposition, aggregate size, and viscosity of asphaltenes.

    PubMed

    Aslan, Seyma; Firoozabadi, Abbas

    2014-04-08

    The aggregation and structure of polar molecules in nonpolar media may have a profound effect on bulk phase properties and transport. In this study, we investigate the aggregation and deposition of water and asphaltenes, the most polar fraction in petroleum fluids. In flow-line experiments, we vary the concentration of water from 500 up to 175,000 ppm and provide the evidence for clear changes in asphaltene deposition. Differential interference contrast (DIC) microscopy and dynamic light scattering (DLS) are used to measure the size of the aggregates. Rheological measurements are performed to get fixed ideas on the structural changes that water induces at different concentrations. This study demonstrates the significant effect of water on asphaltene aggregation and deposition and explores the molecular basis of water-asphaltene interaction. Our aggregate size measurements show that while asphaltene molecules increase the solubilization of water, there is no increase in the aggregate size. Our aggregation size measurements are different from the reports in the literature.

  3. Studies on recycled aggregates-based concrete.

    PubMed

    Rakshvir, Major; Barai, Sudhirkumar V

    2006-06-01

    Reduced extraction of raw materials, reduced transportation cost, improved profits, reduced environmental impact and fast-depleting reserves of conventional natural aggregates has necessitated the use of recycling, in order to be able to conserve conventional natural aggregate. In this study various physical and mechanical properties of recycled concrete aggregates were examined. Recycled concrete aggregates are different from natural aggregates and concrete made from them has specific properties. The percentages of recycled concrete aggregates were varied and it was observed that properties such as compressive strength showed a decrease of up to 10% as the percentage of recycled concrete aggregates increased. Water absorption of recycled aggregates was found to be greater than natural aggregates, and this needs to be compensated during mix design.

  4. Mesoscale Simulation of Asphaltene Aggregation.

    PubMed

    Wang, Jiang; Ferguson, Andrew L

    2016-08-18

    Asphaltenes constitute a heavy aromatic crude oil fraction with a propensity to aggregate and precipitate out of solution during petroleum processing. Aggregation is thought to proceed according to the Yen-Mullins hierarchy, but the molecular mechanisms underlying mesoscopic assembly remain poorly understood. By combining coarse-grained molecular models parametrized using all-atom data with high-performance GPU hardware, we have performed molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microsecond time scales. Our simulations reveal a hierarchical self-assembly mechanism consistent with the Yen-Mullins model, but the details are sensitive and depend on asphaltene chemistry and environment. At low concentrations asphaltenes exist predominantly as dispersed monomers. Upon increasing concentration, we first observe parallel stacking into 1D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates associated by offset, T-shaped, and edge-edge stacking. Asphaltenes possessing long aliphatic side chains cannot form nanoaggregate clusters due to steric repulsions between their aliphatic coronae. At very high concentrations, we observe a porous percolating network of rod-like nanoaggregates suspended in a sea of interpenetrating aliphatic side chains with a fractal dimension of ∼2. The lifetime of the rod-like aggregates is described by an exponential distribution reflecting a dynamic equilibrium between coagulation and fragmentation.

  5. RAGG - R EPISODIC AGGREGATION PACKAGE

    EPA Science Inventory

    The RAGG package is an R implementation of the CMAQ episodic model aggregation method developed by Constella Group and the Environmental Protection Agency. RAGG is a tool to provide climatological seasonal and annual deposition of sulphur and nitrogen for multimedia management. ...

  6. Sequence-dependent internalization of aggregating peptides.

    PubMed

    Couceiro, José R; Gallardo, Rodrigo; De Smet, Frederik; De Baets, Greet; Baatsen, Pieter; Annaert, Wim; Roose, Kenny; Saelens, Xavier; Schymkowitz, Joost; Rousseau, Frederic

    2015-01-02

    Recently, a number of aggregation disease polypeptides have been shown to spread from cell to cell, thereby displaying prionoid behavior. Studying aggregate internalization, however, is often hampered by the complex kinetics of the aggregation process, resulting in the concomitant uptake of aggregates of different sizes by competing mechanisms, which makes it difficult to isolate pathway-specific responses to aggregates. We designed synthetic aggregating peptides bearing different aggregation propensities with the aim of producing modes of uptake that are sufficiently distinct to differentially analyze the cellular response to internalization. We found that small acidic aggregates (≤500 nm in diameter) were taken up by nonspecific endocytosis as part of the fluid phase and traveled through the endosomal compartment to lysosomes. By contrast, bigger basic aggregates (>1 μm) were taken up through a mechanism dependent on cytoskeletal reorganization and membrane remodeling with the morphological hallmarks of phagocytosis. Importantly, the properties of these aggregates determined not only the mechanism of internalization but also the involvement of the proteostatic machinery (the assembly of interconnected networks that control the biogenesis, folding, trafficking, and degradation of proteins) in the process; whereas the internalization of small acidic aggregates is HSF1-independent, the uptake of larger basic aggregates was HSF1-dependent, requiring Hsp70. Our results show that the biophysical properties of aggregates determine both their mechanism of internalization and proteostatic response. It remains to be seen whether these differences in cellular response contribute to the particular role of specific aggregated proteins in disease.

  7. Multicomponent Gas Diffusion and an Appropriate Momentum Boundary Condition

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1994-01-01

    Multicomponent gas diffusion is reviewed with particular emphasis on gas flows near solid boundaries-the so-called Kramers-Kistemaker effect. The aim is to derive an appropriate momentum boundary condition which governs many gaseous species diffusing together. The many species' generalization of the traditional single gas condition, either as slip or stick (no-slip), is not obvious, particularly for technologically important cases of lower gas pressures and very dissimilar molecular weight gases. No convincing theoretical case exists for why two gases should interact with solid boundaries equally but in opposite flow directions, such that the total gas flow exactly vanishes. ln this way, the multicomponent no-slip boundary requires careful treatment The approaches discussed here generally adopt a microscopic model for gas-solid contact. The method has the advantage that the mathematics remain tractable and hence experimentally testable. Two new proposals are put forward, the first building in some molecular collision physics, the second drawing on a detailed view of surface diffusion which does not unphysically extrapolate bulk gas properties to govern the adsorbed molecules. The outcome is a better accounting of previously anomalous experiments. Models predict novel slip conditions appearing even for the case of equal molecular weight components. These approaches become particularly significant in view of a conceptual contradiction found to arise in previous derivations of the appropriate boundary conditions. The analogous case of three gases, one of which is uniformly distributed and hence non-diffusing, presents a further refinement which gives unexpected flow reversals near solid boundaries. This case is investigated alone and for aggregating gas species near their condensation point. In addition to predicting new physics, this investigation carries practical implications for controlling vapor diffusion in the growth of crystals used in medical diagnosis (e

  8. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  9. First principles Monte Carlo simulations of aggregation in the vapor phase of hydrogen fluoride

    SciTech Connect

    McGrath, Matthew J.; Ghogomu, Julius. N.; Mundy, Christopher J.; Kuo, I-F. Will; Siepmann, J. Ilja

    2010-01-01

    The aggregation of superheated hydrogen fluoride vapor is explored through the use of Monte Carlo simulations employing Kohn-Sham density functional theory with the exchange/correlation functional of Becke-Lee-Yang-Parr to describe the molecular interactions. Simulations were carried out in the canonical ensemble for a system consisting of ten molecules at constant density (2700 Å3/molecule) and at three different temperatures (T = 310, 350, and 390 K). Aggregation-volume-bias and configurational-bias Monte Carlo approaches (along with pre-sampling with an approximate potential) were employed to increase the sampling efficiency of cluster formation and destruction.

  10. Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface.

    PubMed

    Dalgicdir, Cahit; Sayar, Mehmet

    2015-12-10

    Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LKα14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LKα14 in bulk water. Next, in order to analyze the aggregation tendency of LKα14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LKα14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the α-helix conformation for a single molecule, it significantly reduces the attraction between two LKα14 peptides, along with their aggregation tendency.

  11. Complex Kepler Orbits and Particle Aggregation in Charged Microscopic Grains

    NASA Astrophysics Data System (ADS)

    Lee, Victor; Waitukaitis, Scott; Miskin, Marc; Jaeger, Heinrich

    2015-03-01

    Kepler orbits are usually associated with the motion of astronomical objects such as planets or comets. Here we observe such orbits at the microscale in a system of charged, insulating grains. By letting the grains fall freely under vacuum, we eliminate the effects of air drag and gravity, and by imaging them with a co-falling high-speed camera we track the relative positions of individual particles with high spatial and temporal precision. This makes it possible to investigate the behaviors caused by the combination of long-range electrostatic interactions and short-range, dissipative, contact interactions in unprecedented detail. We make the first direct observations of microscopic elliptical and hyperbolic Kepler orbits, collide-and-capture events between pairs of charged grains, and particle-by-particle aggregation into larger clusters. Our findings provide experimental evidence for electrostatic mechanisms that have been suspected, but not previously observed at the single-event level, as driving the early stages of particle aggregation in systems ranging from fluidized particle bed reactors to interstellar protoplanetary disks. Furthermore, since particles of different net charge and size are seen to aggregate into characteristic spatial configurations, our results suggest new possibilities for the formation of charge-stabilized ``granular molecules''. We can reproduce the observed molecule configurations by taking many-body, dielectric polarization effects into account.

  12. Cooling molecules in a cell for FTMW spectroscopy

    NASA Astrophysics Data System (ADS)

    Patterson, David; Doyle, John M.

    2012-08-01

    Gas phase benzonitrile, acetone, 1-2 propanediol, fluorobenzene, and anisole molecules are produced in a cell at a temperature of 8 K, and detected via Fourier transform microwave spectroscopy (FTMW). Helium buffer gas is used to cool the molecules originating from a high flux room temperature beam. This general, continuous source of cold molecules offers comparable spectral resolution to existing seeded pulsed supersonic beam/FTMW spectroscopy experiments but with higher number sensitivity. It is also an attractive tool for quantitative studies of cold molecule-helium and molecule-molecule elastic and inelastic collisions. Preliminary data on helium-molecule low temperature rotational and vibrational relaxation cross-sections are presented. Applications of the technique as a sensitive broad spectrum mixture analyser and a high resolution slow-beam spectrometer are discussed.

  13. Structure determination of molecules of biochemical interest

    NASA Astrophysics Data System (ADS)

    Honzatko, R. B.

    1985-10-01

    In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.

  14. Intrinsic disorder modulates protein self-assembly and aggregation.

    PubMed

    De Simone, Alfonso; Kitchen, Craig; Kwan, Ann H; Sunde, Margaret; Dobson, Christopher M; Frenkel, Daan

    2012-05-01

    Protein molecules have evolved to adopt distinctive and well-defined functional and soluble states under physiological conditions. In some circumstances, however, proteins can self-assemble into fibrillar aggregates designated as amyloid fibrils. In vivo these processes are normally associated with severe pathological conditions but can sometimes have functional relevance. One such example is the hydrophobins, whose aggregation at air-water interfaces serves to create robust protein coats that help fungal spores to resist wetting and thus facilitate their dispersal in the air. We have performed multiscale simulations to address the molecular determinants governing the formation of functional amyloids by the class I fungal hydrophobin EAS. Extensive samplings of full-atom replica-exchange molecular dynamics and coarse-grained simulations have allowed us to identify factors that distinguish aggregation-prone from highly soluble states of EAS. As a result of unfavourable entropic terms, highly dynamical regions are shown to exert a crucial influence on the propensity of the protein to aggregate under different conditions. More generally, our findings suggest a key role that specific flexible structural elements can play to ensure the existence of soluble and functional states of proteins under physiological conditions.

  15. Tubular aggregates of cyclic oligothiophenes. A theoretical study.

    PubMed

    Flores, Paola; Guadarrama, Patricia; Ramos, Estrella; Fomine, Serguei

    2008-05-01

    The geometries of neutral, mono-, and dioxidized tubular aggregates of cyclo[8]thiophenes containing up to 5 repeating units were fully optimized at the MPWB1K/3-21G* level of theory. Calculated interplane distances between macrocycles were found to be close to 3.1 A for neutral and charged aggregates. The binding energies between macrocycles in neutral intermediates were in the range of 40-45 kcal/mol, increasing for monocations and dropping strongly for dicationic species due to electrostatic repulsion between polarons. It was established that there exists a noticeable interaction between pi-orbitals of individual macrocycles in tubular aggregates as follows from decreasing of the band gap with a number of repeating units in aggregates and the polaron delocalization toward tube axes in oxidized species. A polaron pair is the most stable dicationic state for all studied molecules according to the calculations. A singlet polaron pair is more stable than a triplet one. The energy difference between singlet and triplet states is growing smaller with the size of the system, becoming zero for the pentamer corresponding to a completely dissociated bipolaron.

  16. Quantitative thermophoretic study of disease-related protein aggregates

    PubMed Central

    Wolff , Manuel; Mittag, Judith J.; Herling, Therese W.; Genst, Erwin De; Dobson, Christopher M.; Knowles, Tuomas P. J.; Braun, Dieter; Buell, Alexander K.

    2016-01-01

    Amyloid fibrils are a hallmark of a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. A detailed understanding of the physico-chemical properties of the different aggregated forms of proteins, and of their interactions with other compounds of diagnostic or therapeutic interest, is crucial for devising effective strategies against such diseases. Protein aggregates are situated at the boundary between soluble and insoluble structures, and are challenging to study because classical biophysical techniques, such as scattering, spectroscopic and calorimetric methods, are not well adapted for their study. Here we present a detailed characterization of the thermophoretic behavior of different forms of the protein α-synuclein, whose aggregation is associated with Parkinson’s disease. Thermophoresis is the directed net diffusional flux of molecules and colloidal particles in a temperature gradient. Because of their low volume requirements and rapidity, analytical methods based on this effect have considerable potential for high throughput screening for drug discovery. In this paper we rationalize and describe in quantitative terms the thermophoretic behavior of monomeric, oligomeric and fibrillar forms of α-synuclein. Furthermore, we demonstrate that microscale thermophoresis (MST) is a valuable method for screening for ligands and binding partners of even such highly challenging samples as supramolecular protein aggregates. PMID:26984748

  17. Quantitative thermophoretic study of disease-related protein aggregates.

    PubMed

    Wolff, Manuel; Mittag, Judith J; Herling, Therese W; Genst, Erwin De; Dobson, Christopher M; Knowles, Tuomas P J; Braun, Dieter; Buell, Alexander K

    2016-03-17

    Amyloid fibrils are a hallmark of a range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. A detailed understanding of the physico-chemical properties of the different aggregated forms of proteins, and of their interactions with other compounds of diagnostic or therapeutic interest, is crucial for devising effective strategies against such diseases. Protein aggregates are situated at the boundary between soluble and insoluble structures, and are challenging to study because classical biophysical techniques, such as scattering, spectroscopic and calorimetric methods, are not well adapted for their study. Here we present a detailed characterization of the thermophoretic behavior of different forms of the protein α-synuclein, whose aggregation is associated with Parkinson's disease. Thermophoresis is the directed net diffusional flux of molecules and colloidal particles in a temperature gradient. Because of their low volume requirements and rapidity, analytical methods based on this effect have considerable potential for high throughput screening for drug discovery. In this paper we rationalize and describe in quantitative terms the thermophoretic behavior of monomeric, oligomeric and fibrillar forms of α-synuclein. Furthermore, we demonstrate that microscale thermophoresis (MST) is a valuable method for screening for ligands and binding partners of even such highly challenging samples as supramolecular protein aggregates.

  18. Using bacterial inclusion bodies to screen for amyloid aggregation inhibitors

    PubMed Central

    2012-01-01

    Background The amyloid-β peptide (Aβ42) is the main component of the inter-neuronal amyloid plaques characteristic of Alzheimer's disease (AD). The mechanism by which Aβ42 and other amyloid peptides assemble into insoluble neurotoxic deposits is still not completely understood and multiple factors have been reported to trigger their formation. In particular, the presence of endogenous metal ions has been linked to the pathogenesis of AD and other neurodegenerative disorders. Results Here we describe a rapid and high-throughput screening method to identify molecules able to modulate amyloid aggregation. The approach exploits the inclusion bodies (IBs) formed by Aβ42 when expressed in bacteria. We have shown previously that these aggregates retain amyloid structural and functional properties. In the present work, we demonstrate that their in vitro refolding is selectively sensitive to the presence of aggregation-promoting metal ions, allowing the detection of inhibitors of metal-promoted amyloid aggregation with potential therapeutic interest. Conclusions Because IBs can be produced at high levels and easily purified, the method overcomes one of the main limitations in screens to detect amyloid modulators: the use of expensive and usually highly insoluble synthetic peptides. PMID:22553999

  19. A model of comb-like association with branches of arbitrary lengths: The mean statistical anisotropy of the polarizability tensor of liquid molecules

    NASA Astrophysics Data System (ADS)

    Durov, V. A.; Shilov, I. Yu.

    2008-01-01

    Analytic methods for calculating the mean anisotropy of the polarizability of liquid molecules consisting of chain aggregates of arbitrary lengths and branched comb-like aggregates with branches of arbitrary lengths were developed. The dependences of the mean anisotropy of the polarizability of methanol molecules on the thermodynamic parameters (equilibrium constants) of chain and branched aggregation and the structural characteristics of supramolecular aggregates were calculated. Special attention was paid to the influence of the degree of branching of comb-like aggregates on anisotropic light scattering. The calculation results were compared with the experimental data.

  20. Super-resolution fluorescence of huntingtin reveals growth of globular species into short fibers and coexistence of distinct aggregates.

    PubMed

    Duim, Whitney C; Jiang, Yan; Shen, Koning; Frydman, Judith; Moerner, W E

    2014-12-19

    Polyglutamine-expanded huntingtin, the protein encoded by HTT mutations associated with Huntington's disease, forms aggregate species in vitro and in vivo. Elucidation of the mechanism of growth of fibrillar aggregates from soluble monomeric protein is critical to understanding the progression of Huntington's disease and to designing therapeutics for the disease, as well as for aggregates implicated in Alzheimer's and Parkinson's diseases. We used the technique of multicolor single-molecule, super-resolution fluorescence imaging to characterize the growth of huntingtin exon 1 aggregates. The huntingtin exon 1 aggregation followed a pathway from exclusively spherical or globular species of ∼80 nm to fibers ∼1 μm in length that increased in width, but not length, over time with the addition of more huntingtin monomers. The fibers further aggregated with one another into aggregate assemblies of increasing size. Seeds created by sonication, which were comparable in shape and size to the globular species in the pathway, were observed to grow through multidirectional elongation into fibers, suggesting a mechanism for growth of globular species into fibers. The single-molecule sensitivity of our approach made it possible to characterize the aggregation pathway across a large range of size scales, from monomers to fiber assemblies, and revealed the coexistence of different aggregate species (globular species, fibers, fiber assemblies) even at late time points.

  1. Role of streams in myxobacteria aggregate formation

    NASA Astrophysics Data System (ADS)

    Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

    2004-10-01

    Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

  2. Aggregation of carbon dioxide sequestration storage assessment units

    USGS Publications Warehouse

    Blondes, Madalyn S.; Schuenemeyer, John H.; Olea, Ricardo A.; Drew, Lawrence J.

    2013-01-01

    The U.S. Geological Survey is currently conducting a national assessment of carbon dioxide (CO2) storage resources, mandated by the Energy Independence and Security Act of 2007. Pre-emission capture and storage of CO2 in subsurface saline formations is one potential method to reduce greenhouse gas emissions and the negative impact of global climate change. Like many large-scale resource assessments, the area under investigation is split into smaller, more manageable storage assessment units (SAUs), which must be aggregated with correctly propagated uncertainty to the basin, regional, and national scales. The aggregation methodology requires two types of data: marginal probability distributions of storage resource for each SAU, and a correlation matrix obtained by expert elicitation describing interdependencies between pairs of SAUs. Dependencies arise because geologic analogs, assessment methods, and assessors often overlap. The correlation matrix is used to induce rank correlation, using a Cholesky decomposition, among the empirical marginal distributions representing individually assessed SAUs. This manuscript presents a probabilistic aggregation method tailored to the correlations and dependencies inherent to a CO2 storage assessment. Aggregation results must be presented at the basin, regional, and national scales. A single stage approach, in which one large correlation matrix is defined and subsets are used for different scales, is compared to a multiple stage approach, in which new correlation matrices are created to aggregate intermediate results. Although the single-stage approach requires determination of significantly more correlation coefficients, it captures geologic dependencies among similar units in different basins and it is less sensitive to fluctuations in low correlation coefficients than the multiple stage approach. Thus, subsets of one single-stage correlation matrix are used to aggregate to basin, regional, and national scales.

  3. Steroidal Surfactants: Detection of Premicellar Aggregation, Secondary Aggregation Changes in Micelles, and Hosting of a Highly Charged Negative Substance.

    PubMed

    Barnadas-Rodríguez, Ramon; Cladera, Josep

    2015-08-25

    CHAPSO and CHAPS are zwitterionic surfactants derived from bile salts which are usually employed in protein purification and for the preparation of liposomes and bicelles. Despite their spread use, there are significant discrepancies on the critical concentrations that determine their aggregation behavior. In this work, we study the interaction between these surfactants with the negative fluorescent dye pyranine (HPTS) by absorbance, fluorescence, and infrared spectrometry to establish their concentration-dependent aggregation. For the studied surfactants, we detect three critical concentrations showing their concentration-dependent presence as a monomeric form, premicellar aggregates, micelles, and a second type of micelle in aqueous medium. The nature of the interaction of HPTS with the surfactants was studied using analogues of their tails and the negative bile salt taurocholate (TC) as reference for the sterol ring. The results indicate that the chemical groups involved are the hydroxyl groups of the polar face of the sterol ring and the sulfonate groups of the dye. This interaction causes not only the incorporation of the negative dye in CHAPSO and CHAPS micelles but also its association with their premicellar aggregates. Surprisingly, this hosting behavior for a negative charged molecule was also detected for the negative bile salt TC, bypassing, in this way, the electrostatic repulsion between the guest and the host.

  4. A Protein Aggregation Based Test for Screening of the Agents Affecting Thermostability of Proteins

    PubMed Central

    Eronina, Tatyana; Borzova, Vera; Maloletkina, Olga; Kleymenov, Sergey; Asryants, Regina; Markossian, Kira; Kurganov, Boris

    2011-01-01

    To search for agents affecting thermal stability of proteins, a test based on the registration of protein aggregation in the regime of heating with a constant rate was used. The initial parts of the dependences of the light scattering intensity (I) on temperature (T) were analyzed using the following empiric equation: I = Kagg(T−T0)2, where Kagg is the parameter characterizing the initial rate of aggregation and T0 is a temperature at which the initial increase in the light scattering intensity is registered. The aggregation data are interpreted in the frame of the model assuming the formation of the start aggregates at the initial stages of the aggregation process. Parameter T0 corresponds to the moment of the origination of the start aggregates. The applicability of the proposed approach was demonstrated on the examples of thermal aggregation of glycogen phosphorylase b from rabbit skeletal muscles and bovine liver glutamate dehydrogenase studied in the presence of agents of different chemical nature. The elaborated approach to the study of protein aggregation may be used for rapid identification of small molecules that interact with protein targets. PMID:21760963

  5. Self-assembly of cyclodextrin complexes: effect of temperature, agitation and media composition on aggregation.

    PubMed

    Messner, Martin; Kurkov, Sergey V; Maraver Palazón, Marta; Álvarez Fernández, Berta; Brewster, Marcus E; Loftsson, Thorsteinn

    2011-10-31

    Recently it has been shown that aggregation of drug/cyclodextrin inclusion complexes is strongly influenced by the drug molecule in addition to self-assembling tendencies of the cyclodextrin itself in aqueous media. Whereas the mechanistic basis of cyclodextrin self-assembly is known, the driving forces for complex aggregation are still unknown. In the present study, the influence of temperature on hydrocortisone/2-hydroxypropyl-β-cyclodextrin complex aggregation is investigated as are influences associated with the addition of ethanol or water soluble polymers to the aqueous systems. Furthermore the effect of stirring on the aggregation is assessed. Size exclusion permeability studies were conducted to estimate complex aggregation tendencies. The results indicate that self-assembled complex aggregates are metastable and notably become smaller with increasing temperature and the addition of ethanol. Water soluble polymers also reduce the size of the complex aggregates. Specifically, hexadimethrine bromide had the greatest impact, since addition of this compound eliminated aggregates from the systems or reduced their size below the molecular weight cut-off of the sizing membrane (8 kDa). Similar observations are made when aqueous solutions of hydrocortisone and 2-hydroxypropyl-β-cyclodextrin are equilibrated by stirred.

  6. Decelerating and Trapping Large Polar Molecules.

    PubMed

    Patterson, David

    2016-11-18

    Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.

  7. Formation of Ultracold Molecules

    SciTech Connect

    Cote, Robin

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  8. Virus-induced aggregates in infected cells.

    PubMed

    Moshe, Adi; Gorovits, Rena

    2012-10-17

    During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. Identification of aggregates has become a useful diagnostic tool for certain viral infections. There is wide variety of viral aggregates, which differ by their location, size, content and putative function. The role of aggregation in the context of a specific virus is often poorly understood, especially in the case of plant viruses. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intra- and intercellular transportation. Aggregated structures may protect viral functional complexes from the cellular degradation machinery. Alternatively, the activation of host defense mechanisms may involve sequestration of virus components in aggregates, followed by their neutralization as toxic for the host cell. The diversity of virus-induced aggregates in mammalian and plant cells is the subject of this review.

  9. Aggregation-induced emission—fluorophores and applications

    NASA Astrophysics Data System (ADS)

    Hong, Yuning

    2016-06-01

    Aggregation-induced emission (AIE) is a novel photophysical phenomenon found in a group of luminogens that are not fluorescent in solution but are highly emissive in the aggregate or solid state. Since the first publication of AIE luminogens in 2001, AIE has become a hot research area in which the number of research papers regarding new AIE molecules and their applications has been increasing in an exponential manner. Thomson Reuters Essential Science Indicators ranked AIE no.3 among the Top 100 Research Frontiers in the field of Chemistry and Materials Science in 2013. In this review, I will give a general introduction of the AIE phenomenon, discuss the structure-property relationship of the AIE lumingens and summarize the recent progress in the applications including as light-emitting materials in optoelectronics, as chemosensors and bioprobes, and for bioimaging (total 69 references cited).

  10. Aggregation of inorganic nanoparticles mediated by biomimetic oligomers.

    PubMed

    Tigger-Zaborov, Hagar; Maayan, Galia

    2015-09-14

    Assemblies of nanoparticles (NPs) have been broadly used for the construction of materials with unique spectroscopic and chiral properties for applications in various scientific disciplines such as sensing, bio-nanotechnology and medicine. Mediating the aggregation of NPs by synthetic biomimetic oligomers, namely, DNA, PNA, peptides and peptide mimics, rather than by small organic molecules has been shown to produce interesting supramolecular structures and enable the combination of the biocompatibility of the mediators and the spectroscopic properties of the NPs. Yet, the key to using this powerful approach for designing new functional materials is to understand the NPs aggregation patterns induced by biopolymers and biomimetic oligomers. Herein we describe the important developments in this field, from early studies to recent work with an emphasis on synthetic methods and tools for controlled assembly of metal NPs by biomimetic polymers and oligomers.

  11. The formation of molecular aggregates of sulfophthalocyanine in complexes with semiconductor nanocrystals

    NASA Astrophysics Data System (ADS)

    Dadadzhanov, D. R.; Martynenko, I. V.; Orlova, A. O.; Maslov, V. G.; Fedorov, A. V.; Baranov, A. V.

    2015-11-01

    In this study, complexes of CdSe/ZnS quantum dots and quantum rods with sulfophthalocyanine molecules have been formed. Analysis of spectral and luminescent properties of solutions of the complexes has revealed that an increase in the number of molecules per one nanocrystal in a mixed solution results in a noticeable decrease in the intensity of the luminescence of the quantum dots and quantum rods. In addition, it has been found that, upon an increase in the concentration of sulfophthalocyanine molecules, the absorption spectra of the samples in the region of their first absorption band have signs of formation of nonluminiscent aggregates of sulfophthalocyanine molecules. Analysis of the absorption spectra of the mixed solutions has made it possible to demonstrate that the complexes with the quantum rods have a content of the sulfophthalocyanine aggregates significantly lower than the complexes with the quantum dots.

  12. Archean Earth Atmosphere Fractal Haze Aggregates: Light Scattering Calculations and the Faint Young Sun Paradox

    NASA Astrophysics Data System (ADS)

    Boness, D. A.; Terrell-Martinez, B.

    2010-12-01

    As part of an ongoing undergraduate research project of light scattering calculations involving fractal carbonaceous soot aggregates relevant to current anthropogenic and natural sources in Earth's atmosphere, we have read with interest a recent paper [E.T. Wolf and O.B Toon,Science 328, 1266 (2010)] claiming that the Faint Young Sun paradox discussed four decades ago by Carl Sagan and others can be resolved without invoking heavy CO2 concentrations as a greenhouse gas warming the early Earth enough to sustain liquid water and hence allow the origin of life. Wolf and Toon report that a Titan-like Archean Earth haze, with a fractal haze aggregate nature due to nitrogen-methane photochemistry at high altitudes, should block enough UV light to protect the warming greenhouse gas NH3 while allowing enough visible light to reach the surface of the Earth. To test this hypothesis, we have employed a rigorous T-Matrix arbitrary-particle light scattering technique, to avoid the simplifications inherent in Mie-sphere scattering, on haze fractal aggregates at UV and visible wavelenths of incident light. We generate these model aggregates using diffusion-limited cluster aggregation (DLCA) algorithms, which much more closely fit actual haze fractal aggregates than do diffusion-limited aggregation (DLA) algorithms.

  13. Protein aggregation in salt solutions

    PubMed Central

    Kastelic, Miha; Kalyuzhnyi, Yurij V.; Hribar-Lee, Barbara; Dill, Ken A.; Vlachy, Vojko

    2015-01-01

    Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein–protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim’s thermodynamic perturbation theory. The necessary condition required for such modeling to be realistic is that proteins in solution during the experiment remain in their compact form. Within this limitation our model gives accurate liquid–liquid coexistence curves for lysozyme and γ IIIa-crystallin solutions in respective buffers. It provides good fits to the cloud-point curves of lysozyme in buffer–salt mixtures as a function of the type and concentration of salt. It than predicts full coexistence curves, osmotic compressibilities, and second virial coefficients under such conditions. This treatment may also be relevant to protein crystallization. PMID:25964322

  14. Molecular aggregation of naphthalimide dyes in Langmuir-Blodgett films

    NASA Astrophysics Data System (ADS)

    Bielejewska, Natalia; Bauman, Danuta

    2011-05-01

    Langmuir-Blodgett (LB) films formed of some naphthalimide dyes, namely derivatives of 4-aminonaphthalimide, mixed with arachidic acid have been studied. The electronic absorption and fluorescence spectra were recorded. The results obtained have led to conclusions about formation of self-aggregates of dye molecules. The absorption spectra have indicated that in the ground electronic state, depending on the molecular structure of substituents to the main core of the dye molecule, some fractions of J-type and/or H-type aggregates can be created. The fluorescence spectra have been dominated by the emission from excimer states. The efficiency of fluorescence has been dependent on the dye content and the number of layers in LB films. Comparison of the results of this study with those obtained previously for these same dyes mixed with the thermotropic liquid crystal 4-heptyl-4'-cyanobiphenyl has revealed that the interactions among dye molecules in monolayers formed at interfaces are strongly affected by a compound used as a supporting matrix.

  15. Unique Gold Nanoparticle Aggregates as a Highly Active SERS Substrate

    SciTech Connect

    Schwartzberg, A M; Grant, C D; Wolcott, A; Talley, C E; Huser, T R; Bogomolni, R; Zhang, J Z

    2004-04-06

    A unique gold nanoparticle aggregate (GNA) system has been shown to be an excellent substrate for surface-enhanced Raman scattering (SERS) applications. Rhodamine 6G (R6G), a common molecule used for testing SERS activity on silver, but generally difficult to detect on gold substrates, has been found to readily bind to the GNA and exhibit strong SERS activity due to the unique surface chemistry afforded by sulfur species on the surface. This GNA system has yielded a large SERS enhancement of 10{sup 7}-10{sup 9} in bulk solution for R6G, on par with or greater than any previously reported gold SERS substrate. SERS activity has also been successfully demonstrated for several biological molecules including adenine, L-cysteine, L-lysine, and L-histidine for the first time on a gold SERS substrate, showing the potential of this GNA as a convenient and powerful SERS substrate for biomolecular detection. In addition, SERS spectrum of R6G on single aggregates has been measured. We have shown that the special surface properties of the GNA, in conjunction with strong near IR absorption, make it useful for SERS analysis of a wide variety of molecules.

  16. Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.

    PubMed

    Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni

    2015-10-14

    In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved

  17. A new understanding of inert gas narcosis

    NASA Astrophysics Data System (ADS)

    Meng, Zhang; Yi, Gao; Haiping, Fang

    2016-01-01

    Anesthetics are extremely important in modern surgery to greatly reduce the patient’s pain. The understanding of anesthesia at molecular level is the preliminary step for the application of anesthetics in clinic safely and effectively. Inert gases, with low chemical activity, have been found to cause anesthesia for centuries, but the mechanism is unclear yet. In this review, we first summarize the progress of theories about general anesthesia, especially for inert gas narcosis, and then propose a new hypothesis that the aggregated rather than the dispersed inert gas molecules are the key to trigger the narcosis to explain the steep dose-response relationship of anesthesia. Project supported by the Supercomputing Center of Chinese Academy of Sciences in Beijing, China, the Shanghai Supercomputer Center, China, the National Natural Science Foundation of China (Grant Nos. 21273268, 11290164, and 11175230), the Startup Funding from Shanghai Institute of Applied Physics, Chinese Academy of Sciences (Grant No. Y290011011), “Hundred People Project” from Chinese Academy of Sciences, and “Pu-jiang Rencai Project” from Science and Technology Commission of Shanghai Municipality, China (Grant No. 13PJ1410400).

  18. Aggregation of Heterogeneously Charged Colloids.

    PubMed

    Dempster, Joshua M; Olvera de la Cruz, Monica

    2016-06-28

    Patchy colloids are attractive as programmable building blocks for metamaterials. Inverse patchy colloids, in which a charged surface is decorated with patches of the opposite charge, are additionally noteworthy as models for heterogeneously charged biological materials such as proteins. We study the phases and aggregation behavior of a single charged patch in an oppositely charged colloid with a single-site model. This single-patch inverse patchy colloid model shows a large number of phases when varying patch size. For large patch sizes we find ferroelectric crystals, while small patch sizes produce cross-linked gels. Intermediate values produce monodisperse clusters and unusual worm structures that preserve finite ratios of area to volume. The polarization observed at large patch sizes is robust under extreme disorder in patch size and shape. We examine phase-temperature dependence and coexistence curves and find that large patch sizes produce polarized liquids, in contrast to mean-field predictions. Finally, we introduce small numbers of unpatched charged colloids. These can either suppress or encourage aggregation depending on their concentration and the size of the patches on the patched colloids. These effects can be exploited to control aggregation and to measure effective patch size.

  19. Porous silicon ammonia gas sensor

    NASA Astrophysics Data System (ADS)

    Chaillou, A.; Charrier, J.; Lorrain, N.; Sarret, M.; Haji, L.

    2006-04-01

    A planar optical waveguide is manufactured by the functionnalisation of oxidised mesoporous silicon with Bromothymol Blue to achieve a sensitive ammonia sensor suitable for low gas concentrations. The propagated light intensity is measured at the output of the waveguide. The sensitivity at low concentrations and the short time of reaction of the sensor are enhanced by a confinement effect of the gas molecules inside the pores. The dependence of the output signal with gas concentration is demonstrated. When the ammonia flow is stopped, the reversibility of the initial characteristics of the propagated light is naturally obtained with the disappearance of the gas molecules.

  20. Purification and preliminary characterization of an aggregation-sensitive chemoattractant of Dictyostelium minutum.

    PubMed Central

    Kakebeeke, P I; Mato, J M; Konijn, T M

    1978-01-01

    Aggregative amoebae of Dictyostelium minutum are not attracted by cyclic AMP; they are sensitive to various attracting sources from which yeast extract was chosen to purify the chemoattractant. A small acrasin-like species-specific molecule which contains glycine and C5H5N5 has been purified 30,000-fold. Several characteristics of this chemotactic molecule, which is inactivated by an enzyme that is not species specific, are described. PMID:563394

  1. Differential anion effects on thermal stability of collagen in the dispersed and aggregated states.

    PubMed

    Russell, A E

    1974-03-01

    The effects of KCNS and KI on thermal transition temperatures of calf skin collagen molecules in dilute acid solution and precipitated collagen fibrils from the same source were compared as a function of salt concentration and pH. The two salts produced qualitatively similar effects on each collagen form, but the response shown by single collagen molecules in dilute solution differed from that observed for molecular aggregates present in native-type fibrils.

  2. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project...

  3. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project...

  4. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project...

  5. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project...

  6. Mineral resource of the month: aggregates

    USGS Publications Warehouse

    Willett, Jason C.

    2012-01-01

    Crushed stone and construction sand and gravel, the two major types of natural aggregates, are among the most abundant and accessible natural resources on the planet. The earliest civilizations used aggregates for various purposes, mainly construction. Today aggregates provide the basic raw materials for the foundation of modern society.

  7. 78 FR 68945 - Aggregation of Positions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-15

    ... the aggregation provisions of part 150 of the Commission's regulations that are substantially similar... modifications proposed here to the aggregation provisions of part 150 would apply to the position limits regimes... position limits because it believes that these proposed amendments regarding aggregation of...

  8. Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

    NASA Astrophysics Data System (ADS)

    McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

    2017-04-01

    We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

  9. Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

    NASA Astrophysics Data System (ADS)

    McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

    2016-11-01

    We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

  10. Therapeutic Antioxidant Medical Gas

    PubMed Central

    Nakao, Atsunori; Sugimoto, Ryujiro; Billiar, Timothy R; McCurry, Kenneth R

    2009-01-01

    Medical gases are pharmaceutical gaseous molecules which offer solutions to medical needs and include traditional gases, such as oxygen and nitrous oxide, as well as gases with recently discovered roles as biological messenger molecules, such as carbon monoxide, nitric oxide and hydrogen sulphide. Medical gas therapy is a relatively unexplored field of medicine; however, a recent increasing in the number of publications on medical gas therapies clearly indicate that there are significant opportunities for use of gases as therapeutic tools for a variety of disease conditions. In this article, we review the recent advances in research on medical gases with antioxidant properties and discuss their clinical applications and therapeutic properties. PMID:19177183

  11. [Endothelial cell adhesion molecules].

    PubMed

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  12. Gas-phase chemical dynamics

    SciTech Connect

    Weston, R.E. Jr.; Sears, T.J.; Preses, J.M.

    1993-12-01

    Research in this program is directed towards the spectroscopy of small free radicals and reactive molecules and the state-to-state dynamics of gas phase collision, energy transfer, and photodissociation phenomena. Work on several systems is summarized here.

  13. Chirality affects aggregation kinetics of single-walled carbon nanotubes.

    PubMed

    Khan, Iftheker A; Afrooz, A R M Nabiul; Flora, Joseph R V; Schierz, P Ariette; Ferguson, P Lee; Sabo-Attwood, Tara; Saleh, Navid B

    2013-02-19

    Aggregation kinetics of chiral-specific semiconducting single-walled carbon nanotubes (SWNTs) was systematically studied through time-resolved dynamic light scattering. Varied monovalent (NaCl) and divalent (CaCl(2)) electrolyte composition was used as background solution chemistry. Suwannee River humic acid (SRHA) was used to study the effects of natural organic matter on chirally separated SWNT aggregation. Increasing salt concentration and introduction of divalent cations caused aggregation of SWNT clusters by suppressing the electrostatic repulsive interaction from the oxidized surfaces. The (6,5) SWNTs, i.e., SG65, with relatively lower diameter tubes compared to (7,6), i.e., SG76, showed substantially higher stability (7- and 5-fold for NaCl and CaCl(2), respectively). The critical coagulation concentration (CCC) values were 96 and 13 mM NaCl in the case of NaCl and 2.8 and 0.6 mM CaCl(2) for SG65 and SG76, respectively. The increased tube diameter for (7,6) armchair SWNTs likely presented with higher van der Waals interaction and thus increased the aggregation propensity substantially. The presence of SRHA enhanced SWNT stability in divalent CaCl(2) environment through steric interaction from adsorbed humic molecules; however showed little or no effects for monovalent NaCl. The mechanism of aggregation-describing favorable interaction tendencies for (7,6) SWNTs-is probed through ab initio molecular modeling. The results suggest that SWNT stability can be chirality dependent in typical aquatic environment.

  14. Effects of osmolytes on protein folding and aggregation in cells.

    PubMed

    Ignatova, Zoya; Gierasch, Lila M

    2007-01-01

    Nature has developed many strategies to ensure that the complex and challenging protein folding reaction occurs in vivo with adequate efficiency and fidelity for the success of the organism. Among the strategies widely employed in a huge range of species and cell types is the elaboration of small organic molecules called osmolytes that offset the potentially damaging effects of osmotic stress. While considerable knowledge has been gained in vitro regarding the influence of osmolytes on protein structure and folding, it is of great interest to probe the effects of osmolytes in cells. We have developed an in-cell fluorescent-labeling method that enables the study of protein stability and also protein aggregation in vivo. We utilize a genetically encoded tag called a tetra-Cys motif that binds specifically to a bis-arsenical fluorescein-based dye "FlAsH"; we inserted the tetra-Cys motif into a protein of interest in such a way that the FlAsH signal reported on the state of folding or aggregation of the protein. Then, we designed protocols to assess how various osmolytes influence the stability and propensity to aggregate of our protein of interest. These are described here. Not only are there potential biotechnological applications of osmolytes in the quest to produce greater quantities of well-folded proteins, but also osmolytes may serve as tools and points of departure for therapeutic intervention in protein folding and aggregation diseases. Having in vivo methods to analyze how osmolytes affect folding and aggregation enhances our ability to further these goals greatly.

  15. Hsp70 and antifibrillogenic peptides promote degradation and inhibit intracellular aggregation of amyloidogenic light chains.

    SciTech Connect

    Dul, J. L.; Davis, D. P.; Williamson, E. K.; Stevens, F. J.; Argon, Y.; Univ. of Chicago

    2001-02-19

    In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its {beta} sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocated out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach.

  16. Comparing the energy landscapes for native folding and aggregation of PrP.

    PubMed

    Dee, Derek R; Woodside, Michael T

    2016-05-03

    Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.

  17. COMMERCIAL DEMONSTRATION OF THE MANUFACTURED AGGREGATE PROCESSING TECHNOLOGY UTILIZING SPRAY DRYER ASH

    SciTech Connect

    Roy Scandrol

    2003-04-01

    Universal Aggregates, LLC proposes to design, construct and operate a lightweight aggregate manufacturing plant at the Birchwood Power Facility in King George, Virginia. The installation and start-up expenses for the Birchwood Aggregate Facility are $19.5 million. The DOE share is $7.2 million (37%) and the Universal Aggregates share is $12.3 (63%). The project team consists of CONSOL Energy Inc., P.J. Dick, Inc., SynAggs, LLC, and Universal Aggregates, LLC. The Birchwood Facility will transform 115,000 tons per year of spray dryer by-products that are currently being disposed of in an offsite landfill into 167,000 tons of a useful product, lightweight aggregates that can be used to manufacture lightweight aggregates that can be used to manufacture lightweight and medium weight masonry blocks. In addition to the environmental benefits, the Birchwood Facility will create eight (8) manufacturing jobs plus additional employment in the local trucking industry to deliver the aggregate to customers or reagents to the facility. A successful demonstration would lead to additional lightweight aggregate manufacturing facilities in the United States. There are currently twenty-one (21) spray dryer facilities operating in the United States that produce an adequate amount of spray dryer by-product to economically justify the installation of a lightweight aggregate manufacturing facility. Industry sources believe that as additional scrubbing is required, dry flue gas desulfurization (FGD) technologies will be the technology of choice. Letters from potential lightweight aggregate customers indicate that there is a market for the product once the commercialization barriers are eliminated by this demonstration project.

  18. [Lysophosphatidic acid and human erythrocyte aggregation].

    PubMed

    Sheremet'ev, Iu A; Popovicheva, A N; Levin, G Ia

    2014-01-01

    The effects of lysophosphatidic acid on the morphology and aggregation of human erythrocytes has been studied. Morphology of erythrocytes and their aggregates were studied by light microscopy. It has been shown that lysophosphatidic acid changes the shape of red blood cells: diskocyte become echinocytes. Aggregation of red blood cells (rouleaux) was significantly reduced in autoplasma. At the same time there is a strong aggregation of echinocytes. This was accompanied by the formation of microvesicles. Adding normal plasma to echinocytes restores shape and aggregation of red blood cells consisting of "rouleaux". A possible mechanism of action of lysophosphatidic acid on erythrocytes is discussed.

  19. [AGGREGATION OF METABOLICALLY DEPLETED HUMAN ERYTHROCYTES].

    PubMed

    Sheremet'ev, Yu A; Popovicheva, A N; Rogozin, M M; Levin, G Ya

    2016-01-01

    An aggregation of erythrocytes in autologous plasma after blood storage for 14 days at 4 °C was studied using photometry and light microscopy. The decrease of ATP content, the formation of echinocytes and spheroechinocytes, the decrease of rouleaux form of erythrocyte aggregation were observed during the storage. On the other hand the aggregates of echinocytes were formed in the stored blood. The addition of plasma from the fresh blood didn't restore the normal discocytic shape and aggregation of erythrocytes in the stored blood. The possible mechanisms of erythrocytes and echinocytes aggregation are discussed.

  20. Beneficiation of natural aggregates by polymer impregnation

    SciTech Connect

    Webster, R.P.; Fontana, J.J.

    1980-09-01

    The use of polymer impregnation as a means of upgrading natural aggregates has been investigated. The effect of polymer impregnation on the physical and mechanical properties was evaluated in a series of tests performed using four aggregates of varying quality. The strength of concrete cast with polymer impregnated coarse aggregate was also tested. Two monomer systems were used in the investigation; a methyl methacrylate-based system and a styrene-based system. In general, significant improvements in the physical and mechanical properties of each of the four aggregates resulted from polymer impregnation. The strength of concrete cast with impregnated aggregates varied, being increased in some cases and decreased in others.