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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. 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.

  3. Lack of Aggregation of Molecules on Ice Nanoparticles.

    PubMed

    Pysanenko, Andriy; Habartová, Alena; Svrčková, Pavla; Lengyel, Jozef; Poterya, Viktoriya; Roeselová, Martina; Fedor, Juraj; Fárník, Michal

    2015-08-27

    Multiple molecules adsorbed on the surface of nanosized ice particles can either remain isolated or form aggregates, depending on their mobility. Such (non)aggregation may subsequently drive the outcome of chemical reactions that play an important role in atmospheric chemistry or astrochemistry. We present a molecular beam experiment in which the controlled number of guest molecules is deposited on the water and argon nanoparticles in a pickup chamber and their aggregation is studied mass spectrometrically. The studied molecules (HCl, CH3Cl, CH3CH2CH2Cl, C6H5Cl, CH4, and C6H6) form large aggregates on argon nanoparticles. On the other hand, no aggregation is observed on ice nanoparticles. Molecular simulations confirm the experimental results; they reveal a high degree of aggregation on the argon nanoparticles and show that the molecules remain mostly isolated on the water ice surface. This finding will influence the efficiency of ice grain-mediated synthesis (e.g., in outer space) and is also important for the cluster science community because it shows some limitations of pickup experiments on water clusters. PMID:26214577

  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. Mechanism of cellular response to nanoscale aggregates of small molecules

    NASA Astrophysics Data System (ADS)

    Kuang, Yi

    This dissertation research focused on the illustration of the molecular mechanism of cellular response to nanoscale aggregates formed by small molecules. There are five chapters in this dissertation. Chapter 1 summarizes the current research on the evaluation of cell response (i.e., biocompatibility/cytotoxicity) to small molecular hydrogelators. Chapter 2 describes an interesting phenomenon that supramolecular hydrogelators consisting of N-terminated dipeptides, which exhibit selective inhibitory effects against cancer cells. This study calls for the development of a new approach for identification of protein targets of the hydrogelators. Chapter 3 describes the evaluation of interactions between cytosol proteins of a mammalian cell line and morphologically different nanoscale molecular aggregates formed by small peptidic molecules. Chapter 4 describes the research on the mechanism of a type of molecular aggregates, which cluster short microtubules to prevent the growth of microtubule. This unprecedented mechanism of "self-assembly to interfere with self-organization " contributes to inhibiting growth of cancer cells in several mammalian cell based assays and a xenograft tumor mice model. At the end, Chapter 5 reports a novel supramolecular hydrogelator, which consists of fluorene and the pentapeptide epitope (TIGYG) of potassium ion (K+) channels, to self-assemble in water to form the tunable, hierarchical nanostructures dictated by the concentration of K+. In conclusion, this dissertation research demonstrates a new approach for investigating cellular target and molecular mechanism of self-assembled aggregates formed by small peptide derivatives based hydrogelators, which will make contribution to the development of supramolecular hydrogelators as biomaterials. Moreover, the differential cytotoxicity of molecular aggregates illustrated in this research promises a new direction for developing anti-cancer drug based on interactions between molecular aggregates and

  6. Charged supramolecular assemblies of surfactant molecules in gas phase.

    PubMed

    Bongiorno, David; Ceraulo, Leopoldo; Indelicato, Sergio; Turco Liveri, Vincenzo; Indelicato, Serena

    2016-01-01

    The aim of this review is to critically analyze recent literature on charged supramolecular assemblies formed by surfactant molecules in gas phase. Apart our specific interest on this research area, the stimuli to undertake the task arise from the widespread theoretical and applicative benefits emerging from a comprehensive view of this topic. In fact, the study of the formation, stability, and physicochemical peculiarities of non-covalent assemblies of surfactant molecules in gas phase allows to unveil interesting aspects such as the role of attractive, repulsive, and steric intermolecular interactions as driving force of supramolecular organization in absence of interactions with surrounding medium and the size and charge state dependence of aggregate structural and dynamical properties. Other interesting aspects worth to be investigated are joined to the ability of these assemblies to incorporate selected solubilizates molecules as well as to give rise to chemical reactions within a single organized structure. In particular, the incorporation of large molecules such as proteins has been of recent interest with the objective to protect their structure and functionality during the transition from solution to gas phase. Exciting fall-out of the study of gas phase surfactant aggregates includes mass and energy transport in the atmosphere, origin of life and simulation of supramolecular aggregation in the interstellar space. Moreover, supramolecular assemblies of amphiphilic molecules in gas phase could find remarkable applications as atmospheric cleaning agents, nanosolvents and nanoreactors for specialized chemical processes in confined space. Mass spectrometry techniques have proven to be particularly suitable to generate these assemblies and to furnish useful information on their size, size polydispersity, stability, and structural organization. On the other hand molecular dynamics simulations have been very useful to rationalize many experimental findings and to

  7. Hybrid molecules synergistically acting against protein aggregation diseases.

    PubMed

    Korth, Carsten; Klingenstein, Ralf; Müller-Schiffmann, Andreas

    2013-01-01

    An emerging common feature of the age-associated neurodegenerative disorders like Alzheimer's disease (AD) and Creutzfeldt-Jakob disease (CJD) is the ability of many disease-associated protein aggregates to induce conversion of a normal counterpart conformer leading to an acceleration of disease progression. Curative pharmacotherapy has not been achieved so far despite successes in elucidating pathomechanisms. Here, we review the pharmaceutical strategy of generating hybrid compounds, i.e. compounds consisting of several independently acting moieties with synergistic effects, on key molecular players in AD and CJD. For prion diseases, we review hybrid compounds consisting of two different heterocyclic compounds, their synergistic effects on prion replication in a cell culture model and their ability to prolong survival of experimentally prion-infected mice in vivo. While a combination therapy of several antiprion compounds including quinacrine, clomipramine, simvastatin and tocopherol prolonged survival time to 10-25%, administration of hybrid compound quinpramine alone, a chimera of acridine and iminodibenzyl scaffolds, led to 10% survival time extension. For AD, we review a hybrid compound consisting of an Aβ recognizing D-peptide fused to a small molecule β-sheet breaker, an aminopyrazole. This molecule was able to diminish Aβ oligomers in cell culture and significantly decrease synaptotoxicity as measured by miniature excitatory postsynaptic responses in vitro. Hybrid compounds can dramatically increase potency of their single moieties and lead to novel functions when they act in a simultaneous or sequential manner thereby revealing synergistic properties. Their systematic generation combining different classes of compounds from peptides to small molecules has the potential to significantly accelerate drug discovery. PMID:24059335

  8. Identification of small molecule aggregators from large compound libraries by support vector machines.

    PubMed

    Rao, Hanbing; Li, Zerong; Li, Xiangyuan; Ma, Xiaohua; Ung, Choongyong; Li, Hu; Liu, Xianghui; Chen, Yuzong

    2010-03-01

    Small molecule aggregators non-specifically inhibit multiple unrelated proteins, rendering them therapeutically useless. They frequently appear as false hits and thus need to be eliminated in high-throughput screening campaigns. Computational methods have been explored for identifying aggregators, which have not been tested in screening large compound libraries. We used 1319 aggregators and 128,325 non-aggregators to develop a support vector machines (SVM) aggregator identification model, which was tested by four methods. The first is five fold cross-validation, which showed comparable aggregator and significantly improved non-aggregator identification rates against earlier studies. The second is the independent test of 17 aggregators discovered independently from the training aggregators, 71% of which were correctly identified. The third is retrospective screening of 13M PUBCHEM and 168K MDDR compounds, which predicted 97.9% and 98.7% of the PUBCHEM and MDDR compounds as non-aggregators. The fourth is retrospective screening of 5527 MDDR compounds similar to the known aggregators, 1.14% of which were predicted as aggregators. SVM showed slightly better overall performance against two other machine learning methods based on five fold cross-validation studies of the same settings. Molecular features of aggregation, extracted by a feature selection method, are consistent with published profiles. SVM showed substantial capability in identifying aggregators from large libraries at low false-hit rates. PMID:19569201

  9. Cluster Growth Mechanism in Sputtering Gas-Aggregation Nanocluster Source

    NASA Astrophysics Data System (ADS)

    Tarsem Singh, M.; Han, H.; Sundararajan, J. A.; Qiang, Y.

    2010-03-01

    We have studied the influence of some parameters for cluster growth of core shell iron- iron oxide magnetic nanoparticles (MNPs). The nanocluster source which combines a magnetron sputtering gun with a gas aggregation chamber is used to produce MNPs. Nanoclusters of various mean sizes ranging from 1-100 nm can be synthesized by varying the aggregation distance, Ar to He gas ratio, pressure in the aggregation tube, sputter power, and temperature of the aggregation tube. Physical properties -- magnetic measurements by VSM and SQUID and size distribution by SEM and TEM were studied for different MNPs. The significance of this research is to understand the growth mechanism and physical properties as the size of particles grow from few nanometer to hundred of nanometer. Growth of the particles is theoretically explained by the homogenous and heterogeneous growth process. Based on this study, different size of MNPs fits into different category of applications from data storage to biomedical field.

  10. Gas biology: tiny molecules controlling metabolic systems.

    PubMed

    Kajimura, Mayumi; Nakanishi, Tsuyoshi; Takenouchi, Toshiki; Morikawa, Takayuki; Hishiki, Takako; Yukutake, Yoshinori; Suematsu, Makoto

    2012-11-15

    It has been recognized that gaseous molecules and their signaling cascades play a vital role in alterations of metabolic systems in physiologic and pathologic conditions. Contrary to this awareness, detailed mechanisms whereby gases exert their actions, in particular in vivo, have been unclear because of several reasons. Gaseous signaling involves diverse reactions with metal centers of metalloproteins and thiol modification of cysteine residues of proteins. Both the multiplicity of gas targets and the technical limitations in accessing local gas concentrations make dissection of exact actions of any gas mediator a challenge. However, a series of advanced technologies now offer ways to explore gas-responsive regulatory processes in vivo. Imaging mass spectrometry combined with quantitative metabolomics by capillary-electrophoresis/mass spectrometry reveals spatio-temporal profiles of many metabolites. Comparing the metabolic footprinting of murine samples with a targeted deletion of a specific gas-producing enzyme makes it possible to determine sites of actions of the gas. In this review, we intend to elaborate on the ideas how small gaseous molecules interact with metabolic systems to control organ functions such as cerebral vascular tone and energy metabolism in vivo. PMID:22516267

  11. Harnessing Chaperones to Generate Small-Molecule Inhibitors of Amyloid β Aggregation

    NASA Astrophysics Data System (ADS)

    Gestwicki, Jason E.; Crabtree, Gerald R.; Graef, Isabella A.

    2004-10-01

    Protein aggregation is involved in the pathogenesis of neurodegenerative diseases and hence is considered an attractive target for therapeutic intervention. However, protein-protein interactions are exceedingly difficult to inhibit. Small molecules lack sufficient steric bulk to prevent interactions between large peptide surfaces. To yield potent inhibitors of β-amyloid (Aβ) aggregation, we synthesized small molecules that increase their steric bulk by binding to chaperones but also have a moiety available for interaction with Aβ. This strategy yields potent inhibitors of Aβ aggregation and could lead to therapeutics for Alzheimer's disease and other forms of neurodegeneration.

  12. Gas phase charged aggregates of bis(2-ethylhexyl)sulfosuccinate (AOT) and divalent metal ions: first evidence of AOT solvated aggregates.

    PubMed

    Giorgi, Gianluca; Pini, Ivana; Ceraulo, Leopoldo; Liveri, Vincenzo Turco

    2011-09-01

    Assembling and chelating properties of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) towards divalent metal ions have been investigated in the gas phase by electrospray ionization mass spectrometry. A variety of positively charged monometallated and mixed metal aggregates are formed. Interestingly, several ions contain solvent (MeOH, H(2)O) molecules and constitute the most abundant AOT cationic aggregates not containing sodium. These species are the first example of solvated AOT-metal ion aggregates in the gas phase. By increasing the surfactant aggregation number, the abundance of solvated species becomes lower than that of unsolvated ones. Decompositions of ionic species have been studied by tandem mass spectrometry, and their stability has been determined through energy resolved mass spectrometry. In contrast with positively charged AOT-alkaline metal ion aggregates, whose decompositions are dominated by the loss of individual surfactant molecules, AOTNa-divalent ion aggregates mainly dissociate through the cleavage of the AOT H(2)C-O bond followed by further intramolecular fragmentations. This finding, that is consistent with an enhanced chelation of divalent ions with AOT(-) head groups, has been taken as an indication that such aggregates are characterized by a reverse micelle-like organization with a ionic core formed by the metal cations interacting with the negatively charged surfactant polar heads, whereas the surfactant alkyl chains point outside. PMID:21915957

  13. 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

  14. 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. PMID:25769517

  15. Aggregation phenomena in a system of molecules with two internal states

    NASA Astrophysics Data System (ADS)

    Gaspari, R.; Gliozzi, A.; Ferrando, R.

    2007-10-01

    A model for the aggregation of molecules with two internal states is studied by kinetic Monte Carlo simulations. Molecules are represented by simple beads, discarding all stereochemical specificity. Monomers are placed in a three-dimensional lattice and diffusion processes are simulated, as well as internal state conversions of the molecules. The two internal states feature a stable (S) not assembly competent configuration, and an unstable assembly competent (A) configuration. Monomers in A state are given a higher energy if isolated, but they can reach the lowest energy level through short-range interactions between each other, so that their aggregation is promoted. Kinetics of cluster formation are examined, as well as the basic mechanisms ruling growth in our system. The simulations show that the aggregation process is preceded by a lag phase, which is followed by a fast growth phase. The duration of the lag phase is determined by the strength of the A-A interaction, whereas the time slope of the growth phase is mainly influenced by the conversion rate between internal states. The whole work has been inspired by the biological problem of amyloid aggregation, whose aggregation curves often present a sigmoidal behavior which is reproduced by the present model.

  16. 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

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

    PubMed

    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. PMID:27435961

  18. The optical properties of molecules and chromogenic aggregates of xanthene dyes

    NASA Astrophysics Data System (ADS)

    Mikheev, Yu. A.; Guseva, L. N.; Ershov, Yu. A.

    2009-05-01

    The UV absorption spectra of rhodamine B and G molecules isolated from industrial dye samples were obtained. Two procedures were used. In one of them, rhodamine B molecules were displaced with water into a heptane layer from a solution of the dye in an alcohol-heptane mixture. The second procedure involved heating of the dye introduced into cellulose triacetate films. Individual rhodamine molecules (namely, dye cation-chlorine anion ion pairs) prepared by both methods did not absorb visible light. The spectra of individual rhodamine molecules coincided with the spectra of so-called pseudoleucobases of xanthene dyes reported in the literature. The conclusion was drawn that the chromaticity property in the series of xanthene dyes appeared because of the formation of supramolecular dimeric and larger aggregates, as was earlier established for triphenylmethane dyes (TPMDs) and copper phthalocyanine (CuPc). At the same time, individual xanthene dye molecules, like TPMD and CuPc molecules, are not chromogens.

  19. Aggregation of dye molecules and its influence on the spectral luminescent properties of solutions

    NASA Astrophysics Data System (ADS)

    Yuzhakov, V. I.

    1992-06-01

    The principal results of studies carried out in recent years on the molecular aggregation of organic dyes and pigments in solutions are examined and surveyed in the present review. Attention is concentrated on the influence of association on the photoenergetics of the dye molecules. Theoretical studies on the spectral-luminescent spectroscopic characteristics of the molecular aggregates are briefly considered. Studies on the anisotropy of the absorption and on the emission from the associated species are described. Investigations of the concentration depolarisation and concentration quenching of the fluorescence of dye solutions are subjected to a critical analysis. The results of studies of the mixed association of dye molecules and of its influence on the lasing characteristics of the solutions are presented. The physicochemical conditions affecting the efficiency of the association process are examined. The bibliography includes 251 references.

  20. A Cell Surface Molecule Involved in Aggregation of Embryonic Liver Cells

    NASA Astrophysics Data System (ADS)

    Bertolotti, Roger; Rutishauser, Urs; Edelman, Gerald M.

    1980-08-01

    Aggregation of chicken embryo hepatocytes can be inhibited by Fab' fragments of antibodies prepared against the cells. An aqueous extract of liver cell membranes contained antigens that neutralized the adhesion-blocking properties of the Fab' fragments. This neutralization activity was associated with a polypeptide of Mr 68,000 in NaDodSO4; the polypeptide was distinct from serum albumin. Specific antibodies prepared against the 80-fold purified active fraction inhibited liver cell adhesion and immunoprecipitated the 68,000 Mr polypeptide from active fractions as well as from a detergent extract of liver cell membranes. In hepatocyte cultures, Fab' fragments of antibodies against the liver molecule prevented both colony formation and appearance of histotypic patterns. Liver cell adhesion was compared at the cellular and molecular levels to that of embryonic neural retina cells. Antibodies against the cell adhesion molecule from neural tissue inhibited retinal but not liver cell aggregation; conversely, antibodies against the liver polypeptide inhibited liver but not retinal cell aggregation. By means of antibody absorption and immunoprecipitation, it was confirmed that the two cell adhesion molecules are antigenically unrelated.

  1. The homophilic adhesion molecule sidekick-1 contributes to augmented podocyte aggregation in HIV-associated nephropathy.

    PubMed

    Kaufman, Lewis; Yang, Guozhe; Hayashi, Kayo; Ashby, James R; Huang, Li; Ross, Michael J; Klotman, Mary E; Klotman, Paul E

    2007-05-01

    The collapsing glomerulopathy of HIV-associated nephropathy (HIVAN) is characterized by podocyte dedifferentiation and proliferation. In affected glomeruli, proliferating podocytes adhere in aggregates to form glomerular pseudocrescents and fill an enlarged Bowman's space. Previously, we reported that sidekick-1 (sdk-1), an adhesion molecule of the immunoglobulin superfamily, was highly up-regulated in HIV-1 transgenic podocytes. In the current work, we explore how sdk-1 overexpression contributes to HIVAN pathogenesis. Murine podocytes infected with HIV-1 virus expressed significantly more sdk-1 than control-infected cells. Podocytes stably transfected with an sdk-1 expression construct grew in large aggregates with a simplified morphology characterized by a disorganized actin cytoskeleton, changes similar to podocytes in HIVAN. In contrast to controls, HIV-1 infected podocytes adhered to stably transfected sdk-1 podocyte aggregates in mixing studies. Furthermore, substrate-released cell sheets of wild-type podocytes were readily dissociated by mechanical stress, whereas HIV-1 podocytes remained in aggregates. The number of HIV-1 podocyte aggregates was significantly reduced in cells expressing a short hairpin RNA (shRNA) construct specific for sdk-1 compared with cells expressing control shRNA. Finally, in a HIVAN mouse model, sdk-1 protein was detected in podocytes in collapsed glomerular tufts and in glomerular pseudocrescents. These findings suggest that sdk-1 is an important mediator of cellular adhesion in HIV-infected podocytes and may contribute to podocyte clustering that is characteristic of pseudocrescent formation in HIVAN. PMID:17307840

  2. PRODUCTION OF CONSTRUCTION AGGREGATES FROM FLUE GAS DESULFURIZATION SLUDGE

    SciTech Connect

    1998-12-01

    Through a cooperative agreement with DOE, the Research and Development Department of CONSOL Inc. (CONSOL R and D) is teaming with SynAggs, Inc. and Duquesne Light to design, construct, and operate a 500 lb/h continuous pilot plant to produce road construction aggregate from a mixture of wet flue gas desulfurization (FGD) sludge, fly ash, and other components. The proposed project is divided into six tasks: (1) Project Management; (2) Mix Design Evaluation; (3) Process Design; (4) Construction; (5) Start-Up and Operation; and (6) Reporting. In this quarter, Tasks 1 and 2 were completed. A project management plan (Task 1) was issued to DOE on October 22, 1998 . The mix design evaluation (Task 2) with Duquesne Light Elrama Station FGD sludge and Allegheny Power Hatfields Ferry Station fly ash was completed. Eight semi-continuous bench-scale tests were conducted to examine the effects of mix formulation on aggregate properties. A suitable mix formulation was identified to produce aggregates that meet specifications of the American Association of State High Transport Officials (AASHTO) as Class A aggregate for use in highway construction. The mix formulation was used in designing the flow sheet of the pilot plant. The process design (Task 3) is approximately 80% completed. Equipment was evaluated to comply with design requirements. The design for the curing vessel was completed by an outside engineering firm. All major equipment items for the pilot plant, except the curing vessel, were ordered. Pilot plant construction (Task 4) was begun in October. The Hazardous Substance Plan was issued to DOE. The Allegheny County (PA) Heat Department determined that an air emission permit is not required for operation of the pilot plant.

  3. Electroluminescence from Spontaneously Generated Single-Vesicle Aggregates Using Solution-Processed Small Organic Molecules.

    PubMed

    Tsai, Yu-Tang; Tseng, Kuo-Pi; Chen, Yan-Fang; Wu, Chung-Chih; Fan, Gang-Lun; Wong, Ken-Tsung; Wantz, Guillaume; Hirsch, Lionel; Raffy, Guillaume; Del Guerzo, Andre; Bassani, Dario M

    2016-01-26

    Self-assembled aggregates offer great potential for tuning the morphology of organic semiconductors, thereby controlling their size and shape. This is particularly interesting for applications in electroluminescent (EL) devices, but there has been, to date, no reports of a functional EL device in which the size and color of the emissive domains could be controlled using self-assembly. We now report a series of molecules that spontaneously self-organize into small EL domains of sub-micrometer dimensions. By tailoring the emissive chromophores in solution, spherical aggregates that have an average size of 300 nm in diameter and emit any one color, including CIE D65 white, are spontaneously formed in solution. We show that the individual aggregates can be used in EL devices built either using small patterned electrodes or using a sandwich architecture to produce devices emitting in the blue, green, red, and white. Furthermore, sequential deposition of the three primary colors yields an RGB device in which single aggregates of each color are present in close proximity. PMID:26730851

  4. 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.

  5. β-Amyloid amorphous aggregates induced by the small natural molecule ferulic acid.

    PubMed

    Bramanti, Emilia; Fulgentini, Lorenzo; Bizzarri, Ranieri; Lenci, Francesco; Sgarbossa, Antonella

    2013-11-01

    There is an emerging interest in small natural molecules for their potential therapeutic use in neurodegenerative disorders like Alzheimer's disease (AD). Ferulic acid (FA), an antioxidant phenolic compound present in fruit and vegetables, has been proposed as an inhibitor of beta amyloid (Aβ) pathological aggregation. Using fluorescence and Fourier transform infrared spectroscopy, electrophoresis techniques, chromatographic analysis, and confocal microscopy, we investigated the effects of FA in the early stages of Aβ fibrillogenesis in vitro. Our results show that FA interacts promptly with Aβ monomers/oligomers, interfering since the beginning with its self-assembly and finally forming amorphous aggregates more prone to destabilization. These findings highlight the molecular basis underlying FA antiamyloidogenic activity in AD. PMID:24168390

  6. 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.

  7. 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.

  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. PMID:26572350

  9. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

    PubMed

    Ebrahimi, Ali; Or, Dani

    2016-09-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. PMID:27152862

  10. A quantum gas of polar molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Moses, Steven A.

    Ultracold polar molecules, because of their long-range, spatially anisotropic interactions, are a new quantum system in which to study novel many-body phenomena. In our lab, we have produced the first quantum gas of 40K 87Rb polar molecules. These molecules were found to undergo exothermic chemical reactions, and this led to interesting studies of chemistry near absolute zero. By creating the molecules at individual sites of a 3D optical lattice, we completely suppress these chemical reactions, and the polar molecule gas becomes stable and lives for tens of seconds. This thesis documents our efforts to explore coherent, many-body phenomena resulting from long-range dipolar interactions in the lattice. By encoding a spin-1/2 system in the rotational states of the molecules, we were able to realize spin-exchange interactions based on a spin Hamiltonian, which is one of the first steps in studying quantum magnetism with polar molecules. While this study was the first realization of such coherent dipolar interactions with polar molecules in a lattice, its full potential was limited by the low lattice filling fractions. Using our ability to exquisitely control the initial atomic gas mixture, we loaded a Mott insulator of Rb and a band insulator of K into the lattice. This quantum synthesis approach led to significantly higher molecular filling fractions and represents the first fully connected system of polar molecules in an optical lattice. This low-entropy quantum gas of polar molecules opens the door to interesting quantum simulations, which should be attainable in the next generation of the experiment.

  11. A plant cell model of polyglutamine aggregation: Identification and characterisation of macromolecular and small-molecule anti-protein aggregation activity in vivo.

    PubMed

    Liu, Guobao; Hu, Yueming; Tunnacliffe, Alan; Zheng, Yizhi

    2015-08-10

    In vitro studies have shown that LEA proteins from plants and invertebrates protect and stabilise other proteins under conditions of water stress, suggesting a role in stress tolerance. However, there is little information on LEA protein function in whole plants or plant cells, particularly with respect to their anti-aggregation activity. To address this, we expressed in tobacco BY-2 suspension cells an aggregation-prone protein based on that responsible for Huntington's disease (HD). In HD, abnormally long stretches of polyglutamine (polyQ) in huntingtin (Htt) protein cause aggregation of Htt fragments within cells. We constructed stably transformed BY-2 cell lines expressing enhanced green fluorescent protein (EGFP)-HttQ23 or EGFP-HttQ52 fusion proteins (encoding 23 or 52 glutamine residues, pertaining to the normal and disease states, respectively), as well as an EGFP control. EGFP-HttQ52 protein aggregated in the cytoplasm of transformed tobacco cells, which showed slow growth kinetics; in contrast, EGFP-HttQ23 or EGFP did not form aggregates and cells expressing these constructs grew normally. To test the effect of LEA proteins on protein aggregation in plant cells, we constructed cell lines expressing both EGFP-HttQ52 and LEA proteins (PM1, PM18, ZLDE-2 or AavLEA1) or a sHSP (PM31). Of these, AavLEA1 and PM31 reduced intracellular EGFP-HttQ52 aggregation and alleviated the associated growth inhibition, while PM18 and ZLDE-2 partially restored growth rates. Treatment of EGFP-HttQ52-expressing BY2 cells with the polyphenol epigallocatechin-3-gallate (EGCG) also reduced EGFP-HttQ52 aggregation and improved cell growth rate. The EGFP-HttQ52 cell line therefore has potential for characterising both macromolecular and small molecule inhibitors of protein aggregation in plant cells. PMID:26003885

  12. 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.

  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. PMID:24527910

  14. 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)

  15. 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

  16. The prebiotic molecules observed in the interstellar gas.

    PubMed

    Thaddeus, P

    2006-10-29

    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 microm, 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

  17. High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles.

    PubMed

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

    2015-02-01

    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

  18. Self-assembly of diphenylalanine peptides into microtubes with "turn on" fluorescence using an aggregation-induced emission molecule.

    PubMed

    Na, Na; Mu, Xiaoyan; Liu, Qiuling; Wen, Jiying; Wang, Fangfang; Ouyang, Jin

    2013-10-01

    The self-assembly of diphenylalanine peptides (l-Phe-l-Phe) into microtubes with "turn on" bright yellow green fluorescence was described, which was achieved using an aggregation-induced emission (AIE) molecule of 9,10-bis[4-(3-sulfonatopropoxyl)-styryl] anthracene (BSPSA) sodium. PMID:24045462

  19. 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.

  20. A supramolecular aggregate of four exchange-biased single-molecule magnets.

    PubMed

    Nguyen, Tu N; Wernsdorfer, Wolfgang; Abboud, Khalil A; Christou, George

    2011-12-28

    The reaction between 3-phenyl-1,5-bis(pyridin-2-yl)pentane-1,5-dione dioxime (pdpdH(2)) and triangular [Mn(III)(3)O(O(2)CMe)(py)(3)](ClO(4)) (1) affords [Mn(12)O(4)(O(2)CMe)(12)(pdpd)(6))](ClO(4))(4) (3). Complex 3 has a rectangular shape and consists of four [Mn(III)(3)O](7+) triangular units linked covalently by the dioximate ligands into a supramolecular [Mn(3)](4) tetramer. Solid-state dc and ac magnetic susceptibility measurements revealed that [Mn(3)](4) contains four Mn(3) single-molecule magnets (SMMs), each with an S = 6 ground state. Magnetization versus dc-field sweeps on a single crystal gave hysteresis loops below 1 K that exhibited exchange-biased quantum tunneling of magnetization steps, confirming 3 to be a supramolecular aggregate of four weakly exchange-coupled SMM units. PMID:22136491

  1. 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.

  2. [Aggregation Behavior of Collagen-Based Surfactant Molecules in Aqueous Solutions Based on Synchronization Fluorescence Spectrum Technology].

    PubMed

    Li, Cong-hu; Tian, Zhen-hua; Liu, Wen-tao; Li, Guo-ying

    2016-01-01

    Due to the intrinsic fluorescence characteristic of tyrosine (Tyr) and phenylalanine (Phe), synchronization fluorescence spectrum technology which adopted the constant wavelength difference (Δλ = 15 nm) was selected to investigate the effects of collagen-based surfactant (CBS) concentration, pH, NaCt concentration and temperature on the aggregation state of CBS molecules in aqueous solutions. Meanwhile, temperature-dependent two-dimensional (2D) synchronization fluorescence correlation analyses was used to investigate the variation order of Tyr and Phe residues in CBS molecules with the change of temperature. The results showed that the characteristic absorption peaks located at 261 and 282 nm were attributed to Phe and Tyr, respectively. With the increase of CBS concentration, the amount of Phe and Tyr residues increased gradually which resulted in the increase of aggregate degree of CBS molecules and then led to the increase of fluorescence intensity. When the pH value (pH 5.0) of CBS solutions was close to the isoelectric point of CBS, the aggregate degree of CBS molecules increased due to the increase of the hydrophobic interaction and the formation ability of hydrogen bond. Additionally, with the increase of NaCl concentration, the repulsion force for inter/intra-molecules of CBS decreased, which helped to improve the aggregation behavior of CBS molecules. However, with the increase of temperature, the aggregation state of CBS was changed to be monomolecular state, and then resulted in the decrease of the fluorescence intensity gradually due to the quenching, the denaturation and the decrease of hydrogen bond formation ability. Furthermore, temperature-dependent 2D synchronization fluorescence correlation spectroscopy demonstrated that at lower temperature (10-40 degrees C), the aggregate state of CBS changed to be loose state and then Phe residues located in the inside of the aggregate varied before Tyr residues; while in the heating process of 45

  3. Gas phase infrared multiple photon dissociation spectra of positively charged sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle-like aggregates.

    PubMed

    Giorgi, Gianluca; Ceraulo, Leopoldo; Berden, Giel; Oomens, Jos; Liveri, Vincenzo Turco

    2011-03-17

    The capability of infrared multiple photon dissociation (IRMPD) spectroscopy to gain structural information on surfactant-based supramolecular aggregates has been exploited to elucidate intermolecular interactions and local organization of positively charged sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) aggregates in the gas phase. A detailed analysis of the stretching modes of the AOTNa CO and SO(3)(-) head groups allows one to directly probe their interactions with sodium counterions and to gain insight in their organization within the aggregate. Similarities and differences of the IRMPD spectra as compared to the infrared absorption spectrum of micellized AOTNa in CCl(4) have been analyzed. They strongly suggest a reverse micelle-like organization of AOTNa charged aggregates in the gas phase. Apart from low-abundance fragmentation channels of the AOTNa (molecule) itself, the main dissociation pathway of singly charged surfactant aggregates is the loss of neutral surfactant molecules, while doubly charged aggregates dissociate preferentially by charge separation forming singly charged species. In both cases, decomposition leads to the formation of the most energetically stable charged fragments. PMID:21341816

  4. Sensing gas molecules using graphitic nanoribbon films and networks

    NASA Astrophysics Data System (ADS)

    An, Yanbin; Johnson, Jason L.; Behnam, Ashkan; Pearton, S. J.; Ural, Ant

    2011-03-01

    We fabricate and study the gas sensing properties of graphitic nanoribbon (GNR) films and networks consisting of multi-layer graphene nanoribbons with an average width of 7 nm. We experimentally demonstrate the high sensitivity of these films and networks for sensing gas molecules at the parts-per-million (ppm) level, in particular hydrogen and ammonia. The sensing response exhibits excellent repeatability and full recovery in air. Furthermore, our results show that functionalization by metal nanoparticles could significantly improve the sensitivity. We characterize the sensing response at various temperatures, gas concentrations, recovery ambients, and film thicknesses. We find that the relative resistance response of the GNR films shows a power-law dependence on the gas concentration, which can be explained by the Freundlich isotherm. The activation energy obtained from the sensing experiments is consistent with the theoretical calculations of the adsorption energies of gas molecules on graphene sheets and nanoribbons. Their simple and low-cost fabrication process and good sensing response open up the possibility of using graphitic nanoribbon films and networks for large-scale sensing applications.

  5. Study of mass and cluster flux in a pulsed gas system with enhanced nanoparticle aggregation

    NASA Astrophysics Data System (ADS)

    Drache, Steffen; Stranak, Vitezslav; Hubicka, Zdenek; Berg, Florian; Tichy, Milan; Helm, Christiane A.; Hippler, Rainer

    2014-10-01

    The paper is focused on investigation of enhanced metal (Cu) cluster growth in a source of Haberland's type using pulsed gas aggregation. The aggregation Ar gas was delivered into the cluster source in a pulse regime, which results in the formation of well pronounced aggregation pressure peaks. The pressure peaks were varied by varying the different pulse gas frequency at the same mean pressure kept for all experiments. Hence, we were able to study the effect of enhanced aggregation pressure on cluster formation. Time-resolved measurements of cluster mass distribution were performed to estimate the mass and particle flux. The paper demonstrates that pulse gas aggregation influences growth of Cu nanoparticles, i.e., cluster mass/size, mass flux, and particle flux emitted from the cluster source. It was found that cluster mass related quantities are strongly influenced by pulsed gas frequency; the highest value of mass flux appears at the most pronounced pressure peaks. On the other hand, the particle flux depends only slightly on the gas pulse frequency. The explanation based on cooling and thermalization of sputtered particles is discussed in the paper.

  6. Using Coupled Harmonic Oscillators to Model Some Greenhouse Gas Molecules

    SciTech Connect

    Go, Clark Kendrick C.; Maquiling, Joel T.

    2010-07-28

    Common greenhouse gas molecules SF{sub 6}, NO{sub 2}, CH{sub 4}, and CO{sub 2} are modeled as harmonic oscillators whose potential and kinetic energies are derived. Using the Euler-Lagrange equation, their equations of motion are derived and their phase portraits are plotted. The authors use these data to attempt to explain the lifespan of these gases in the atmosphere.

  7. Small molecule-mediated stabilization of vesicle-associated helical α-synuclein inhibits pathogenic misfolding and aggregation.

    PubMed

    Fonseca-Ornelas, Luis; Eisbach, Sybille E; Paulat, Maria; Giller, Karin; Fernández, Claudio O; Outeiro, Tiago F; Becker, Stefan; Zweckstetter, Markus

    2014-01-01

    α-synuclein is an abundant presynaptic protein that is important for regulation of synaptic vesicle trafficking, and whose misfolding plays a key role in Parkinson's disease. While α-synuclein is disordered in solution, it folds into a helical conformation when bound to synaptic vesicles. Stabilization of helical, folded α-synuclein might therefore interfere with α-synuclein-induced neurotoxicity. Here we show that several small molecules, which delay aggregation of α-synuclein in solution, including the Parkinson's disease drug selegiline, fail to interfere with misfolding of vesicle-bound α-synuclein. In contrast, the porphyrin phtalocyanine tetrasulfonate directly binds to vesicle-bound α-synuclein, stabilizes its helical conformation and thereby delays pathogenic misfolding and aggregation. Our study suggests that small-molecule-mediated stabilization of helical vesicle-bound α-synuclein opens new possibilities to target Parkinson's disease and related synucleinopathies. PMID:25524885

  8. Comparison of antibody molecules produced from two cell lines with contrasting productivities and aggregate contents.

    PubMed

    Ishii, Yoichi; Imamoto, Yasufumi; Yamamoto, Rie; Tsukahara, Masayoshi; Wakamatsu, Kaori

    2015-01-01

    Cell culture processes that produce therapeutic antibodies with high productivity (titer) and low aggregate content reduce the risk of adverse effects and expense to patients. To elucidate the mechanism of aggregate formation, we compared trastuzumab samples produced from two contrasting cell lines: cell line A, which exhibits high titer and low aggregate content, and cell line B, which exhibits low titer and high aggregate content. Cell line B produced significantly fewer (approximately 1/3) antibodies compared with cell line A and contained higher (approximately 3-fold) percentages of aggregates. The aggregates of antibodies found in the protein A-purified samples of cell line B were associated mostly with noncovalent interactions. Cell line B exhibited a low content of monomers/dimers of light chains in the medium and within cells. Because light chains are essential for the correct folding of heavy chains and secretion of mature antibodies, the characteristics of cell line B may be attributed to low levels of light chain production. In addition, protein A-purified antibodies from cell line B (but not those from cell line A) contained fragments that are expected to expose the hydrophobic CH3 domain, which may serve as nuclei for aggregation. PMID:25501618

  9. 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. )

  10. Molecule formation in quasar broad-line cloud gas

    SciTech Connect

    Kallman, T.; Lepp, S.; Giovannoni, P.

    1987-10-01

    Models for the broad-line emitting clouds of quasars typically assume that the clouds have column densities of at most 10 to the 23rd/sq cm. The consequences of relaxing this assumption are examined, and it is shown that: (1) at slightly larger column densities the gas may cool to about 1000 K as a result of molecule formation; (2) in much of the molecule-forming region the temperature may have either of two values, about 1000 K or 6000-8000 K; (3) the strengths of most observable optical lines, including C II semiforbidden 2326-A lines and Fe II lines, are unaffected by such large column densities; and (4) lines from low-ionization species such as Na I are readily formed at large column densities. Observations of such lines provide evidence for large cloud column densities. 47 references.

  11. Bubble-induced aggregation of platelets: effects of gas species, proteins, and decompression.

    PubMed

    Thorsen, T; Klausen, H; Lie, R T; Holmsen, H

    1993-06-01

    We show that bubbles containing different gases (N2, He, Ne, Ar, or an O2-CO2-N2 mixture) are equally potent platelet agonists. The synergistic effect of different platelet antagonists does not seem to be affected by the type of gas in the bubbles. In contrast to aggregation in platelet-rich plasma (PRP), bubbles cause only a weak response in gel-filtered platelets (GFP), i.e., comparison of aggregation in protein-rich and protein-poor platelet suspensions may shed light on the role of different plasma proteins. Extracellular fibrinogen promotes bubble-induced platelet aggregation similar to known physiologic agonists, whereas albumin counteracts this aggregation. Bubble-induced aggregation is inhibited in GFP-fibrinogen by 2-deoxy-D-glucose plus antimycin A, suggesting dependency on ATP generation in the platelets and evidence for direct exposure of the "cryptic" fibrinogen receptor by bubbles. Hyperbaric compression and subsequent rapid, inadequate decompression of PRP caused little change in the aggregation response to gas bubbles and epinephrine at 1 bar, but reduced the response to ADP. Bubbles tended not to form before the surface film was broken. Pressure-induced aggregation was apparently metabolically active and not due to passive agglutination; electron microscopic studies and PRP with added glutaraldehyde did not show platelet activation, clumping, or reduced platelet count. In contrast to aggregation caused by pressure, bubble-induced aggregation in PRP at 1 bar (after treatment in the pressure chamber) was nearly completely inhibited by theophylline, a phosphodiesterase inhibitor that increases intracellular platelet cyclic AMP. PMID:8392414

  12. Identification of Small Molecule Inhibitors of Tau Aggregation by Targeting Monomeric Tau As a Potential Therapeutic Approach for Tauopathies

    PubMed Central

    Pickhardt, Marcus; Neumann, Thomas; Schwizer, Daniel; Callaway, Kari; Vendruscolo, Michele; Schenk, Dale; St. George-Hyslop, Peter; Mandelkow, Eva M.; Dobson, Christopher M.; McConlogue, Lisa; Mandelkow, Eckhard; Tóth, Gergely

    2015-01-01

    A potential strategy to alleviate the aggregation of intrinsically disordered proteins (IDPs) is to maintain the native functional state of the protein by small molecule binding. However, the targeting of the native state of IDPs by small molecules has been challenging due to their heterogeneous conformational ensembles. To tackle this challenge, we applied a high-throughput chemical microarray surface plasmon resonance imaging screen to detect the binding between small molecules and monomeric full-length Tau, a protein linked with the onset of a range of Tauopathies. The screen identified a novel set of drug-like fragment and lead-like compounds that bound to Tau. We verified that the majority of these hit compounds reduced the aggregation of different Tau constructs in vitro and in N2a cells. These results demonstrate that Tau is a viable receptor of drug-like small molecules. The drug discovery approach that we present can be applied to other IDPs linked to other misfolding diseases such as Alzheimer’s and Parkinson’s diseases.

  13. Identification of small molecule inhibitors of Tau aggregation by targeting monomeric Tau as a potential therapeutic approach for Tauopathies

    PubMed Central

    Pickhardt, Marcus; Neumann, Thomas; Schwizer, Daniel; Callaway, Kari; Vendruscolo, Michele; Schenk, Dale; George-Hyslop, Peter; Mandelkow, Eva M.; Dobson, Christopher M.; McConlogue, Lisa; Mandelkow, Eckhard; Tóth, Gergely

    2016-01-01

    A potential strategy to alleviate the aggregation of intrinsically disordered proteins (IDPs) is to maintain the native functional state of the protein by small molecule binding. However, the targeting of the native state of IDPs by small molecules has been challenging due to their heterogeneous conformational ensembles. To tackle this challenge, we applied a high-throughput chemical microarray surface plasmon resonance imaging screen to detect the binding between small molecules and monomeric full-length Tau, a protein linked with the onset of a range of Tauopathies. The screen identified a novel set of drug-like fragment and lead-like compounds that bound to Tau. We verified that the majority of these hit compounds reduced the aggregation of different Tau constructs in vitro and in N2a cells. These results demonstrate that Tau is a viable receptor of drug-like small molecules. The drug discovery approach that we present can be applied to other IDPs linked to other misfolding diseases such as Alzheimer’s and Parkinson’s diseases. PMID:26510979

  14. Optics of a gas of coherently spinning molecules.

    PubMed

    Steinitz, Uri; Prior, Yehiam; Averbukh, Ilya Sh

    2014-01-10

    We consider the optical properties of a gas of molecules that are brought to fast unidirectional spinning by a pulsed laser field. It is shown that a circularly polarized probe light passing through the medium inverts its polarization handedness and experiences a frequency shift controllable by the sense and the rate of molecular rotation. Our analysis is supported by two recent experiments on the laser-induced rotational Doppler effect in molecular gases and provides a good qualitative and quantitative description of the experimental observations. PMID:24483895

  15. Features of self-aggregation of C60 molecules in toluene prepared by different methods

    NASA Astrophysics Data System (ADS)

    Makhmanov, Urol; Ismailova, Oksana; Kokhkharov, Abdulmutallib; Zakhidov, Erkin; Bakhramov, Sagdilla

    2016-05-01

    Structural and dimensional features of C60 aggregates in toluene solution prepared in two different ways - equilibrium and strongly non-equilibrium - were studied by high-resolution transmission electron microscopy and atomic-force microscopy methods. It was found that in solutions prepared by the non-equilibrium method (stirring of solution of C60 by a mechanical rotator), large quasispherical aggregates (with a diameter of up to ∼ 380 ± 20 nm) of nanoporous structure with fractal size D ≈ 2.13 were synthesized. In the case of solutions C60, which were prepared by the equilibrium method (without the use of external mechanical influences on solution), the formation of densely packed monomolecular fullerene aggregates with a diameter of not more than 50 nm was observed.

  16. Aggregation-induced emission molecules in layered matrices for two-color luminescence films.

    PubMed

    Guan, Weijiang; Lu, Jun; Zhou, Wenjuan; Lu, Chao

    2014-10-14

    We fabricated two-color luminescence ultrathin films (UTFs) composed of the layered double hydroxide host-aggregation-induced emission guests by LBL assembly. The fabricated UTFs were simple, tunable, controllable and highly luminescent. Moreover, reversible thermochromic luminescence further exhibited their potential in practical applications. PMID:25154856

  17. 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.

  18. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  19. Effects of the net charge on abundance and stability of supramolecular surfactant aggregates in gas phase.

    PubMed

    Bongiorno, David; Ceraulo, Leopoldo; Giorgi, Gianluca; Indelicato, Serena; Ferrugia, Mirella; Ruggirello, Angela; Liveri, Vincenzo Turco

    2011-02-01

    Self-assembling of amphiphilic molecules under electrospray ionization (ESI) conditions is characterized by quite unexpected phenomenology. The noticeable differences with respect to the condensed phase are attributable to the absence of the surfactant-solvent interactions, the presence of net charge in the aggregates, and the strong deviation from equilibrium conditions. Aiming to investigate the effects of the net charge on abundance and stability of supramolecular surfactant aggregates, positively and negatively charged aggregates of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) and sodium methane sulfonate (MetS), butane sulfonate (ButS) and octane sulfonate (OctS) have been studied by ESI mass spectrometry, energy resolved mass spectrometry and density functional theory calculations. The negatively charged aggregates are found to be less stable than their positive counterparts. The results are consistent with a self-assembling pattern dominated by electrostatic interactions involving the counterions and head groups of the investigated amphiphilic compounds while the alkyl chains point outwards, protecting the aggregates from unlimited growth processes. PMID:21259391

  20. Aggregation-Induced-Emissive Molecule Incorporated into Polymeric Nanoparticulate as FRET Donor for Observing Doxorubicin Delivery.

    PubMed

    Han, Xiongqi; Liu, De-E; Wang, Tieyan; Lu, Hongguang; Ma, Jianbiao; Chen, Qixian; Gao, Hui

    2015-10-28

    Tetraphenylethene (TPE) derivatives characterized with distinct aggregation-induced-emission, attempted to aggregate with doxorubicin (Dox) to formulate the interior compartment of polymeric nanoparticulate, served as fluorescence resonance energy transfer (FRET) donor to promote emission of acceptor Dox. Accordingly, this FRET formulation allowed identification of Dox in complexed form by detecting FRET. Important insight into the Dox releasing can be subsequently explored by extracting complexed Dox (FRET) from the overall Dox via direct single-photon excitation of Dox. Of note, functional catiomers were used to complex with FRET partners for a template formulation, which was verified to induce pH-responsive release in the targeted subcellular compartment. Hence, this well-defined multifunctional system entitles in situ observation of the drug releasing profile and insight on drug delivery journey from the tip of injection vein to the subcellular organelle of the targeted cells. PMID:26448180

  1. Effects of heparin and related molecules upon neutrophil aggregation and elastase release in vitro

    PubMed Central

    Brown, Rachel A; Lever, Rebecca; Jones, Neil A; Page, Clive P

    2003-01-01

    Neutrophil-derived elastase is an enzyme implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Heparin inhibits the enzymatic activity of elastase and here we provide evidence for the first time that heparin can inhibit the release of elastase from human neutrophils. Unfractionated and low molecular weight heparins (UH and LMWH, 0.01–1000 U ml−1) and corresponding concentrations (0.06–6000 μg ml−1) of nonanticoagulant O-desulphated heparin (ODH), dextran sulphate (DS) and nonsulphated poly-L-glutamic acid (PGA) were compared for their effects on both elastase release from and aggregation of neutrophils. UH, ODH and LMWH inhibited (P<0.05) the homotypic aggregation of neutrophils, in response to both N-formyl-methionyl-leucyl-phenylalanine (fMLP, 10−6 M) and platelet-activating factor (PAF, 10−6 M), as well as elastase release in response to these stimuli, in the absence and presence of the priming agent tumour necrosis factor-alpha (TNF-α, 100 U ml−1). DS inhibited elastase release under all the conditions of cellular activation tested (P<0.05) but had no effect on aggregation. PGA lacked efficacy in either assay, suggesting general sulphation to be important in both effects of heparin on neutrophil function and specific patterns of sulphation to be required for inhibition of aggregation. Further investigation of the structural requirements for inhibition of elastase release confirmed the nonsulphated GAG hyaluronic acid and neutral dextran, respectively, to be without effect, whereas the IP3 receptor antagonist 2-aminoethoxydiphenylborate (2-APB) mimicked the effects of heparin, itself an established IP3 receptor antagonist, suggesting this to be a possible mechanism of action. PMID:12813008

  2. Effects of heparin and related molecules upon neutrophil aggregation and elastase release in vitro.

    PubMed

    Brown, Rachel A; Lever, Rebecca; Jones, Neil A; Page, Clive P

    2003-06-01

    1 Neutrophil-derived elastase is an enzyme implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Heparin inhibits the enzymatic activity of elastase and here we provide evidence for the first time that heparin can inhibit the release of elastase from human neutrophils. 2 Unfractionated and low molecular weight heparins (UH and LMWH, 0.01-1000 U ml(-1)) and corresponding concentrations (0.06-6000 micro g ml(-1)) of nonanticoagulant O-desulphated heparin (ODH), dextran sulphate (DS) and nonsulphated poly-L-glutamic acid (PGA) were compared for their effects on both elastase release from and aggregation of neutrophils. 3 UH, ODH and LMWH inhibited (P<0.05) the homotypic aggregation of neutrophils, in response to both N-formyl-methionyl-leucyl-phenylalanine (fMLP, 10(-6) M) and platelet-activating factor (PAF, 10(-6) M), as well as elastase release in response to these stimuli, in the absence and presence of the priming agent tumour necrosis factor-alpha (TNF-alpha, 100 U ml(-1)). 4 DS inhibited elastase release under all the conditions of cellular activation tested (P<0.05) but had no effect on aggregation. PGA lacked efficacy in either assay, suggesting general sulphation to be important in both effects of heparin on neutrophil function and specific patterns of sulphation to be required for inhibition of aggregation. 5 Further investigation of the structural requirements for inhibition of elastase release confirmed the nonsulphated GAG hyaluronic acid and neutral dextran, respectively, to be without effect, whereas the IP(3) receptor antagonist 2-aminoethoxydiphenylborate (2-APB) mimicked the effects of heparin, itself an established IP(3) receptor antagonist, suggesting this to be a possible mechanism of action. PMID:12813008

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

    SciTech Connect

    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.

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

    PubMed

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

    2016-07-01

    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. PMID:27284590

  5. 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.

  6. Mechanisms of soil aggregate failure by rapid increase in internal gas pressure during low-intensity burns

    NASA Astrophysics Data System (ADS)

    Jian, M.; Ghezzehei, T. A.; Berli, M.

    2015-12-01

    The incidence of low-intensity natural and managed fire is on the rise, especially in the arid and semi-arid parts of the U.S. Southwest. Yet, there is little understanding of the ramifications of such burns on soil characteristics and their associated ecological processes. In particular, effects of low-intensity fires on soil structure have generally been ignored because such fires have little effect on soil organic matter. Recently, we showed that soil aggregates subjected to rapid low-intensity heating (<200°C) deteriorate more than aggregates subjected to the same temperature but at slow heating rate. We hypothesized that rapid heating rate results in high internal gas pressure due to vaporization of pore water that exerts disruptive mechanical stress that exceeds the internal strength of the aggregates. Here, we present in situ measurements of gas pressure of aggregates subjected to low-intensity burns. We compared a wide range of aggregate wetness and temperature levels. In addition, we report direct visualization of aggregate breakdown during rapid gas expansion using dynamic environment scanning electron microscopy. Our observation to date show that the interior gas pressure of moist aggregates rise rapidly to 1.5-4kPa, whereas the pressure inside dry aggregates remain unchanged during rapid heating. These observations show that weakly aggregated soils of arid and semi-arid regions are very vulnerable to low-intensity burns.

  7. 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.

  8. Excited electronic states of complex heteroatomic molecules in series and in different aggregation states of matter

    NASA Astrophysics Data System (ADS)

    Obukhov, Alexandr E.

    1995-01-01

    We investigate the spectroscopic and photophysical properties of new series complex molecules, which is capable of fluorescence and some generating light in solvents of various kinds within the wavelength region 308 - 420 nm with a high fluorescence quantum yield (gamma) equals 0.01 - 0.97 and a low threshold pump density Elp(Plp). We worked from the measured lifetimes and to calculate the rate constants for radiative decay (Kfl) and intercombinational conversion, (KST), the cross section for a stimulated emission ((sigma) 31osc), and the characteristic time tlp in solvents of various types and in the vapor. The latter is the limiting rise time of the pump pulse (tlp) at which the generation of electromagnetic radiation is still possible. The cross sections for the induced singlet-singlet ((sigma) 3S*) and triplet-triplet ((sigma) 2T*) absorption in the generation band, required for calculating tlp, were taken from a variety of sources: experimental and for all other complex molecules, we used results calculated by some semiempirical methods SCF MO LKAO the Pariser-Parr-Pople (PPP/CI) and in complete neglect of differential overlap (INDO/S-CI). The results show that the decrease or increase of in the switch from solution to vapor, or as the properties of the solvent change, stems from dynamic separation or overlap of the lasing and induced absorption bands of the S1* yields Sn* and T1 yields Tn transitions. Lasing does not occur in concentrated acids because of the nearly complete overlap of the limiting gain and induced absorption T1 yields Tn transitions (compare it with the behavior of dyes in their chemo absorbed state). Using the density matrix method, we show that the solvent affects the distribution of electron density among the individual atoms and fragments of the complex geteratomic molecule in the ground state, leading to systematic changes in geometry. As a result, there are changes in the distribution of bond lengths in the rings of the azo

  9. Conventional transmission electron microscopy of 1-1 haptoglobin isolated molecules and paracrystalline aggregates.

    PubMed

    Blonda, C; Albergamo, A; Casale, A; Felluga, B; Bernini, L; Santulli, A; Annunziata, A; Mazza, A

    1986-04-01

    Data are presented relating conventional transmission electron microscope (CTEM) ultrastructural observations of the monomeric phenotypic variant (Hp 1-1) of the haptoglobin class of blood glycoproteins. Through comparison of these findings with homologous published data, obtained by means of scanning transmission electron microscopy (STEM), the validity of CTEM in molecule shape and fine structure determination is confirmed. An experimental procedure for Hp 1-1 crystallization is also reported. PMID:3712515

  10. 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)

  11. 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.

  12. 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. PMID:25416874

  13. ESI-IMS-MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules.

    PubMed

    Young, Lydia M; Saunders, Janet C; Mahood, Rachel A; Revill, Charlotte H; Foster, Richard J; Ashcroft, Alison E; Radford, Sheena E

    2016-02-15

    Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS-MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aβ40 as an example, and reveal two new inhibitors of Aβ40 fibrillation. PMID:26007606

  14. ESI-IMS–MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules

    PubMed Central

    Young, Lydia M.; Saunders, Janet C.; Mahood, Rachel A.; Revill, Charlotte H.; Foster, Richard J.; Ashcroft, Alison E.; Radford, Sheena E.

    2016-01-01

    Electrospray ionisation-ion mobility spectrometry–mass spectrometry (ESI-IMS–MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS–MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aβ40 as an example, and reveal two new inhibitors of Aβ40 fibrillation. PMID:26007606

  15. Heating of interstellar gas by large molecules or small grains

    SciTech Connect

    Lepp, S.; Dalgarno, A.

    1988-12-01

    The heating of the interstellar medium by photoelectric emission from large molecules or small grains is explored. Photodetachment of large negative ions may be a significant heat source in diffuse clouds. For an abundance of large molecules relative to hydrogen greater than 2 x 10 to the -7th, the heating rate from the photoelectrons produced in the photoionization of large molecules and the photodetachment of large molecular negative ions exceeds the standard grain-heating rate. Theoretical models have been used to infer the abundances of large molecules from the C(+)/C abundance ratios in the interstellar clouds toward Zeta Oph and Zeta Per. 33 references.

  16. Surface-Enhanced Raman Spectroscopy of Single Molecules and Single Nano-Aggregates

    NASA Astrophysics Data System (ADS)

    Kleinman, Samuel Louis

    Although plasmonic nanoparticles are widely utilized in spectroscopy and sensing applications, a quantitative structure-function relationship is lacking. In this dissertation, we discuss measurements of single noble metal nanoparticles using localized surface plasmon resonance spectroscopy, surface-enhanced Raman spectroscopy (SERS), and transmission electron microscopy to elucidate structure-function relationships. Correlated studies involving two or all three of these techniques relate optical properties of the same nanoparticle to its structure. Through these correlated techniques we have been able to elucidate some of the structural motifs which give rise to the largest SERS enhancements. A variety of SERS substrates are used and the strengths and weaknesses of each type are compared. This information can be applied to sensing and detection methodologies. The utility of SERS is further explored through the use of SER spectroelectrochemistry. This confluence of techniques provided unique insight into the intermolecular interactions present in self-assembled monolayers of tetrathiafulvalene-modified thiolates on gold. Both ensemble-averaged and single-molecule SERS are thoroughly explored and with their benefits and limitations used synergistically to access the most fundamental physics of the light-matter interaction.

  17. 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.

  18. 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.

  19. Aggregation dynamics in a self-gravitating one-dimensional gas

    SciTech Connect

    Martin, P.A.; Piasecki, J.

    1996-08-01

    Aggregation of mass by perfectly inelastic collisions in a one-dimensional self-gravitating gas is studied. The binary collisions are subject to the laws of mass and momentum conservation. A method to obtain an exact probabilistic description of aggregation is presented. Since the one-dimensional gravitational attraction is confining, all particles will eventually form a single body. The detailed analysis of the probability P{sub n}(t) of such a complete merging before time t is performed for initial states of n equidistant identical particles with uncorrelated velocities. It is found that for a macroscopic amount of matter (n {r_arrow} {infinity}), this probability vanishes before a characteristic time t*. In the limit of a continuous initial mass distribution the exact analytic form of P{sub n}(t) is derived. The analysis of collisions leading to the time-variation of P{sub n}(t) reveals that in fact the merging into macroscopic bodies always occurs in the immediate vicinity of t*. For t>t*, and n large, P{sub n}(t) describes events corresponding to the final aggregation of remaining microscopic fragments.

  20. 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

  1. Amyloid at the nanoscale: AFM and single-molecule investigations of early steps of aggregation and mature fibril growth, structure, and mechanics

    NASA Astrophysics Data System (ADS)

    Subramaniam, Vinod

    2013-03-01

    Misfolding and aggregation of proteins into nanometer-scale fibrillar assemblies is a hallmark of many neurodegenerative diseases. We have investigated the self-assembly of the human intrinsically disordered protein alpha-synuclein, involved in Parkinson's disease, into amyloid fibrils. A particularly relevant question is the role of early oligomeric aggregates in modulating the dynamics of protein nucleation and aggregation. We have used single molecule fluorescence spectroscopy to characterize conformational transitions of alpha-synuclein, and to gain insights into the structure and composition of oligomeric aggregates of alpha-synuclein. Quantitative atomic force microscopy and nanomechanical investigations provide information on amyloid fibril polymorphism and on nanoscale mechanical properties of mature fibrillar species, while conventional optical and super-resolution imaging have yielded insights into the growth of fibrils and into the assembly of suprafibrillar structures. We thank the Foundation for Fundamental Research on Matter (FOM), the Netherlands Organisation for Scientific Research (NWO), and the MESA+ Institute for Nanotechnology for support.

  2. Infrared Spectroscopy of Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Zhang, Keqing

    Fourier transform infrared spectroscopy is applied to the studies of several very different molecular systems. The spectra of the diatomic molecules BF, AlF, and MgF were recorded and analyzed. Dunham coefficients were obtained. The data of two isotopomers, 11BF and 10BF, were used to determine the mass-reduced Dunham coefficients, along with Born-Oppenheimer breakdown constants. Parameterized potential energy functions of BF and AlF were determined by fitting the available data using the solutions of the radial Schrodinger equation. Two vibrational modes of the short-lived and reactive BrCNO molecule were recorded at high resolution. Rotation-vibration transitions of the fundamental bands of both isotopomers 79BrCNO and 81BrCNO were assigned and analyzed. From the rotational constants, it was found that the Br-C bond length in BrCNO anomalously short when a linear geometry was assumed. This may indicate that BrCNO is quasi-linear, simulating the parent HCNO molecule. The emission spectra of the gaseous polycyclic aromatic hydrocarbon (PAH) molecules naphthalene, anthracene, pyrene, and chrysene were recorded in the far-infrared and mid-infrared regions. The assignments of fundamental modes and some combination modes were made. The vibrational bands that lie in the far-infrared are unique for different PAHs and allow discrimination among the four PAH molecules. The far-infrared PAH spectra, therefore, may prove useful in the assignments of unidentified spectral features from astronomical objects.

  3. Direct Observation of a Gas Molecule (H2, Ar) Swallowed by C60

    SciTech Connect

    Sawa, H.; Kakiuchi, T.; Wakabayashi, Y.; Murata, Y.; Murata, M.; Komatsu, K.; Yakigaya, K.; Takagi, H.; Dragoe, N.

    2007-01-19

    Various types of endohedral fullerene complexes are known to date. The well known metallofullerenes are generally produced by arc-discharge method, but the use of such extremely drastic conditions is apparently not suitable for encapsulation of unstable molecules or gases. We recently succeeded in incorporation of a H2 molecule or an Ar atom in 100% into a C60. In order to observe the endohedral gas molecule directly, the X-ray diffraction analysis using synchrotron radiation were carried out. We observed a gas molecule encapsulated in each fullerene cage using structure analysis and the maximum entropy method. These gas molecules are floating inside of the hollow cavities and are completely isolated from the outside.

  4. 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.

  5. Lattice gas cellular automation model for rippling and aggregation in myxobacteria

    NASA Astrophysics Data System (ADS)

    Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.

    2004-05-01

    A lattice gas cellular automation (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 min, a minimum response time of up to 1 min and no maximum oscillation period best reproduce rippling in the experiments of Myxococcus xanthus. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.

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

    PubMed

    Mychaskiw, George

    2011-01-01

    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. PMID:22146602

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

    PubMed Central

    2011-01-01

    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 PMID:22146602

  8. 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

  9. Organic molecules in the gas phase of dense interstellar clouds.

    PubMed

    Irvine, W M

    1995-03-01

    Since a previous COSPAR review on this subject, the number of molecular species identified by astronomers in dense interstellar clouds or in the envelopes expelled by evolved stars has grown from about eighty to approximately one hundred. Recent detections in stellar envelopes include the radical CP, the second phosphorus-containing astronomical molecule; SiN, the first astronomical molecule with a Si-N bond; and the HCCN radical. In the dense interstellar clouds recent detections or verifications of previous possible identifications include the H3O+ ion, which is a critical intermediary in the production of H2O and O2; the CCO radical, which is isoelectronic with HCCN; the SO+ ion, which appears to be diagnostic of shock chemistry; two new isomers of cyanoacetylene, HCCNC and CCCNH; and the two cumulenes H2C3 and H2C4. Some recent work is also described on the mapping of interstellar clouds in multiple molecular transitions in order to separate variations in chemical abundance from gradients in physical parameters. PMID:11539249

  10. 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.

  11. Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules

    SciTech Connect

    Muckerman, J.T.

    1999-05-21

    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-spectrometic 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 the 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.

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

    PubMed

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

    2016-01-01

    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. PMID:27213313

  13. Creation of a low-entropy quantum gas of polar molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Moses, Steven A.; Covey, Jacob P.; Miecnikowski, Matthew T.; Yan, Bo; Gadway, Bryce; Ye, Jun; Jin, Deborah S.

    2015-11-01

    Ultracold polar molecules, with their long-range electric dipolar interactions, offer a unique platform for studying correlated quantum many-body phenomena. However, realizing a highly degenerate quantum gas of molecules with a low entropy per particle is challenging. We report the synthesis of a low-entropy quantum gas of potassium-rubidium molecules (KRb) in a three-dimensional optical lattice. We simultaneously load into the optical lattice a Mott insulator of bosonic Rb atoms and a single-band insulator of fermionic K atoms. Then, using magnetoassociation and optical state transfer, we efficiently produce ground-state molecules in the lattice at those sites that contain one Rb and one K atom. The achieved filling fraction of 25% should enable future studies of transport and entanglement propagation in a many-body system with long-range dipolar interactions.

  14. Creation of a low-entropy quantum gas of polar molecules in an optical lattice.

    PubMed

    Moses, Steven A; Covey, Jacob P; Miecnikowski, Matthew T; Yan, Bo; Gadway, Bryce; Ye, Jun; Jin, Deborah S

    2015-11-01

    Ultracold polar molecules, with their long-range electric dipolar interactions, offer a unique platform for studying correlated quantum many-body phenomena. However, realizing a highly degenerate quantum gas of molecules with a low entropy per particle is challenging. We report the synthesis of a low-entropy quantum gas of potassium-rubidium molecules (KRb) in a three-dimensional optical lattice. We simultaneously load into the optical lattice a Mott insulator of bosonic Rb atoms and a single-band insulator of fermionic K atoms. Then, using magnetoassociation and optical state transfer, we efficiently produce ground-state molecules in the lattice at those sites that contain one Rb and one K atom. The achieved filling fraction of 25% should enable future studies of transport and entanglement propagation in a many-body system with long-range dipolar interactions. PMID:26542566

  15. Superhard Coatings Synthesis Assisted by Pulsed Beams of High-Energy Gas Molecules

    NASA Astrophysics Data System (ADS)

    Metel, Alexander; Bolbukov, Vasily; Volosova, Marina; Grigoriev, Sergei; Melnik, Yury; Department of high-efficiency machining technologies Team

    2015-09-01

    For production of nanocomposite superhard (HV 5000) and fracture-tough coatings on dielectric substrates a source of metal atoms accompanied by pulsed beams of 30-keV neutral molecules was used. The source is equipped with two parallel equipotential grids placed between a magnetron target and a substrate. Negative high-voltage pulses applied to the high-transparency grids accelerate from the magnetron plasma ions, which are transformed into high-energy neutral molecules due to charge-exchange collisions with gas molecules between the grids. Mixing of the substrate and coating materials through bombardment by high-energy gas molecules results in an adequate compressive stress of the coating and interface width exceeding 1 μm, which allows deposition of 100- μm-thick coatings with a perfect adhesion. The work was supported by the Grant No. 14-29-00297 of the Russian Science Foundation.

  16. Formation of van der Waals molecules in buffer-gas-cooled magnetic traps [corrected].

    PubMed

    Brahms, N; Tscherbul, T V; Zhang, P; Kłos, J; Sadeghpour, H R; Dalgarno, A; Doyle, J M; Walker, T G

    2010-07-16

    We predict that a large class of helium-containing cold polar molecules form readily in a cryogenic buffer gas, achieving densities as high as 10(12)  cm(-3). We explore the spin relaxation of these molecules in buffer-gas-loaded magnetic traps and identify a loss mechanism based on Landau-Zener transitions arising from the anisotropic hyperfine interaction. Our results show that the recently observed strong T(-6) thermal dependence of the spin-change rate of silver (Ag) trapped in dense (3)He is accounted for by the formation and spin change of Ag(3)He van der Waals molecules, thus providing indirect evidence for molecular formation in a buffer-gas trap. PMID:20867761

  17. Nonequilibrium vibrational excitation of molecules behind a shock front in a gas mixture

    NASA Astrophysics Data System (ADS)

    Dobkin, S. V.; Son, E. E.

    1981-10-01

    It is shown that when a shock wave propagates in a light gas with a small admixture of heavy gas, the nonequilibrium vibrational excitation of molecules of the heavy gas can occur. In this case, the vibrational temperature can increase to values exceeding the gas temperature behind the shock wave, in contrast to the equilibrium case. Vibrational energy in a shock wave in a mixture of helium and uranium hexafluoride is calculated as an example. The possibility of experimentally observing this effect is discussed.

  18. 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.

  19. 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.

  20. 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. PMID:25554152

  1. Site-selective patterning of organic luminescent molecules via gas phase deposition.

    PubMed

    Hao, Juanyuan; Lu, Nan; Wu, Qiong; Hu, Wei; Chen, Xiaodong; Zhang, Hongyu; Wu, Ying; Wang, Yue; Chi, Lifeng

    2008-05-20

    In this paper, we present a bottom-up approach to pattern organic luminescent molecules with a feature size down to sub-100 nm over wafer-sized areas. This method is based on the selective gas deposition of organic molecules on self-organized patterned structures, which consist of an organic monolayer with two different phases rather than different materials. The site selectivity is controllable by deposition rate and the pattern features. The reason for the site selectivity may be due to the nucleation and diffusion behaviors of the deposited organic molecules on different monolayer phases. PMID:18370416

  2. Creating a quantum degenerate gas of stable molecules via weak photoassociation

    NASA Astrophysics Data System (ADS)

    Mackie, Matt; Phou, Pierre

    2010-07-01

    Quantum degenerate molecules represent a new paradigm for fundamental studies and practical applications. Association of already quantum degenerate atoms into molecules provides a crucial shortcut around the difficulty of cooling molecules to ultracold temperatures. Whereas association can be induced with either laser or magnetic fields, photoassociation requires impractical laser intensity to overcome poor overlap between the atom pair and molecular wave functions, and experiments are currently restricted to magnetoassociation. Here we model realistic production of a quantum degenerate gas of stable molecules via two-photon photoassociation of Bose-condensed atoms. An adiabatic change of the laser frequency converts the initial atomic condensate almost entirely into stable molecular condensate, even for low-intensity lasers. Results for dipolar LiNa provide an upper bound on the necessary photoassociation laser intensity for alkali-metal atoms ~30 W/cm2, indicating a feasible path to quantum degenerate molecules beyond magnetoassociation.

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

    NASA Astrophysics Data System (ADS)

    Adams, N. G.; Fondren, L. D.; McLain, J. L.; Jackson, D. M.

    Several ring compounds have been detected in interstellar gas clouds, ISC, including the aromatic, benzene. Polycyclic aromatic hydrocarbons, PAH's, have been implicated as carriers of diffuse interstellar bands (DIB's) 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 (C_5H_5N, C_4H_4N_2, C_5H_{11}N and C_4H_8O_2) has been tested in the laboratory using charge transfer excitation in ion-molecule reactions. The fragmentation paths, including production of C_4H_4^+, C_3H_3N^+ and HCN, suggest reverse routes to the parent molecules, which are presently under laboratory investigation as production sources.

  4. 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.

  5. A quantum gas of ground state molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Danzl, Johann; Mark, Manfred; Haller, Elmar; Gustavsson, Mattias; Hart, Russell; Nägerl, Hanns-Christoph

    2009-05-01

    Ultracold samples of molecules are ideally suited for fundamental studies in physics and chemistry. For many of the proposed experiments full molecular state control and high phase space densities are needed. We create a dense quantum gas of ground state Cs2 molecules trapped at the wells of a 3D optical lattice, i.e. a molecular Mott-insulator-like state with ground state molecules with vibrational quantum number v = 0. We first efficiently produce weakly bound molecules with v 155 on a Feshbach resonance out of an atomic Mott-insulator state that is obtained from a Bose-Einstein condensate (BEC) of Cs atoms. These molecules are then (coherently) transferred to the ground state by two sequential two-photon STIRAP processes via the intermediate vibrational level v 73 ^1. The molecule production efficiency and the single-step STIRAP transfer efficiency reach 50% and 80%, respectively. We discuss the stability of the system and our progress towards the creation of a BEC of ground state molecules, which is expected to form when the molecular Mott-like state is ``melted'' upon lowering the lattice depth and releasing the molecules from the wells into a large volume trap. ^1J. G. Danzl, E. Haller, M. Gustavsson, M. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, H.-C. Nägerl, Science 321, 1062 (2008).

  6. 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

  7. 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.

  8. 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.

  9. 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…

  10. 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.

  11. Adsorption of gas molecules on monolayer MoS2 and effect of applied electric field

    NASA Astrophysics Data System (ADS)

    Yue, Qu; Shao, Zhengzheng; Chang, Shengli; Li, Jingbo

    2013-10-01

    Using first-principles calculations, we investigate the adsorption of various gas molecules (H2, O2, H2O, NH3, NO, NO2, and CO) on monolayer MoS2. The most stable adsorption configuration, adsorption energy, and charge transfer are obtained. It is shown that all the molecules are weakly adsorbed on the monolayer MoS2 surface and act as charge acceptors for the monolayer, except NH3 which is found to be a charge donor. Furthermore, we show that charge transfer between the adsorbed molecule and MoS2 can be significantly modulated by a perpendicular electric field. Our theoretical results are consistent with the recent experiments and suggest MoS2 as a potential material for gas sensing application.

  12. Adsorption of gas molecules on monolayer MoS2 and effect of applied electric field.

    PubMed

    Yue, Qu; Shao, Zhengzheng; Chang, Shengli; Li, Jingbo

    2013-01-01

    : Using first-principles calculations, we investigate the adsorption of various gas molecules (H2, O2, H2O, NH3, NO, NO2, and CO) on monolayer MoS2. The most stable adsorption configuration, adsorption energy, and charge transfer are obtained. It is shown that all the molecules are weakly adsorbed on the monolayer MoS2 surface and act as charge acceptors for the monolayer, except NH3 which is found to be a charge donor. Furthermore, we show that charge transfer between the adsorbed molecule and MoS2 can be significantly modulated by a perpendicular electric field. Our theoretical results are consistent with the recent experiments and suggest MoS2 as a potential material for gas sensing application. PMID:24134512

  13. 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

  14. Inhibition of Both Hsp70 Activity and Tau Aggregation in Vitro Best Predicts Tau Lowering Activity of Small Molecules.

    PubMed

    Martin, Mackenzie D; Baker, Jeremy D; Suntharalingam, Amirthaa; Nordhues, Bryce A; Shelton, Lindsey B; Zheng, Dali; Sabbagh, Jonathan J; Haystead, Timothy A J; Gestwicki, Jason E; Dickey, Chad A

    2016-07-15

    Three scaffolds with inhibitory activity against the heat shock protein 70 (Hsp70) family of chaperones have been found to enhance the degradation of the microtubule associated protein tau in cells, neurons, and brain tissue. This is important because tau accumulation is linked to neurodegenerative diseases including Alzheimer's disease (AD) and chronic traumatic encephalopathy (CTE). Here, we expanded upon this study to investigate the anti-tau efficacy of additional scaffolds with Hsp70 inhibitory activity. Five of the nine scaffolds tested lowered tau levels, with the rhodacyanine and phenothiazine scaffolds exhibiting the highest potency as previously described. Because phenothiazines also inhibit tau aggregation in vitro, we suspected that this activity might be a more accurate predictor of tau lowering. Interestingly, the rhodacyanines did inhibit in vitro tau aggregation to a similar degree as phenothiazines, correlating well with tau-lowering efficacy in cells and ex vivo slices. Moreover, other Hsp70 inhibitor scaffolds with weaker tau-lowering activity in cells inhibited tau aggregation in vitro, albeit at lower potencies. When we tested six well-characterized tau aggregation inhibitors, we determined that this mechanism of action was not a better predictor of tau-lowering than Hsp70 inhibition. Instead, we found that compounds possessing both activities were the most effective at promoting tau clearance. Moreover, cytotoxicity and PAINS activity are critical factors that can lead to false-positive lead identification. Strategies designed around these principles will likely yield more efficacious tau-lowering compounds. PMID:27177119

  15. Adsorption Mechanism of Inhibitor and Guest Molecules on the Surface of Gas Hydrates.

    PubMed

    Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

    2015-09-23

    The adsorption of guest and kinetic inhibitor molecules on the surface of methane hydrate is investigated by using molecular dynamics simulations. We calculate the free energy profile for transferring a solute molecule from bulk water to the hydrate surface for various molecules. Spherical solutes with a diameter of ∼0.5 nm are significantly stabilized at the hydrate surface, whereas smaller and larger solutes exhibit lower adsorption affinity than the solutes of intermediate size. The range of the attractive force is subnanoscale, implying that this force has no effect on the macroscopic mass transfer of guest molecules in crystal growth processes of gas hydrates. We also examine the adsorption mechanism of a kinetic hydrate inhibitor. It is found that a monomer of the kinetic hydrate inhibitor is strongly adsorbed on the hydrate surface. However, the hydrogen bonding between the amide group of the inhibitor and water molecules on the hydrate surface, which was believed to be the driving force for the adsorption, makes no contribution to the adsorption affinity. The preferential adsorption of both the kinetic inhibitor and the spherical molecules to the surface is mainly due to the entropic stabilization arising from the presence of cavities at the hydrate surface. The dependence of surface affinity on the size of adsorbed molecules is also explained by this mechanism. PMID:26331549

  16. Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution.

    PubMed

    Barone, Vincenzo; Improta, Roberto; Rega, Nadia

    2008-05-01

    Interpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases. In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters. After reporting some recent achievements for the study of excited states by first principle quantum mechanical

  17. 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).

  18. 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

  19. Organic molecules in ices and their release into the gas phase

    NASA Astrophysics Data System (ADS)

    Fayolle, Edith; Oberg, Karin I.; Garrod, Robin; van Dishoeck, Ewine; Rajappan, Mahesh; Bertin, Mathieu; Romanzin, Claire; Michaut, Xavier; Fillion, Jean-Hugues

    2015-08-01

    Organic molecules in the early stages of star formation are mainly produced in icy mantles surrounding interstellar dust grains. Identifying these complex organics and quantifying their abundance during the evolution of young stellar objects is of importance to understand the emergence of life. Simple molecules in ices, up to methanol in size, have been identified in the interstellar medium through their mid-IR vibrations, but band confusion prevents detections of more complex and less abundant organic molecules in interstellar ices. The presence of complex organics on grains can instead be indirectly inferred from observations of their rotational lines in the gas phase following ice sublimation.Thermal sublimation of protostellar ices occurs when icy grains flow toward a central protostar, resulting in the formation of a hot-core or a hot-corinos. The high degree of chemical complexity observed in these dense and warm regions can be the results of i) direct synthesis on the grains followed by desorption, but also to ii) the desorption of precursors from the ice followed by gas-phase chemistry. I will show how spatially resolved millimetric observations of hot cores and cooler protostellar environments, coupled to ice observations can help us pinpoint the ice or gas-phase origin of these organic species.Organic molecules have also recently been observed in cold environments where thermal desorption can be neglected. The presence of these cold molecules in the gas phase is most likely due to non-thermal desorption processes induced by, for e.g., photon-, electron-, cosmic-ray-irradiation, shock, exothermic reactions... I will present laboratory and observational efforts that push our current understanding of these non-thermal desorption processes and how they could be use to quantify the amount of organics in ices.

  20. Site-Specific Fragmentation of Polystyrene Molecule Using Size-Selected Ar Gas Cluster Ion Beam

    NASA Astrophysics Data System (ADS)

    Moritani, Kousuke; Mukai, Gen; Hashinokuchi, Michihiro; Mochiji, Kozo

    2009-04-01

    The secondary ion mass spectrum (SIMS) of a polystyrene thin film was investigated using a size-selected Ar gas cluster ion beam (GCIB). The fragmentation in the SIM spectrum varied by kinetic energy per atom (Eatom); the Eatom dependence of the secondary ion intensity of the fragment species of polystyrene can be essentially classified into three types based on the relationship between Eatom and the dissociation energy of a specific bonding site in the molecule. These results indicate that adjusting Eatom of size-selected GCIB may realize site-specific bond breaking within a molecule.

  1. Quantum Phase Transition Between a Luttinger Liquid and a Gas of Cold Molecules

    SciTech Connect

    Law, K. T.; Feldman, D. E.

    2008-08-29

    We consider cold polar molecules confined in a helical optical lattice similar to those used in holographic microfabrication. An external electric field polarizes molecules along the axis of the helix. The large-distance intermolecular dipolar interaction is attractive but the short-scale interaction is repulsive due to geometric constraints and thus prevents collapse. The interaction strength depends on the electric field. We show that a zero-temperature second-order liquid-gas transition occurs at a critical field. It can be observed under experimentally accessible conditions.

  2. Vascular cell adhesion molecule 1 and alpha 4 and beta 1 integrins in lymphocyte aggregates in Sjögren's syndrome and rheumatoid arthritis.

    PubMed Central

    Edwards, J C; Wilkinson, L S; Speight, P; Isenberg, D A

    1993-01-01

    OBJECTIVES--Interactions between vascular cell adhesion molecule 1 (VCAM-1) and its ligand, the alpha 4/beta 1 integrin, have been shown to be important in a number of cellular events in vitro. To assess the importance of such interactions in the development of lymphocytic infiltration in diseased tissue the distribution of the two ligands has been studied immunohistochemically. METHODS--Cryostat sections of labial tissue from patients with Sjögren's syndrome, normal labial tissues, rheumatoid synovia, and normal tonsils were stained using antibodies to VCAM-1, alpha 4 and beta 1 integrin chains, and markers for T cells, B cells, macrophages, and follicular dendritic reticulum cells (FDRCs), visualised using alkaline phosphatase and fast red. RESULTS--Staining patterns for VCAM-1 and integrin chains in lymphocyte aggregates in synovial and labial tissues were similar. VCAM-1 staining was found on both vascular and ramifying dendritic cells at the centre of large T cell aggregates and in all aggregates where there was a central clustering of B cells. VCAM-1 colocalised with, but also extended beyond, staining for the FDRC marker R4/23. Staining for the alpha 4 and beta 1 integrin chains was more widespread than staining for VCAM-1, with no significant increase in staining at sites of maximum VCAM-1 staining. In tonsils VCAM-1 and R4/23 codistributed in germinal centres, but staining for the alpha 4 and beta 1 integrin chains was chiefly seen in T lymphocyte areas. CONCLUSIONS--VCAM-1 may be more important in determining the distribution of B than T lymphocytes in lymphocytic infiltration of non-lymphoid tissue. Unlike the follicles of lymphoid tissue, ectopic follicle-like structures in non-lymphoid tissues may form by immigration of B cells via VCAM-1+ vessels at the centre of T cell aggregates. Images PMID:7504438

  3. 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.

  4. Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.

    PubMed

    Hjertenæs, Eirik; Trinh, Thuat T; Koch, Henrik

    2016-07-21

    We present chemically accurate potential energy curves of CH4, CO2 and H2 moving through hexagonal water rings, calculated by CCSD(T)/aug-cc-pVTZ with counterpoise correction. The barriers are extracted from a potential energy surface obtained by allowing the water ring to expand while the gas molecule diffuses through. State-of-the-art XC-functionals are evaluated against the CCSD(T) potential energy surface. PMID:27345929

  5. The gas phase origin of complex organic molecules precursors in prestellar cores

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2016-05-01

    Complex organic molecules (COMs) have long been observed in the warm regions surrounding nascent protostars. The recent discovery of oxygen-bearing COMs like methyl formate or dimethyl ether in prestellar cores (Bacmann et al. [2]), where gas and dust temperatures rarely exceed 10-15 K, has challenged the previously accepted models according to which COM formation relied on the diffusion of heavy radicals on warm (˜30 K) grains. Following these detections, new questions have arisen: do non-thermal processes play a role in increasing radical mobility or should new gas-phase routes be explored? The radicals involved in the formation of the aforementioned COMs, HCO and CH3O represent intermediate species in the grain-surface synthesis of methanol which proceeds via successive hydrogenations of CO molecules in the ice. We present here observations of methanol and its grain-surface precursors HCO, H2CO, CH3O in a sample of prestellar cores and derive their relative abundances. We find that the relative abundances HCO:H2CO:CH3O:CH3OH are constant across the core sample, close to 10:100:1:100. Our results also show that the amounts of HCO and CH3O are consistent with a gas-phase synthesis of these species from H2CO and CH3OH via radical-neutral or ion-molecule reactions followed by dissociative recombinations. Thus, while grain chemistry is necessary to explain the abundances of the parent volatile CH3OH, and possibly H2CO, the reactive species HCO and CH3O might be daughter molecules directly produced in the gas-phase.

  6. Rotational relaxation of fluoromethane molecules in low-temperature collisions with buffer-gas helium

    NASA Astrophysics Data System (ADS)

    Li, Xingjia; Xu, Liang; Yin, Yanning; Xu, Supeng; Xia, Yong; Yin, Jianping

    2016-06-01

    We propose a method to study the rotational relaxation of polar molecules [here taking fluoromethane (CH3F ) as an example] in collisions with 3.5 K buffer-gas helium (He) atoms by using an electrostatic guiding technique. The dependence of the guiding signal of CH3F on the injected He flux and the dependence of the guiding efficiency of CH3F on its rotational temperature are investigated both theoretically and experimentally. By comparing the experimental and simulated results, we find that the translational and rotational temperatures of the buffer-gas cooled CH3F molecules can reach to about 5.48 and 0.60 K, respectively, and the ratio between the translational and average rotational collisional cross sections of CH3F -He is γ =σt/σr=36.49 ±6.15 . In addition, the slowing, cooling, and boosting effects of the molecular beam with different injected He fluxes are also observed and their forming conditions are investigated in some detail. Our study shows that our proposed method can not only be used to measure the translational and rotational temperatures of the buffer-gas cooled molecules, but also to measure the ratio of the translational collisional cross section to the average rotational collisional cross section, and even to measure the average rotational collisional cross section when the translational collisional cross section is measured by fitting the lifetime of molecule signal to get a numerical solution from the diffusion equation of buffer-gas He atoms in the cell.

  7. Small hydrocarbon molecules in cloud-forming brown dwarf and giant gas planet atmospheres

    NASA Astrophysics Data System (ADS)

    Bilger, C.; Rimmer, P.; Helling, Ch.

    2013-11-01

    We study the abundances of complex carbon-bearing molecules in the oxygen-rich dust-forming atmospheres of brown dwarfs and giant gas planets. The inner atmospheric regions that form the inner boundary for thermochemical gas-phase models are investigated. Results from DRIFT-PHOENIX atmosphere simulations, which include the feedback of phase-non-equilibrium dust cloud formation on the atmospheric structure and the gas-phase abundances, are utilized. The resulting element depletion leads to a shift in the carbon-to-oxygen ratio such that several hydrocarbon molecules and cyanopolyyne molecules can be present. An increase in surface gravity and/or a decrease in metallicity support the increase in the partial pressures of these species. CO, CO2, CH4 and HCN contain the largest fraction of carbon. In the upper atmosphere of low-metallicity objects, more carbon is contained in C4H than in CO, and also CH3 and C2H2 play an increasingly important role as carbon sink. We determine chemical relaxation time-scales to evaluate if hydrocarbon molecules can be affected by transport-induced quenching. Our results suggest that a considerable amount of C2H6 and C2H2 could be expected in the upper atmospheres not only of giant gas planets, but also of brown dwarfs. However, the exact quenching height strongly depends on the data source used. These results will have an impact on future thermokinetic studies, as they change the inner boundary condition for those simulations.

  8. Gas phase reactions of CH(3)(+) with a series of homo- and heterocyclic molecules.

    PubMed

    Fondren, L Dalila; Adams, Nigel G; Stavish, Leah

    2009-01-22

    In gas phase ion chemistry, the growth of larger molecules is known to occur through association of ions and neutrals. Where the ion attaches to the neutral is important because it can influence the possibility of additional associations, effectively enabling or terminating further molecular growth. This was investigated by using a Selected Ion Flow Tube (SIFT) at 300 K to study the reactions of CH(3)(+) with the following series of single-ring homocyclic and heterocyclic molecules: benzene (C(6)H(6)), cyclohexane (C(6)H(12)), pyridine (C(5)H(5)N), pyrimidine (C(4)H(4)N(2)), piperidine (C(5)H(11)N), 1,4-dioxane (C(4)H(8)O(2)), furan (C(4)H(4)O), pyrrole (C(4)H(5)N), and pyrrolidine (C(4)H(9)N). Most of the reactions, except for 1,4-dioxane, pyrrole, and pyrrolidine, proceed at the gas kinetic rate. In the ion product distributions, charge transfer, hydride ion abstraction, proton transfer, fragmentation, and association were observed. In particular, proton transfer is seen to be small in all cases even though these channels are energetically favorable. Association is appreciable when the molecules are aromatic (except for furan) and nonexistent when there are no pi electrons in the ring. CH(3)(+) ions are an important intermediate in molecular synthesis in interstellar clouds and in the Titan ionosphere and ring molecules have also been detected in these media. The significance of the studied reactions to these media is discussed. PMID:19090756

  9. 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.

  10. 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. PMID:24976309

  11. Ultrafast electron diffraction from laser-aligned molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Yang, Jie

    Ultrafast electron diffraction has emerged since the end of last century, and has become an increasingly important tool for revealing great details of molecular dynamics. In comparison to spectroscopic techniques, ultrafast electron diffraction directly probes time-resolved structure of target molecules, and therefore can potentially provide "molecular movies" of the reactions being studied. These molecular movies are critical for understanding and ultimately controlling the energy conversion pathways and efficiencies of photochemical processes. In this dissertation, I have focused on ultrafast electron diffraction from gas-phase molecules, and have investigated several long-standing challenges that have been preventing researchers from being able to achieve 3-D molecular movies of photochemical reactions. The first challenge is to resolve the full 3-D structure for molecules in the gas phase. The random orientation of molecules in the gas phase smears out the diffraction signal, which results in only 1-D structural information being accessible. The second challenge lies in temporal resolution. In order to resolve coherent nuclear motions on their natural time scale, a temporal resolution of ˜200 femtosecond or better is required. However, due to experimental limitations the shortest temporal resolution that had been achieved was only a few picoseconds in early 2000, by Zewail group from Caltech. The first challenge is tackled by laser-alignment. In the first half of the dissertation, I approach this method both theoretically and experimentally, and demonstrate that by using a short laser pulse to transiently align target molecules in space, 3-D molecular structure can be reconstructed ab-initio from diffraction patterns. The second half of the dissertation presents two experiments, both of which are important steps toward imaging coherent nuclear motions in real time during photochemical reactions. The first experiment simultaneously resolves molecular alignment

  12. Production of a Quantum Gas of Rovibronic Ground-State Molecules in AN Optical Lattice

    NASA Astrophysics Data System (ADS)

    Danzl, Johann G.; Mark, Manfred J.; Haller, Elmar; Gustavsson, Mattias; Hart, Russell; Nägerl, Hanns-Christoph

    2010-02-01

    Recent years have seen tremendous progress in the field of cold and ultracold molecules. A central goal in the field is currently the realization of stable rovibronic ground-state molecular samples in the regime of quantum degeneracy, e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate Fermi gases, or, when an optical lattice is present, molecular Mott-insulator phases. However, molecular samples are not readily cooled to the extremely low temperatures at which quantum degeneracy occurs. In particular, laser cooling, the 'workhorse' for the field of atomic quantum gases, is generally not applicable to molecular samples. Here we take an important step beyond previous work1 and provide details on the realization of an ultracold quantum gas of ground-state dimer molecules trapped in an optical lattice as recently reported in Ref. 2. We demonstrate full control over all internal and external quantum degrees of freedom for the ground-state molecules by deterministically preparing the molecules in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic ground state, while the molecules are trapped in the motional ground state of the individual lattice wells. We circumvent the problem of cooling by associating weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and by transferring these to the absolute ground state in a four-photon STIRAP process. Our preparation procedure directly leads to a long-lived, lattice-trapped molecular many-body state, which we expect to form the platform for many of the envisioned future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy, quantum information science, and dipolar quantum systems.

  13. Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation.

    PubMed

    Paramasivam, Manikandan; Cogoi, Susanna; Filichev, Vyacheslav V; Bomholt, Niels; Pedersen, Erik B; Xodo, Luigi E

    2008-06-01

    Sequence-specific targeting of genomic DNA by triplex-forming oligonucleotides (TFOs) is a promising strategy to modulate in vivo gene expression. Triplex formation involving G-rich oligonucleotides as third strand is, however, strongly inhibited by potassium-induced TFO self-association into G-quartet structures. We report here that G-rich TFOs with bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)-phenylmethyl] glycerol (called twisted intercalating nucleic acids, TINA) show a much lower tendency to aggregate in potassium than wild-type analogues do. We designed purine-motif TINA-TFOs for binding to a regulatory polypurine-polypyrimidine (pur/pyr) motif present in the promoter of the KRAS proto-oncogene. The binding of TINA-TFOs to the KRAS target has been analysed by electrophoresis mobility shift assays and DNase I footprinting experiments. We discovered that in the presence of potassium the wild-type TFOs did not bind to the KRAS target, differently from the TINA analogues, whose binding was observed up to 140 mM KCl. The designed TINA-TFOs were found to abrogate the formation of a DNA-protein complex at the pur/pyr site and to down-regulate the transcription of CAT driven by the murine KRAS promoter. Molecular modelling of the DNA/TINA-TFO triplexes are also reported. This study provides a new and promising approach to create TFOs to target in vivo the genome. PMID:18456705

  14. 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.

  15. Reactions of metal cluster anions with inorganic and organic molecules in the gas phase.

    PubMed

    Zhao, Yan-Xia; Liu, Qing-Yu; Zhang, Mei-Qi; He, Sheng-Gui

    2016-07-28

    The study of gas phase ion-molecule reactions by state-of-the-art mass spectrometric experiments in conjunction with quantum chemistry calculations offers an opportunity to clarify the elementary steps and mechanistic details of bond activation and conversion processes. In the past few decades, a considerable number of publications have been devoted to the ion-molecule reactions of metal clusters, the experimentally and theoretically tractable models for the active phase of condensed phase systems. The focus of this perspective concerns progress on activation and transformation of important inorganic and organic molecules by negatively charged metal clusters. The metal cluster anions cover bare metal clusters as well as ligated systems with oxygen, carbon, and nitrogen, among others. The following important issues have been summarized and discussed: (i) dependence of chemical reactivity and selectivity on cluster structures and sizes, metals and metal oxidation states, odd-even electron numbers, etc. and (ii) effects of doping, ligation, and pre-adsorption on the reactivity of metal clusters toward rather inert molecules. PMID:27346242

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

    DOE PAGESBeta

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

    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

  17. 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.

  18. 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

    2016-01-01

    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

  19. 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

  20. Polaron-molecule transitions in a two-dimensional Fermi gas

    SciTech Connect

    Parish, Meera M.

    2011-05-15

    We address the problem of a single 'spin-down' impurity atom interacting attractively with a spin-up Fermi gas in two dimensions (2D). We consider the case where the mass of the impurity is greater than or equal to the mass of a spin-up fermion. Using a variational approach, we resolve the questions raised by previous studies and show that there is, in fact, a transition between polaron and molecule (dimer) ground states in 2D. For the molecule state, we use a variational wave function with a single particle-hole excitation on the Fermi sea and we find that its energy matches that of the exact solution in the limit of infinite impurity mass. Thus, we expect the variational approach to provide a reliable tool for investigating 2D systems.

  1. 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.

  2. Unique Y-shaped lanthanide aggregates and single-molecule magnet behaviour for the Dy4 analogue.

    PubMed

    Xue, Shufang; Guo, Yun-Nan; Zhao, Lang; Zhang, Peng; Tang, Jinkui

    2014-01-28

    The assembly of N'-(amino-(pyrimidin-2-yl)methylene)-o-vanilloyl hydrazine ligands (H2L, Scheme 1) with different lanthanide perchlorates produces novel Y-shaped tetranuclear complexes, [Ln4(μ3-OH)(L(2-))4(H2O)6]·(ClO4)3·6H2O, where Ln = Tb (1), Dy (2) and Ho (3). The formation of this unprecedented Y-shaped topology is largely ascribed to the versatility of the mixed-donor hydrazone ligands in terms of their potential denticity. Analysis of the susceptibility data shows that only the Dy-based molecule features SMM-like behaviour. The synthetic methodology of employing H2L and related ligands has provided a very promising route towards new families of magnetic coordination clusters with novel metal topologies and properties. PMID:24213812

  3. 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

  4. Rationally designed micropores within a metal-organic framework for selective sorption of gas molecules.

    PubMed

    Chen, Banglin; Ma, Shengqian; Zapata, Fatima; Fronczek, Frank R; Lobkovsky, Emil B; Zhou, Hong-Cai

    2007-02-19

    A microporous metal-organic framework, MOF, Cu(FMA)(4,4'-Bpe)0.5 (3a, FMA = fumarate; 4,4'-Bpe = 4,4'-Bpe = trans-bis(4-pyridyl)ethylene) was rationally designed from a primitive cubic net whose pores are tuned by double framework interpenetration. With pore cavities of about 3.6 A, which are interconnected by pore windows of 2.0 x 3.2 A, 3a shows highly selective sorption behaviors of gas molecules. PMID:17291116

  5. Laser-driven rotational dynamics of gas-phase molecules: Control and applications

    NASA Astrophysics Data System (ADS)

    Ren, Xiaoming

    In this thesis, our work on developing new techniques to measure and enhance field-free molecular alignment and orientation is described. Non-resonant femtosecond laser pulses are used to align and orient rotationally-cold gas-phase molecules. The time-dependent Schrodinger equation is solved to simulate the experimental results. A single-shot kHz velocity map imaging (VMI) spectrometer is developed for characterizing 1D and 3D alignment. Stimulated by a novel metric for 3D alignment proposed by Makhija et al. [Phys. Rev. A 85,033425 (2012)], a multi-pulse scheme to improve 3D alignment is demonstrated experimentally on difluoro-iodobenzene molecules and the best field-free 3D alignment is achieved. A degenerate four wave mixing probe is developed to overcome limitations in VMI measurement; experiments on different types of molecules show good agreement with computational results. Highly aligned linear molecules are used for high harmonic generation experiments. Due to the high degree of alignment, fractional revivals, variation of revival structure with harmonic order and the shape resonance and Cooper minimum in the photoionization cross section of molecular nitrogen are all observed directly in experiment for the first time. Enhanced orientation from rotationally cold heteronuclear molecules is also demonstrated. We follow the theory developed by Zhang et al. [Phys. Rev. A 83, 043410 (2011)] and demonstrate experimentally for the first time that for rotationally cold carbon monoxide an aligning laser pulse followed by a two-color laser pulse can increase field-free orientation level by almost a factor of three compared to using just the two-color pulse.

  6. Properties of clusters in the gas phase. V - Complexes of neutral molecules onto negative ions

    NASA Technical Reports Server (NTRS)

    Keesee, R. G.; Lee, N.; Castleman, A. W., Jr.

    1980-01-01

    Ion-molecules association reactions of the form A(-)(B)n-1 + B = A(-)(B)n were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl(-), I(-), and NO2(-) with n ranging from one to three or four, and onto SO2(-) and SO3(-) with n equal to one; and (2) carbon dioxide onto Cl(-), I(-), NO2(-), CO3(-), and SO3(-) with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions.

  7. 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

  8. 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.

  9. 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. PMID:26640032

  10. 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.

  11. Gas-phase ion/molecule reactions of corannulene, a fullerene subunit

    SciTech Connect

    Becker, H.; Schwarz, H. ); Javahery, G.; Petrie, S.; Bohme, D.K. ); Cheng, P.C.; Scott, L.T. )

    1993-12-01

    Corannulene is intriguing, not only because of its highly-strained bowl-like structure, but also as a subunit of C[sub 60] and other fullerenes. The carbon skeleton of corannulene appears several times in C[sub 60], and its curvature mimics the curvature of C[sub 60]. Inspired by this curiosity, and having previously investigated ion/molecule reactions of C[sub 60] cations, we began an unprecedented experimental investigation of ion/molecule reactions of corannulene. Here we report the first observations of gas-phase ion/molecule reactions with corannulene: reactions of the corannulene cation (cor[sup [sm bullet]+]) with C[sub 60] and of neutral corannulene with Ar[sup [sm bullet]+], cor[sup [sm bullet]+], C[sub 60][sup [sm bullet]+], C[sub 60][sup 2+], and C[sub 60][sup [sm bullet]3+]. Both electronic and topographical features are expected to be of consequence in many of these reactions. 22 refs., 1 tab.

  12. Adsorption of gas molecules on Cu impurities embedded monolayer MoS2: A first- principles study

    NASA Astrophysics Data System (ADS)

    Zhao, B.; Li, C. Y.; Liu, L. L.; Zhou, B.; Zhang, Q. K.; Chen, Z. Q.; Tang, Z.

    2016-09-01

    Adsorption of small gas molecules (O2, NO, NO2 and NH3) on transition-metal Cu atom embedded monolayer MoS2 was investigated by first-principles calculations based on the density-functional theory (DFT). The embedded Cu atom is strongly constrained on the sulfur vacancy of monolayer MoS2 with a high diffusion barrier. The stable adsorption geometry, charge transfer and electronic structures of these gas molecules on monolayer MoS2 embedded with transition-metal Cu atom are discussed in detail. It is found that the monolayer MoS2 with embedded Cu atom can effectively capture these gas molecules with high adsorption energy. The NH3 molecule acts as electron donor after adsorption, which is different from the other gas molecules (O2, NO, and NO2). The results suggest that MoS2-Cu system may be promising for future applications in gas molecules sensing and catalysis, which is similar to those of the transition-metal embedded graphene.

  13. Influence of the presence of small gas molecules in the structure of comblike polyacrylates: a Monte Carlo study.

    PubMed

    León, Salvador; Zanuy, David; Alemán, Carlos

    2002-05-01

    A theoretical strategy has been developed to study the motion of small molecules through ordered polymeric systems. The strategy, which has been incorporated into a computer program denoted MCDP/2, is especially useful to study comblike polymers organized in biphasic arrangements. This is because it is based on a configurational bias Monte Carlo algorithm, which is more efficient than conventional methods to study dense systems. The MCDP/2 program has been used to investigate the influence of CH(4) and CO(2) gas molecules in the structure of isotactic poly(octadecyl acrylate), a typical comblike polymer. For this purpose, the pure polymer and different molecular systems constituted by several gas molecules dissolved in the polymer matrix have been simulated. Results indicated that the structural relaxation of the polymer is not coupled to the motion of gas molecules. The importance of these results in the field of molecular modeling of transport properties in comblike polymers is discussed. PMID:11948586

  14. Interaction of gas molecules with crystalline polymer separation membranes: Atomic-scale modeling and first-principles calculations

    SciTech Connect

    Sergey N. Rashkeev; Eric S. Peterson

    2011-11-01

    Carbon dioxide (CO2)-induced plasticization can significantly decrease the gas separation performance of membranes in high-temperature or high pressure conditions, such as industrial methane (CH4) separations. In this paper, we investigated the crystalline phase of three polymers (polybenzimidazole (PBI), Bis(isobutylcarboxy)polybenzimidazole (PBI-Butyl), and KaptonTM) and interactions between gas molecules (CO2 and N2) and these polymers. A novel, molecular dynamics (MD) based, computational technique was employed to find unknown crystalline structures of these polymer materials. The interaction of CO2 and N2 gases with these crystals was studied by first-principles calculations and by classical MD simulations. The results showed that the packing structure and the interlayer coupling in polymer crystals determine the permeability and diffusivity of gas molecules. This methodology also allows prediction of plastic swelling in these materials caused by gas molecules absorbed in the polymer matrix.

  15. 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

  16. 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. PMID:27198064

  17. Aggregated silver nanoparticles based surface-enhanced Raman scattering enzyme-linked immunosorbent assay for ultrasensitive detection of protein biomarkers and small molecules.

    PubMed

    Liang, Jiajie; Liu, Hongwu; Huang, Caihong; Yao, Cuize; Fu, Qiangqiang; Li, Xiuqing; Cao, Donglin; Luo, Zhi; Tang, Yong

    2015-06-01

    Lowering the detection limit is critical to the design of bioassays required for medical diagnostics, environmental monitoring, and food safety regulations. The current sensitivity of standard color-based analyte detection limits the further use of enzyme-linked immunosorbent assays (ELISAs) in research and clinical diagnoses. Here, we demonstrate a novel method that uses the Raman signal as the signal-generating system of an ELISA and combines surface-enhanced Raman scattering (SERS) with silver nanoparticles aggregation for ultrasensitive analyte detection. The enzyme label of the ELISA controls the dissolution of Raman reporter-labeled silver nanoparticles through hydrogen peroxide and generates a strong Raman signal when the analyte is present. Using this assay, prostate-specific antigen (PSA) and the adrenal stimulant ractopamine (Rac) were detected in whole serum and urine at the ultralow concentrations of 10(-9) and 10(-6) ng/mL, respectively. The methodology proposed here could potentially be applied to other molecules detection as well as PSA and Rac. PMID:25928837

  18. 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. PMID:27110099

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

    PubMed Central

    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. PMID:27110099

  20. The physical basis for absorption of light. [effects on wave functions of gas molecules and atoms

    NASA Technical Reports Server (NTRS)

    Pickett, H. M.

    1979-01-01

    The effects of light absorption on the wave functions of gas-phase molecules and atoms are investigated by high resolution spectral measurements of radiation emerging from a sample. A Stark-modulated sample of methyl fluoride was irradiated at the 102 GHz rotational transition and the emergent radiation was resolved by means of a spectrum analyzer. For signal oscillator frequencies below or above the molecular resonance by one modulation frequency, the amplitudes of the upper and lower modulation sidebands are found to be of nonuniform intensity, which is inconsistent with amplitude modulation. Emission due to polarization is, however, calculated to be consistent with the results observed, indicating that light absorption should be considered as a subtractive stimulated emission.

  1. 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.

  2. 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

  3. First-principles investigation of armchair boron nitride nanoribbons for sensing PH3 gas molecules

    NASA Astrophysics Data System (ADS)

    Srivastava, Pankaj; Jaiswal, Neeraj K.; Sharma, Varun

    2014-09-01

    The present work exhibits density functional theory (DFT) based first-principles calculations to explore the sensing properties of bare armchair boron nitride nanoribbons (ABNNR) for PH3 gas molecules. Edges of the ribbon were considered as the sites of possible adsorption with two different configurations i.e. adsorption at one edge and adsorption at both edges of the ribbon. It is revealed that B atoms of the ribbons are more energetically favorable sites for the adsorption of PH3 molecules as compared with N atoms. The adsorption of PH3 affects the electronic properties of nanoribbons. One edge PH3 adsorbed ribbons are metallic whereas in both edges PH3 adsorption, the band gap is decreased than that of bare ribbon. The changes in electronic properties caused by PH3 adsorption are further supported by the current-voltage (I-V) characteristics of the considered configurations. The results show that ABNNR can serve as a potential candidate for PH3 sensing applications.

  4. Does Moisture Influence the Chemical Detection of Gas Molecules Adsorbed on Single-Wall Carbon Nanotubes?

    NASA Astrophysics Data System (ADS)

    Yu, Ming; Tian, W. Q.; Jayanthi, C. S.; Wu, S. Y.

    2009-03-01

    In this work, the role of water in the detection of hydrazine (N2H4) by a single-wall carbon nanotube (SWCNT) is investigated using first principles electronic structure calculations (DFT/GGA--USPP)[1]. This calculation is undertaken to interpret the experimental resistivity measurements for N2H4 adsorbed on SWCNT that reveal an n-type behavior [2]. Our preliminary theoretical studies of the adsorption of N2H4 on SWCNT revealed physisorption for N2H4 and an unaltered band structure for the SWCNT [3]. This prompted us to look into the role of water on the bonding of N2H4 to the SWCNT. We found that, by introducing a monolayer of water film on the (8,0) SWCNT, the adsorption of N2H4 can introduce occupied states near the Fermi level, exhibiting an n-type behavior. However, the introduction of just few water molecules was not sufficient to influence the electronic structure of N2H4/SWCNT. Presently, we are studying the influence of water films on the chemical detection of a variety of other gas molecules (N2, NH3, etc.) by SWCNTs, and the results from such studies will also be reported. [1]. G. Kresse et al. Phys. Rev. B 54, 11169 (1996). [2]. S. Desai, et al. (APS, March 2008). [3]. M. Yu, et al. (APS, March 2008).

  5. Adsorption of gas molecules on transition metal embedded graphene: a search for high-performance graphene-based catalysts and gas sensors

    NASA Astrophysics Data System (ADS)

    Zhou, Miao; Lu, Yun-Hao; Cai, Yong-Qing; Zhang, Chun; Feng, Yuan-Ping

    2011-09-01

    We report an investigation on the adsorption of small gas molecules (O2, CO, NO2 and NH3) on pristine and various transition metal embedded graphene samples using a first-principles approach based on density-functional theory (DFT). The most stable adsorption geometry, energy, charge transfer, and magnetic moment of these molecules on graphene embedded with different transition metal elements are thoroughly discussed. Our calculations found that embedded transition metal elements in general can significantly enhance the interactions between gas molecules and graphene, and for applications of graphene-based catalysis, Ti and Au may be the best choices among all transition metal elements. We also expect a detailed analysis of the electronic structures and magnetic properties of these systems to shed light on future applications of graphene-based gas sensing and spintronics.

  6. Detection of the Elusive Triazane Molecule (N3 H5 ) in the Gas Phase.

    PubMed

    Förstel, Marko; Maksyutenko, Pavlo; Jones, Brant M; Sun, Bing-Jian; Chen, Shih-Hua; Chang, Agnes H-H; Kaiser, Ralf I

    2015-10-26

    We report the detection of triazane (N3 H5 ) in the gas phase. Triazane is a higher order nitrogen hydride of ammonia (NH3 ) and hydrazine (N2 H4 ) of fundamental importance for the understanding of the stability of single-bonded chains of nitrogen atoms and a potential key intermediate in hydrogen-nitrogen chemistry. The experimental results along with electronic-structure calculations reveal that triazane presents a stable molecule with a nitrogen-nitrogen bond length that is a few picometers shorter than that of hydrazine and has a lifetime exceeding 6±2 μs at a sublimation temperature of 170 K. Triazane was synthesized through irradiation of ammonia ice with energetic electrons and was detected in the gas phase upon sublimation of the ice through soft vacuum ultraviolet (VUV) photoionization coupled with a reflectron-time-of-flight mass spectrometer. Isotopic substitution experiments exploiting [D3 ]-ammonia ice confirmed the identification through the detection of its fully deuterated counterpart [D5 ]-triazane (N3 D5 ). PMID:26331382

  7. 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...

  8. Efficiency of excimer molecule formation in plasma jets of inert gas mixtures with SF6 and CCl4

    NASA Astrophysics Data System (ADS)

    Rogulich, V. S.; Starodub, V. P.; Shevera, V. S.

    1988-10-01

    The formation of krypton and xenon monofluorides and monochlorides in continuous plasma jets of inert gas mixtures with SF6 and CCl4 molecules is investigated experimentally. Absolute concentrations of KrF, XeF, KrCl, and XeCl excimer molecules in the jet are determined. The energy efficiency of specific input power conversion to the spontaneous B-X emission in the KrF band is estimated at 2-4 percent. Ways of increasing the concentration of excimer molecules in the plasma jet are analyzed.

  9. Metastable BrO2+ and NBr2+ molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Aoto, Yuri Alexandre; de Oliveira-Filho, Antonio Gustavo S.; Franzreb, Klaus; Ornellas, Fernando R.

    2011-03-01

    The doubly positively charged gas-phase molecules BrO2+ and NBr2+ have been produced by prolonged high-current energetic oxygen (17 keV 16O-) ion surface bombardment (ion beam sputtering) of rubidium bromide (RbBr) and of ammonium bromide (NH4Br) powdered ionic salt samples, respectively, pressed into indium foil. These novel species were observed at half-integer m/z values in positive ion mass spectra for ion flight times of roughly ˜12 μs through a magnetic-sector secondary ion mass spectrometer. Here we present these experimental results and combine them with a detailed theoretical investigation using high level ab initio calculations of the ground states of BrO2+ and NBr2+, and a manifold of excited electronic states. NBr2+ and BrO2+, in their ground states, are long-lived metastable gas-phase molecules with well depths of 2.73 × 104 cm-1 (3.38 eV) and 1.62 × 104 cm-1 (2.01 eV); their fragmentation channels into two monocations lie 2.31 × 103 cm-1 (0.29 eV) and 2.14 × 104 cm-1 (2.65 eV) below the ground state minimum. The calculated lifetimes for NBr2+ (v″ < 35) and BrO2+ (v″ < 18) are large enough to be considered stable against tunneling. For NBr2+, we predicted Re = 3.051 a0 and ωe = 984 cm-1; for BrO2+, we obtained 3.033 a0 and 916 cm-1, respectively. The adiabatic double ionization energies of BrO and NBr to form metastable BrO2+ and NBr2+ are calculated to be 30.73 and 29.08 eV, respectively. The effect of spin-orbit interactions on the low-lying (Λ + S) states is also discussed.

  10. 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.

  11. 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)

  12. Role of interspecies interactions in the preparation of a low-entropy gas of polar molecules in a lattice

    NASA Astrophysics Data System (ADS)

    Safavi-Naini, A.; Wall, M. L.; Rey, A. M.

    2015-12-01

    The preparation of a quantum degenerate gas of heteronuclear molecules has been an outstanding challenge. We use path-integral quantum Monte Carlo simulations to understand the role of interactions and finite temperature effects in the protocol currently employed to adiabatically prepare a low-entropy gas of polar molecules in a lattice starting from an ultracold Bose-Fermi mixture. We find that interspecies interactions affect the final temperature of the mixture after the adiabatic loading procedure and detrimentally limit the molecular peak filling. Our conclusions are in agreement with recent experimental measurements [Moses et al., Science 350, 659 (2015), 10.1126/science.aac6400] and therefore are of immediate relevance for the myriad experiments that aim to form molecules from dual-species atomic gases.

  13. 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.

  14. 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.

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

    PubMed

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

    2012-11-28

    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. PMID:23206013

  16. 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.

  17. 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.

  18. Mechanism of charge transfer and its impacts on Fermi-level pinning for gas molecules adsorbed on monolayer WS2.

    PubMed

    Zhou, Changjie; Yang, Weihuang; Zhu, Huili

    2015-06-01

    Density functional theory calculations were performed to assess changes in the geometric and electronic structures of monolayer WS2 upon adsorption of various gas molecules (H2, O2, H2O, NH3, NO, NO2, and CO). The most stable configuration of the adsorbed molecules, the adsorption energy, and the degree of charge transfer between adsorbate and substrate were determined. All evaluated molecules were physisorbed on monolayer WS2 with a low degree of charge transfer and accept charge from the monolayer, except for NH3, which is a charge donor. Band structure calculations showed that the valence and conduction bands of monolayer WS2 are not significantly altered upon adsorption of H2, H2O, NH3, and CO, whereas the lowest unoccupied molecular orbitals of O2, NO, and NO2 are pinned around the Fermi-level when these molecules are adsorbed on monolayer WS2. The phenomenon of Fermi-level pinning was discussed in light of the traditional and orbital mixing charge transfer theories. The impacts of the charge transfer mechanism on Fermi-level pinning were confirmed for the gas molecules adsorbed on monolayer WS2. The proposed mechanism governing Fermi-level pinning is applicable to the systems of adsorbates on recently developed two-dimensional materials, such as graphene and transition metal dichalcogenides. PMID:26049513

  19. Pulse gas chromatographic study of adsorption of substituted aromatics and heterocyclic molecules on MIL-47 at zero coverage.

    PubMed

    Duerinck, Tim; Couck, Sarah; Vermoortele, Frederik; De Vos, Dirk E; Baron, Gino V; Denayer, Joeri F M

    2012-10-01

    The low coverage adsorptive properties of the MIL-47 metal organic framework toward aromatic and heterocyclic molecules are reported in this paper. The effect of molecular functionality and size on Henry adsorption constants and adsorption enthalpies of alkyl and heteroatom functionalized benzene derivates and heterocyclic molecules was studied using pulse gas chromatography. By means of statistical analysis, experimental data was analyzed and modeled using principal component analysis and partial least-squares regression. Structure-property relationships were established, revealing and confirming several trends. Among the molecular properties governing the adsorption process, vapor pressure, mean polarizability, and dipole moment play a determining role. PMID:22958218

  20. 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.

  1. Diffusion, thermalization, and optical pumping of YbF molecules in a cold buffer-gas cell

    NASA Astrophysics Data System (ADS)

    Skoff, S. M.; Hendricks, R. J.; Sinclair, C. D. J.; Hudson, J. J.; Segal, D. M.; Sauer, B. E.; Hinds, E. A.; Tarbutt, M. R.

    2011-02-01

    We produce YbF molecules with a density of 1018 m-3 using laser ablation inside a cryogenically cooled cell filled with a helium buffer gas. Using absorption imaging and absorption spectroscopy we study the formation, diffusion, thermalization, and optical pumping of the molecules. The absorption images show an initial rapid expansion of molecules away from the ablation target followed by a much slower diffusion to the cell walls. We study how the time constant for diffusion depends on the helium density and temperature and obtain values for the YbF-He diffusion cross section at two different temperatures. We measure the translational and rotational temperatures of the molecules as a function of time since formation, obtain the characteristic time constant for the molecules to thermalize with the cell walls, and elucidate the process responsible for limiting this thermalization rate. Finally, we make a detailed study of how the absorption of the probe laser saturates as its intensity increases, showing that the saturation intensity is proportional to the helium density. We use this to estimate collision rates and the density of molecules in the cell.

  2. 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.

  3. 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.

  4. Hot-Wire Chemical Vapor Deposition Of Polycrystalline Silicon : From Gas Molecule To Solar Cell

    NASA Astrophysics Data System (ADS)

    van Veenendaal, P. A. T. T.

    2002-10-01

    Although the effort to investigate the use of renewable energy sources, such as wind and solar energy, has increased, their contribution to the total energy consumption remains insignificant. The conversion of solar energy into electricity through solar cells is one of the most promising techniques, but the use of these cells is limited by the high cost of electricity. The major contributions to these costs are the material and manufacturing costs. Over the past decades, the development of silicon based thin film solar cells has received much attention, because the fabrication costs are low. A promising material for use in thin film solar cells is polycrystalline silicon (poly-Si:H). A relatively new technique to deposit poly-Si:H is Hot-Wire Chemical Vapor Deposition (Hot-Wire CVD), in which the reactant gases are catalytically decomposed at the surface of a hot filament, mainly tungsten and tantalum. The main advantages of Hot-Wire CVD over PE-CVD are absence of ion bombardment, high deposition rate, low equipment cost and high gas utilization. This thesis deals with the full spectrum of deposition, characterization and application of poly-Si:H thin films, i.e. from gas molecule to solar cell. Studies on the decomposition of silane on the filament showed that the process is catalytic of nature and that silane is decomposed into Si and 4H. The dominant gas phase reaction is the reaction of Si and H with silane, resulting in SiH3, Si2H6, Si3H6 and H2SiSiH2. The film growth precursors are Si, SiH3 and Si2H4. Also, XPS results on used tantalum and tungsten filaments are discussed. The position dependent measurements show larger silicon contents at the ends of the tungsten filament, as compared to the middle, due to a lower filament temperature. This effect is insignificant for a tantalum filament. Deposition time dependent measurements show an increase in silicon content of the tungsten filament with time, while the silicon content on the tantalum filament saturates

  5. Magnetic-field-induced quadrupole coupling in the nuclear magnetic resonance of noble-gas atoms and molecules

    SciTech Connect

    Manninen, Pekka; Vaara, Juha; Pyykkoe, Pekka

    2004-10-01

    An analytic response theory formulation for the leading-order magnetic field-induced and field-dependent quadrupole splitting in nuclear magnetic resonance spectra is presented and demonstrated with first-principles calculations for {sup 21}Ne, {sup 36}Ar, and {sup 83}Kr in noble gas atoms. The case of molecules was studied for {sup 33}S in the sulphur hexafluoride molecule, as well as for {sup 47/49}Ti, {sup 91}Zr, and {sup 177,179}Hf in group(IV) tetrahalides. According to our calculations, the hitherto experimentally unknown field-induced quadrupole splitting in molecules rises to 10{sup 2} Hz for {sup 177,179}Hf nuclei in HfF{sub 4} and 10{sup 1} Hz for {sup 47/49}Ti in TiCl{sub 4}, and is hence of observable magnitude.

  6. Electron-impact-induced tryptophan molecule fragmentation

    NASA Astrophysics Data System (ADS)

    Tamuliene, Jelena; Romanova, Liudmila G.; Vukstich, Vasyl S.; Papp, Alexander V.; Snegursky, Alexander V.

    2015-01-01

    The fragmentation of a gas-phase tryptophan molecule by a low-energy (<70 eV) electron impact was studied both experimentally and theoretically. Various positively charged fragments were observed and analyzed. A special attention was paid to the energy characteristics of the ionic fragment yield. The geometrical parameters of the initial molecule rearrangement were also analyzed. The fragmentation observed was due to either a simple bond cleavage or more complex reactions involving molecular rearrangements. Contribution to the Topical Issue "Elementary Processes with Atoms and Molecules in Isolated and Aggregated States", edited by Friedrich Aumayr, Bratislav Marinkovic, Stefan Matejcik, John Tanis and Kurt H. Becker.

  7. 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.

  8. Optically pumped gas laser using electronic transitions in the NaRb molecule

    SciTech Connect

    Kaslin, V.M.; Yakushev, O.F.

    1983-12-01

    Laser superradiance was achieved for the first time as a result of an electronic transition in a diatomic heteronuclear molecule as a result of direct optical pumping. This superradiance was observed in the region of 670 nm due to a transition to the ground state X/sup 1/..sigma../sup +/ of the intermetallic alkali molecule NaRb pumped by radiation from a pulsed copper vapor laser (lambda = 510.6 nm).

  9. 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.

  10. 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.

  11. Formation of Complex Organics by Gas Phase and Intracluster Ion-Molecule Reactions Involving Acetylene and Hydrogen Cyanide

    NASA Astrophysics Data System (ADS)

    El-Shall, S.; Hamed, A.; Soliman, A. R.; Momoh, P. O.

    2011-05-01

    Many complex organics including polycyclic aromatic hydrocarbons are present in flames and combustion processes as well as in interstellar clouds and solar nebulae. Here, we present evidence for the formation of complex covalent organics by gas phase and intracluster reactions of the benzene, phenylium, pyridine, pyrimidine, phenylacetylene and benzonitrile cations with acetylene and hydrogen cyanide molecules. These reactions are studied using mass-selected ion mobility, chemical reactivity, collisional dissociation, and ab initio calculations. Measurements of collision cross sections in helium provide structural information on the adducts and allow probing structural changes at different temperatures (isomerization). We observed multiple additions of five acetylene molecules on the pyridine cation at room temperature. This is a remarkable result considering that only two acetylene molecules were added to the phenyl cation and no addition was observed on the benzene cation at room temperature. The experimental results are in full agreement with the ab initio calculations which predict that the first and second acetylenes add to the pyridine ion in barrierless, highly exothermic reactions. Similar reactions have been observed for the pyrimidine radical cation although the extent of the addition reactions is limited to only two acetylene molecules at room temperature. The results provide the first evidence for the incorporation of nitrogen in the formation cyclic hydrocarbons via the gas phase reactions of pyridine and pyrimidine ions with acetylene molecules. In addition, the formation of covalent adducts in the ionized acetylene/HCN system will be reported for the first time. Sequential reactions leading to the formation of pyridine and pyrimidine radical cations and higher adducts are observed over a wide range of temperature and pressure. The formation of these covalent adducts may represent a general class of addition reactions that can form complex

  12. 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.

  13. Creation of an Ultracold Gas of Ground-State Dipolar 23Na 87 Molecules

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    We report the successful production of an ultracold sample of absolute ground-state 23Na 87Rb molecules. Starting from weakly bound Feshbach molecules formed via magnetoassociation, the lowest rovibrational and hyperfine level of the electronic ground state is populated following a high-efficiency and high-resolution two-photon Raman process. The high-purity absolute ground-state samples have up to 8000 molecules and densities of over 1011 cm-3 . By measuring the Stark shifts induced by external electric fields, we determined the permanent electric dipole moment of the absolute ground-state 23Na 87Rb and demonstrated the capability of inducing an effective dipole moment over 1 D. Bimolecular reaction between ground-state 23Na 87Rb molecules is endothermic, but we still observed a rather fast decay of the molecular sample. Our results pave the way toward investigation of ultracold molecular collisions in a fully controlled manner and possibly to quantum gases of ultracold bosonic molecules with strong dipolar interactions.

  14. Polarized fluorescence of polyatomic fragments produced through photodissociation of polyatomic molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Blokhin, A. P.; Gelin, M. F.; Kalosha, I. I.; Polubisok, S. A.; Tolkachev, V. A.

    1999-01-01

    A combined theoretical and experimental study is carried of the polarized emission of polyatomic products produced through photodissociation of polyatomic molecules. A general approach, based on the formalism of dissociation kernels and orientational correlation functions, is developed to predict anisotropy of the fluorescence of photoproducts. We consider the most general case of asymmetric top parent and product molecules. The rotational predissociation effect is taken into account. Various kinds of photoreactions are studied: those when fragments after dissociation are in the electronically excited states and those when fragments are in the ground electronic states so that additional laser pulse is necessary to excite their fluorescence. Particular attention is concentrated on those practically important extreme cases, when predissociation times and lifetimes of the electronically excited states of photoproducts are short or long as compared to the averaged period of free rotation. The steady state polarized fluorescence of radicals produced through dissociation of several disulfides into two identical radicals is measured. The results are interpreted in the framework of the free recoil model (FRM). In this model, photoproducts are assumed to experience no torque and fly apart freely, so that the only origin of the fragment rotation is rotation of the parent molecule. Predictions of the impulsive model (IM), in which fragments are supposed to suffer instantaneous torque due to the rupture of the chemical bonds of the parent molecule, are demonstrated to disagree strongly with our experimental data. This gives an additional confirmation of the validity of the FRM in describing dissociation of polyatomic molecules into polyatomic fragments. The FRM can therefore be invoked to estimate interrelation between the characteristic times, governing the processes of dissociation and emission, and the averaged period of free molecular rotation. Also, the FRM can be used

  15. Electron swarm parameters in SiH sub 4 -rare gas mixtures and collision cross sections for monosilane molecules

    SciTech Connect

    Kurachi, M.; Nakamura, Y. . Faculty of Science and Technology)

    1991-04-01

    Previously measured drift velocity and longitudinal diffusion coefficient in SiH{sub 4}-Ar mixtures were re-analyzed, and the new vibrational excitation cross sections for monosilane molecules were obtained. Not only were the new cross sections consistent with swarm parameters, but also the ratio of their magnitudes at the resonance peak agreed with recent measurements of the electron beam experiment. Having known the vibrational excitation cross sections, the analysis of the primary ionization coefficient measured in SiH{sub 4}-Kr mixtures led to a consistent inelastic cross section, which possibly corresponds to the total cross section for neutral dissociations for the molecule. In this paper it was confirmed that the derived set of the cross sections also gave good agreement with the electron swarm parameters measured in pure monosilane gas.

  16. Molecule-modulated photoconductivity and gain-amplified selective gas sensing in polar GaN nanowires

    NASA Astrophysics Data System (ADS)

    Chen, R. S.; Lu, C. Y.; Chen, K. H.; Chen, L. C.

    2009-12-01

    We report the strong molecular effects on the surface-dominant photoconductivity with high-gain transport in the polar GaN nanowires. Both the transient and steady-state photocurrents are sensitive and selective to the adsorptions of oxygen and hydrogen. The surface band bending of GaN nanowires is proposed to be effectively reduced or enhanced by oxygen or hydrogen, respectively, as a donorlike or acceptorlike surface state. The molecular effect, corroborated with the high-gain photoresponse nature of GaN nanowires is found to amplify the molecule-selective photocurrent signal by near three orders of magnitude higher than its counterpart in dark current. The molecule-tunable photoconductivity, as demonstrated here, would benefit a variety of applications, ranging from the high-gain optoelectronic devices, photoelectric energy transducer, as well as gas and chemical sensors.

  17. 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.

  18. 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.

  19. Measuring the internal energy content of molecules transported across the liquid-gas interface

    NASA Astrophysics Data System (ADS)

    Maselli, Olivia J.; Gascooke, Jason R.; Lawrance, Warren D.; Buntine, Mark A.

    2009-09-01

    Many details concerning the mechanism associated with the liberation of molecules from a liquid surface remain to be elucidated. We use the liquid microjet technique coupled with laser spectroscopy to measure the rotational and vibrational energy content of benzene spontaneously evaporating from a water-ethanol solution. These measurements provide molecular level insight into the mass and energy transfer processes associated with evaporation.

  20. 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.

  1. 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.

  2. Interaction of various gas molecules with paddle-wheel-type open metal sites of porous coordination polymers: theoretical investigation.

    PubMed

    Hijikata, Yuh; Sakaki, Shigeyoshi

    2014-03-01

    We theoretically evaluated binding energies (Eb's) between various gas molecules and the Cu center open metal site (Cu-OMS) of Cu paddle-wheel units, [Cu2(O2CR)4] (R = H, Me, or Ph) using density functional theory (DFT) and MP2-MP4. The optimized geometry of the model system [Cu2(O2CPh)4] agrees with the experimental structure. The Eb of CO with [Cu2(O2CH)4] is only slightly different between the open-shell singlet and triplet states. The calculated Eb decreases in the order MeNC > H2O > MeCN > C2H4 > C2H2 > CO > CO2 > N2 > CH4 > H2. The trend is discussed in terms of the electrostatic interaction energy (ES), exchange repulsion energy (EX), and charge-transfer (CT) + polarization (Pol) interaction energy at the Hartree-Fock level and the electron correlation effect. The ES increases linearly with an increase in Eb, while the EX decreases linearly with an increase in Eb. These relationships indicate that the ES compensates for the EX. In other words, the Eb does not depend on the sum of ES and EX, which corresponds to the static energy. The electron correlation effect contributes little to the above-mentioned decreasing order of Eb. The total Eb roughly increases with an increase in the CT+Pol term, suggesting that the CT+Pol term plays important roles in determining the trend of Eb. The shift of the stretching frequency of adsorbed gas molecules on the Cu-OMS is reproduced well by the DFT calculation with the model system [Cu2(O2CH)4(L)2] (L = gas molecule). We found that the positive charge on the Cu significantly contributes to the shift in the end-on coordination gas molecules such as CO, MeNC, MeCN, and N2. Although the shift has been generally discussed in terms of donation and back-donation, the present result indicates that the electrostatic potential field in the porous coordination polymer should be considered in the discussion of the frequency shift. PMID:24512503

  3. 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.

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

    PubMed

    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. PMID:27627388

  5. 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.

  6. Stability of metal organic frameworks and interaction of small gas molecules in these materials

    NASA Astrophysics Data System (ADS)

    Tan, Kui

    The work in this dissertation combines spectroscopy ( in-situ infrared absorption and Raman), powder X-ray diffraction and DFT calculations to study the stability of metal organic frameworks materials (MOFs) in the presence of water vapor and other corrosive gases (e.g., SO 2, NO2 NO), and the interaction and competitive co-adsorption of several gases within MOFs by considering two types of prototypical MOFs: 1) a MOF with saturated metal centers based on paddlewheel secondary building units: M(bdc)(ted)0.5 [M=Cu, Zn, Ni, Co, bdc = 1,4-benzenedicarboxylate, ted = triethylenediamine], and 2) a MOF with unsaturated metal centers: M2(dobdc) [M=Mg2+, Zn2+, Ni2+, Co2+ and dobdc = 2,5-dihydroxybenzenedicarboxylate]. We find that the stability of MOFs to water vapor critically depends on their structure and the specific metal cation in the building units. For M(bdc)(ted)0.5, the metal-bdc bond is the most vulnerable for Cu(bdc)(ted)0.5, while the metal-ted bond is first attacked for the Zn and Co analogs. In contrast, Ni(bdc)(ted)0.5 remains stable under the same conditions. For M2(dobdc), or MOF-74, the weak link is the dobdc-metal bond. The water molecule is dissociatively adsorbed at the metal-oxygen group with OH adsorption directly on the metal center and H adsorption on the bridging O of the phenolate group in the dobdc linker. Other technologically important molecules besides water, such as NO, NO2, SO2, tend to poison M2(dobdc) through dissociative or molecular adsorption onto the open metal sites. A high uptake SO2 capacity was measured in M(bdc)(ted)0.5, attributed to multipoint interactions between the guest SO2 molecule and the MOF host. In the case of competitive co-adsorption between CO2 and other small molecules, we find that binding energy alone is not a good indicator of molecular site occupation within the MOF (i.e., it cannot successfully predict and evaluate the displacement of CO2 by other molecules). Instead, we show that the kinetic barrier for the

  7. Half-quantum vortex molecules in a binary dipolar Bose gas.

    PubMed

    Shirley, Wilbur E; Anderson, Brandon M; Clark, Charles W; Wilson, Ryan M

    2014-10-17

    We study the ground state phases of a rotating two-component, or binary, Bose-Einstein condensate, wherein one component possesses a large permanent magnetic dipole moment. A variety of nontrivial phases emerge in this system, including a half-quantum vortex (HQV) chain phase and a HQV molecule phase, where HQVs bind at short distances. We attribute these phases to the development of a minimum in the HQV interaction potential, which emerges without coherent coupling or attractive interactions between the components. Thus, we show that the presence of dipolar interactions in this system provides a unique mechanism for the formation of HQV molecules and results in a rich ground state phase diagram. PMID:25361261

  8. Rotational excitation of hydrogen molecules by collisions with hydrogen atoms. [interstellar gas energetics

    NASA Technical Reports Server (NTRS)

    Green, S.; Truhlar, D. G.

    1979-01-01

    Rate constants for rotational excitation of hydrogen molecules by collisions with hydrogen atoms have been obtained from quantum-mechanical calculations for kinetic temperatures between 100 and 5000 K. These calculations involve the rigid-rotator approximation, but other possible sources of error should be small. The calculations indicate that the early values of Nishimura are larger than accurate rigid-rotator values by about a factor of 20 or more.

  9. Mössbauer spectroscopy of trimethyl tin halide molecules matrix-isolated in solid rare gas

    NASA Astrophysics Data System (ADS)

    Bukshpan, S.

    1991-02-01

    The study of matrix-isolated (CH 3) 3SnCl, (CH 3) 3SnBr and (CH 3) 3SnI reveals a tetrahedral molecular structure similar to the corresponding phenyl molecules. The results confirm that in the crystalline state of these compounds the tin atom is five-coordinated while in the matrix-isolated state the coordination number is four.

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

    DOE PAGESBeta

    Kierspel, Thomas; Wiese, Joss; Mullins, Terry; Robinson, Joseph; Aquila, Andy; Barty, Anton; Bean, Richard; Boll, Rebecca; Boutet, Sebastien; Bucksbaum, Philip; et al

    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

  11. 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.

  12. 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.

  13. Fluorescent turn-on sensing of bacterial lipopolysaccharide in artificial urine sample with sensitivity down to nanomolar by tetraphenylethylene based aggregation induced emission molecule.

    PubMed

    Jiang, Guoyu; Wang, Jianguo; Yang, Yang; Zhang, Guanxin; Liu, Yaling; Lin, He; Zhang, Guilan; Li, Yongdong; Fan, Xiaolin

    2016-11-15

    A tetraphenylethylene based aggregation induced emission (AIE) probe, TPEPyE, bearing a positively charged pyridinium pendant was designed and synthesized. The positively charged TPEPyE can efficiently bind to the negatively charged lipopolysaccharide (LPS) through electrostatic interactions between the two oppositely charged species. As a result, upon the addition of LPS into the PBS solution of TPEPyE, this probe aggregated immediately onto the surface of LPS and resulted over 22-fold of fluorescence enhancement. TPEPyE exhibited good selectivity and high sensitivity toward LPS in PBS buffer solution and the detection limit was calculated to be 370 pM (3.7ng/mL). More notably, TPEPyE also retained good sensitivity and selectivity in artificial urine system (with much higher ionic strength) with the detection limit down to nanomolar. Moreover, this probe can also make a distinction between gram-positive bacteria Staphylococcus aureus (S. aureus) and gram-negative bacteria Escherichia coli (E. coli), making it a promising sensor for clinical monitoring of urinary tract infections. PMID:27155117

  14. An Aggregation Advisor for Ligand Discovery.

    PubMed

    Irwin, John J; Duan, Da; Torosyan, Hayarpi; Doak, Allison K; Ziebart, Kristin T; Sterling, Teague; Tumanian, Gurgen; Shoichet, Brian K

    2015-09-10

    Colloidal aggregation of organic molecules is the dominant mechanism for artifactual inhibition of proteins, and controls against it are widely deployed. Notwithstanding an increasingly detailed understanding of this phenomenon, a method to reliably predict aggregation has remained elusive. Correspondingly, active molecules that act via aggregation continue to be found in early discovery campaigns and remain common in the literature. Over the past decade, over 12 thousand aggregating organic molecules have been identified, potentially enabling a precedent-based approach to match known aggregators with new molecules that may be expected to aggregate and lead to artifacts. We investigate an approach that uses lipophilicity, affinity, and similarity to known aggregators to advise on the likelihood that a candidate compound is an aggregator. In prospective experimental testing, five of seven new molecules with Tanimoto coefficients (Tc's) between 0.95 and 0.99 to known aggregators aggregated at relevant concentrations. Ten of 19 with Tc's between 0.94 and 0.90 and three of seven with Tc's between 0.89 and 0.85 also aggregated. Another three of the predicted compounds aggregated at higher concentrations. This method finds that 61 827 or 5.1% of the ligands acting in the 0.1 to 10 μM range in the medicinal chemistry literature are at least 85% similar to a known aggregator with these physical properties and may aggregate at relevant concentrations. Intriguingly, only 0.73% of all drug-like commercially available compounds resemble the known aggregators, suggesting that colloidal aggregators are enriched in the literature. As a percentage of the literature, aggregator-like compounds have increased 9-fold since 1995, partly reflecting the advent of high-throughput and virtual screens against molecular targets. Emerging from this study is an aggregator advisor database and tool ( http://advisor.bkslab.org ), free to the community, that may help distinguish between

  15. Generation, detection and characterization of gas-phase transition metal aggregates and compounds. Final technical report, September 15, 1991--July 14, 1994

    SciTech Connect

    Steimle, T.C.

    1994-11-12

    The goal of this research project has been to identify and characterize small gas-phase metal containing molecules and relate these properties to proposed reaction mechanisms. Of particular emphasis has been the elucidation of the mechanism for activation of C-H, N-H, S-H, and C-C bonds in CH{sub 4}, HCCH, H{sub 2}S and NH{sub 3} by platinum, titanium, molybdenum, and niobium.

  16. A triply interpenetrated microporous metal-organic framework for selective sorption of gas molecules.

    PubMed

    Chen, Banglin; Ma, Shengqian; Hurtado, Eric J; Lobkovsky, Emil B; Zhou, Hong-Cai

    2007-10-15

    A microporous metal-organic framework Zn(ADC)(4,4'-Bpe)(0.5).xG [1; ADC = 4,4'-azobenzenedicarboxylate, 4,4'-Bpe = trans-bis(4-pyridyl)ethylene, G = guest molecules] with a triply interpenetrative primitive cubic net was synthesized and characterized. With pores of about 3.4 x 3.4 A, the activated 1a exhibits highly selective sorption behavior toward H(2)/N(2), H(2)/CO, and CO(2)/CH(4). PMID:17854181

  17. 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.

  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. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules

    PubMed Central

    Hasty, Jeff; Tsimring, Lev

    2016-01-01

    The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems. PMID:27148743

  20. Greenhouse Gas Molecule CO2 Detection Using a Capacitive Micromachined Ultrasound Transducer.

    PubMed

    Barauskas, Dovydas; Pelenis, Donatas; Virzonis, Darius; Baltrus, John P; Baltrusaitis, Jonas

    2016-07-01

    We manufactured and tested a capacitive micromachined ultrasound transducer (CMUT)-based sensor for CO2 detection at environmentally relevant concentrations using polyethylenimine as a CO2 binding material. The assembly of a sensing chip was 10 × 20 mm, and up to 5 gases can potentially be detected simultaneously using a masking technique and different sensing materials. The limit of detection was calculated to be 0.033 CO2 vol % while the limit of quantification was calculated to be 0.102%. The sensor exhibited a linear response between 0.06% and 0.30% CO2 while concentrations close to those in flue gas can also be measured using dilution with inert gas. PMID:27321769

  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 Inter- and Intra-aggregate Pore Space on the Soil-Gas Diffusivity Behavior in Unsaturated, Undisturbed Volcanic Ash Soils

    NASA Astrophysics Data System (ADS)

    Resurreccion, A. C.; Kawamoto, K.; Komatsu, T.; Moldrup, P.

    2006-12-01

    Volcanic ash soils (Andisols) have a unique dual porosity structure that results in good drainage and high soil- water retention. Despite of the complicated and highly developed soil structure, recent studies have reported a simple, highly linear relation between the soil-gas diffusion coefficient, Dp, and the soil-air content, ɛ, for several Japanese Andisols. In this study, we explain the linear Dp(ɛ) behavior from the effects of the inter- and intra-aggregate pore-size distributions. We couple the bimodal van Genuchten soil-water retention model with a general Dp(ɛ) model, ɛ^{X}, allowing the tortuosity- connectivity factor X to vary with pF (= log(-ψ; the soil-water matric potential in cm H2O)). Measured data suggest that the tortuosity-connectivity parameter X is at the minimum at pF 3 (where X ~ 2, following Buckingham, 1904), equal to the water retention point where a separation of inter- and intra-aggregate effects on Dp is observed. At pF < 3, the X values increased as pF decreased because of inactive/remote air-filled pore space entrapped by the inter-connected water films between inter-aggregate pore spaces. At pF > 3, X increased to a high value at very dry conditions due to remote air-filled space inside the intra-aggregate pores. By combining the complex dual porosity soil-water retention model with the power- law gas diffusivity model using a parabolic X(pF) function, the surprisingly simple linear behavior of Dp with ɛ was captured while the variation of Dp with pF followed a dual s-shaped curve similar to the water retention curve. A simple linear model to predict Dp(ɛ) is suggested, with slope C and threshold soil-air content, ɛth, calculated from the power-law model ɛ^{X} at pF 2 (near field capacity) and at pF 4.1 (near wilting point) using the same X value (= 2.3) at both pF in agreement with measured data. This linear Dp(ɛ) model performed better, especially at dry conditions, compared to the traditionally-used predictive models when

  3. 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

  4. Chemical reactions between cold trapped Ba+ ions and neutral molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Roth, B.; Offenberg, D.; Zhang, C. B.; Schiller, S.

    2008-10-01

    Using a laser-cooled ion trapping apparatus, we have investigated laser-induced chemical reactions between cold trapped Ba+ ions and several neutral molecular gases at room temperature, O2 , CO2 , and N2O , leading to the production of cold trapped (≈20mK) BaO+ ions. The BaO+ ions were converted back to Ba+ ions via reaction with room-temperature CO. Reaction rates were determined by employing molecular dynamics simulations. The cold mixed-species ion ensembles produced were used for studying the efficiency of sympathetic cooling, by variation of the ratio of laser-cooled to sympathetically cooled ion numbers. In one extreme case, 20 laser-cooled Ba+138 ions were capable of maintaining the translational temperature of 120 sympathetically cooled barium isotopes (Ba+135-137) and 430 Ba16138O+ molecules at approximately 25mK .

  5. 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.

  6. Post-translational modification in the gas phase: mechanism of cysteine S-nitrosylation via ion-molecule reactions

    PubMed Central

    Osburn, Sandra; O'Hair, Richard A.J.; Black, Stephen M.; Ryzhov, Victor

    2013-01-01

    The gas-phase mechanism of S-nitrosylation of thiols was studied in a quadrupole ion trap mass spectrometer. This was done via ion-molecule reactions of protonated cysteine and many of its derivatives and other thiol ions with neutral tert-butyl nitrite or nitrous acid. Our results showed that the presence of the carboxylic acid functional group, –COOH, in the vicinity of the thiol group is essential for the gas-phase nitrosylation of thiols. When the carboxyl proton is replaced by a methyl group (cysteine methyl ester) no nitrosylation was observed. Other thiols lacking a carboxylic acid functional group displayed no S-nitrosylation, strongly suggesting that the carboxyl hydrogen plays a key role in the nitrosylation process. These results are in excellent agreement with a solution-phase mechanism proposed by Stamler et al. (J. S. Stamler, E. J. Toone, S. A. Lipton, N. J. Sucher. Neuron 1997, 18, 691–696) who suggested a catalytic role for the carboxylic acid group adjacent to cysteine residues and with later additions by Ascenzi et al. (P. Ascenzi, M. Colasanti, T. Persichini, M. Muolo, F. Polticelli, G. Venturini, D. Bordo, M. Bolognesi. Biol. Chem. 2000, 381, 623–627) who postulated that the presence of the carboxyl in the cysteine microenvironment in proteins is crucial for S-nitrosylation. A concerted mechanism for the gas-phase S-nitrosylation was proposed based on our results and was further studied using theoretical calculations. Our calculations showed that this proposed pathway is exothermic by 44.0 kJ mol−1. This is one of the few recent examples when a gas-phase mechanism matches one in solution. PMID:22006383

  7. Post-translational modification in the gas phase: mechanism of cysteine S-nitrosylation via ion-molecule reactions.

    PubMed

    Osburn, Sandra; O'Hair, Richard A J; Black, Stephen M; Ryzhov, Victor

    2011-11-15

    The gas-phase mechanism of S-nitrosylation of thiols was studied in a quadrupole ion trap mass spectrometer. This was done via ion-molecule reactions of protonated cysteine and many of its derivatives and other thiol ions with neutral tert-butyl nitrite or nitrous acid. Our results showed that the presence of the carboxylic acid functional group, -COOH, in the vicinity of the thiol group is essential for the gas-phase nitrosylation of thiols. When the carboxyl proton is replaced by a methyl group (cysteine methyl ester) no nitrosylation was observed. Other thiols lacking a carboxylic acid functional group displayed no S-nitrosylation, strongly suggesting that the carboxyl hydrogen plays a key role in the nitrosylation process. These results are in excellent agreement with a solution-phase mechanism proposed by Stamler et al. (J. S. Stamler, E. J. Toone, S. A. Lipton, N. J. Sucher. Neuron 1997, 18, 691-696) who suggested a catalytic role for the carboxylic acid group adjacent to cysteine residues and with later additions by Ascenzi et al. (P. Ascenzi, M. Colasanti, T. Persichini, M. Muolo, F. Polticelli, G. Venturini, D. Bordo, M. Bolognesi. Biol. Chem. 2000, 381, 623-627) who postulated that the presence of the carboxyl in the cysteine microenvironment in proteins is crucial for S-nitrosylation. A concerted mechanism for the gas-phase S-nitrosylation was proposed based on our results and was further studied using theoretical calculations. Our calculations showed that this proposed pathway is exothermic by 44.0 kJ mol(-1). This is one of the few recent examples when a gas-phase mechanism matches one in solution. PMID:22006383

  8. 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.

  9. 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.

  10. Weighted aggregation

    NASA Technical Reports Server (NTRS)

    Feiveson, A. H. (Principal Investigator)

    1979-01-01

    The use of a weighted aggregation technique to improve the precision of the overall LACIE estimate is considered. The manner in which a weighted aggregation technique is implemented given a set of weights is described. The problem of variance estimation is discussed and the question of how to obtain the weights in an operational environment is addressed.

  11. 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

    2015-08-01

    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. PMID:26141277

  12. Kohn-Sham approach to Fermi gas superfluidity: The bilayer of fermionic polar molecules

    NASA Astrophysics Data System (ADS)

    Ancilotto, Francesco

    2016-05-01

    By using a well-established "ab initio" theoretical approach developed in the past to quantitatively study the superconductivity of condensed matter systems, based on the Kohn-Sham density functional theory, I study the superfluid properties and the BCS-BEC crossover of two parallel bi-dimensional layers of fermionic dipolar molecules, where the pairing mechanism leading to superfluidity is provided by the interlayer coupling between dipoles. The finite temperature superfluid properties of both the homogeneous system and one where the fermions in each layer are confined by a square optical lattice are studied at half filling conditions, and for different values of the strength of the confining optical potential. The T = 0 results for the homogeneous system are found to be in excellent agreement with diffusion Monte Carlo results. The superfluid transition temperature in the BCS region is found to increase, for a given interlayer coupling, with the strength of the confining optical potential. A transition occurs at sufficiently small interlayer distances, where the fermions becomes localized within the optical lattice sites in a square geometry with an increased effective lattice constant, forming a system of localized composite bosons. This transition should be signaled by a sudden drop in the superfluid fraction of the system.

  13. 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.

  14. Gas-phase ion-molecule reactions of small nitroalkanes and their deprotonated anions.

    PubMed

    Kato, Shuji; Carrigan, Kathleen E; DePuy, Charles H; Bierbaum, Veronica M

    2004-01-01

    Gas-phase reactions of nitromethane (1), nitroethane (2), 2-nitropropane (3), 2-methyl-2-nitropropane (4) and nitrocyclopropane (5) were studied at 300 K using the flowing afterglow technique. These nitroalkanes react with gas-phase bases HO(-), CH(3)O(-) and HOO(-) very rapidly with rate coefficients of (2.5-4.3) x 10(-9) cm(3) s(-1) and reaction efficiencies of 60-100%, for example, k = 3.2 x 10(-9) cm(3) s(-1) (86%) for 5 reacting with hydroperoxide anion. Proton transfer (PT) is the only reaction observed for 1 while elimination (E2) is the exclusive pathway for 4 yielding isobutene and NO(2)(-). Both PT and E2 reactions are observed for 2, 3 and 5, the former being the major pathway. Deprotonated anions of 1, 2, 3 and 5 were subjected to reactivity studies with CH(3)I, CO(2), CS(2) and SO(2). Nucleophilic substitution (S(N)2) reaction occurs with CH(3)I while characteristic products CS(2)O(-) and SO(3)(-) are formed from CS(2) and SO(2), respectively, along with competing adduct formation. The SN(2) rate is greater, whereas the reactivities with the triatomic reagents are smaller for deprotonated nitrocyclopropane than for the other acyclic anions. These observations strongly suggest that the reactions of nitroalkane [M - H](-) anions occur through initial attack from the terminal oxygen; the nitrocyclopropane carbanion is more strained and, thus, less stabilized by resonance [R(2)C(-) - NO2 <--> R(2)=NO(2)(-)] resulting in the greater basicity/nucleophilicy and the less negative charge on the oxygen site. PMID:15103100

  15. H-bonding of an NH3 gas molecule to H2O/Pt(111) — A barrier-free path

    NASA Astrophysics Data System (ADS)

    Henkelman, Graeme; Feibelman, Peter J.

    2016-02-01

    Does an OH-flipping barrier hinder H-bond formation between a gas phase molecule and a water monolayer whose free OH ligands point toward a substrate? According to density functional theory calculations for water on Pt(111) the answer is yes, when the molecule is CO or N2, but no when it is NH3. The difference is the relatively strong attraction of the NH3 lone pair to free OH ligands.

  16. 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.

  17. 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.

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

    DOE PAGESBeta

    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

  19. 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

  20. Ion Molecule Reactions of Gas-Phase Chromium Oxyanions:CrxOyHz- + O2

    SciTech Connect

    Anita K. Gianotto; Brittany D. M. Hodges; Peter de B. Harrington; Anthony Appelhans; John E. Olson; Gary S. Groenewold

    2003-10-01

    Chromium oxyanions, CrxOyHz-, were generated in the gas-phase using a quadrupole ion trap secondary ion mass spectrometer (IT-SIMS), where they were reacted with O2. Only CrO2- of the Cr1OyHz- envelope was observed to react with oxygen, producing primarily CrO3-. The rate constant for the reaction of CrO2- with O2 was 38% of the Langevin collision constant at 310 K. CrO3-, CrO4-, and CrO4H- were unreactive with O2 in the ion trap. In contrast, Cr2O4- was observed to react with O2 producing CrO3- + CrO3 via oxidative degradation at a rate that was 15% efficient. The presence of background water facilitated the reaction of Cr2O4- + H2O to form Cr2O5H2-; the hydrated product ion Cr2O5H2- reacted with O2 to form Cr2O6- (with concurrent elimination of H2O) at a rate that was 6% efficient. Cr2O5- also reacted with O2 to form Cr2O7- (4% efficient) and Cr2O6- + O (2% efficient); these reactions proceeded in parallel. By comparison, Cr2O6- was unreactive with O2, and in fact, no further O2 addition could be observed for any of the Cr2O6Hz- anions. Generalizing, CrxOyHz- species that have low coordinate, low oxidation state metal centers are susceptible to O2 oxidation. However, when the metal coordination is >3, or when the formal oxidation state is =5, reactivity stops.

  1. Construction aggregates

    USGS Publications Warehouse

    Langer, W.H.; Tepordei, V.V.; Bolen, W.P.

    2000-01-01

    Construction aggregates consist primarily of crushed stone and construction sand and gravel. Total estimated production of construction aggregates increased in 1999 by about 2% to 2.39 Gt (2.64 billion st) compared with 1998. This record production level continued an expansion that began in 1992. By commodities, crushed stone production increased 3.3%, while sand and gravel production increased by about 0.5%.

  2. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1994-01-01

    Part of a special section on industrial minerals in 1993. The 1993 production of construction aggregates increased 6.3 percent over the 1992 figure, to reach 2.01 Gt. This represents the highest estimated annual production of combined crushed stone and construction sand and gravel ever recorded in the U.S. The outlook for construction aggregates and the issues facing the industry are discussed.

  3. Structural organization of surfactant aggregates in vacuo: a molecular dynamics and well-tempered metadynamics study.

    PubMed

    Longhi, Giovanna; Fornili, Sandro L; Turco Liveri, Vincenzo

    2015-07-01

    Experimental investigations using mass spectrometry have established that surfactant molecules are able to form aggregates in the gas phase. However, there is no general consensus on the organization of these aggregates and how it depends on the aggregation number and surfactant molecular structure. In the present paper we investigate the structural organization of some surfactants in vacuo by molecular dynamics and well-tempered metadynamics simulations to widely explore the space of their possible conformations in vacuo. To study how the specific molecular features of such compounds affect their organization, we have considered as paradigmatic surfactants, the anionic single-chain sodium dodecyl sulfate (SDS), the anionic double-chain sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and the zwitterionic single-chain dodecyl phosphatidyl choline (DPC) within a wide aggregation number range (from 5 to 100). We observe that for low aggregation numbers the aggregates show in vacuo the typical structure of reverse micelles, while for large aggregation numbers a variety of globular aggregates occur that are characterized by the coexistence of interlaced domains formed by the polar or ionic heads and by the alkyl chains of the surfactants. Well-tempered metadynamics simulations allows us to confirm that the structural organizations obtained after 50 ns of molecular dynamics simulations are practically the equilibrium ones. Similarities and differences of surfactant aggregates in vacuo and in apolar media are also discussed. PMID:26050747

  4. 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 ...

  5. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  6. Radial diffusion and penetration of gas molecules and aerosol particles through laminar flow reactors, denuders, and sampling tubes.

    PubMed

    Knopf, Daniel A; Pöschl, Ulrich; Shiraiwa, Manabu

    2015-04-01

    Flow reactors, denuders, and sampling tubes are essential tools for many applications in analytical and physical chemistry and engineering. We derive a new method for determining radial diffusion effects and the penetration or transmission of gas molecules and aerosol particles through cylindrical tubes under laminar flow conditions using explicit analytical equations. In contrast to the traditional Brown method [Brown, R. L. J. Res. Natl. Bur. Stand. (U. S.) 1978, 83, 1-8] and CKD method (Cooney, D. O.; Kim, S. S.; Davis, E. J. Chem. Eng. Sci. 1974, 29, 1731-1738), the new approximation developed in this study (known as the KPS method) does not require interpolation or numerical techniques. The KPS method agrees well with the CKD method under all experimental conditions and also with the Brown method at low Sherwood numbers. At high Sherwood numbers corresponding to high uptake on the wall, flow entry effects become relevant and are considered in the KPS and CKD methods but not in the Brown method. The practical applicability of the KPS method is demonstrated by analysis of measurement data from experimental studies of rapid OH, intermediate NO3, and slow O3 uptake on various organic substrates. The KPS method also allows determination of the penetration of aerosol particles through a tube, using a single equation to cover both the limiting cases of high and low deposition described by Gormley and Kennedy (Proc. R. Ir. Acad., Sect. A. 1949, 52A, 163-169). We demonstrate that the treatment of gas and particle diffusion converges in the KPS method, thus facilitating prediction of diffusional loss and penetration of gases and particles, analysis of chemical kinetics data, and design of fluid reactors, denuders, and sampling lines. PMID:25744622

  7. The gas phase ion/molecule chemistry of four carbanions generated from vinylene carbonate and its methyl and dimethyl derivatives

    NASA Astrophysics Data System (ADS)

    Robinson, Marin S.; Breitbeil, Fred W.

    1992-09-01

    The gas phase ion/molecule chemistry of four carbanions generated by the reaction of vinylene carbonate, and its methyl and dimethyl derivatives with hydroxide ion has been investigated. From the parent the sole product is the ketenyl anion, HC[triple bond; length as m-dash]C---O-, arising from vinylic proton abstraction and loss of CO2. From the dimethyl derivative, abstraction of an allylic proton from one of the methyl groups followed by loss of CO2 leads exclusively to CH2=CC(O)CH3. Both pathways are observed for the monomethyl derivative, leading to a mixture of the ions CH3C[triple bond; length as m-dash]C---O- and CH2=CCHO. The ketenyl and methyl ketenyl ions do not exchange hydrogen for deuterium with D2O or CH3OD, but they do react with CS2 and COS to form the corresponding thioketenyl anions, HC[triple bond; length as m-dash]C---S- and CH3C=C---S-. The ions CH2=CC(O)CH3 and CH2=CCHO exchange one and three hydrogen atoms for deuterium atoms with D2O respectively, and react with CS2 to form thioketenyl anions by addition and loss of thioformaldehyde. Possible mechanisms for these reactions are discussed.

  8. Volume shrinkage of a metal-organic framework host induced by the dispersive attraction of guest gas molecules.

    PubMed

    Joo, Jaeyong; Kim, Hyungjun; Han, Sang Soo

    2013-11-21

    Using a density functional theory calculation including van der Waals (vdW) corrections, we report that H2 adsorption in a cubic-crystalline microporous metal-organic framework (MOF-5) leads to volume shrinkage, which is in contrast to the intuition that gas adsorption in a confined system (e.g., pores in a material) increases the internal pressure and then leads to volumetric expansion. This extraordinary phenomenon is closely related to the vdW interactions between MOF and H2 along with the H2-H2 interaction, rather than the Madelung-type electrostatic interaction. At low temperatures, H2 molecules adsorbed in the MOF-5 form highly symmetrical interlinked nanocages that change from a cube-like shape to a sphere-like shape with H2 loading, helping to exert centrosymmetric forces and hydrostatic (volumetric) stresses from the collection of dispersive interactions. The generated internal negative stress is sufficient to overcome the stiffness of the MOF-5 which is a soft material with a low bulk modulus (15.54 GPa). PMID:24072185

  9. Mechanism of charge transfer and its impacts on Fermi-level pinning for gas molecules adsorbed on monolayer WS{sub 2}

    SciTech Connect

    Zhou, Changjie; Zhu, Huili; Yang, Weihuang

    2015-06-07

    Density functional theory calculations were performed to assess changes in the geometric and electronic structures of monolayer WS{sub 2} upon adsorption of various gas molecules (H{sub 2}, O{sub 2}, H{sub 2}O, NH{sub 3}, NO, NO{sub 2}, and CO). The most stable configuration of the adsorbed molecules, the adsorption energy, and the degree of charge transfer between adsorbate and substrate were determined. All evaluated molecules were physisorbed on monolayer WS{sub 2} with a low degree of charge transfer and accept charge from the monolayer, except for NH{sub 3}, which is a charge donor. Band structure calculations showed that the valence and conduction bands of monolayer WS{sub 2} are not significantly altered upon adsorption of H{sub 2}, H{sub 2}O, NH{sub 3}, and CO, whereas the lowest unoccupied molecular orbitals of O{sub 2}, NO, and NO{sub 2} are pinned around the Fermi-level when these molecules are adsorbed on monolayer WS{sub 2}. The phenomenon of Fermi-level pinning was discussed in light of the traditional and orbital mixing charge transfer theories. The impacts of the charge transfer mechanism on Fermi-level pinning were confirmed for the gas molecules adsorbed on monolayer WS{sub 2}. The proposed mechanism governing Fermi-level pinning is applicable to the systems of adsorbates on recently developed two-dimensional materials, such as graphene and transition metal dichalcogenides.

  10. 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

  11. 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.

  12. 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

    2016-01-01

    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

  13. Selective detection of toxic cyanogen gas in the presence of O2, and H2O molecules using a AlN nanocluster

    NASA Astrophysics Data System (ADS)

    Solimannejad, Mohammad; Kamalinahad, Saeedeh; Shakerzadeh, Ehsan

    2016-08-01

    The interaction of cyanogen molecule with Al12N12 nanocage has been studied using density functional theory (DFT) at CAM-B3LYP/6-31+G(d) level. Geometric, electronic structure and natural bond orbitals (NBO) analysis display that adsorption of cyanogen onto exterior surface of Al12N12 is physisorption with adsorption energy (Eads) equal to -55.36 kJ/mol. UV-vis study shows a high intensity peak in 388.9 nm due to interaction of gas with nanocage. It is expected that Al12N12 will be used in designing novel materials for potential applications to detect toxic cyanogen molecule.

  14. Supramolecular aggregates in vacuum: positively monocharged sodium alkanesulfonate clusters.

    PubMed

    Bongiorno, David; Ceraulo, Leopoldo; Giorgi, Gianluca; Indelicato, Serena; Ruggirello, Angela; Turco Liveri, Vincenzo

    2010-01-01

    The formation and structural features of positively monocharged aggregates of sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and sodium methane--(MetS), butane--(ButS) and octane--(OctS) sulfonate molecules in gas phase have been investigated by electrospray ionization mass spectrometry, energy resolved mass spectrometry and density functional theory (DFT) calculations. The experimental results show that the center-of-mass collision energy required to dissociate 50% of these monocharged aggregates scantly depends on the length of the alkyl chain as well as on the aggregation number. This, together with the large predominance of monocharged species in the mass spectra, was rationalized in terms of an aggregation pattern mainly driven by the counter ions and head groups electrostatic interactions while minor effects were attributed to the steric hindrance caused by the size of the surfactant head group and alkyl chain. DFT calculations show that the most favoured structural arrangement of these aggregates is always characterized by an internal polar core constituted by the sodium counter ions and surfactant head groups surrounded by an external layer composed by the surfactant alkyl chains. PMID:20065519

  15. Gas-phase ion-molecule reactions for resolution of atomic isobars: AMS and ICP-MS perspectives

    NASA Astrophysics Data System (ADS)

    Bandura, Dmitry R.; Baranov, Vladimir I.; Litherland, A. E.; Tanner, Scott D.

    2006-09-01

    Ion-molecule reactions that can be used for resolution of spectral overlaps of long-lived or stable (T1/2 > 100 years) atomic isobars on the long-lived radio-isotopes (100 < T1/2 < 1012 years) in mass spectrometry are considered. Results for the separations of isobaric overlaps via cation reactions with NO, N2O, O2, CO2, C2H2, CH3F studied with the Inductively Coupled Plasma Dynamic Reaction Cell(TM) Mass Spectrometer (ICP-DRC(TM)-MS) with use of stable isotopes are presented. Overview of potential and reported reactions for separation of 35 isobars is given. Potential for the following isobaric pairs separation is shown (reaction gas and the extent of separation achieved to date in parenthesis): 32Si+/32S+(NO, 5 x 104), 40K+/40Ar+(N2O, 1.9 x 103), 40K+/40Ca+(N2O, 50), 59Ni+/59Co+(N2O, 6), 79Se+/79Br+(O2, 7.2 x 103), 81Kr+/81Br+(C2H2, 1.5 x 104), 93Mo+/93Nb+(N2O, 100), 93Mo+/93Zr+(N2O, 150), 135Cs+/135Ba+(N2O, 8 x 104), 137,138La+/137,138Ba+(O2, 40), 146Sm+/146Nd+(CO2, 1.5 x 105), 176Lu+/176Hf+(NO, 2.8 x 103), 187Re+/187Os+(N2O, 2.8 x 104). Effect of instrumental parameters on reactivity is discussed. The relevance of this work to accelerator mass spectrometry is discussed briefly.

  16. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1993-01-01

    Part of a special section on the market performance of industrial minerals in 1992. Production of construction aggregates increased by 4.6 percent in 1992. This increase was due, in part, to the increased funding for transportation and infrastructure projects. The U.S. produced about 1.05 Gt of crushed stone and an estimated 734 Mt of construction sand and gravel in 1992. Demand is expected to increase by about 5 percent in 1993.

  17. 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.

  18. 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.

  19. 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

  20. Ion-Molecule Reaction of Gas-Phase Chromium Oxyanions: CrxOyHz- + H2O

    SciTech Connect

    Gianotto, Anita Kay; Hodges, Brittany DM; Benson, Michael Timothy; Harrington, Peter Boves; Appelhans, Anthony David; Olson, John Eric; Groenewold, Gary Steven

    2003-08-01

    Chromium oxyanions having the general formula CrxOyHz- play a key role in many industrial, environmental, and analytical processes, which motivated investigations of their intrinsic reactivity. Reactions with water are perhaps the most significant, and were studied by generating CrxOyHz- in the gas phase using a quadrupole ion trap secondary ion mass spectrometer. Of the ions in the Cr1OyHz envelope (y = 2, 3, 4; z = 0, 1), only CrO2- was observed to react with H2O, producing the hydrated CrO3H2- at a slow rate (~0.07% of the ion-molecule collision constant at 310 K). CrO3-, CrO4-, and CrO4H- were unreactive. In contrast, Cr2O4-, Cr2O5-, and Cr2O5H2- displayed a considerable tendency to react with H2O. Cr2O4- underwent sequential reactions with H2O, initially producing Cr2O5H2- at a rate that was ~7% efficient. Cr2O5H2- then reacted with a second H2O by addition to form Cr2O6H4- (1.8% efficient) and by OH abstraction to form Cr2O6H3- (0.6% efficient). The reactions of Cr2O5- were similar to those of Cr2O5H2-: Cr2O5- underwent addition to form Cr2O6H2- (3% efficient) and OH abstraction to form Cr2O6H- (<1% efficient). By comparison, Cr2O6- was unreactive with H2O, and in fact, no further H2O addition could be observed for any of the Cr2O6Hz- anions. Hartree-Fock ab initio calculations showed that reactive CrxOyHz- species underwent nucleophilic attack by the incoming H2O molecules, which produced an initially formed adduct in which the water O was bound to a Cr center. The experimental and computational studies suggested that Cr2OyHz- species that have bi- or tricoordinated Cr centers are susceptible to attack by H2O; however, when the metal becomes tetracoordinate, reactivity stops. For the Cr2OyHz- anions the lowest energy structures all contained rhombic Cr2O2 rings with pendant O atoms and/or OH groups. The initially formed [Cr2Oy- + H2O] adducts underwent H rearrangement to a gem O atom to produce stable dihydroxy structures. The calculations indicated that

  1. Construction aggregates

    USGS Publications Warehouse

    Bolen, W.P.; Tepordei, V.V.

    2001-01-01

    The estimated production during 2000 of construction aggregates, crushed stone, and construction sand and gravel increased by about 2.6% to 2.7 Gt (3 billion st), compared with 1999. The expansion that started in 1992 continued with record production levels for the ninth consecutive year. By commodity, construction sand and gravel production increased by 4.5% to 1.16 Gt (1.28 billion st), while crushed stone production increased by 1.3% to 1.56 Gt (1.72 billion st).

  2. 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.

  3. The electronic spectrum of CUONg4 (Ng = Ne, Ar, Kr, Xe): New insights in the interaction of the CUO molecule with noble gas matrices

    NASA Astrophysics Data System (ADS)

    Tecmer, Paweł; van Lingen, Henk; Gomes, André Severo Pereira; Visscher, Lucas

    2012-08-01

    The electronic spectrum of the CUO molecule was investigated with the IHFSCC-SD (intermediate Hamiltonian Fock-space coupled cluster with singles and doubles) method and with TD-DFT (time-dependent density functional theory) employing the PBE and PBE0 exchange-correlation functionals. The importance of both spin-orbit coupling and correlation effects on the low-lying excited-states of this molecule are analyzed and discussed. Noble gas matrix effects on the energy ordering and vibrational frequencies of the lowest electronic states of the CUO molecule were investigated with density functional theory (DFT) and TD-DFT in a supermolecular as well as a frozen density embedding (FDE) subsystem approach. This data is used to test the suitability of the FDE approach to model the influence of different matrices on the vertical electronic transitions of this molecule. The most suitable potential was chosen to perform relativistic wave function theory in density functional theory calculations to study the vertical electronic spectra of the CUO and CUONg4 with the IHFSCC-SD method.

  4. 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. PMID:26523809

  5. Pine Pyrolysis Vapor Phase Upgrading Over ZSM-5 Catalyst: Effect of Temperature, Hot Gas Filtration, and Hydrogen Donor Molecule on the Rate of Deactivation of Catalyst

    SciTech Connect

    Mukarakate, C.; Zhang, X.; Nimlos, M.; Robichaud, D.; Donohoe, B.

    2013-01-01

    The conversion of primary vapors from pine pyrolysis over a ZSM-5 catalyst was characterized using a micro-reactor coupled to a molecular beam mass spectrometer (MBMS) to allow on-line measurement of the upgraded vapors. This micro-reacor-MBMS system was used to investigate the effects of hot gas filtration, temperature and hydrogen donor molecules on the rate of deactivation of the UPV2 catalyst. Our results show that the life of catalyst is significantly improved by using better filtration. Temperature had an effect on both product distribution and catalyst deactivation. The hydrogen donor molecules (HDM) used in this study show better reduction in catalyst deactivation rates at high temperatures.

  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. Ultracold polar KRb molecules

    NASA Astrophysics Data System (ADS)

    Neyenhuis, Brian; Chotia, Amodsen; Moses, Steven; Ye, Jun; Jin, Deborah

    2011-05-01

    Ultracold polar molecules in the quantum degenerate regime open the possibility of realizing quantum gases with long-range, and spatially anisotropic, interparticle interactions. Currently, we can create a gas of ultracold fermionic ground-state KRb molecules in with a peak density of 1012 cm-3 and a temperature just 1.4 times the Fermi temperature. We will report on efforts to further cool this gas of molecules. One possibility is to evaporatively cool a spin-polarized molecular Fermi gas confined in quasi-2D, where we would rely on dipole-dipole interactions for rethermalization. We acknowledge funding from NIST, NSF, and AFOSR-MURI.

  8. 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 Technical Reports Server (NTRS)

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

    1993-01-01

    A comparison is made of the stratospheric water vapor measurements made by the satellite sensors of the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus-7 LIMS, and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. It was found that, despite differences in the measurement techniques, sampling bias, and observational periods, the three experiments have disclosed a generally consistent pattern of stratospheric water vapor distribution. The only significant difference occurs at high southern altitudes in May below 18 km, where LIMS measurements were 2-3 ppmv greater than those of SAGE II and ATMOS.

  9. Determination of local concentration of H{sub 2}O molecules and gas temperature in the process of hydrogen - oxygen gas mixture heating by means of linear and nonlinear laser spectroscopy

    SciTech Connect

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

    2013-01-31

    Employing the methods of linear absorption spectroscopy and nonlinear four-wave mixing spectroscopy using laserinduced gratings we have simultaneously measured the local concentrations of H{sub 2}O molecules and the gas temperature in the process of the H{sub 2} - O{sub 2} mixture heating. During the measurements of the deactivation rates of pulsed-laser excited singlet oxygen O{sub 2} (b {sup 1}{Sigma}{sup +}{sub g}) in collisions with H{sub 2} 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, H{sub 2}O molecules are formed by 'dark' reactions of H{sub 2} with O{sub 2} 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 H{sub 2}O concentration in the O{sub 2} laser excitation volume, if the gas temperature in this volume is known. When studying the collisional deactivation of O{sub 2} (b {sup 1}{Sigma}{sup +}{sub g}) molecules, the necessary measurements of the local temperature can be implemented using laser-induced gratings, arising due to spatially periodic excitation of O{sub 2} (X{sup 3}{Sigma}{sup -}{sub g}) molecules to the b {sup 1}{Sigma}{sup +}{sub g} state by radiation of the pump laser of the four-wave mixing spectrometer. (laser spectroscopy)

  10. Fluorescent H-Aggregates Hosted by a Charged Cyclodextrin Cavity.

    PubMed

    Mudliar, Niyati H; Singh, Prabhat K

    2016-05-23

    Most macrocyclic host molecules, including cyclodextrins, usually prevent self-aggregation of the guest organic molecules, by exploiting inclusion complexation of the guest with the host. In this work, it was found that a negatively charged β-cylcodextrin derivative induces aggregation of a well-known amyloid sensing dye, Thioflavin-T, and leads to an unprecedented formation of the rarely observed emissive H-type aggregates of the dye. PMID:27028039

  11. 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

  12. Molecular Aggregation in Disodium Cromoglycate

    NASA Astrophysics Data System (ADS)

    Singh, Gautam; Agra-Kooijman, D.; Collings, P. J.; Kumar, Satyendra

    2012-02-01

    Details of molecular aggregation in the mesophases of the anti-asthmatic drug disodium cromoglycate (DSCG) have been studied using x-ray synchrotron scattering. The results show two reflections, one at wide angles corresponding to π-π stacking (3.32 å) of molecules, and the other at small angles which is perpendicular to the direction of molecular stacking and corresponds to the distance between the molecular aggregates. The latter varies from 35 - 41 å in the nematic (N) phase and 27 -- 32 å in the columnar (M) phase. The temperature evolution of the stack height, positional order correlations in the lateral direction, and orientation order parameter were determined in the N, M, and biphasic regions. The structure of the N and M phases and the nature of the molecular aggregation, together with their dependence on temperature and concentration, will be presented.

  13. Kinetics of disilane molecule decomposition on the growth surface of silicon in vacuum gas-phase epitaxy reactors

    NASA Astrophysics Data System (ADS)

    Orlov, L. K.; Smyslova, T. N.

    2012-11-01

    The range of the characteristic decomposition rates of dihydride molecule radicals adsorbed by the silicon surface in the temperature interval 450-700°C is experimentally found for a number of kinetic models. A relationship between the rate of silicon atom incorporation into a growing crystal and the characteristic rate of disilane molecule pyrolysis on the silicon surface is found. The temperature dependence of the rate of disilane fragment decomposition on the silicon surface is nonmonotonic, and its run depends on temperature conditions. It is shown that the temperature dependence of the molecular decomposition rate on the growth surface is described by a superposition of two activation curves with various activation energies. The activation energies depend on the peculiarity of interaction between the molecular beam and the silicon surface when the filling of surface states with hydrogen is low and high.

  14. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation. PMID:27264846

  15. 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)

  16. 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}.

  17. Gas-phase ion-molecule reactions: a model for the determination of biologically reactive electrophilic contaminants in the environment.

    PubMed

    Freeman, J A; Johnson, J V; Yost, R A; Kuehl, D W

    1994-06-01

    A promising instrumental technique has been investigated to rapidly screen complex environmental samples for chemical contaminants having the propensity to covalently bond to biomacromolecules such as DNA. Radical molecular ions of pyridine, a model compound for nucleophilic bases of DNA, were mass-selected and allowed to react with electrophilic environmental contaminants in the collision cell of a triple quadrupole mass spectrometer. Analytes were introduced into the collision cell via a gas chromatographic column. Reactive chemicals are then characterized by scanning Q3 to identify associative reaction products. A good qualitative correlation was observed for the gas-phase reactivity of a series of electrophilic reagents with both their alkylating reactivity in solution (4-(4-nitrobenzyl)pyridine) and AMES test mutagenicity which had been previously published. Femtomole limits of detection for specific associative reaction products were demonstrated. Gas-phase reactions of ions of environmental contaminants (introduced into the source) with neutral pyridine (in the collision cell) were also investigated. Reactions of the radical molecular ion of the allyl reagents with neutral pyridine were similar to results from the mass-selected reaction of the pyridine radical molecular ion with neutral allylic reagents. PMID:8030792

  18. BRIEF COMMUNICATIONS: Investigation of the vibrational relaxation of CO2 molecules in a heterogeneous gas-cluster system

    NASA Astrophysics Data System (ADS)

    Vostrikov, A. A.; Mironov, S. G.; Rebrov, A. K.; Semyachkin, B. E.

    1981-06-01

    An investigation was made of the relaxation of monomers and clusters of carbon dioxide excited in a glow discharge maintained in a condensing supersonic free jet. Measurements were made of the intensity of the output radiation emitted from the 001 vibrational level of the CO2 molecule in a band at 4.3 μ, and also of the intensity and energy of the molecular beam. It was found that the relaxation of the excited monomers as a result of their collisions with clusters occurred at a rate much higher than the rate of VT relaxation in the gaseous phase, and it increased on increase in the average size of the cluster. The clusters which have received the excitation energy directly from the discharge and indirectly from monomers were found to lose this energy with time: in ≲1 msec the excitation was converted into heat and this resulted in partial evaporation of the clusters.

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

    SciTech Connect

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

    2014-07-21

    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.

  20. 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. PMID:26313978

  1. 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

  2. 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

  3. Theoretical predictions of the spectroscopic parameters in noble-gas molecules: HXeOH and its complex with water.

    PubMed

    Cukras, Janusz; Sadlej, Joanna

    2011-09-14

    We employ state-of-the-art methods and basis sets to study the effect of inserting the Xe atom into the water molecule and the water dimer on their NMR parameters. Our aim is to obtain predictions for the future experimental investigation of novel xenon complexes by NMR spectroscopy. Properties such as molecular structure and energetics have been studied by supermolecular approaches using HF, MP2, CCSD, CCSD(T) and MP4 methods. The bonding in HXeOH···H(2)O complexes has been analyzed by Symmetry-Adapted Perturbation Theory to provide the intricate insight into the nature of the interaction. We focus on vibrational spectra, NMR shielding and spin-spin coupling constants-experimental signals that reflect the electronic structures of the compounds. The parameters have been calculated at electron-correlated and Dirac-Hartree-Fock relativistic levels. This study has elucidated that the insertion of the Xe atom greatly modifies the NMR properties, including both the electron correlation and relativistic effects, the (129)Xe shielding constants decrease in HXeOH and HXeOH···H(2)O in comparison to Xe atom; the (17)O, as a neighbour of Xe, is deshielded too. The HXeOH···H(2)O complex in its most stable form is stabilized mainly by induction and dispersion energies. PMID:21804992

  4. Experimental and theoretical study on gas-phase ion/molecule reactions of silver trimer cation, Ag{sub 3}{sup +}, with 12-crown-4

    SciTech Connect

    Kumondai, Kousuke; Toyoda, Michisato; Ishihara, Morio; Katakuse, Itsuo; Takeuchi, Takae; Ikeda, Mai; Iwamoto, Kenichi

    2005-07-08

    The reaction mechanisms of silver trimer cation, Ag{sub 3}{sup +}, with 12-crown-4 (12C4) were studied experimentally and theoretically. Using a cylindrical ion trap time-of-flight mass spectrometer, gas-phase ion/molecule reactions of Ag{sub 3}{sup +} with 12C4 were observed. Metal-ligand complexes of [Ag(12C4)]{sup +}, [Ag{sub 3}(12C4)]{sup +} and [Ag{sub 3}(12C4){sub 2}]{sup +}, and of [Ag(12C4){sub 2}]{sup +} and [Ag{sub 3}(12C4){sub 3}]{sup +}, were observed as the reaction intermediates and terminal products, respectively. The formations of the [Ag(12C4)]{sup +} and [Ag(12C4){sub 2}]{sup +} complexes indicated that the neutral dimer (Ag{sub 2}) had been eliminated from the trimer cation. From the results of ab initio calculations at the HF/LanL2DZ level of theory and the experiments, it is suggested that three 12C4 molecules can attach to Ag{sub 3}{sup +} through consecutive reactions and that neutral Ag{sub 2} can be easily eliminated from [Ag{sub 3}(12C4)]{sup +}.

  5. Vibrational effects in a weakly-interacting quantum solvent: The CO molecule in 4He gas and in 4He droplets

    NASA Astrophysics Data System (ADS)

    Paesani, F.; Gianturco, F. A.

    2002-06-01

    The coupling between the intermolecular motion and the internal vibrational coordinate in the He-CO system is computed at the post-Hartree-Fock level using the DFT+DISP model already employed by us for similar systems and reviewed here in the main text. The quality of the computation of such weak effects is compared with other, earlier model calculations and then used for the evaluation of the vibrational relaxation cross sections of the CO molecule diluted in 4He gas. A further assessment of the vibrational coupling is carried out by computing, with a stochastic approach that employs the Diffusion Monte Carlo method, the effects on the vibrational frequency of the CO impurity from its immersion in 4He droplets of variable size. Both sets of results are analyzed and discussed to gauge the reliability of the computed coupling vis-a-vis one of those suggested by earlier calculations. This study provides further evidence on the difficulty of quantitatively obtaining from calculations the extremely small effects connected with molecular vibrational features in this system and caused by the weak interaction between the title molecule and a quantum solvent like 4He.

  6. Collisional properties of cold spin-polarized nitrogen gas: Theory, experiment, and prospects as a sympathetic coolant for trapped atoms and molecules

    SciTech Connect

    Tscherbul, T. V.; Dalgarno, A.; Klos, J.; Zygelman, B.; Pavlovic, Z.; Hummon, M. T.; Lu, H.-I.; Tsikata, E.; Doyle, J. M.

    2010-10-15

    We report a combined experimental and theoretical study of collision-induced dipolar relaxation in a cold spin-polarized gas of atomic nitrogen (N). We use buffer gas cooling to create trapped samples of {sup 14}N and {sup 15}N atoms with densities (5{+-}2)x10{sup 12} cm{sup -3} and measure their magnetic relaxation rates at milli-Kelvin temperatures. These measurements, together with rigorous quantum scattering calculations based on accurate ab initio interaction potentials for the {sup 7}{Sigma}{sub u}{sup +} electronic state of N{sub 2} demonstrate that dipolar relaxation in N+N collisions occurs at a slow rate of {approx}10{sup -13} cm{sup 3}/s over a wide range of temperatures (1 mK to 1 K) and magnetic fields (10 mT to 2 T). The calculated dipolar relaxation rates are insensitive to small variations of the interaction potential and to the magnitude of the spin-exchange interaction, enabling the accurate calibration of the measured N atom density. We find consistency between the calculated and experimentally determined rates. Our results suggest that N atoms are promising candidates for future experiments on sympathetic cooling of molecules.

  7. The detection of optical asymmetry in biogenic molecules by gas chromatography for extraterrestrial space exploration: sample processing studies.

    PubMed

    Pollock, G E; Miyamoto, A K; Oyama, V I

    1970-01-01

    Life detection instrumentation proposed for space missions is necessarily based on fundamental properties of life as we know it. Most biological life detection experiments attempt to elicit biological activity such as metabolism, growth, or reproduction. In addition to these approaches, which could be definitive, it is desirable to attack the problem of life detection as depending on some chemical attribute, since it may be most difficult to elicit a biological response. Fortunately, the property of natural optical activity in organics is synonymous with life, and can be measured by physicochemical methods. The phenomenon of optical activity arising from the selection of one of two possible isomers in living systems has been explained previously. Its detection in extraterrestrial samples would be prima facie evidence for the existence of life. For this reason, among others, gas chromatographic methods for the detection of optical asymmetry have been investigated and developed in recent years. We have preferred the diastereomeric route using (+)-2-butyl derivatives of amino acids and recently we have successfully made and separated derivatives of carbohydrates from glyceraldehyde through some hexoses. A scheme for isolating, purifying and derivatizing amino acids from soils has been devised and applied to rich and poor soils alike. Since the operations involved are simple as shown schematically, the utility of automated wet chemical approaches in space exploration is a distinct possibility. PMID:11826894

  8. Polar vortex dynamics during spring and fall diagnosed using trace gas observations from the Atmospheric Trace Molecule Spectroscopy instrument

    NASA Astrophysics Data System (ADS)

    Manney, G. L.; Michelsen, H. A.; Santee, M. L.; Gunson, M. R.; Irion, F. W.; Roche, A. E.; Livesey, N. J.

    1999-08-01

    Trace gases measured by the Atmospheric Trace Molecule Spectroscopy (ATMOS) instrument during three Atmospheric Laboratory for Applications and Science (ATLAS) space-shuttle missions, in March/April 1992 (AT-1), April 1993 (AT-2), and November 1994 (AT-3) have been mapped into equivalent latitude/potential temperature (EqL/θ) coordinates. The asymmetry of the spring vortices results in coverage of subtropical to polar EqLs. EqL/θ fields of long-lived tracers in spring in both hemispheres show the net effects of descent at high EqL throughout the winter, reflecting strong descent in the upper stratosphere, decreasing descent at lower altitudes, and evidence of greater descent at the edge of the lower stratospheric vortex than in the vortex center; these results are consistent with trajectory calculations examining the history of the air measured by ATMOS in the month prior to each mission. EqL/θ tracer fields, the derived fields CH4-CH4* (CH4* is the expected CH4 calculated from a prescribed relationship with N2O for fall) and NOy-NOy* (analogous to CH4*), and parcel histories all indicate regions of strong mixing in the 1994 Southern Hemisphere (SH) spring vortex above 500 K, with the strongest mixing confined to the vortex edge region between 500 and 700 K, and mixing throughout the Northern Hemisphere (NH) spring vortex in 1993 below about 850 K. Parcel histories indicate mixing of extravortex air with air near the vortex edge below 500 K in the SH but not with air in the vortex core; they show extravortex air mixing well into the vortex above ˜450 K in the NH and into the vortex edge region below. The effects of severe denitrification are apparent in EqL/θ HNO3 in the SH lower stratospheric spring vortex. The morphology of HNO3 in the Arctic spring lower stratospheric vortex is consistent with the effects of descent. EqL/θ fields of ATMOS NOy-NOy* show decreases consistent with the effects of mixing throughout the NH lower stratospheric vortex. The Eq

  9. Platelet aggregation test

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/003669.htm Platelet aggregation test To use the sharing features on this page, please enable JavaScript. The platelet aggregation blood test checks how well platelets , a ...

  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. Platelet aggregation test

    MedlinePlus

    The platelet aggregation blood test checks how well platelets , a part of blood, clump together and cause blood to clot. ... Decreased platelet aggregation may be due to: Autoimmune ... Fibrin degradation products Inherited platelet function defects ...

  12. Determining β2-Integrin and Intercellular Adhesion Molecule 1 Binding Kinetics in Tumor Cell Adhesion to Leukocytes and Endothelial Cells by a Gas-driven Micropipette Assay*

    PubMed Central

    Fu, Changliang; Tong, Chunfang; Wang, Manliu; Gao, Yuxin; Zhang, Yan; Lü, Shouqin; Liang, Shile; Dong, Cheng; Long, Mian

    2011-01-01

    Interactions between polymorphonuclear neutrophils (PMNs) and tumor cells have been reported to facilitate the adhesion and subsequent extravasation of tumor cells through the endothelium under blood flow, both of which are mediated by binding β2-integrin to intercellular adhesion molecule 1 (ICAM-1). Here the adhesions between human WM9 metastatic melanoma cells, PMNs, and human pulmonary microvascular endothelial cells (HPMECs) were quantified by a gas-driven micropipette aspiration technique (GDMAT). Our data indicated that the cellular binding affinity of PMN-WM9 pair was 3.9-fold higher than that of the PMN-HPMEC pair. However, the effective binding affinities per molecular pair were comparable between the two cell pairs no matter whether WM9 cells or HPMECs were quiescent or cytokine-activated, indicating that the stronger adhesion between PMN-WM9 pair is mainly attributed to the high expression of ICAM-1 on WM9 cells. These results proposed an alternative mechanism, where WM9 melanoma cells adhere first with PMNs near vessel-wall regions and then bind to endothelial cells via PMNs under blood flow. In contrast, the adhesions between human MDA-MB-231 metastatic breast carcinoma cells and PMNs showed a comparable cellular binding affinity to PMN-HPMEC pair because the ICAM-1 expressions on MDA-MB-231 cells and HPMECs are similar. Furthermore, differences were observed in the intrinsic forward and reverse rates of the β2-integrin-ICAM-1 bond between PMN-TC and PMN-EC pairs. This GDMAT assay enables us to quantify the binding kinetics of cell adhesion molecules physiologically expressed on nucleated cells. The findings also further the understanding of leukocyte-facilitated tumor cell adhesion from the viewpoint of molecular binding kinetics. PMID:21840991

  13. 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.

  14. 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.

  15. Electrosonic spray ionization. A gentle technique for generating folded proteins and protein complexes in the gas phase and for studying ion-molecule reactions at atmospheric pressure.

    PubMed

    Takáts, Zoltán; Wiseman, Justin M; Gologan, Bogdan; Cooks, R Graham

    2004-07-15

    Electrosonic spray ionization (ESSI), a variant on electrospray ionization (ESI), employs a traditional micro ESI source with supersonic nebulizing gas. The high linear velocity of the nebulizing gas provides efficient pneumatic spraying of the charged liquid sample. The variable electrostatic potential can be tuned to allow efficient and gentle ionization. This ionization method is successfully applied to aqueous solutions of various proteins at neutral pH, and its performance is compared to that of the nanospray and micro ESI techniques. Evidence for efficient desolvation during ESSI is provided by the fact that the peak widths for various multiply charged protein ions are an order of magnitude narrower than those for nanospray. Narrow charge-state distributions compared to other ESI techniques are observed also; for most of the proteins studied, more than 90% of the protein ions can be accumulated in one charge state using ESSI when optimizing conditions. The fact that the abundant charge state is normally as low or lower than that recorded by ESI or nanospray indicates that folded protein ions are generated. The sensitivity of the ionization technique to high salt concentrations is comparable to that of nanospray, but ESSI is considerably less sensitive to high concentrations of organic additives such as glycerol or 2-amino-2-(hydroxymethyl)-1,3-propanediol (Tris base). Noncovalent complexes are observed in the case of myoglobin, protein kinase A/ATP complex, and other proteins. The extent of dissociation of protein ions in ESSI is comparable to or even smaller than that in the case of nanospray, emphasizing the gentle nature of the method. The unique features of ESSI are ascribed to very efficient spraying and the low internal energy supplied to the ions. Evidence is provided that the method is capable of generating fully desolvated protein ions at atmospheric pressure. This allows the technique to be used for the study of ion-molecule reactions at atmospheric

  16. 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.

  17. The effectiveness of plug-in hybrid electric vehicles and renewable power in support of holistic environmental goals: Part 1 - Evaluation of aggregate energy and greenhouse gas performance

    NASA Astrophysics Data System (ADS)

    Tarroja, Brian; Eichman, Joshua D.; Zhang, Li; Brown, Tim M.; Samuelsen, Scott

    2014-07-01

    A study that analyzes the effectiveness of plug-in hybrid vehicles (PHEVs) to meet holistic environmental goals has been performed across the combined electricity and light-duty transportation sectors. PHEV penetration levels are varied from 0 to 60% and base renewable penetration levels are varied from 10 to 45%. Part 1 of the study focuses on CO2 emissions, fuel usage, and the renewable penetration level of individual and combined energy sectors. The effect on grid renewable penetration level depends on two factors: the additional vehicle load demand acting to decrease renewable penetration, and the controllability of vehicle charging acting to reduce curtailment of renewable power. PHEV integration can reduce CO2 emissions and fuel usage and increase the aggregate renewable energy share compared to the no-vehicle case. The benefits of isolated PHEV integration are slightly offset by increased CO2 emissions and fuel usage by the electric grid. Significant benefits are only realized when PHEVs are appropriately deployed in conjunction with renewable energy resources, highlighting important synergies between the electric and light-duty transportation sectors for meeting sustainability goals.

  18. Orientational ordering, site structure, and dynamics for octahedral molecules in low temperature matrices: SF6 and SeF6 in rare gas solidsa)

    NASA Astrophysics Data System (ADS)

    Jones, Llewellyn H.; Swanson, Basil I.

    1983-08-01

    From polarization studies of high resolution IR spectra of SF6 and SeF6 trapped in noble gas solids we show that much of the structure observed for the stretching mode represents site symmetry split components for low symmetry trapping sites, the triply-degenerate ν3 mode being split into a doubly- and singly-degenerate mode. Most of the sites showing polarization are orientationally ordered with the singly-degenerate component perpendicular to the substrate. We attribute the driving force for ordering to guest-host interaction potentials which result in registry between the molecules and the (111) growth plane during deposition. The observed orientational ordering combined with high temperature annealing studies has allowed the identification of the symmetry of certain trapping sites and further analysis of vibrational dephasing dynamics. Several sites with the same nominal symmetry and structure can be tracked through the matrices discussed herein. The implications of the ordering of impurity structure in a host lattice formed by vapor deposition are discussed.

  19. Orientational ordering, site structure, and dynamics for octahedral molecules in low temperature matrices: SF/sub 6/ and SeF/sub 6/ in rare gas solids

    SciTech Connect

    Jones, L.H.; Swanson, B.I.

    1983-08-01

    From polarization studies of high resolution IR spectra of SF/sub 6/ and SeF/sub 6/ trapped in noble gas solids we show that much of the structure observed for the stretching mode represents site symmetry split components for low symmetry trapping sites, the triply-degenerate ..nu../sub 3/ mode being split into a doubly- and singly-degenerate mode. Most of the sites showing polarization are orientationally ordered with the singly-degenerate component perpendicular to the substrate. We attribute the driving force for ordering to guest--host interaction potentials which result in registry between the molecules and the (111) growth plane during deposition. The observed orientational ordering combined with high temperature annealing studies has allowed the identification of the symmetry of certain trapping sites and further analysis of vibrational dephasing dynamics. Several sites with the same nominal symmetry and structure can be tracked through the matrices discussed herein. The implications of the ordering of impurity structure in a host lattice formed by vapor deposition are discussed.

  20. Detergent-mediated protein aggregation

    PubMed Central

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

    2016-01-01

    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. PMID:23466535

  1. 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.

  2. Bio-molecule assisted aggregation of ZnWO4 nanoparticles (NPs) into chain-like assemblies: material for high performance supercapacitor and as catalyst for benzyl alcohol oxidation.

    PubMed

    Ede, Sivasankara Rao; Ramadoss, Ananthakumar; Nithiyanantham, U; Anantharaj, S; Kundu, Subrata

    2015-04-20

    ZnWO4 nanoparticles (NPs) that are assembled and aggregated together as chain-like morphology have been synthesized via the reaction of Zn(II) salt solution with sodium tungstate in the presence of the DNA scaffold under 5 min of microwave heating. The reaction parameters have been tuned to control the size of the individual particles and diameter of the chains. The significance of different reaction parameters and specific growth mechanism for the formation of particles is elaborated. The DNA-ZnWO4 nanoassemblies have been used in two potential applications for the first time, namely, supercapacitor and catalysis studies. Supercapacitor study revealed that DNA-ZnWO4 nanoassemblies exhibited good electrochemical properties having high specific capacitance value ∼72 F/g at 5 mV s(-1), and electrodes possessed a good cyclic stability with more than 1000 consecutive times of cycling. Catalysis studies have been done for benzyl alcohol oxidation, and it was observed that DNA-ZnWO4 nanoassemblies having smaller diameter gives better catalytic efficiency compared to other morphology. This is further authenticated from their BET surface area analysis. In the future, the self-assembled DNA-ZnWO4 nanoassemblies could be a promising candidate for the synthesis of other mixed metal oxides and should be applicable in various emerging fields like Li ion batteries or photocatalysis, or as luminescent materials. PMID:25843144

  3. Mechanisms of carbon nanotube aggregation and the reversion of carbon nanotube aggregates in aqueous medium.

    PubMed

    Koh, Byumseok; Cheng, Wei

    2014-09-16

    Single-walled carbon nanotubes (SWCNTs) dispersed in aqueous medium have many potential applications in chemistry, biology, and medicine. Reversible aggregation of SWCNTs dispersed in water has been frequently reported, but the mechanisms behind are not well understood. Here we show that SWCNTs dispersed into aqueous medium assisted by various charged molecules can be reversibly aggregated by a variety of electrolytes with two distinct mechanisms. Direct binding of counterions to SWCNTs leads to aggregation when the surface charge is neutralized from 74 to 86%. This aggregation is driven by electrostatic instead of van der Waals interactions, thus showing similarity to that of DNA condensation induced by multivalent cations. Sequestration of counterions by chelating reagents leads to the redispersion of SWCNT aggregates. In contrast to various metal ions, polyelectrolytes have the unique ability to induce SWCNT aggregation by bridging between individual SWCNTs. Aggregation through the latter mechanism can be engineered to be reversible by exploiting various mechanisms of chain breaking, including reduction of disulfide bond in the polymer chain, and the cleavage action of proteolytic enzymes. These findings clarify the mechanisms of SWCNT aggregation, and have broad implications in various applications of SWCNTs in water. PMID:25144606

  4. Lanosterol reverses protein aggregation in cataracts.

    PubMed

    Zhao, Ling; Chen, Xiang-Jun; Zhu, Jie; Xi, Yi-Bo; Yang, Xu; Hu, Li-Dan; Ouyang, Hong; Patel, Sherrina H; Jin, Xin; Lin, Danni; Wu, Frances; Flagg, Ken; Cai, Huimin; Li, Gen; Cao, Guiqun; Lin, Ying; Chen, Daniel; Wen, Cindy; Chung, Christopher; Wang, Yandong; Qiu, Austin; Yeh, Emily; Wang, Wenqiu; Hu, Xun; Grob, Seanna; Abagyan, Ruben; Su, Zhiguang; Tjondro, Harry Christianto; Zhao, Xi-Juan; Luo, Hongrong; Hou, Rui; Perry, J Jefferson P; Gao, Weiwei; Kozak, Igor; Granet, David; Li, Yingrui; Sun, Xiaodong; Wang, Jun; Zhang, Liangfang; Liu, Yizhi; Yan, Yong-Bin; Zhang, Kang

    2015-07-30

    The human lens is comprised largely of crystallin proteins assembled into a highly ordered, interactive macro-structure essential for lens transparency and refractive index. Any disruption of intra- or inter-protein interactions will alter this delicate structure, exposing hydrophobic surfaces, with consequent protein aggregation and cataract formation. Cataracts are the most common cause of blindness worldwide, affecting tens of millions of people, and currently the only treatment is surgical removal of cataractous lenses. The precise mechanisms by which lens proteins both prevent aggregation and maintain lens transparency are largely unknown. Lanosterol is an amphipathic molecule enriched in the lens. It is synthesized by lanosterol synthase (LSS) in a key cyclization reaction of a cholesterol synthesis pathway. Here we identify two distinct homozygous LSS missense mutations (W581R and G588S) in two families with extensive congenital cataracts. Both of these mutations affect highly conserved amino acid residues and impair key catalytic functions of LSS. Engineered expression of wild-type, but not mutant, LSS prevents intracellular protein aggregation of various cataract-causing mutant crystallins. Treatment by lanosterol, but not cholesterol, significantly decreased preformed protein aggregates both in vitro and in cell-transfection experiments. We further show that lanosterol treatment could reduce cataract severity and increase transparency in dissected rabbit cataractous lenses in vitro and cataract severity in vivo in dogs. Our study identifies lanosterol as a key molecule in the prevention of lens protein aggregation and points to a novel strategy for cataract prevention and treatment. PMID:26200341

  5. Collision simulation of sintered dust aggregates

    NASA Astrophysics Data System (ADS)

    Sirono, Sin-iti; Ueno, Haruta

    Collisional evolution of dust aggregates is the initial process of the planet formation. Sticking velocity, below which collisional sticking of an aggregate happens, is a crucial quantity in the collisional evolution. In the standard model of protoplanetary nebula, the maximum collisional velocity is around 50m/s. Therefore, if a planetesimal is formed through direct collisional sticking, the sticking velocity should be higher than 50m/s. Even if a planetesimal is formed by other mechanism such as anticyclonic vortices, substantial growth of an aggregate is required because the motion of an aggregate should be decoupled from that of gas. Collisional simulation of icy dust aggregates (Wada et al. 2009, ApJ 702, 1490) showed that the sticking velocity was larger than 50m/s and planetesimal formation by collisional sticking was possible. However, sintering of ice proceeds in a wide area of a protoplanetary nebula (Sirono 2011, ApJ 765, 50). Sintering enlarges a neck, connection between adjacent dust grains, and changes the mechanical properties of a dust aggregate. Here we performed collisional simulations between sintered dust aggregates taking account of sintering. We found that the sticking velocity was decreased substantially down to 20m/s. This result suggests that a planetesimal is not formed by direct collisional sticking and that the planetesimal formation proceeded in particular regions in a protoplanetary nebula.

  6. Mass Spectrometry Study of Multiply Negatively Charged, Gas-Phase NaAOT Micelles: How Does Charge State Affect Micellar Structure and Encapsulation?

    NASA Astrophysics Data System (ADS)

    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 [Nan-zAOTn]z- ( n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Nan-1AOTnH2O]- of n = 3-9. Incorporation of glycine and tryptophan into [Nan-zAOTn]z- aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Nan-zAOTn]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 [Nan+zAOTn]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.

  7. 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. PMID:23247969

  8. 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.

  9. Theoretical Investigation of the Reaction Paths of the Aluminum Cluster Cation with Water Molecule in the Gas Phase: A Facile Route for Dihydrogen Release.

    PubMed

    Moc, Jerzy

    2015-08-13

    The gas-phase reaction of the Al6(+) cation with a water molecule is investigated computationally by coupled cluster and density functional theories. Several low-energy paths of the mechanism for dihydrogen production from H2O by the positively charged aluminum cluster are identified. This reaction involves the initial formation of the association complex, exothermic by 25 kcal/mol, followed by the water dissociation and H2 elimination major steps, yielding the Al6O(+) product oxide with either the nonplanar or planar structure. The H2O dissociation on Al6(+) is the rate-determining step. Of the paths probed, the one kinetically most preferred leads from the O-H bond dissociation transition state lying below the separated reactants to the immediate HAl6OH(+) intermediate of the "open" type and involves further the more compact intermediate from which H2 is eliminated. The other reaction paths explored involve the activation enthalpy (at 0 K) for the rate-determining step of less than 2 kcal/mol relative to the Al6(+) + H2O. Natural population analysis based charges indicate that forming of H2 along the elimination coordinate is facilitated by the interaction of the hydridic and protic hydrogens. For the kinetically most favorable route detected, the coupled cluster singles and doubles with perturbative triples (CCSD(T)) relative energies calculated with the unrestricted and restricted HF references are in a good agreement. This investigation is relevant specifically to the recent mass spectrometric study of the reactivity of Aln(+) with water by Arakawa et al., and it provides a mechanistic insight into the formation of the observed AlnO(+) product oxide with n = 6. PMID:26200102

  10. 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.

  11. 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

  12. Fluorescent aggregates Cyan 40 and Thiazole Orange dyes in solution

    NASA Astrophysics Data System (ADS)

    Nizomov, Negmat; Kurtaliev, Eldar N.; Rahimov, Sherzod I.

    2012-12-01

    Absorption and fluorescence electronic spectra of cyanine dyes Cyan 40 and Thiazole Orange (TO) in water and in binary mixtures: water + ethanol, water + DMF, water + dioxane and chloroform + hexane were studied. It was revealed, that increase of concentration of Cyan 40 and TO dyes in water and chloroform + hexane binary mixture promotes the formation of fluorescent H-aggregates. Meanwhile, in contrary to the well-known fluorescent aggregates, electronic absorption band of aggregated molecules is shifted to the shorter wavelengths and fluorescence band is shifted to the longer wavelengths relative to the bands of the monomer molecules. Observed spectral changes are explained on the basis of Davidov's theory of molecular excitons as splitting of the electron-excited states due to the aggregation of dye molecules.

  13. 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.

  14. 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)

  15. 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)

  16. 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)

  17. 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.

  18. 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.

  19. 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.

  20. Mesoscale simulation of asphaltene aggregation

    NASA Astrophysics Data System (ADS)

    Wang, Jiang; Ferguson, Andrew

    Asphaltenes constitute a heavy aromatic crude oil fraction that can aggregate and precipitate out of solution. Association is thought to proceed hierarchically according to the Yen-Mullins model, but the molecular mechanisms and pathways remain poorly understood. In this study, we perform molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microseconds using the coarse-grained Martini force field. We identified a hierarchical self-assembly mechanism consistent with Yen-Mullins model, but the details of which are strongly dependent on asphaltene molecular structure. Monomeric asphaltenes first self-assemble into 1-D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates. At high concentrations, asphaltenes with short aliphatic side chains assemble into a percolating network with the binding of 1-D rods. Conversely, molecules with more and longer side chains cannot efficiently stack, producing a fractal network of 1-D rods suspended in a sea of interpenetrating aliphatic side chains. Our results provide the first molecularly-detailed validation of the full Yen-Mullins hierarchy, and are in good agreement with recent computational and experimental studies. ACS Petroleum Research Fund.

  1. 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.

  2. 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

  3. Molecules on ice

    SciTech Connect

    Clary, D.C.

    1996-03-15

    The ozone hole that forms in the spring months over the Antarctic is thought to be produced through a network of chemical reactions catalyzed by the surfaces of ice crystals in polar stratospheric clouds (PSCs). A reaction between chlorine reservoir molecules, such as HCl + ClONO{sub 2} > HNO{sub 3} + Cl{sub 2}, is kinetically forbidden in the gas phase but proceeds quickly on the surface of ice and produces Cl{sub 2} molecules that are photodissociated by sunlight to yield the Cl atoms that destroy ozone. This destructive chain of events begins when HCl molecules stick to the ice crystals, and the mechanism for this crucial sticking process has been the subject of much debate. Recent work describes a mechanism that explains how HCl sticks to ice. This article goes on to detail research focusing surface reactions in stratospheric chemistry. 9 refs., 1 fig.

  4. 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. PMID:26136234

  5. Aggregation risk prediction for antibodies and its application to biotherapeutic development

    PubMed Central

    Obrezanova, Olga; Arnell, Andreas; de la Cuesta, Ramón Gómez; Berthelot, Maud E; Gallagher, Thomas RA; Zurdo, Jesús; Stallwood, Yvette

    2015-01-01

    Aggregation is a common problem affecting biopharmaceutical development that can have a significant effect on the quality of the product, as well as the safety to patients, particularly because of the increased risk of immune reactions. Here, we describe a new high-throughput screening algorithm developed to classify antibody molecules based on their propensity to aggregate. The tool, constructed and validated on experimental aggregation data for over 500 antibodies, is able to discern molecules with a high aggregation propensity as defined by experimental criteria relevant to bioprocessing and manufacturing of these molecules. Furthermore, we show how this tool can be combined with other computational approaches during early drug development to select molecules with reduced risk of aggregation and optimal developability properties. PMID:25760769

  6. Optical characterization of Prodan aggregates in water medium.

    PubMed

    Vequi-Suplicy, Cíntia C; Coutinho, Kaline; Teresa Lamy, M

    2013-07-28

    The fluorescent probe Prodan (2-dimethylamino-6-propionylnaphthalene) has been widely used in biological systems, mainly due to the high sensitivity of its emission spectrum to the medium polarity. Though mostly used as a membrane probe, in lipid dispersions Prodan partitions in water, mainly in the presence of gel-phase bilayers. Here, optical properties of Prodan in aqueous medium are experimentally studied using absorption and emission spectroscopies, and compared with those of the probe in cyclohexane, where it is supposed to be very soluble. In parallel, theoretical calculations of the absorption spectrum of a monomer and aggregated Prodan in water were performed. Moreover, to understand Prodan-water and Prodan-Prodan interactions, solvation free energies of Prodan in water and in liquid Prodan were calculated. A light scattering profile underneath the optical absorption spectrum of Prodan in water clearly indicates the presence of aggregates at very low Prodan concentrations (0.9 μM). Experimental evidence of Prodan aggregation is theoretically supported by solvation free energy calculations, which demonstrate that Prodan molecules interact preferentially with other Prodan molecules than with water molecules. Theoretical calculations for electronic transition energies of monomers and aggregated Prodan in water show that a Prodan optical absorption band at 358 nm is related to the monomeric form of Prodan. This band saturates as Prodan concentration increases, indicating that aggregated Prodan prevails at higher concentrations. The relative increase in Prodan aggregated population is monitored by the increase in an absorption band at higher energies, at around 250 nm, and by the disappearance of a band at around 280 nm. Surprisingly, it was observed that the fluorescent emission spectrum of Prodan is not sensitive to probe aggregation up to around 15 μM. Hence, Prodan aggregation in water medium, even at very low concentrations, must be considered when using

  7. 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. PMID:24423378

  8. 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.

  9. Colloidal aggregation in polymer blends.

    PubMed

    Benhamou, M; Ridouane, H; Hachem, E-K; Derouiche, A; Rahmoune, M

    2005-06-22

    We consider here a low-density assembly of colloidal particles immersed in a critical polymer mixture of two chemically incompatible polymers. We assume that, close to the critical point of the free mixture, the colloids prefer to be surrounded by one polymer (critical adsorption). As result, one is assisted to a reversible colloidal aggregation in the nonpreferred phase, due the existence of a long-range attractive Casimir force between particles. This aggregation is a phase transition driving the colloidal system from dilute to dense phases, as the usual gas-liquid transition. We are interested in a quantitative investigation of the phase diagram of the immersed colloids. We suppose that the positions of particles are disordered, and the disorder is quenched and follows a Gaussian distribution. To apprehend the problem, use is made of the standard phi(4) theory, where the field phi represents the composition fluctuation (order parameter), combined with the standard cumulant method. First, we derive the expression of the effective free energy of colloids and show that this is of Flory-Huggins type. Second, we find that the interaction parameter u between colloids is simply a linear combination of the isotherm compressibility and specific heat of the free mixture. Third, with the help of the derived effective free energy, we determine the complete shape of the phase diagram (binodal and spinodal) in the (Psi,u) plane, with Psi as the volume fraction of immersed colloids. The continuous "gas-liquid" transition occurs at some critical point K of coordinates (Psi(c) = 0.5,u(c) = 2). Finally, we emphasize that the present work is a natural extension of that, relative to simple liquid mixtures incorporating colloids. PMID:16035822

  10. 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.

  11. 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.

  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. 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.

  14. 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. PMID:24784502

  15. 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

  16. Surface chemistry of deuterated molecules

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    1983-03-01

    The chemical composition of grain mantles is calculated in order to determine the concentration of deuterated molecules relative to their hydrogenated counterparts in grain mantles. The computation takes into account reactions involving deuterium in the gas phase and on grain surfaces. The results show that the abundance of deuterium molecules in grain mantles is much higher than expected on the basis of the cosmic abundance ratio of D to H. HDCO has a relatively high abundance in grain mantles as compared to other deuterated molecules, due to the fact that H abstraction from HDCO has a lower activation barrier than D abstraction. The infrared characteristics of the calculated grain mantles are discussed and observational tests of the model calcultions are suggested. The contribution of grain surface chemistry to the concentration of molecules in the gas phase is briefly considered.

  17. Molecules in interstellar clouds

    NASA Astrophysics Data System (ADS)

    Irvine, W. M.; Hjalmarson, A.; Rydbeck, O. E. H.

    The physical conditions and chemical compositions of the gas in interstellar clouds are reviewed in light of the importance of interstellar clouds for star formation and the origin of life. The Orion A region is discussed as an example of a giant molecular cloud where massive stars are being formed, and it is pointed out that conditions in the core of the cloud, with a kinetic temperature of about 75 K and a density of 100,000-1,000,000 molecules/cu cm, may support gas phase ion-molecule chemistry. The Taurus Molecular Clouds are then considered as examples of cold, dark, relatively dense interstellar clouds which may be the birthplaces of solar-type stars and which have been found to contain the heaviest interstellar molecules yet discovered. The molecular species identified in each of these regions are tabulated, including such building blocks of biological monomers as H2O, NH3, H2CO, CO, H2S, CH3CN and H2, and more complex species such as HCOOCH3 and CH3CH2CN.

  18. Collisional decoherence of polar molecules

    NASA Astrophysics Data System (ADS)

    Walter, Kai; Stickler, Benjamin A.; Hornberger, Klaus

    2016-06-01

    The quantum state of motion of a large and rotating polar molecule can lose coherence through the collisions with gas atoms. We show how the associated quantum master equation for the center of mass can be expressed in terms of the orientationally averaged differential and total scattering cross sections, for which we provide approximate analytic expressions. The master equation is then utilized to quantify collisional decoherence in a interference experiment with polar molecules.

  19. 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

    2016-01-01

    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. PMID:26877167

  20. 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

  1. A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters

    SciTech Connect

    Iftner, Christophe; Simon, Aude; Korchagina, Kseniia; Rapacioli, Mathias; Spiegelman, Fernand

    2014-01-21

    We propose in the present paper a SCC-DFTB/FF (Self-Consistent-Charge Density Functional based Tight Binding/Force-Field) scheme adapted to the investigation of molecules trapped in rare gas environments. With respect to usual FF descriptions, the model involves the interaction of quantum electrons in a molecule with rare gas atoms in an anisotropic scheme. It includes polarization and dispersion contributions and can be used for both neutral and charged species. Parameters for this model are determined for hydrocarbon-argon complexes and the model is validated for small hydrocarbons. With the future aim of studying polycyclic aromatic hydrocarbons in Ar matrices, extensive benchmark calculations are performed on (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters against DFT and CCSD(T) calculations for the smaller sizes, and more generally against other experimental and theoretical data. Results on the structures and energetics (isomer ordering and energy separation, cohesion energy per Ar atom) are presented in detail for n = 1–8, 13, 20, 27, and 30, for both neutrals and cations. We confirm that the clustering of Ar atoms leads to a monotonous decrease of the ionization potential of benzene for n ⩽ 20, in line with previous experimental and FF data.

  2. 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.

  3. Photophoretic force on aggregate grains

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin S.; Kimery, Jesse B.; Wurm, Gerhard; de Beule, Caroline; Kuepper, Markus; Hyde, Truell W.

    2016-01-01

    The photophoretic force may impact planetary formation by selectively moving solid particles based on their composition and structure. This generates collision velocities between grains of different sizes and sorts the dust in protoplanetary discs by composition. This numerical simulation studied the photophoretic force acting on fractal dust aggregates of μm-scale radii. Results show that aggregates tend to have greater photophoretic drift velocities than spheres of similar mass or radii, though with a greater spread in the velocity. While the drift velocities of compact aggregates continue to increase as the aggregates grow larger in size, fluffy aggregates have drift velocities which are relatively constant with size. Aggregates formed from an initially polydisperse size distribution of dust grains behave differently from aggregates formed from a monodisperse population, having smaller drift velocities with directions which deviate substantially from the direction of illumination. Results agree with microgravity experiments which show the difference of photophoretic forces with aggregation state.

  4. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231- 235.

  5. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231-235.

  6. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  7. 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.

  8. 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

  9. An in vivo platform for identifying inhibitors of protein aggregation.

    PubMed

    Saunders, Janet C; Young, Lydia M; Mahood, Rachel A; Jackson, Matthew P; Revill, Charlotte H; Foster, Richard J; Smith, D Alastair; Ashcroft, Alison E; Brockwell, David J; Radford, Sheena E

    2016-02-01

    Protein aggregation underlies an array of human diseases, yet only one small-molecule therapeutic targeting this process has been successfully developed to date. Here, we introduce an in vivo system, based on a β-lactamase tripartite fusion construct, that is 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 islet amyloid polypeptide 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

  10. 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.

  11. 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.

  12. High-repetition-rate and high-photon-flux 70 eV high-harmonic source for coincidence ion imaging of gas-phase molecules.

    PubMed

    Rothhardt, Jan; Hädrich, Steffen; Shamir, Yariv; Tschnernajew, Maxim; Klas, Robert; Hoffmann, Armin; Tadesse, Getnet K; Klenke, Arno; Gottschall, Thomas; Eidam, Tino; Limpert, Jens; Tünnermann, Andreas; Boll, Rebecca; Bomme, Cedric; Dachraoui, Hatem; Erk, Benjamin; Di Fraia, Michele; Horke, Daniel A; Kierspel, Thomas; Mullins, Terence; Przystawik, Andreas; Savelyev, Evgeny; Wiese, Joss; Laarmann, Tim; Küpper, Jochen; Rolles, Daniel

    2016-08-01

    Unraveling and controlling chemical dynamics requires techniques to image structural changes of molecules with femtosecond temporal and picometer spatial resolution. Ultrashort-pulse x-ray free-electron lasers have significantly advanced the field by enabling advanced pump-probe schemes. There is an increasing interest in using table-top photon sources enabled by high-harmonic generation of ultrashort-pulse lasers for such studies. We present a novel high-harmonic source driven by a 100 kHz fiber laser system, which delivers 1011 photons/s in a single 1.3 eV bandwidth harmonic at 68.6 eV. The combination of record-high photon flux and high repetition rate paves the way for time-resolved studies of the dissociation dynamics of inner-shell ionized molecules in a coincidence detection scheme. First coincidence measurements on CH3I are shown and it is outlined how the anticipated advancement of fiber laser technology and improved sample delivery will, in the next step, allow pump-probe studies of ultrafast molecular dynamics with table-top XUV-photon sources. These table-top sources can provide significantly higher repetition rates than the currently operating free-electron lasers and they offer very high temporal resolution due to the intrinsically small timing jitter between pump and probe pulses. PMID:27505779

  13. Spin-spin coupling in the HD molecule determined from 1H and 2H NMR experiments in the gas-phase

    NASA Astrophysics Data System (ADS)

    Garbacz, Piotr

    2014-10-01

    The indirect spin-spin coupling of hydrogen deuteride, J(D, H), was determined from a series of 1H and 2H NMR spectra acquired at various densities of gaseous solvents (He, Ar, CO2, and N2O). The analysis of these spectra shows that accurate determination of J(D, H) from this experimental data requires careful examination of the effects of nuclear relaxation and of HD-solvent gas interactions on hydrogen deuteride line shapes. Particularly, it was found that the first-order corrections of the peak-to-peak separations between HD multiplet peaks due to weak van der Waals interactions are proportional to solvent gas density, while these corrections for nuclear relaxation of the proton and the deuteron are proportional to the second power of the inverse of the gas density. Analysis of the data indicates that J(D, H), obtained by correcting for the effects of nuclear relaxation and intermolecular interactions, is 43.136(7) Hz at 300 K.

  14. 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

  15. Dynamics of fire ant aggregations

    NASA Astrophysics Data System (ADS)

    Tennenbaum, Michael; Hu, David; Fernandez-Nieves, Alberto

    Fire ant aggregations are an inherently active system. Each ant harvests its own energy and can convert it into motion. The motion of individual ants contributes non-trivially to the bulk material properties of the aggregation. We have measured some of these properties using plate-plate rheology, where the response to an applied external force or deformation is measured. In this talk, we will present data pertaining to the aggregation behavior in the absence of any external force. We quantify the aggregation dynamics by monitoring the rotation of the top plate and by measuring the normal force. We then compare the results with visualizations of 2D aggregations.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Activation of Alpha Chymotrypsin by Three Phase Partitioning Is Accompanied by Aggregation

    PubMed Central

    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 λmax 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. PMID:23239966

  1. Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers.

    PubMed

    Luo, Zhouyang; Zhu, Ningbo; Zhao, Dahui

    2016-07-25

    The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n-hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self-aggregation of unfolded chains, as a minor component, gradually drives the folding-unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH3 OH/H2 O) both folded and unfolded oligomer 2 appear to undergo self-association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H2 O content, self-aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded-unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers. PMID:27374725

  2. Synthesis and aggregation behavior of a hexameric quaternary ammonium surfactant.

    PubMed

    Fan, Yaxun; Hou, Yanbo; Xiang, Junfeng; Yu, Defeng; Wu, Chunxian; Tian, Maozhang; Han, Yuchun; Wang, Yilin

    2011-09-01

    A star-shaped hexameric quaternary ammonium surfactant (PAHB), bearing six hydrophobic chains and six charged hydrophilic headgroups connected by an amide-type spacer group, was synthesized. The self-assembly behavior of the surfactant in aqueous solution was studied by surface tension, electrical conductivity, isothermal titration microcalorimetry, dynamic light scattering, cryogenic transmission electron microscopy, and NMR techniques. The results reveal that there are two critical aggregate concentrations during the process of aggregation, namely C(1) and C(2). The aggregate transitions are proved to be caused by the changes of the surfactant configuration through hydrophobic interaction among the hydrocarbon chains. Below C(1), PAHB may present a star-shaped molecular configuration due to intramolecular electrostatic repulsion among the charged headgroups, and large aggregates with network-like structure are observed. Between C(1) and C(2), the hydrophobic interaction among the hydrophobic chains may become stronger to make the hydrophobic chains of the PAHB molecules curve back and pack more closely, and then the network-like aggregates transfer to large spherical aggregates of ∼100 nm. Beyond C(2), the hydrophobic interaction may become strong enough to cause the PAHB molecular configuration to turn into a pyramid-like shape, resulting in the transition of the spherical large aggregates to spherical micelles of ∼10 nm. Interestingly, the PAHB displays high emulsification ability to linear fatty alkyls even at very low concentration. PMID:21797217

  3. 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.

  4. Making Graphene Resist Aggregation

    NASA Astrophysics Data System (ADS)

    Luo, Jiayan

    Graphene-based sheets have stimulated great interest in many scientific disciplines and shown promise for wide potential applications. Among various ways of creating single atomic layer carbon sheets, a promising route for bulk production is to first chemically exfoliate graphite powders to graphene oxide (GO) sheets, followed by reduction to form chemically modified graphene (CMG). Due to the strong van der Waals attraction between graphene sheets, CMG tends to aggregate. The restacking of sheets is largely uncontrollable and irreversible, thus it reduces their processability and compromises properties such as accessible surface area. Strategies based on colloidal chemistry have been applied to keep CMG dispersed in solvents by introducing electrostatic repulsion to overcome the van der Waals attraction or adding spacers to increase the inter-sheet spacing. In this dissertation, two very different ideas that can prevent CMG aggregation without extensively modifying the material or introducing foreign spacer materials are introduced. The van der Waals potential decreases with reduced overlapping area between sheets. For CMG, reducing the lateral dimension from micrometer to nanometer scale should greatly enhance their colloidal stability with additional advantages of increased charge density and decreased probability to interact. The enhanced colloidal stability of GO and CMG nanocolloids makes them especially promising for spectroscopy based bio-sensing applications. For potential applications in a compact bulk solid form, the sheets were converted into paper-ball like structure using capillary compression in evaporating aerosol droplets. The crumpled graphene balls are stabilized by locally folded pi-pi stacked ridges, and do not unfold or collapse during common processing steps. They can tightly pack without greatly reducing the surface area. This form of graphene leads to scalable performance in energy storage. For example, planer sheets tend to aggregate and

  5. 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.

  6. 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.

  7. Light-induced self-assembly and decay of J aggregates of thiamonomethinecyanine dyes.

    PubMed

    Petrenko, Volodymyr Yu; Dimitriev, Oleg P

    2014-12-15

    Formation of J aggregates, that is, one-dimensional supramolecular self-organizations in which the transition moments of individual molecules are aligned parallel to the line joining their centers through a "head-to-tail" arrangement, normally proceed via electrostatic interactions between oppositely charged molecular groups; this is facilitated by an electrolyte medium. Here, we show that J aggregates of thiamonomethinecyanine dyes in a solution can be assembled from dye dimers by illuminating the solution with light of the appropriate wavelength to induce excitation of the dye dimers. The reverse process is also demonstrated by application of light of the correct wavelength to induce excitation of the J aggregates. Our results indicate that spontaneous J aggregation in the dark and formation of J aggregates through illumination proceed through different mechanisms; the former resulting in an increase in the number of the aggregates and the latter in an increase in the size of the aggregates. PMID:25294591

  8. Aggregation-Enhanced Raman Scattering by a Water-Soluble Porphyrin

    NASA Technical Reports Server (NTRS)

    Akins, Daniel L.

    1995-01-01

    Much interest in our laboratory has focused on aggregation of organic compounds, particularly cyanine dyes and porphyrins. For this discussion we have applied absorption and Raman scattering spectroscopies to characterize aggregated TSPP (tetrakis-(p-sulfonatophynyl) porphyrin) in aqueous solution. Based on concentration, pH and ionic strength dependence of TSPP absorption, we deduce that aggregation evolves through the formation of TSPP diacid and that the diacid is the repeating unit in the aggregate. The Raman bands of TSPP in strongly acidic solution lead us further to conclude that vibrations of adjacent molecules are perturbed in a fashion that is consistent with the pyrrolic ring in the porphinato macrocycle being ruffled, and that two aggregate arrangements occur: specifically J- and H-type aggregates. Furthermore, aggregation enhancement is advanced as a viable mechanism to explain enhanced Raman Scattering for homogeneous aqueous phase TSPP, where the surface-enhancement mechanism is not applicable.

  9. Exciton Theory for Supramolecular Chlorosomal Aggregates: 1. Aggregate Size Dependence of the Linear Spectra

    PubMed Central

    Prokhorenko, V. I.; Steensgaard, D. B.; Holzwarth, A. R.

    2003-01-01

    The interior of chlorosomes of green bacteria forms an unusual antenna system organized without proteins. The steady-spectra (absorption, circular dichroism, and linear dichroism) have been modeled using the Frenkel Hamiltonian for the large tubular aggregates of bacteriochlorophylls with geometries corresponding to those proposed for Chloroflexus aurantiacus and Chlorobium tepidum chlorosomes. For the Cf. aurantiacus aggregates we apply a structure used previously (V. I. Prokhorenko., D. B. Steensgaard, and A. R. Holzwarth, Biophys. J. 2000, 79:2105–2120), whereas for the Cb. tepidum aggregates a new extended model of double-tube aggregates, based on recently published solid-state nuclear magnetic resonance studies (B.-J. van Rossum, B. Y. van Duhl, D. B. Steensgaard, T. S. Balaban, A. R. Holzwarth, K. Schaffner, and H. J. M. de Groot, Biochemistry 2001, 40:1587–1595), is developed. We find that the circular dichroism spectra depend strongly on the aggregate length for both types of chlorosomes. Their shape changes from “type-II” (negative at short wavelengths to positive at long wavelengths) to the “mixed-type” (negative-positive-negative) in the nomenclature proposed in K. Griebenow, A. R. Holzwarth, F. van Mourik, and R. van Grondelle, Biochim. Biophys. Acta 1991, 1058:194–202, for an aggregate length of 30–40 bacteriochlorophyll molecules per stack. This “size effect” on the circular dichroism spectra is caused by appearance of macroscopic chirality due to circular distribution of the transition dipole moment of the monomers. We visualize these distributions, and also the corresponding Frenkel excitons, using a novel presentation technique. The observed size effects provide a key to explain many previously puzzling and seemingly contradictory experimental data in the literature on the circular and linear dichroism spectra of seemingly identical types of chlorosomes. PMID:14581217

  10. Thermodynamically reversible generalization of diffusion limited aggregation.

    PubMed

    D'Souza, R M; Margolus, N H

    1999-07-01

    We introduce a lattice gas model of cluster growth via the diffusive aggregation of particles in a closed system obeying a local, deterministic, microscopically reversible dynamics. This model roughly corresponds to placing the irreversible diffusion limited aggregation model (DLA) in contact with a heat bath. Particles release latent heat when aggregating, while singly connected cluster members can absorb heat and evaporate. The heat bath is initially empty, hence we observe the flow of entropy from the aggregating gas of particles into the heat bath, which is being populated by diffusing heat tokens. Before the population of the heat bath stabilizes, the cluster morphology (quantified by the fractal dimension) is similar to a standard DLA cluster. The cluster then gradually anneals, becoming more tenuous, until reaching configurational equilibrium when the cluster morphology resembles a quenched branched random polymer. As the microscopic dynamics is invertible, we can reverse the evolution, observe the inverse flow of heat and entropy, and recover the initial condition. This simple system provides an explicit example of how macroscopic dissipation and self-organization can result from an underlying microscopically reversible dynamics. We present a detailed description of the dynamics for the model, discuss the macroscopic limit, and give predictions for the equilibrium particle densities obtained in the mean field limit. Empirical results for the growth are then presented, including the observed equilibrium particle densities, the temperature of the system, the fractal dimension of the growth clusters, scaling behavior, finite size effects, and the approach to equilibrium. We pay particular attention to the temporal behavior of the growth process and show that the relaxation to the maximum entropy state is initially a rapid nonequilibrium process, then subsequently it is a quasistatic process with a well defined temperature. PMID:11969759

  11. 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.

  12. Taurine and platelet aggregation

    SciTech Connect

    Nauss-Karol, C.; VanderWende, C.; Gaut, Z.N.

    1986-03-01

    Taurine is a putative neurotransmitter or neuromodulator. The endogenous taurine concentration in human platelets, determined by amino acid analysis, is 15 ..mu..M/g. In spite of this high level, taurine is actively accumulated. Uptake is saturable, Na/sup +/ and temperature dependent, and suppressed by metabolic inhibitors, structural analogues, and several classes of centrally active substances. High, medium and low affinity transport processes have been characterized, and the platelet may represent a model system for taurine transport in the CNS. When platelets were incubated with /sup 14/C-taurine for 30 minutes, then resuspended in fresh medium and reincubated for one hour, essentially all of the taurine was retained within the cells. Taurine, at concentrations ranging from 10-1000 ..mu..M, had no effect on platelet aggregation induced by ADP or epinephrine. However, taurine may have a role in platelet aggregation since 35-39% of the taurine taken up by human platelets appears to be secreted during the release reaction induced by low concentrations of either epinephrine or ADP, respectively. This release phenomenon would imply that part of the taurine taken up is stored directly in the dense bodies of the platelet.

  13. Coupled cluster calculations of mean excitation energies of the noble gas atoms He, Ne and Ar and of the H2 molecule

    NASA Astrophysics Data System (ADS)

    Sauer, Stephan P. A.; Haq, Inam Ul; Sabin, John R.; Oddershede, Jens; Christiansen, Ove; Coriani, Sonia

    2014-03-01

    Using an asymmetric Lanczos chain algorithm for the calculation of the coupled cluster linear response functions at the coupled cluster singles and doubles (CCSD) and coupled cluster singles and approximate iterative doubles (CC2) levels of approximation, we have calculated the mean excitation energies of the noble gases He, Ne and Ar, and of the hydrogen molecule (H2). Convergence with respect to the one-electron basis set was investigated in detail for families of correlation-consistent basis sets including both augmentation and core-valence functions. We find that the electron correlation effects at the CCSD level change the mean excitation energies obtained at the uncorrelated Hartree-Fock level by about 1%. For the two-electron systems He and H2, our CCSD results (for a Lanczos chain length equal to the full excitation space), I0 = 42.28 eV (helium) and I0 = 19.62 eV (H2), correspond to full configuration interaction results and are therefore the exact, non-relativistic theoretical values for the mean excitation energy of these two systems within the Bethe theory for the chosen basis set and, in the case of H2, at the experimental equilibrium geometry.

  14. Synthesis and characterization of silicon carbonitride films by plasma enhanced chemical vapor deposition (PECVD) using bis(dimethylamino)dimethylsilane (BDMADMS), as membrane for a small molecule gas separation

    NASA Astrophysics Data System (ADS)

    Kafrouni, W.; Rouessac, V.; Julbe, A.; Durand, J.

    2010-12-01

    Silicon carbonitride thin films have been deposited by plasma enhanced chemical vapor deposition (PECVD) from bis(dimethylamino)dimethylsilane (BDMADMS) as a function of X = (BDMADMS/(BDMADMS + NH 3)) between 0.1 and 1, and plasma power P (W) between 100 and 400 W. The microstructure of obtained materials has been studied by SEM, FTIR, EDS, ellipsometrie, and contact angle of water measurements. The structure of the materials is strongly depended on plasma parameters; we can pass from a material rich in carbon to a material rich in nitrogen. Single gas permeation tests have been carried out and we have obtained a helium permeance of about 10 -7 mol m -2 s -1 Pa -1 and ideal selectivity of helium over nitrogen of about 20.

  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. 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.

  17. Bio-/Chemosensors and Imaging with Aggregation-Induced Emission Luminogens.

    PubMed

    Zhan, Chi; You, Xue; Zhang, Guanxin; Zhang, Deqing

    2016-08-01

    Aggregation-induced emission (AIE) luminogens show abnormal fluorescent behavior; they are non-emissive in solution, but they become strongly emissive after aggregation. Sensing and imaging are the major applications of AIE luminogens. By properly manipulating the aggregation and deaggregation of AIE molecules, various bio-/chemosensors have been developed. Moreover, AIE molecules with targeting groups have been devised for imaging of organelles and cancer cells. In this account, we report our recent work on the application of AIE luminogens for the construction of bio-/chemosensors and imaging. PMID:27427427

  18. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.

    PubMed

    McLaughlin, Christopher K; Duan, Da; Ganesh, Ahil N; Torosyan, Hayarpi; Shoichet, Brian K; Shoichet, Molly S

    2016-04-15

    Small molecule aggregates are considered nuisance compounds in drug discovery, but their unusual properties as colloids could be exploited to form stable vehicles to preserve protein activity. We investigated the coaggregation of seven molecules chosen because they had been previously intensely studied as colloidal aggregators, coformulating them with bis-azo dyes. The coformulation reduced colloid sizes to <100 nm and improved uniformity of the particle size distribution. The new colloid formulations are more stable than previous aggregator particles. Specifically, coaggregation of Congo Red with sorafenib, tetraiodophenolphthalein (TIPT), or vemurafenib produced particles that are stable in solutions of high ionic strength and high protein concentrations. Like traditional, single compound colloidal aggregates, the stabilized colloids adsorbed and inhibited enzymes like β-lactamase, malate dehydrogenase, and trypsin. Unlike traditional aggregates, the coformulated colloid-protein particles could be centrifuged and resuspended multiple times, and from resuspended particles, active trypsin could be released up to 72 h after adsorption. Unexpectedly, the stable colloidal formulations can sequester, stabilize, and isolate enzymes by spin-down, resuspension, and release. PMID:26741163

  19. Cellular pattern formation during Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Höfer, Thomas; Sherratt, Jonathan A.; Maini, Philip K.

    The development of multicellularity in the life cycle of Dictyostelium discoideum provides a paradigm model system for biological pattern formation. Previously, mathematical models have shown how a collective pattern of cell communication by waves of the messenger molecule cyclic adenosine 3‧5‧-monophosphate (cAMP) arises from excitable local cAMP kinetics and cAMP diffusion. Here we derive a model of the actual cell aggregation process by considering the chemotactic cell response to cAMP and its interplay with the cAMP dynamics. Cell density, which previously has been treated as a spatially homogeneous parameter, is a crucial variable of the aggregation model. We find that the coupled dynamics of cell chemotaxis and cAMP reaction-diffusion lead to the break-up of the initially uniform cell layer and to the formation of the striking cell stream morphology which characterizes the aggregation process in situ. By a combination of stability analysis and two-dimensional simulations of the model equations, we show cell streaming to be the consequence of the growth of a small-amplitude pattern in cell density forced by the large-amplitude cAMP waves, thus representing a novel scenario of spatial patterning in a cell chemotaxis system. The instability mechanism is further analysed by means of an analytic caricature of the model, and the condition for chemotaxis-driven instability is found to be very similar to the one obtained for the standard (non-oscillatory) Keller-Segel system. The growing cell stream pattern feeds back into the cAMP dynamics, which can explain in some detail experimental observations on the time evolution of the cAMP wave pattern, and suggests the characterization of the Dictyostelium aggregation field as a self-organized excitable medium.

  20. 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.

  1. 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.

  2. 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.

  3. A new interstellar molecule - Tricarbon monoxide

    NASA Technical Reports Server (NTRS)

    Matthews, H. E.; Irvine, W. M.; Friberg, P.; Brown, R. D.; Godfrey, P. D.

    1984-01-01

    The C3O molecule, whose pure rotational spectrum has only recently been studied in the laboratory, has been detected in the cold, dark interstellar Taurus Molecular Cloud 1. Since C3O is the first interstelar carbon chain molecule to contain oxygen, its existence places an important new constraint on chemical schemes for cold interstellar clouds. The abundance of C3O can be understood in terms of purely gas-phase ion-molecule chemistry.

  4. Nanomagnets La0.8Pb0.2(Fe0.8Co0.2)O3 assembled with a bonded surface graphene oxide: sensitive for sensing small gas molecules.

    PubMed

    Bhargav, K K; Ram, S; Majumder, S B

    2012-04-01

    Nanocrystallites La0.8Pb0.2(Fe0.8Co0.2)O3 (LPFC) when bonded through a surface layer (carbon) in small ensembles display surface sensitive magnetism useful for biological probes, electrodes, and toxic gas sensors. A simple dispersion and hydrolysis of the salts in ethylene glycol (EG) in water is explored to form ensembles of the nanocrystallites (NCs) by combustion of a liquid precursor gel slowly in microwave at 70-80 dgrees C (apparent) in a closed container in air. In a dilute sample, the EG molecules mediate hydrolyzed species to configure in small groups in process to form a gel. Proposed models describe how a residual carbon bridges a stable bonded layer of a graphene-oxide-like hybrid structure on the LPFC-NCs in attenuating the magnetic structure. SEM images, measured from a pelletized sample which was used to study the gas sensing features in terms of the electrical resistance, describe plate shaped NCs, typically 30-60 nm widths, 60-180 nm lengths and -50 m2/g surface area (after heating at -750 degrees C). These NCs are arranged in ensembles (200-900 nm size). As per the X-ray diffraction, the plates (a Pnma orthorhombic structure) bear only small strain -0.0023 N/m2 and oxygen vacancies. The phonon and electronic bands from a bonded surface layer disappear when it is etched out slowly by heating above 550 degrees C in air. The surface layer actively promotes selective H2 gas sensor properties. PMID:22849054

  5. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    PubMed

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  6. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    PubMed Central

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  7. Orientational Alignment of Amyloidogenic Proteins in Pre-Aggregated Solutions

    NASA Astrophysics Data System (ADS)

    Schröder, C.; Steinhauser, O.; Sasisanker, P.; Weingärtner, H.

    2015-03-01

    In the present study we combine dielectric relaxation spectroscopy with generalized Born simulations to explore the role of orientational order for protein aggregation in solutions of bovine pancreatic insulin at various p H conditions. Under aggregation-prone conditions at low p H , insulin monomers prefer antiparallel dipole alignments, which are consistent with the orientation of the monomeric subunits in the dimer structure. This alignment is also true for two dimers, suggesting that already at moderate protein concentrations the species assemble in equilibrium clusters, in which the molecules adopt preferred orientations also found for the protomers of the corresponding oligomers.

  8. Frequency Factors in a Landscape Model of Filamentous Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Buell, Alexander K.; Jamie R. Blundell; Dobson, Christopher M.; Welland, Mark E.; Terentjev, Eugene M.; Knowles, Tuomas P. J.

    2010-06-01

    Using quantitative measurements of protein aggregation rates, we develop a kinetic picture of protein conversion from a soluble to a fibrillar state which shows that a single free energy barrier to aggregation controls the addition of protein molecules into amyloid fibrils, while the characteristic sublinear concentration dependence emerges as a natural consequence of finite diffusion times. These findings suggest that this reaction does not follow a simple chemical mechanism, but rather operates in a way analogous to the landscape models of protein folding defined by stochastic dynamics on a characteristic energy surface.

  9. Inhibition of amyloid-β aggregation in Alzheimer's disease.

    PubMed

    Wang, Qiuming; Yu, Xiang; Li, Lingyan; Zheng, Jie

    2014-01-01

    The assembly of naturally occurring amyloid peptides into cytotoxic oligomeric and fibrillar aggregates is believed to be a major pathologic event in over 25 human diseases. Blocking of or interfering with the aggregation of amyloid peptides such as amyloid-β (Aβ) using small organic molecules, peptides and peptidomimetics, and nanoparticles that selectively bind or inhibit Aβ aggregates is a promising strategy for the development of novel pharmaceutical approaches and agents to treat Alzheimer's disease (AD). In a broad sense, considering many common features in structure, kinetics, and biological activity of amyloid peptides, potent inhibitors and associated inhibition strategies that are developed for targeting Aβ aggregation could also be generally applied to other amyloid-forming peptides in "protein-aggregation diseases". Due to the complex nature of Aβ self-assembly process, increasing knowledge in high-resolution structures of Aβ oligomers, atomic-level Aβ-inhibitor binding information, and cost-effective high-throughput screening method will improve our fundamental understanding of amyloid formation and inhibition mechanisms, as well as practical design of pharmaceutical strategies and drugs to treat AD. This review summarizes major findings, recent advances, and future challenges for the development of new Aβ-aggregation inhibitors, mainly focusing on three major classes of Aβ inhibitors with associated inhibition mechanisms and practical. examples. PMID:23713775

  10. 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

  11. Dipolar molecules in optical lattices.

    PubMed

    Sowiński, Tomasz; Dutta, Omjyoti; Hauke, Philipp; Tagliacozzo, Luca; Lewenstein, Maciej

    2012-03-16

    We study the extended Bose-Hubbard model describing an ultracold gas of dipolar molecules in an optical lattice, taking into account all on-site and nearest-neighbor interactions, including occupation-dependent tunneling and pair tunneling terms. Using exact diagonalization and the multiscale entanglement renormalization ansatz, we show that these terms can destroy insulating phases and lead to novel quantum phases. These considerable changes of the phase diagram have to be taken into account in upcoming experiments with dipolar molecules. PMID:22540482

  12. On the dynamics of the TPPS4 aggregation in aqueous solutions: successive formation of H and J aggregates.

    PubMed

    Aggarwal, Lucimara P F; Borissevitch, Iouri E

    2006-01-01

    The dynamics of aggregation of meso-tetrakis (p-sulfonatofenyl) porphyrin (TPPS4) in function of its concentration, pH and ionic strength was studied by optical absorption, fluorescence and resonance light scattering (RLS) techniques. In the region of pH, where TPPS4 exists in biprotonated form, the addition of NaCl induces the TPPS4 aggregation due to the formation of the "cloud" of counter ions around the TPPS4 molecule thus reducing electrostatic repulsion between the porphyrin molecules. The formation of this "cloud" shifts the pKa value to acid region (from 5.0 in the absence of salt to 4.5 at [NaCl] = 0.4 M), reduces the TPPS4 absorption in all spectral range and quantum yield and lifetime of fluorescence (from 0.27 to 0.17 and from 4.00+/-0.04 to 3.00+/-0.03 ns in the absence of salt and in the presence of NaCl, respectively). The aggregation process involves two successive stages: initially H aggregates are formed, which in time are transformed in J ones. The existence of these two stages was confirmed by the fluorescence and RLS data. The kinetics of the formation of J aggregates is characterized by the induction time t1 and the average growth time t2, which depend on both TPPS4 and salt concentrations. The induction period t1 appears as a result of initial formation of H aggregates and their successive transformation in J ones. At very high TPPS4 concentrations, the J aggregates are united in more complex structures such as hollow cylinders or helixes. PMID:15955725

  13. 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

  14. Scaling of transverse nuclear magnetic relaxation due to magnetic nanoparticle aggregation.

    PubMed

    Brown, Keith A; Vassiliou, Christophoros C; Issadore, David; Berezovsky, Jesse; Cima, Michael J; Westervelt, R M

    2010-10-01

    The aggregation of superparamagnetic iron oxide (SPIO) nanoparticles decreases the transverse nuclear magnetic resonance (NMR) relaxation time T2CP of adjacent water molecules measured by a Carr-Purcell-Meiboom-Gill (CPMG) pulse-echo sequence. This effect is commonly used to measure the concentrations of a variety of small molecules. We perform extensive Monte Carlo simulations of water diffusing around SPIO nanoparticle aggregates to determine the relationship between T2CP and details of the aggregate. We find that in the motional averaging regime T2CP scales as a power law with the number N of nanoparticles in an aggregate. The specific scaling is dependent on the fractal dimension d of the aggregates. We find T2CP∝N-0.44 for aggregates with d = 2.2, a value typical of diffusion limited aggregation. We also find that in two-nanoparticle systems, T2CP is strongly dependent on the orientation of the two nanoparticles relative to the external magnetic field, which implies that it may be possible to sense the orientation of a two-nanoparticle aggregate. To optimize the sensitivity of SPIO nanoparticle sensors, we propose that it is best to have aggregates with few nanoparticles, close together, measured with long pulse-echo times. PMID:20689678

  15. Peptide aggregation in neurodegenerative disease.

    PubMed

    Murphy, Regina M

    2002-01-01

    In the not-so-distant past, insoluble aggregated protein was considered as uninteresting and bothersome as yesterday's trash. More recently, protein aggregates have enjoyed considerable scientific interest, as it has become clear that these aggregates play key roles in many diseases. In this review, we focus attention on three polypeptides: beta-amyloid, prion, and huntingtin, which are linked to three feared neurodegenerative diseases: Alzheimer's, "mad cow," and Huntington's disease, respectively. These proteins lack any significant primary sequence homology, yet their aggregates possess very similar features, specifically, high beta-sheet content, fibrillar morphology, relative insolubility, and protease resistance. Because the aggregates are noncrystalline, secrets of their structure at nanometer resolution are only slowly yielding to X-ray diffraction, solid-state NMR, and other techniques. Besides structure, the aggregates may possess similar pathways of assembly. Two alternative assembly pathways have been proposed: the nucleation-elongation and the template-assisted mode. These two modes may be complementary, not mutually exclusive. Strategies for interfering with aggregation, which may provide novel therapeutic approaches, are under development. The structural similarities between protein aggregates of dissimilar origin suggest that therapeutic strategies successful against one disease may have broad utility in others. PMID:12117755

  16. 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…

  17. 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.

  18. Noble-gas hydrides: new chemistry at low temperatures.

    PubMed

    Khriachtchev, Leonid; Räsänen, Markku; Gerber, R Benny

    2009-01-20

    ; however, the decomposition is prevented by high barriers, for instance, about 2 eV for HXeCCH. The other decomposition channel HNgY --> H + Ng + Y is endothermic for all prepared molecules.Areas that appear promising for further study include the extension of argon chemistry, preparation of new bonds with noble-gas atoms (such as Xe-Si bond), and studies of radon compounds. The calculations suggest the existence of related polymers, aggregates, and even HNgY crystals, and their experimental preparation is a major challenge. Another interesting task, still in its early stages, is the preparation of HNgY molecules in the gas phase. PMID:18720951

  19. 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.

  20. Mechanics of fire ant aggregations

    NASA Astrophysics Data System (ADS)

    Tennenbaum, Michael; Liu, Zhongyang; Hu, David; Fernandez-Nieves, Alberto

    2016-01-01

    Fire ants link their bodies to form aggregations; these can adopt a variety of structures, they can drip and spread, or withstand applied loads. Here, by using oscillatory rheology, we show that fire ant aggregations are viscoelastic. We find that, at the lowest ant densities probed and in the linear regime, the elastic and viscous moduli are essentially identical over the spanned frequency range, which highlights the absence of a dominant mode of structural relaxation. As ant density increases, the elastic modulus rises, which we interpret by alluding to ant crowding and subsequent jamming. When deformed beyond the linear regime, the aggregation flows, exhibiting shear-thinning behaviour with a stress load that is comparable to the maximum load the aggregation can withstand before individual ants are torn apart. Our findings illustrate the rich, collective mechanical behaviour that can arise in aggregations of active, interacting building blocks.

  1. Mechanics of fire ant aggregations.

    PubMed

    Tennenbaum, Michael; Liu, Zhongyang; Hu, David; Fernandez-Nieves, Alberto

    2016-01-01

    Fire ants link their bodies to form aggregations; these can adopt a variety of structures, they can drip and spread, or withstand applied loads. Here, by using oscillatory rheology, we show that fire ant aggregations are viscoelastic. We find that, at the lowest ant densities probed and in the linear regime, the elastic and viscous moduli are essentially identical over the spanned frequency range, which highlights the absence of a dominant mode of structural relaxation. As ant density increases, the elastic modulus rises, which we interpret by alluding to ant crowding and subsequent jamming. When deformed beyond the linear regime, the aggregation flows, exhibiting shear-thinning behaviour with a stress load that is comparable to the maximum load the aggregation can withstand before individual ants are torn apart. Our findings illustrate the rich, collective mechanical behaviour that can arise in aggregations of active, interacting building blocks. PMID:26501413

  2. Imbibition kinetics of spherical aggregates

    NASA Astrophysics Data System (ADS)

    Hébraud, Pascal; Lootens, Didier; Debacker, Alban

    The imbibition kinetics of a millimeter-sized aggregate of 300 nm diameter colloidal particles by a wetting pure solvent is studied. Three successive regimes are observed : in the first one, the imbibition proceeds by compressing the air inside the aggregate. Then, the solvent stops when the pressure of the compressed air is equal to the Laplace pressure at the meniscus of the wetting solvent in the porous aggregate. The interface is pinned and the aggregate slowly degases, up to a point where the pressure of the entrapped air stops decreasing and is controlled by the Laplace pressure of small bubbles. Depending on the curvature of the bubble, the system may then be in an unstable state. The imbibition then starts again, but with an inner pressure in equilibrium with these bubbles. This last stage leads to the complete infiltration of the aggregate.

  3. Immunogenicity of Therapeutic Protein Aggregates.

    PubMed

    Moussa, Ehab M; Panchal, Jainik P; Moorthy, Balakrishnan S; Blum, Janice S; Joubert, Marisa K; Narhi, Linda O; Topp, Elizabeth M

    2016-02-01

    Therapeutic proteins have a propensity for aggregation during manufacturing, shipping, and storage. The presence of aggregates in protein drug products can induce adverse immune responses in patients that may affect safety and efficacy, and so it is of concern to both manufacturers and regulatory agencies. In this vein, there is a lack of understanding of the physicochemical determinants of immunological responses and a lack of standardized analytical methods to survey the molecular properties of aggregates associated with immune activation. In this review, we provide an overview of the basic immune mechanisms in the context of interactions with protein aggregates. We then critically examine the literature with emphasis on the underlying immune mechanisms as they relate to aggregate properties. Finally, we highlight the gaps in our current understanding of this issue and offer recommendations for future research. PMID:26869409

  4. Medicinal Chemistry Focusing on Aggregation of Amyloid-β.

    PubMed

    Sohma, Youhei

    2016-01-01

    The aggregation of peptides/proteins is intimately related to a number of human diseases. More than 20 have been identified which aggregate into fibrils containing extensive β-sheet structures, and species generated in the aggregation processes (i.e., oligomers and fibrils) contribute to disease development. Amyloid-β peptide (designated Aβ), related to Alzheimer's disease (AD), is the representative example. The intensive aggregation property of Aβ also leads to difficulty in its synthesis. To improve the synthetic problem, we developed an O-acyl isopeptide of Aβ1-42, in which the N-acyl linkage (amide bond) of Ser(26) was replaced with an O-acyl linkage (ester bond) at the side chain. The O-acyl isopeptide demonstrated markedly higher water-solubility than that of Aβ1-42, while it quickly converted to intact monomer Aβ1-42 via an O-to-N acyl rearrangement under physiological conditions. Inhibition of the pathogenic aggregation of Aβ1-42 might be a therapeutic strategy for curing AD. We succeeded in the rational design and identification of a small molecule aggregation inhibitor based on a pharmacophore motif obtained from cyclo[-Lys-Leu-Val-Phe-Phe-]. Moreover, the inhibition of Aβ aggregation was achieved via oxygenation (i.e., incorporation of oxygen atoms to Aβ) using an artificial catalyst. We identified a selective, cell-compatible photo-oxygenation catalyst of Aβ, a flavin catalyst attached to an Aβ-binding peptide, which markedly decreased the aggregation potency and neurotoxicity of Aβ. PMID:26726739

  5. Two Dimensional Aggregation Behaviors of Quinoxaline Dendrimers.

    PubMed

    Choi, Soyoung; Lee, Hoik; Kim, Hwan Kyu; Lee, Sang Uck; Sohn, Daewon

    2015-02-01

    This study focuses on the molecular behavior of two dendrimers containing a hydrophilic core group (carboxyl group) and hydrophobic branches (quinoxaline and methoxyphenyl groups), 2,3-bis(4-(2,3- bis(4-methoxyphenyl)quinoxalin-6-yloxy)phenyl)quinoxaline-6-carb-oxylic acid (G2) and 2,3-bis(4-(2,3-bis(4-(2,3-bis(4-methoxyphenyl)quinoxalin-6-yloxy)phe-nyl)quinoxalin-6-y-oxy)phenyl) quin oxaline-6-carboxylic acid (G3) at the air-water interface. To understand the mechanism of the self-assembly of these molecules, we measured the surface pressure-area (III-A) isotherm and investigated the surface morphology of Langmuir-Blodgett films transferred onto hydrophilic silicon wafers using atomic force microscopy (AFM). Upon compression, G2 molecules stand up and steadily make close-packed monolayer whereas G3 molecules form circular domains and gradually make aggregates of domains. These results were confirmed by the X-ray Reflectivity (XRR) profiles of G2 and G3 monolayers transferred onto silicon substrates. PMID:26353682

  6. Energy transfer in aggregates of bacteriochlorophyll c self-assembled with azulene derivatives.

    PubMed

    Matěnová, Martina; Lorelei Horhoiu, Viviana; Dang, Florian-Xuan; Pospíšil, Petr; Alster, Jan; Burda, Jaroslav V; Balaban, Teodor Silviu; Pšenčík, Jakub

    2014-08-21

    Bacteriochlorophyll (BChl) c is the main light-harvesting pigment of certain photosynthetic bacteria. It is found in the form of self-assembled aggregates in the so-called chlorosomes. Here we report the results of co-aggregation experiments of BChl c with azulene and its tailored derivatives. We have performed spectroscopic and quantum chemical characterization of the azulenes, followed by self-assembly experiments. The results show that only azulenes with sufficient hydrophobicity are able to induce aggregation of BChl c. Interestingly, only azulene derivatives possessing a conjugated phenyl ring were capable of efficient (∼50%) excitation energy transfer to BChl molecules. These aggregates represent an artificial light-harvesting complex with enhanced absorption between 220 and 350 nm compared to aggregates of pure BChl c. The results provide insight into the principles of self-assembly of BChl aggregates and suggest an important role of the π-π interactions in efficient energy transfer. PMID:24999619

  7. Perspectives on Preference Aggregation.

    PubMed

    Regenwetter, Michel

    2009-07-01

    For centuries, the mathematical aggregation of preferences by groups, organizations, or society itself has received keen interdisciplinary attention. Extensive theoretical work in economics and political science throughout the second half of the 20th century has highlighted the idea that competing notions of rational social choice intrinsically contradict each other. This has led some researchers to consider coherent democratic decision making to be a mathematical impossibility. Recent empirical work in psychology qualifies that view. This nontechnical review sketches a quantitative research paradigm for the behavioral investigation of mathematical social choice rules on real ballots, experimental choices, or attitudinal survey data. The article poses a series of open questions. Some classical work sometimes makes assumptions about voter preferences that are descriptively invalid. Do such technical assumptions lead the theory astray? How can empirical work inform the formulation of meaningful theoretical primitives? Classical "impossibility results" leverage the fact that certain desirable mathematical properties logically cannot hold in all conceivable electorates. Do these properties nonetheless hold true in empirical distributions of preferences? Will future behavioral analyses continue to contradict the expectations of established theory? Under what conditions do competing consensus methods yield identical outcomes and why do they do so? PMID:26158988

  8. 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

  9. 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

  10. 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

  11. Self-assembly of phenylalanine-based molecules.

    PubMed

    German, Helen W; Uyaver, Sahin; Hansmann, Ulrich H E

    2015-03-01

    Using molecular dynamics, we study the self-assembly of phenylalanine with charged end-groups at various temperatures and concentrations. As in the case of diphenylalanine, we observe the formation of nanotubes; however, phenylalanine aggregates in layers of four, not six, molecules. The observed aggregates are consistent with recent experimental measurements of fibrils obtained from mice with phenylketonuria. We investigate the stability and the mechanism by which these tubular structures form and discuss potential toxicity mechanisms. PMID:25347763

  12. 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.

  13. 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.

  14. Prion-like features of misfolded Aβ and tau aggregates.

    PubMed

    Morales, Rodrigo; Callegari, Keri; Soto, Claudio

    2015-09-01

    Recent findings have shown that several misfolded proteins can transmit disease pathogenesis in a prion-like manner by transferring their conformational properties to normally folded units. However, the extent by which these molecule-to-molecule or cell-to-cell spreading processes reflect the entire prion behavior is now subject of controversy, especially due to the lack of epidemiological data supporting inter-individual transmission of non-prion protein misfolding diseases. Nevertheless, extensive research has shown that several of the typical characteristics of prions can be observed for Aβ and tau aggregates when administered in animal models. In this article we review recent studies describing the prion-like features of both proteins, highlighting the similarities with bona fide prions in terms of inter-individual transmission, their strain-like conformational diversity, and the transmission of misfolded aggregates by different routes of administration. PMID:25575736

  15. Fundamentals of gas measurement I

    SciTech Connect

    Dodds, D.E.

    1995-12-01

    To truly understand gas measurement, a person must understand gas measurement fundamentals. This includes the units of measurement, the behavior of the gas molecule, the property of gases, the gas laws, and the methods and means of measuring gas. Since the quality of gas is often the responsibility of the gas measurement technician, it is important that he or she have a knowledge of natural gas chemistry.

  16. Self-Assembling NanoLuc Luciferase Fragments as Probes for Protein Aggregation in Living Cells.

    PubMed

    Zhao, Jia; Nelson, Travis J; Vu, Quyen; Truong, Tiffany; Stains, Cliff I

    2016-01-15

    Given the clear role of protein aggregation in human disease, there is a critical need for assays capable of quantifying protein aggregation in living systems. We hypothesized that the inherently low background and biocompatibility of luminescence signal readouts could provide a potential solution to this problem. Herein, we describe a set of self-assembling NanoLuc luciferase (Nluc) fragments that produce a tunable luminescence readout that is dependent upon the solubility of a target protein fused to the N-terminal Nluc fragment. To demonstrate this approach, we employed this assay in bacteria to assess mutations known to disrupt amyloid-beta (Aβ) aggregation as well as disease-relevant mutations associated with familial Alzheimer's diseases. The luminescence signal from these experiments correlates with the reported aggregation potential of these Aβ mutants and reinforces the increased aggregation potential of disease-relevant mutations in Aβ1-42. To further demonstrate the utility of this approach, we show that the effect of small molecule inhibitors on Aβ aggregation can be monitored using this system. In addition, we demonstrate that aggregation assays can be ported into mammalian cells. Taken together, these results indicate that this platform could be used to rapidly screen for mutations that influence protein aggregation as well as inhibitors of protein aggregation. This method offers a novel, genetically encodable luminescence readout of protein aggregation in living cells. PMID:26492083

  17. Molecules in the early universe

    SciTech Connect

    Lepp, S.; Shull, J.M.

    1984-05-15

    We present calculations of the formation of astrophysically interesting molecules (H/sub 2/, HD, LiH, and HeH/sup +/) by gas-phase reactions during the postrecombination epoch (redshifts z = 300-30). In standard Friedmann cosmological models, H/sub 2//Hroughly-equal10/sup -6/, HD/H/sub 2/roughly-equal10/sup -4.5/, and LiH/H/sub 2/roughly-equal10/sup -6.5/. These molecules may dominate the cooling and trigger the collapse of primordial gas clouds. The dipole rotational transitions of HD and LiH are particularly important at high density and low temperature. Additional molecules form during spherical collapse of these clouds, their rotational cooling keeps the gas temperature between 400 and 1500 K over 12 decades of density increase until the H/sub 2/ lines become optically thick. The existence of molecular coolants at high redshift has significant implications for the first generation of stars and for thermal instabilities in intergalactic matter.

  18. 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.

  19. 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.

  20. Investigation of critical lines and global phase behavior of unequal size of molecules in binary gas-liquid mixtures in the combined pressure-temperature-concentration planes around the van Laar point

    NASA Astrophysics Data System (ADS)

    Gençaslan, Mustafa; Keskin, Mustafa

    2016-09-01

    We investigate critical curves and global phase behavior of unequal size of molecules in binary gas-liquid mixtures at the van Laar point and its vicinity. The van Laar point is only point at which the mathematical double point curve is stable, and also the intersection of the tricritical point and the double critical end point. The critical line structure is displayed for various combinations of the chain length and system parameters in the reduced pressure (P∗) temperature (T∗) plane, as is usually done with experimental results and temperature-concentration (T, x) plane. The P∗,T∗ diagrams are discussed in accordance with the Scott and van Konynenburg binary phase diagram classification. We found that our P∗,T∗ plots correspond to the type II, type III, type IV phase diagram behaviors and they are in good agreement with the theoretical and experimental studies. It is also found that the critical lines and phase behavior are extremely sensitive to small modifications in the system parameters.

  1. 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. PMID:18327313

  2. 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

  3. Monosized aggregates -- A new model

    SciTech Connect

    Gopal, M.

    1997-08-01

    For applications requiring colloidal particles, it is desirable that they be monosized to better control the structure and the properties. In a number of systems, the monosized particles come together to form aggregates that are also monosized. A model is presented here to explain the formation of these monosized aggregates. This is of particular importance in the fields of ceramics, catalysis, pigments, pharmacy, photographic emulsions, etc.

  4. Aggregation of model asphaltenes: a molecular dynamics study.

    PubMed

    Costa, J L L F S; Simionesie, D; Zhang, Z J; Mulheran, P A

    2016-10-01

    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. PMID:27465036

  5. 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.

  6. 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.

  7. 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.

  8. Modifiers of mutant huntingtin aggregation

    PubMed Central

    Teuling, Eva; Bourgonje, Annika; Veenje, Sven; Thijssen, Karen; de Boer, Jelle; van der Velde, Joeri; Swertz, Morris; Nollen, Ellen

    2011-01-01

    Protein aggregation is a common hallmark of a number of age-related neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and polyglutamine-expansion disorders such as Huntington’s disease, but how aggregation-prone proteins lead to pathology is not known. Using a genome-wide RNAi screen in a C. elegans-model for polyglutamine aggregation, we previously identified 186 genes that suppress aggregation. Using an RNAi screen for human orthologs of these genes, we here present 26 human genes that suppress aggregation of mutant huntingtin in a human cell line. Among these are genes that have not been previously linked to mutant huntingtin aggregation. They include those encoding eukaryotic translation initiation, elongation and translation factors, and genes that have been previously associated with other neurodegenerative diseases, like the ATP-ase family gene 3-like 2 (AFG3L2) and ubiquitin-like modifier activating enzyme 1 (UBA1). Unravelling the role of these genes will broaden our understanding of the pathogenesis of Huntington’s disease. PMID:21915392

  9. Kinetic model for erythrocyte aggregation.

    PubMed

    Bertoluzzo, S M; Bollini, A; Rasia, M; Raynal, A

    1999-01-01

    It is well known that light transmission through blood is the most widely utilized method for the study of erythrocyte aggregation. The curves obtained had been considered empirically as exponential functions. In consequence, the process becomes characterized by an only parameter that varies with all the process factors without discrimination. In the present paper a mathematical model for RBC aggregation process is deduced in accordance with von Smoluchowski's theory about the kinetics of colloidal particles agglomeration. The equation fitted the experimental pattern of the RBC suspension optical transmittance closely and contained two parameters that estimate the most important characteristics of the aggregation process separately, i.e., (1) average size of rouleaux at equilibrium and (2) aggregation rate. The evaluation of the method was assessed by some factors affecting erythrocyte aggregation, such as temperature, plasma dilutions, Dextran 500, Dextran 70 and PVP 360, at different media concentrations, cellular membrane alteration by the alkylating agent TCEA, and decrease of medium osmolarity. Results were interpreted considering the process characteristics estimated by the parameters, and there were also compared with similar studies carried out by other authors with other methods. This analysis allowed us to conclude that the equation proposed is reliable and useful to study erythrocyte aggregation. PMID:10660481

  10. A covalent homodimer probing early oligomers along amyloid aggregation.

    PubMed

    Halabelian, Levon; Relini, Annalisa; Barbiroli, Alberto; Penco, Amanda; Bolognesi, Martino; Ricagno, Stefano

    2015-01-01

    Early oligomers are crucial in amyloid aggregation; however, due to their transient nature they are among the least structurally characterized species. We focused on the amyloidogenic protein beta2-microglobulin (β2m) whose early oligomers are still a matter of debate. An intermolecular interaction between D strands of facing β2m molecules was repeatedly observed, suggesting that such interface may be relevant for β2m dimerization. In this study, by mutating Ser33 to Cys, and assembling the disulphide-stabilized β2m homodimer (DimC33), such DD strand interface was locked. Although the isolated DimC33 display a stability similar to wt β2m under native conditions, it shows enhanced amyloid aggregation propensity. Three distinct crystal structures of DimC33 suggest that dimerization through the DD interface is instrumental for enhancing DimC33 aggregation propensity. Furthermore, the crystal structure of DimC33 in complex with the amyloid-specific dye Thioflavin-T pinpoints a second interface, which likely participates in the first steps of β2m aggregation. The present data provide new insight into β2m early steps of amyloid aggregation. PMID:26420657

  11. A covalent homodimer probing early oligomers along amyloid aggregation

    PubMed Central

    Halabelian, Levon; Relini, Annalisa; Barbiroli, Alberto; Penco, Amanda; Bolognesi, Martino; Ricagno, Stefano

    2015-01-01

    Early oligomers are crucial in amyloid aggregation; however, due to their transient nature they are among the least structurally characterized species. We focused on the amyloidogenic protein beta2-microglobulin (β2m) whose early oligomers are still a matter of debate. An intermolecular interaction between D strands of facing β2m molecules was repeatedly observed, suggesting that such interface may be relevant for β2m dimerization. In this study, by mutating Ser33 to Cys, and assembling the disulphide-stabilized β2m homodimer (DimC33), such DD strand interface was locked. Although the isolated DimC33 display a stability similar to wt β2m under native conditions, it shows enhanced amyloid aggregation propensity. Three distinct crystal structures of DimC33 suggest that dimerization through the DD interface is instrumental for enhancing DimC33 aggregation propensity. Furthermore, the crystal structure of DimC33 in complex with the amyloid-specific dye Thioflavin-T pinpoints a second interface, which likely participates in the first steps of β2m aggregation. The present data provide new insight into β2m early steps of amyloid aggregation. PMID:26420657

  12. Patterning microparticles on a template of aggregated cationic dye.

    PubMed

    Wexler, Allan; Switalski, Steven; Bennett, Grace; Lindner, Kimberly; Baptiste, Kenny; Slater, Gary

    2015-02-01

    Patternwise aggregation of charged molecules on a surface is potentially a facile approach to generate a template on which to pattern oppositely charged microparticles. We report on the patterning of silica microparticles by a system comprising a photopatternable copolymer and an aggregate forming penta-cationic cyanine dye. A thin film of the copolymer, composed of a molar excess of styrenesulfonic acid oxime ester to cross-linkable glycidyl methacrylate monomomers, was exposed through a mask and neutralized, resulting in a pattern of hydrophobic areas, and where exposed, a hydrophilic cross-linked film with sodium poly(styrenesulfonate) domains. The occurrence and locus of aggregation of an aqueous solution of the dye, applied to the patterned surface was established by absorbance and fluorescence spectroscopy and atomic force microscopy. In exposed areas, dye is imbibed and aggregation induced in sodium styrenesulfonate domains internal to the layer, whereas in the unexposed areas the dye aggregates on the hydrophobic surface. Aqueous anionic silica microparticles applied to the dye treated patterned surface and then rinsed, are retained in the unexposed areas having cationic surface aggregates, but rejected from the exposed areas with internal dye aggregates as these areas retain net negative charge. Mask exposure, absent dye treatment, did not result in patterning as negatively charged microparticles were nowhere retained, and positively charged particles were everywhere retained. The extent of surface coverage by the dye in unexposed areas was deposition time dependent, and ranged from isolated patches covering about 20 percent of the polymer surface to a surface saturated layer, with silica particle patterning robust over the range of dye surface coverages studied. The force requirements to pattern the denser than water silica microparticles are identified, and particle and polymer film surface potentials that meet the critical repulsion force requirement

  13. 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

  14. Electrospray ion mobility mass spectrometry of positively charged sodium bis[2-ethythexyl)sulfosuccinate aggregates.

    PubMed

    Bongiorno, David; Indelicato, Serena; Giorgi, Gianluca; Scarpella, Simona; Liveri, Vincenzo Turco; Ceraulo, Leopoldo

    2014-01-01

    Collision cross-sections (CCS) of positively singly and multiply charged aggregates of the surfactant sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) in the gas phase have been measured by quadrupole ion mobility time-of-flight mass spectrometry. Calibration of the observed drift times to the CCS of the AOTNa non-covalent aggregates was achieved by collecting, under the same experimental conditions, the drift times of a range of singly and multiply charged polyalanine peptides whose CCS had been obtained by conventional ion mobility spectrometry. Together with an obvious increase of the aggregate cross-section with the aggregation number, it was found that the aggregate cross-section increases with the charge state due to the sodium counterions steric effect and the augmented electrostatic repulsion. This finding is consistent with the result of a previous molecular dynamics study on positively charged AOTNa aggregates in the gas phase showing that, by increasing the charge state, the aggregates become progressively more oblate; implying a rise of their CCS. Moreover, the occurrence at each aggregation number and extra charge of a unique value of cross section points toward aggregates whose conformations do not show discernible shape change in the experiment time scale. PMID:24895777

  15. Crystal aggregation in kidney stones; a polymer aggregation problem?

    NASA Astrophysics Data System (ADS)

    Wesson, J.; Beshensky, A.; Viswanathan, P.; Zachowicz, W.; Kleinman, J.

    2008-03-01

    Kidney stones most frequently form as aggregates of calcium oxalate monohydrate (COM) crystals with organic layers between them, and the organic layers contain principally proteins. The pathway leading to the formation of these crystal aggregates in affected people has not been identified, but stone forming patients are thought to have a defect in the structure or distribution of urinary proteins, which normally protect against stone formation. We have developed two polyelectrolyte models that will induce COM crystal aggregation in vitro, and both are consistent with possible urinary protein compositions. The first model was based on mixing polyanionic and polycationic proteins, in portions such that the combined protein charge is near zero. The second model was based on reducing the charge density on partially charged polyanionic proteins, specifically Tamm-Horsfall protein, the second most abundant protein in urine. Both models demonstrated polymer phase separation at solution conditions where COM crystal aggregation was observed. Correlation with data from other bulk crystallization measurements suggest that the anionic side chains form critical binding interactions with COM surfaces that are necessary along with the phase separation process to induce COM crystal aggregation.

  16. Bistable aggregate of all-trans-astaxanthin in an aqueous solution

    NASA Astrophysics Data System (ADS)

    Mori, Yuso; Yamano, Kuniko; Hashimoto, Hideki

    1996-05-01

    The temperature dependence of the optical absorption spectra for astaxanthin aggregate has been studied between 2 and 32°C. Red-shifted absorption bands as compared to the monomer absorption band are found above 21°C in addition to the blue-shifted band of the aggregate. The spectra suggest that the molecular arrangement in the aggregate is a bistable one consisting of head-to-tail and card-packed arrangements. A diagram describing the bistability together with the monomer state is proposed in the space defined by the free energy and the quantity of Σi = 1 N< θ12 + < σθ12 for the ith molecule in the N-molecule aggregate.

  17. 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.

  18. 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

  19. Aggregation-Induced Emission Mechanism of Dimethoxy-Tetraphenylethylene in Water Solution: Molecular Dynamics and QM/MM Investigations.

    PubMed

    Sun, Guangxu; Zhao, Yi; Liang, WanZhen

    2015-05-12

    Molecular dynamics simulations and combined quantum mechanics and molecular mechanics calculations are employed to investigate dimethoxy-tetraphenylethylene (DMO-TPE) molecules in water solution for their detailed aggregation process and the mechanism of aggregation-induced emission. The molecular dynamics simulations show that the aggregates start to appear in the nanosecond time scale, and small molecular aggregates appear at low concentration; whereas the large aggregates with a chain-type structure appear at high concentration, and the intramolecular rotation is largely restricted by a molecular aggregated environment. The average radical distribution demonstrates that the waters join the aggregation process and that two types of hydrogen bonds between DMO-TPE and water molecules are built with the peaks at about 0.5 and 0.7 nm, respectively. The spectral features further reveal that the aggregates dominantly present J-type aggregation although they fluctuate between J-type and H-type at a given temperature. The statistical absorption, emission spectra, and the aggregation-induced emission enhancement with respect to the solution concentration agree well with the experimental measurements, indicating the significant effect of molecular environments on the molecular properties. PMID:26574424

  20. 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…

  1. Aggregation of intrinsically disordered fibrinogen as the influence of backbone conformation.

    PubMed

    Naeem, Aabgeena; Bhat, Sheraz Ahmad; Iram, Afshin; Khan, Rizwan Hasan

    2016-08-01

    Fib having intrinsically disordered αC domains is involved in coagulation cascade and thrombosis. Fib molecules forms prefibrillar oligomers at 30%, and associate in 40 and 50% TFE to proceed α to β transition, suggesting the formation of an intermolecular β-structure. AFM images confirmed the nature of Fib aggregates at 40 and 50% TFE to be prefibrillar and fibrillar respectively. These aggregates possess high thioflavin T fluorescence with a shifted Congo red absorbance. Kinetics of Fib aggregation data at 50% TFE supports nucleation-dependent polymerization mechanism. At 60 and 70% TFE, no aggregation was observed. The inhibition of protein aggregation appears due to weakening of the hydrophobic interactions that were initially stabilizing the intermolecular β-sheet structure in the protein aggregation. The loss of hydrophobic contacts seems to favor the formation of intramolecular hydrogen bonds over intermolecular hydrogen bonds leading to helix formation. To conclude, protein aggregation is accompanied by the formation of β-sheet conformation, and induction of non-native helical segments in the protein inhibits aggregation. The discrepancy of the secondary structures on aggregation is proposed to stem from the disparity in the nature of the hydrogen bonds and packing of hydrophobic residues of the side chains in the β-sheet and α-helix conformation. PMID:27150313

  2. 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

  3. Aggregated recommendation through random forests.

    PubMed

    Zhang, Heng-Ru; Min, Fan; He, Xu

    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

  4. The Lantibiotic Nisin Induces Lipid II Aggregation, Causing Membrane Instability and Vesicle Budding

    PubMed Central

    Scherer, Katharina M.; Spille, Jan-Hendrik; Sahl, Hans-Georg; Grein, Fabian; Kubitscheck, Ulrich

    2015-01-01

    The antimicrobial peptide nisin exerts its activity by a unique dual mechanism. It permeates the cell membranes of Gram-positive bacteria by binding to the cell wall precursor Lipid II and inhibits cell wall synthesis. Binding of nisin to Lipid II induces the formation of large nisin-Lipid II aggregates in the membrane of bacteria as well as in Lipid II-doped model membranes. Mechanistic details of the aggregation process and its impact on membrane permeation are still unresolved. In our experiments, we found that fluorescently labeled nisin bound very inhomogeneously to bacterial membranes as a consequence of the strong aggregation due to Lipid II binding. A correlation between cell membrane damage and nisin aggregation was observed in vivo. To further investigate the aggregation process of Lipid II and nisin, we assessed its dynamics by single-molecule microscopy of fluorescently labeled Lipid II molecules in giant unilamellar vesicles using light-sheet illumination. We observed a continuous reduction of Lipid II mobility due to a steady growth of nisin-Lipid II aggregates as a function of time and nisin concentration. From the measured diffusion constants of Lipid II, we estimated that the largest aggregates contained tens of thousands of Lipid II molecules. Furthermore, we observed that the formation of large nisin-Lipid II aggregates induced vesicle budding in giant unilamellar vesicles. Thus, we propose a membrane permeation mechanism that is dependent on the continuous growth of nisin-Lipid II aggregation and probably involves curvature effects on the membrane. PMID:25762323

  5. The lantibiotic nisin induces lipid II aggregation, causing membrane instability and vesicle budding.

    PubMed

    Scherer, Katharina M; Spille, Jan-Hendrik; Sahl, Hans-Georg; Grein, Fabian; Kubitscheck, Ulrich

    2015-03-10

    The antimicrobial peptide nisin exerts its activity by a unique dual mechanism. It permeates the cell membranes of Gram-positive bacteria by binding to the cell wall precursor Lipid II and inhibits cell wall synthesis. Binding of nisin to Lipid II induces the formation of large nisin-Lipid II aggregates in the membrane of bacteria as well as in Lipid II-doped model membranes. Mechanistic details of the aggregation process and its impact on membrane permeation are still unresolved. In our experiments, we found that fluorescently labeled nisin bound very inhomogeneously to bacterial membranes as a consequence of the strong aggregation due to Lipid II binding. A correlation between cell membrane damage and nisin aggregation was observed in vivo. To further investigate the aggregation process of Lipid II and nisin, we assessed its dynamics by single-molecule microscopy of fluorescently labeled Lipid II molecules in giant unilamellar vesicles using light-sheet illumination. We observed a continuous reduction of Lipid II mobility due to a steady growth of nisin-Lipid II aggregates as a function of time and nisin concentration. From the measured diffusion constants of Lipid II, we estimated that the largest aggregates contained tens of thousands of Lipid II molecules. Furthermore, we observed that the formation of large nisin-Lipid II aggregates induced vesicle budding in giant unilamellar vesicles. Thus, we propose a membrane permeation mechanism that is dependent on the continuous growth of nisin-Lipid II aggregation and probably involves curvature effects on the membrane. PMID:25762323

  6. Aggregation operations for multiaspect fuzzy soft sets

    NASA Astrophysics Data System (ADS)

    Sulaiman, Nor Hashimah; Mohamad, Daud

    2015-10-01

    Multiaspect fuzzy soft set (MAFSS) is one of the generalized forms of fuzzy soft sets. In this paper, we introduce two types of aggregation operations for MAFSSs, namely the weighted arithmetic mean (WAM)-based MAFSS aggregation, and the ordered weighted aggregation (OWA)-based MAFSS aggregation. The applicability of the two MAFSS-aggregation operations is illustrated with numerical examples in group decision making.

  7. Real-time imaging of Huntingtin aggregates diverting target search and gene transcription.

    PubMed

    Li, Li; Liu, Hui; Dong, Peng; Li, Dong; Legant, Wesley R; Grimm, Jonathan B; Lavis, Luke D; Betzig, Eric; Tjian, Robert; Liu, Zhe

    2016-01-01

    The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells - 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells. PMID:27484239

  8. Tunneling electron induced molecular electroluminescence from individual porphyrin J-aggregates

    NASA Astrophysics Data System (ADS)

    Meng, Qiushi; Zhang, Chao; Zhang, Yang; Zhang, Yao; Liao, Yuan; Dong, Zhenchao

    2015-07-01

    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.

  9. 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.

  10. 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.

  11. Aggregation induced enhanced emission of 2-(2'-hydroxyphenyl)benzimidazole.

    PubMed

    Malakar, Ashim; Kumar, Manishekhar; Reddy, Anki; Biswal, Himadree T; Mandal, Biman B; Krishnamoorthy, G

    2016-07-01

    In this study, the aggregation induced emission enhancement (AIEE) of 2-(2'-hydroxyphenyl)benzimidazole (HPBI) is reported. To investigate the AIEE process of HPBI, absorption/fluorescence spectroscopy, fluorescence imaging and field emission scanning electron microscopy were employed. A comparative study with 2-phenylbenzimidazole (PBI) divulges the significance of the hydroxyl group in the AIEE process. Further, molecular dynamics simulations have been carried out with explicit solvent molecules to follow the aggregation process of HPBI with time. The obtained molecular dynamics simulation results not only predicted the formation of aggregates but also provided detailed insight and information on the molecular interactions. The cellular studies showed aggregates yield higher fluorescence in the visible region inside HeLa cells in comparison to monomeric compounds which failed to exhibit any visible fluorescence inside the cell. The obtained aggregates were further found to be biocompatible and therefore can be used for bio-imaging applications. PMID:27334264

  12. Glass/Jamming Transition in Colloidal Aggregation

    NASA Technical Reports Server (NTRS)

    Segre, Philip N.; Prasad, Vikram; Weitz, David A.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    We have studied colloidal aggregation in a model colloid plus polymer system with short-range attractive interactions. By varying the colloid concentration and the strength of the attraction, we explored regions where the equilibrium phase is expected to consist of colloidal crystallites in coexistance with colloidal gas (i.e. monomers). This occurs for moderate values of the potential depth, U approximately equal to 2-5 kT. Crystallization was not always observed. Rather, over an extended sub-region two new metastable phases appear, one fluid-like and one solid-like. These were examined in detail with light scattering and microscopy techniques. Both phases consist of a near uniform distribution of small irregular shaped clusters of colloidal particles. The dynamical and structural characteristics of the ergodic-nonergodic transition between the two phases share much in common with the colloidal hard sphere glass transition.

  13. Evaporation effects in elastocapillary aggregation

    NASA Astrophysics Data System (ADS)

    Vella, Dominic; Hadjittofis, Andreas; Singh, Kiran; Lister, John

    2015-11-01

    We consider the effect of evaporation on the aggregation of a number of elastic objects due to a liquid's surface tension. In particular, we consider an array of spring-block elements in which the gaps between blocks are filled by thin liquid films that evaporate during the course of an experiment. Using lubrication theory to account for the fluid flow within the gaps, we study the dynamics of aggregation. We find that a non-zero evaporation rate causes the elements to aggregate more quickly and, indeed, to contact within finite time. However, we also show that the number of elements within each cluster decreases as the evaporation rate increases. We explain these results quantitatively by comparison with the corresponding two-body problem and discuss their relevance for controlling pattern formation in carbon nanotube forests.

  14. Global kinetic analysis of seeded BSA aggregation.

    PubMed

    Sahin, Ziya; Demir, Yusuf Kemal; Kayser, Veysel

    2016-04-30

    Accelerated aggregation studies were conducted around the melting temperature (Tm) to elucidate the kinetics of seeded BSA aggregation. Aggregation was tracked by SEC-HPLC and intrinsic fluorescence spectroscopy. Time evolution of monomer, dimer and soluble aggregate concentrations were globally analysed to reliably deduce mechanistic details pertinent to the process. Results showed that BSA aggregated irreversibly through both sequential monomer addition and aggregate-aggregate interactions. Sequential monomer addition proceeded only via non-native monomers, starting to occur only by 1-2°C below the Tm. Aggregate-aggregate interactions were the dominant mechanism below the Tm due to an initial presence of small aggregates that acted as seeds. Aggregate-aggregate interactions were significant also above the Tm, particularly at later stages of aggregation when sequential monomer addition seemed to cease, leading in some cases to insoluble aggregate formation. The adherence (or non-thereof) of the mechanisms to Arrhenius kinetics were discussed alongside possible implications of seeding for biopharmaceutical shelf-life and spectroscopic data interpretation, the latter of which was found to often be overlooked in BSA aggregation studies. PMID:26970282

  15. Photoactivatable aggregation-induced emission fluorophores with multiple-color fluorescence and wavelength-selective activation.

    PubMed

    Peng, Lu; Zheng, Yue; Wang, Xiaoyan; Tong, Aijun; Xiang, Yu

    2015-03-01

    Photoactivatable (caged) fluorophores are widely used in chemistry, materials, and biology. However, the development of such molecules exhibiting photoactivable solid-state fluorescence is still challenging due to the aggregation-caused quenching (ACQ) effect of most fluorophores in their aggregate or solid states. In this work, we developed caged salicylaldehyde hydrazone derivatives, which are of aggregation-induced emission (AIE) characteristics upon light irradiation, as efficient photoactivatable solid-state fluorophores. These compounds displayed multiple-color emissions and ratiometric (photochromic) fluorescence switches upon wavelength-selective photoactivation, and were successfully applied for photopatterning and photoactivatable cell imaging in a multiple-color and stepwise manner. PMID:25644036

  16. 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.

  17. Aggregation-induced emission: a simple strategy to improve chemiluminescence resonance energy transfer.

    PubMed

    Zhang, Lijuan; He, Nan; Lu, Chao

    2015-01-20

    The emergence of aggregation-induced emission (AIE) has opened up a new avenue for scientists. There is a great demand for the development of a new generation chemiluminescence resonance energy transfer (CRET) acceptors with AIE characteristics due to the aggregation-caused chemiluminescence (CL) quenching effect commonly observed in the conventional fluorophore CL acceptors at high concentrations. However, the systematical studies involving in AIE-amplified CL are still scarce. Herein, it is the first report that the gold nanocluster aggregates (a type of well-defined AIE molecules) are used to study their influence on the bis(2,4,6-trichlorophenyl) oxalate (TCPO)-H2O2 CL reaction. Interestingly, the AIE molecules in the diluted solution are unable to boost the CL signal of the TCPO-H2O2 system, but their aggregates display a strongly enhanced CL emission compared to their counterparts of fluorophore molecules, thanks to the unique AIE effect of gold nanoclusters. In comparison to rhodamine B with the aid of an imidazole catalyst, the detection limit of the gold nanocluster aggregate-amplified CL probe for H2O2 (S/N = 3) is low in the absence of any catalyst. Finally, the other two typical AIE molecules, Au(I)-thiolate complexes and 9,10-bis[4-(3-sulfonatopropoxyl)-styryl]anthracene (BSPSA), are investigated to verify the generality of the AIE molecule-amplified CL emissions. These results demonstrate effective access to highly fluorescent AIE molecules with practical applications in avoiding the aggregation-induced CL quenching at high concentrations, which can be expected to provide a novel and sensitive platform for the CL amplified detection. PMID:25526522

  18. Preparation of biocatalytic nanofibres with high activity and stability via enzyme aggregate coating on polymer nanofibres

    NASA Astrophysics Data System (ADS)

    Kim, Byoung Chan; Nair, Sujith; Kim, Jungbae; Kwak, Ja Hun; Grate, Jay W.; Kim, Seong H.; Gu, Man Bock

    2005-07-01

    We have developed a unique approach for the fabrication of enzyme aggregate coatings on the surfaces of electrospun polymer nanofibres. This approach employs covalent attachment of seed enzymes onto nanofibres consisting of a mixture of polystyrene and poly(styrene-co-maleic anhydride), followed by a glutaraldehyde (GA) treatment that cross-links additional enzyme molecules and aggregates from the solution onto the covalently attached seed enzyme molecules. These cross-linked enzyme aggregates, covalently attached to the nanofibres via the linkers of seed enzyme molecules, are expected to improve the enzyme activity due to increased enzyme loading, and also the enzyme stability. To demonstrate the principle, we coated α-chymotrypsin (CT) on nanofibres electrospun from a mixture of polystyrene and poly(styrene-co-maleic anhydride). The initial activity of CT-aggregate-coated nanofibres was nine times higher than nanofibres with just a layer of covalently attached CT molecules. The enzyme stability of CT-aggregate-coated nanofibres was greatly improved with essentially no measurable loss of activity over a month of observation under rigorous shaking conditions. This new approach of enzyme coating on nanofibres, yielding high activity and stability, creates a useful new biocatalytic immobilized enzyme system with potential applications in bioconversion, bioremediation, and biosensors.

  19. Effect of water on deposition, aggregate size, and viscosity of asphaltenes.

    PubMed

    Aslan, Seyma; Firoozabadi, Abbas

    2014-04-01

    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. PMID:24650340

  20. Sulfate anion delays the self-assembly of human insulin by modifying the aggregation pathway.

    PubMed

    Owczarz, Marta; Arosio, Paolo

    2014-07-01

    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

  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. 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

  3. Simple Statistical Model for Branched Aggregates: Application to Cooee Bitumen.

    PubMed

    Lemarchand, Claire A; Hansen, Jesper S

    2015-11-01

    We propose a statistical model that can reproduce the size distribution of any branched aggregate, including amylopectin, dendrimers, molecular clusters of monoalcohols, and asphaltene nanoaggregates. It is based on the conditional probability for one molecule to form a new bond with a molecule, given that it already has bonds with others. The model is applied here to asphaltene nanoaggregates observed in molecular dynamics simulations of Cooee bitumen. The variation with temperature of the probabilities deduced from this model is discussed in terms of statistical mechanics arguments. The relevance of the statistical model in the case of asphaltene nanoaggregates is checked by comparing the predicted value of the probability for one molecule to have exactly i bonds with the same probability directly measured in the molecular dynamics simulations. The agreement is satisfactory. PMID:26458140

  4. Properties of substances inhibiting aggregation of oxidized GAPDH: Data on the interaction with the enzyme and the impact on its intracellular content.

    PubMed

    Lazarev, Vladimir F; Nikotina, Alina D; Semenyuk, Pavel I; Evstafyeva, Diana B; Mikhaylova, Elena R; Muronetz, Vladimir I; Shevtsov, Maxim A; Tolkacheva, Anastasia V; Dobrodumov, Anatoly V; Shavarda, Alexey L; Guzhova, Irina V; Margulis, Boris A

    2016-06-01

    This data is related to our paper "Small molecules preventing GAPDH aggregation are therapeutically applicable in cell and rat models of oxidative stress" (Lazarev et al. [1]) where we explore therapeutic properties of small molecules preventing GAPDH aggregation in cell and rat models of oxidative stress. The present article demonstrates a few of additional properties of the chemicals shown to block GAPDH aggregation such as calculated site for targeting the enzyme, effects on GAPDH glycolytic activity, influence on GAPDH intracellular level and anti-aggregate activity of pure polyglutamine exemplifying a denatured protein. PMID:27054152

  5. 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.

  6. Nucleic acid-induced tetraphenylethene probe noncovalent self-assembly and the superquenching of aggregation-induced emission.

    PubMed

    Chen, Jian; Wang, Yan; Li, Wenying; Zhou, Huipeng; Li, Yongxin; Yu, Cong

    2014-10-01

    Superquenching of aggregation-induced emission (AIE) has been utilized in biosensing for the first time. A positively charged tetraphenylethene derivative (compound 1) showed no emission in an aqueous buffer solution. A single-stranded DNA (a polyanion) induced aggregation of compound 1, and strong compound 1 aggregate emission was observed. When the DNA was labeled with a quencher molecule, compound 1 aggregate emission was efficiently quenched. On the basis of this observation, a new, simple, sensitive and selective DNA methyltransferase (MTase) assay has been developed. A quencher-labeled double-stranded DNA could induce aggregation of compound 1, and superquenching of compound 1 AIE was observed. In the presence of MTase and an endonuclease, the DNA could be specifically methylated and cleaved into single-stranded DNA fragments. The quencher molecule was released, and a turn-on emission signal was detected. PMID:25203656

  7. Fluorescence from an H-aggregated naphthalenediimide based peptide: photophysical and computational investigation of this rare phenomenon.

    PubMed

    Basak, Shibaji; Nandi, Nibedita; Bhattacharyya, Kalishankar; Datta, Ayan; Banerjee, Arindam

    2015-11-11

    Fluorescence associated with J-aggregated naphthalenediimides (NDIs) is common. However, in this study an NDI based synthetic peptide molecule is found to form a fluorescent H-aggregate in a chloroform (CHCl3)-methylcyclohexane (MCH) mixture. An attempt has been made to explain the unusual fluorescence property of this H-aggregated NDI derivative. Time correlated single photon counting (TCSPC) shows that the average lifetime of the NDI based molecule is on the order of a few nanoseconds. It is revealed from the computational study that the transition from the second exited state (S2) to the ground energy state (S0) is responsible for the fluorescence as S1 is a dark state. Such rare violation of Kasha's rule accounts for the unusual fluorescence properties of this type of NDI molecule in the H-aggregated state. PMID:26508537

  8. 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.

  9. 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.

  10. Aqueous Self-Sorting in Extended Supramolecular Aggregates

    PubMed Central

    Rest, Christina; Mayoral, María José; Fernández, Gustavo

    2013-01-01

    Self-organization and self-sorting processes are responsible for the regulation and control of the vast majority of biological processes that eventually sustain life on our planet. Attempts to unveil the complexity of these systems have been devoted to the investigation of the binding processes between artificial molecules, complexes or aggregates within multicomponent mixtures, which has facilitated the emergence of the field of self-sorting in the last decade. Since, artificial systems involving discrete supramolecular structures, extended supramolecular aggregates or gel-phase materials in organic solvents or—to a lesser extent—in water have been investigated. In this review, we have collected diverse strategies employed in recent years to construct extended supramolecular aggregates in water upon self-sorting of small synthetic molecules. We have made particular emphasis on co-assembly processes in binary mixtures leading to supramolecular structures of remarkable complexity and the influence of different external variables such as solvent and concentration to direct recognition or discrimination processes between these species. The comprehension of such recognition phenomena will be crucial for the organization and evolution of complex matter. PMID:23344056

  11. 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. PMID:27455391

  12. 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. ...

  13. 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

  14. Morphology and structure of photosensitive dye J-aggregates adsorbed on AgBr microcrystals grown in gelatin.

    PubMed

    Saijo, H; Shiojiri, M

    1998-07-15

    Though the cyanine dye J-aggregates carry the role to sense the exposing light in the silver halide photographic system, little research on the morphology of the aggregates in adsorption has been made with modern surface analytical methods. In this paper, we describe the size, epitaxy, multi-layered array formation, nucleation and preferential adsorption, and irregular distribution of population between particles and the segregation on a particle, of J-aggregates adsorbed on AgBr grown in gelatin. We employed cathodoluminescence microscopy, low energy high resolution scanning electron microscopy, and atomic force microscopy. Dye molecules aggregate together near the surface of AgBr and adsorb on the surface. The growth of adsorbed aggregates is controlled by the diffusion of dye molecules from the surrounding solution. The population of J-aggregates adsorbed on an AgBr particle varies from almost none to full coverage. Each aggregate is about (20-30) x (30-50) nm in size and is 2.1 nm thick for thiacarbocyanine with sodium ion, 1.04 nm for thiacarbocyanine with tosyl ion, and 0.5 nm for an oxacarbocyanine. The aggregates connect their longer edges to each other to form arrays, and the arrays build up multi-layered stacks. The arrays align parallel and segregate to form terraces. The longer edges of J-aggregates align along [210] on AgBr (100) or [632] on AgBr (111). PMID:9728883

  15. 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. PMID:25330023

  16. Super-Resolution Fluorescence of Huntingtin Reveals Growth of Globular Species into Short Fibers and Coexistence of Distinct Aggregates

    PubMed Central

    2015-01-01

    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. PMID:25330023

  17. 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

  18. Efficient Inhibition of Protein Aggregation, Disintegration of Aggregates, and Lowering of Cytotoxicity by Green Tea Polyphenol-Based Self-Assembled Polymer Nanoparticles.

    PubMed

    Debnath, Koushik; Shekhar, Shashi; Kumar, Vipendra; Jana, Nihar R; Jana, Nikhil R

    2016-08-10

    Green tea polyphenol epigallocatechin-3-gallate (EGCG) is known for its antiamyloidogenic property, and it is observed that molecular EGCG binds with amyloid structure, redirects fibrillation kinetics, remodels mature fibril, and lowers the amyloid-derived toxicity. However, this unique property of EGCG is difficult to utilize because of their poor chemical stability and substandard bioavailability. Here we report a nanoparticle form of EGCG of 25 nm size (nano-EGCG) which is 10-100 times more efficient than molecular EGCG in inhibiting protein aggregation, disintegrating mature protein aggregates, and lowering amyloidogenic cytotoxicity. The most attractive advantage of nano-EGCG is that it efficiently protects neuronal cells from the toxic effect of extracellular amyloid beta or intracellular mutant huntingtin protein aggregates by preventing their aggregation. We found that the better performance of nano-EGCG is due to the combined effect of increased chemical stability of EGCG against degradation, stronger binding with protein aggregates, and efficient entry into the cell for interaction with aggregated protein structure. This result indicates that the nanoparticle form of antiamyloidogenic molecules can be more powerful in prevention and curing of protein aggregation derived diseases. PMID:27427935

  19. Time-dependent aggregation-induced enhanced emission, absorption spectral broadening, and aggregation morphology of a novel perylene derivative with a large D-π-A structure.

    PubMed

    Yang, Long; Yu, Yuyan; Zhang, Jin; Ge, Feijie; Zhang, Jianling; Jiang, Long; Gao, Fang; Dan, Yi

    2015-05-01

    Strong aggregation-caused quenching of perylene diimides (PDI) is changed successfully by simple chemical modification with two quinoline moieties through C=C at the bay positions to obtain aggregation-induced enhanced emission (AIEE) of a perylene derivative (Cya-PDI) with a large π-conjugation system. Cya-PDI is weakly luminescent in the well-dispersed CH(3)CN or THF solutions and exhibits an evident time-dependent AIEE and absorption spectra broadening in the aggregated state. In addition, morphological inspection demonstrates that the morphology of the aggregated form of Cya-PDI molecules changed from plate-shaped to rod-like aggregates under the co-effects of time and water. An edge-to-face arrangement of aggregation was proposed and discussed. The fact that the Cya-PDI aggregates show a broad absorption covering the whole visible-light range and strong intermolecular interaction through π-π stacking in the solid state makes them promising materials for optoelectric applications. PMID:25643930

  20. Inhibition of β-amyloid1-40 Peptide Aggregation and Neurotoxicity by Citrate

    PubMed Central

    Park, Yong Hoon; Kim, Young-Jin; Son, Il Hong

    2009-01-01

    The accumulation of β-amyloid (Aβ) aggregates is a characteristic of Alzheimer's disease (AD). Furthermore, these aggregates have neurotoxic effects on cells, and thus, molecules that inhibit Aβ aggregate formation could be valuable therapeutics for AD. It is well known that aggregation of Aβ depends on its hydrophobicity, and thus, in order to increase the hydrophilicity of Aβ, we considered using citrate, an anionic surfactant with three carboxylic acid groups. We hypothesized that citrate could reduce hydrophobicity and increase hydrophilicity of Aβ1-40 molecules via hydrophilic/electrostatic interactions. We found that citrate significantly inhibited Aβ1-40 aggregation and significantly protected SH-SY5Y cell line against Aβ1-40 aggregates-induced neurotoxicity. In details, we examined the effects of citrate on Aβ1-40 aggregation and on Aβ1-40 aggregates-induced cytotoxicity, cell viability, and apoptosis. Th-T assays showed that citrate significantly inhibited Aβ1-40 aggregation in a concentration-dependent manner (Th-T intensity: from 91.3% in 0.01 mM citrate to 82.1% in 1.0 mM citrate vs. 100.0% in Aβ1-40 alone). In cytotoxicity and viability assays, citrate reduced the toxicity of Aβ1-40 in a concentration-dependent manner, in which the cytotoxicity decreased from 107.5 to 102.3% as compared with Aβ1-40 aggregates alone treated cells (127.3%) and the cell viability increased from 84.6 to 93.8% as compared with the Aβ1-40 aggregates alone treated cells (65.3%). Furthermore, Hoechst 33342 staining showed that citrate (1.0 mM) suppressed Aβ1-40 aggregates-induced apoptosis in the cells. This study suggests that citrate can inhibit Aβ1-40 aggregation and protect neurons from the apoptotic effects of Aβ1-40 aggregates. Accordingly, our findings suggest that citrate administration should be viewed as a novel neuroprotective strategy for AD. PMID:19885010

  1. Unraveling the aggregation effect on amorphous phase AIE luminogens: a computational study.

    PubMed

    Zheng, Xiaoyan; Peng, Qian; Zhu, Lizhe; Xie, Yujun; Huang, Xuhui; Shuai, Zhigang

    2016-08-18

    To achieve the efficient and precise regulation of aggregation-induced emission (AIE), unraveling the aggregation effects on amorphous AIE luminogens is of vital importance. Using a theoretical protocol combining molecular dynamics simulations and quantum mechanics/molecular mechanics calculations, we explored the relationship between molecular packing, optical spectra and fluorescence quantum efficiency of amorphous AIE luminogens hexaphenylsilole (HPS). We confirmed that the redshifted emission of amorphous aggregates as compared to crystalline HPS is caused by the lower packing density of amorphous HPS aggregates and the reduced restrictions on their intramolecular low-frequency vibrational motions. Strikingly, our calculations revealed the size independent fluorescence quantum efficiency of nanosized HPS aggregates and predicted the linear relationship between the fluorescence intensity and aggregate size. This is because the nanosized aggregates are dominated by embedded HPS molecules which exhibit similar fluorescence quantum efficiency at different aggregate sizes. In addition, our results provided a direct explanation for the crystallization-enhanced emission phenomenon of propeller-shaped AIE luminogens in experiments. Our theoretical protocol is general and applicable to other AIE luminogens, thus laying solid foundation for the rational design of advanced AIE materials. PMID:27417250

  2. 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

  3. Kinetic regime of dithiothreitol-induced aggregation of bovine serum albumin.

    PubMed

    Borzova, Vera A; Markossian, Kira A; Kara, Dmitriy A; Kurganov, Boris

    2015-09-01

    A search for agents, which are capable of effectively suppressing protein aggregation, and elaboration of the appropriate test systems, are among important problems of modern biochemistry and biotechnology. One such test system is based on dithiothreitol (DTT)-induced aggregation of bovine serum albumin (BSA). Study of the kinetics of DTT-induced aggregation of BSA by asymmetric flow field flow fractionation showed that a decrease in the portion of the non-aggregated protein in time followed the exponential law, the rate constant of the first order remaining unchanged at varying protein concentration (0.1M Na-phosphate buffer, pH 7.0; 45 °C). The obtained results indicate that the rate-limiting stage of the general aggregation process is that of unfolding of the protein molecule. When studying the kinetics of DTT-induced aggregation of BSA by dynamic light scattering, we proposed to use parameter K(LS) as a measure of the initial rate of aggregation. Parameter K(LS) corresponds to the initial slope of the dependence of (I-I0)(0.5) on time (I0 and I are the initial and current values of the light scattering intensity, respectively). The K(LS) value has been applied to estimate anti-aggregation activity of chemical chaperones (arginine, its derivatives and proline). PMID:26116389

  4. Platelet aggregation inhibitors from Philippine marine invertebrate samples screened in a new microplate assay.

    PubMed

    Pimentel, Sheila Marie V; Bojo, Zenaida P; Roberto, Amy V D; Lazaro, Jose Enrico H; Mangalindan, Gina C; Florentino, Leila M; Lim-Navarro, Pilar; Tasdemir, Deniz; Ireland, Chris M; Concepcion, Gisela P

    2003-01-01

    A new microplate assay for Ca(2+)-induced platelet aggregation as detected by Giemsa dye was used to screen marine invertebrate samples from the Philippines for inhibitors of human platelet aggregation. Out of 261 crude methanol extracts of marine sponges and tunicates, 25 inhibited aggregation at 2 mg/ml. Inhibition of agonist-induced aggregation in an aggregometer was used to confirm results of the microplate assay and to determine the specific mode of inhibition of 2 samples. The marine sponge Xestospongia sp. yielded a xestospongin/araguspongine-type molecule that inhibited collagen-induced aggregation by 87% at 2 micro g/ml, and epinephrine-induced aggregation by 78% at 20 micro g/ml, while the marine sponge Aplysina sp. yielded 5,6-dibromotryptamine, which inhibited epinephrine-induced aggregation by 51% at 20 micro g/ml. In this study we have found that the microplate assay is a simple, inexpensive, yet useful preliminary tool to qualitatively screen a large number of marine samples for antiplatelet aggregation activity. PMID:14719168

  5. 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.

  6. Acceleration of Individual, Decimetre-sized Aggregates in the Lower Coma of Comet 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Agarwal, Jessica; A'Hearn, M. F.; Vincent, J.-B.; Güttler, C.; Höfner, S.; Sierks, H.; Tubiana, C.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; Barucci, M. A.; Bertaux, J.-L.; Bertini, I.; Boudreault, S.; Cremonese, G.; Da Deppo, V.; Davidsson, B.; Debei, S.; De Cecco, M.; Deller, J.; Fornasier, S.; Fulle, M.; Gicquel, A.; Groussin, O.; Gutiérrez, P. J.; Hofmann, M.; Hviid, S. F.; Ip, W.-H.; Jorda, L.; Keller, H. U.; Knollenberg, J.; Kramm, J.-R.; Kührt, E.; Küppers, M.; Lara, L. M.; Lazzarin, M.; Lopez Moreno, J. J.; Marzari, F.; Naletto, G.; Oklay, N.; Shi, X.; Thomas, N.

    2016-09-01

    We present OSIRIS/NAC observations of decimetre-sized, likely ice-containing aggregates ejected from a confined region on the surface of comet 67P/Churyumov-Gerasimenko. The images were obtained in January 2016 when the comet was at 2 AU from the Sun out-bound from perihelion. We measure the acceleration of individual aggregates through a two-hour image series. Approximately 50% of the aggregates are accelerated away from the nucleus, and 50% towards it, and likewise towards either horizontal direction. The accelerations are up to one order of magnitude stronger than local gravity, and are most simply explained by the combined effect of gas drag accelerating all aggregates upwards, and the recoil force from asymmetric outgassing, either from rotating aggregates with randomly oriented spin axes and sufficient thermal inertia to shift the temperature maximum away from an aggregate's subsolar region, or from aggregates with variable ice content. At least 10% of the aggregates will escape the gravity field of the nucleus and feed the comet's debris trail, while others may fall back to the surface and contribute to the deposits covering parts of the northern hemisphere. The rocket force plays a crucial role in pushing these aggregates back towards the surface. Our observations show the future back fall material in the process of ejection, and provide the first direct measurement of the acceleration of aggregates in the innermost coma (<2km) of a comet, where gas drag is still significant.

  7. 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).

  8. Water and formic acid aggregates: a molecular dynamics study.

    PubMed

    Vardanega, Delphine; Picaud, Sylvain

    2014-09-14

    Water adsorption around a formic acid aggregate has been studied by means of molecular dynamics simulations in a large temperature range including tropospheric conditions. Systems of different water contents have been considered and a large number of simulations has allowed us to determine the behavior of the corresponding binary formic acid-water systems as a function of temperature and humidity. The results clearly evidence a threshold temperature below which the system consists of water molecules adsorbed on a large formic acid grain. Above this temperature, formation of liquid-like mixed aggregates is obtained. This threshold temperature depends on the water content and may influence the ability of formic acid grains to act as cloud condensation nuclei in the Troposphere. PMID:25217941

  9. 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.

  10. 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.

  11. Aggregation of metallochlorophylls - Examination by spectroscopy

    NASA Technical Reports Server (NTRS)

    Boucher, L. J.; Katz, J. J.

    1969-01-01

    Nuclear magnetic resonance measurements determine which metallochlorophylls, besides magnesium-containing chlorophylls, possess coordination aggregation properties. Infrared spectroscopy reveals that only zinc pheophytin and zinc methyl pheophorbide showed significant coordination aggregation, whereas divalent nickel and copper did not.

  12. 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

  13. Aggregated Authentication (AMAC) Using Universal Hash Functions

    NASA Astrophysics Data System (ADS)

    Znaidi, Wassim; Minier, Marine; Lauradoux, Cédric

    Aggregation is a very important issue to reduce the energy consumption in Wireless Sensors Networks (WSNs). There is currently a lack of cryptographic primitives for authentication of aggregated data. The theoretical background for Aggregated Message Authentication Codes (AMACs) has been proposed by Chan and Castelluccia at ISIT 08.

  14. 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.

  15. 28 CFR 2.5 - Sentence aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Sentence aggregation. 2.5 Section 2.5 Judicial Administration DEPARTMENT OF JUSTICE PAROLE, RELEASE, SUPERVISION AND RECOMMITMENT OF PRISONERS... aggregation. When multiple sentences are aggregated by the Bureau of Prisons pursuant to 18 U.S.C. 4161...

  16. Cytotoxic effects of aggregated nanomaterials.

    PubMed

    Soto, Karla; Garza, K M; Murr, L E

    2007-05-01

    This study deals with cytotoxicity assays performed on an array of commercially manufactured inorganic nanoparticulate materials, including Ag, TiO(2), Fe(2)O(3), Al(2)O(3), ZrO(2), Si(3)N(4), naturally occurring mineral chrysotile asbestos and carbonaceous nanoparticulate materials such as multiwall carbon nanotube aggregates and black carbon aggregates. The nanomaterials were characterized by TEM, as the primary particles, aggregates or long fiber dimensions ranged from 2nm to 20microm. Cytotoxicological assays of these nanomaterials were performed utilizing a murine alveolar macrophage cell line and human macrophage and epithelial lung cell lines as comparators. The nanoparticulate materials exhibited varying degrees of cytoxicity for all cell lines and the general trends were similar for both the murine and human macrophage cell lines. These findings suggest that representative cytotoxic responses for humans might be obtained by nanoparticulate exposures to simple murine macrophage cell line assays. Moreover, these results illustrate the utility in performing rapid in vitro assays for cytotoxicity assessments of nanoparticulate materials as a general inquiry of potential respiratory health risks in humans. PMID:17275430

  17. 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. PMID:27253725

  18. Weighted Random Mixing and Exact Finite Lattice Descriptions of Molecular Aggregation Equilibria

    NASA Astrophysics Data System (ADS)

    Ben-Amotz, Dor

    2014-03-01

    Entropic and energetic contributions to a broad class of molecular aggregation and self-assembly processes are described by performing a mean field Boltzmann average over aggregate size distributions pertaining to an idealized random mixture. Predictions obtained using the resulting weighted random mixing (WRM) model are compared with exact finite lattice and fluid molecular dynamics simulation results for systems in which each aggregate resembles a central molecule with multiple ligand binding sites. Good agreement between the exact and WRM results is found for systems with interaction energies of various magnitudes (and signs), both in the large and small cohesive interaction energy regimes (or at low and high temperature, respectively). The latter two regimes are separated by a critical point on either side of which qualitatively different aggregation behavior is predicted and observed. More specifically, both the WRM model and exact finite lattice aggregation results reveal that when half the ligand binding sites are filled, the corresponding aggregate size distributions are bimodal below and unimodal above the corresponding critical temperature, whose value depends on the ligand-ligand interaction energy, but is independent of the binding energy of each ligand to the central molecule. This work was carried out in collaboration with Blake M. Rankin and B. Widom (at Cornell University), and was supported by NSF Grant Number CHE-1213338.

  19. Aggregation behavior of a gemini surfactant with a tripeptide spacer.

    PubMed

    Wang, Meina; Han, Yuchun; Qiao, Fulin; Wang, Yilin

    2015-02-28

    A peptide gemini surfactant, 12-G(NH2)LG(NH2)-12, has been constructed with two dodecyl chains separately attached to the two terminals of a glutamic acid-lysine-glutamic acid peptide and the aggregation behavior of the surfactant was studied in aqueous solution. The 12-G(NH2)LG(NH2)-12 molecules form fiber-like precipitates around pH 7.0, and the precipitation range is widened on increasing the concentration. At pHs 3.0 and 11.0, 12-G(NH2)LG(NH2)-12 forms soluble aggregates because each molecule carries two positively charged amino groups at the two ends of the peptide spacer at pH 3.0, while each molecule carries one negatively charged carboxyl group in the middle of the peptide spacer at pH 11.0. 12-G(NH2)LG(NH2)-12 displays a similar concentration-dependent process at these two pHs: forming small micelles above the critical micelle concentration and transferring to fibers at pH 3.0 or twisted ribbons at pH 11.0 above the second critical concentration. The fibers formed at pH 3.0 tend to aggregate into bundles with twisted structure. Both the twisted fibers at pH 3.0 and the twisted ribbons at pH 11.0 contain β-sheet structure formed by the peptide spacer. PMID:25588349

  20. Full counting statistics of laser excited Rydberg aggregates in a one-dimensional geometry.

    PubMed

    Schempp, H; Günter, G; Robert-de-Saint-Vincent, M; Hofmann, C S; Breyel, D; Komnik, A; Schönleber, D W; Gärttner, M; Evers, J; Whitlock, S; Weidemüller, M

    2014-01-10

    We experimentally study the full counting statistics of few-body Rydberg aggregates excited from a quasi-one-dimensional atomic gas. We measure asymmetric excitation spectra and increased second and third order statistical moments of the Rydberg number distribution, from which we determine the average aggregate size. Estimating rates for different excitation processes we conclude that the aggregates grow sequentially around an initial grain. Direct comparison with numerical simulations confirms this conclusion and reveals the presence of liquidlike spatial correlations. Our findings demonstrate the importance of dephasing in strongly correlated Rydberg gases and introduce a way to study spatial correlations in interacting many-body quantum systems without imaging. PMID:24483893